Pathway of Allosteric Control as Revealed by Intermediate States of Hemoglobin / J.M. Holt ; G.K. Ackers
Probes of Energy Transduction in Enzyme Catalysis / Y. Huang ; D.W. Bolen
Macromolecules and Water: Probing with Osmotic Stress / V.A. Parsegian ; R.P. Rand ; D.C. Rau
Linkage of Protein Assembly to Protein-DNA Binding / I. Wong ; T.M. Lohman
Linkage at Steady State: Allosteric Transitions of Thrombin / E. Di Cera ; Q.D. Dang ; Y. Ayala ; A. Vindigni
Thermal Denaturation Methods in Study of Protein Folding / E. Freire
Kinetics of Lipid Membrane Phase Transitions: A Volume Perturbation Calorimeter Study / L. Chen ; R.L. Biltonen ; M.L. Johnson
Tight Binding Affinities Determined from the Thermodynamic Linkage to Protons by Titration Calorimetry / M.L. Doyle ; G. Louie ; P. Dal Monte ; T. Sokoloski
Calorimetric Methods for Interpreting Protein-Ligand Interactions / H.F. Fisher ; N. Singh
Extracting Thermodynamic Data from Equilibrium Melting Curves for Oligonucleotide Order-Disorder Transitions / K.J. Breslauer
Thermodynamics and Mutations in RNA-Protein Interactions / K.B. Hall ; J.K. Kranz
Melting Studies of RNA Unfolding and RNA-Ligand Interactions / D.E. Draper ; T.C. Gluick
Structural-Perturbation Approaches to Thermodynamics of Site-Specific Protein-DNA Interactions / L. Jen-Jacobson
Thermodynamic Parameters from Hydrogen Exchange Measurements / Y. Bai ; J.J. Englander ; L. Mayne ; J.S. Milne ; S.W. Englander
Application of Pressure to Biochemical Equilibria: The Other Thermodynamic Variable / C.A. Royer
Molecular Volume / L.M. Rellick ; W.J. Becktel
Hydrostatic and Osmotic Pressure as Tools to Study Macromolecular Recognition / C.R. Robinson ; S.G. Sligar
Sedimentation Equilibrium as Thermodynamic Tool / T.M. Laue
Footprint Phenotypes: Structural Models of DNA-Binding Proteins from Chemical Modification Analysis of DNA / J. Yang ; J. Carey
Low-Temperature Electrophoresis Methods / M. Perrella ; I. Denisov
Use of Multiple Spectroscopic Methods to Monitor Equilibrium Unfolding of Proteins / M.R. Eftink
Probing Structural and Physical Basis of Protein Energetics Linked to Protons and Salt / B. Garcia-Moreno
Evaluating Contribution of Hydrogen Bonding and Hydrophobic Bonding to Protein Folding / C.N. Pace
Analyzing Solvent Reorganization and Hydrophobicity / B. Lee
Simple Force Field for Study of Peptide and Protein Conformational Properties / T.P. Creamer ; G.D. Rose
Probes for Analysis of Stability of Different Variants of Aspartate Aminotransferase / M. Martinez-Carrion ; A. Artigues ; A. Berezov ; M.L. Bianconi ; A.M. Reyes ; A. Iriarte
Jo M.; Johnson, Michael L.; Ackers, Gary K.; Ackers, Gary K Holt, Gary K. Ackers, Jo M. Holt, Michael L. Johnson, Gary K. Ackers, Michael L. Johnson, Jo M. Holt
Pathway of Allosteric Control as Revealed by Intermediate States of Hemoglobin / J.M. Holt ; G.K. Ackers
Probes of Energy Transduction in Enzyme Catalysis / Y. Huang ; D.W. Bolen
Macromolecules and Water: Probing with Osmotic Stress / V.A. Parsegian ; R.P. Rand ; D.C. Rau
Linkage of Protein Assembly to Protein-DNA Binding / I. Wong ; T.M. Lohman
Linkage at Steady State: Allosteric Transitions of Thrombin / E. Di Cera ; Q.D. Dang ; Y. Ayala ; A. Vindigni
Thermal Denaturation Methods in Study of Protein Folding / E. Freire
Kinetics of Lipid Membrane Phase Transitions: A Volume Perturbation Calorimeter Study / L. Chen ; R.L. Biltonen ; M.L. Johnson
Tight Binding Affinities Determined from the Thermodynamic Linkage to Protons by Titration Calorimetry / M.L. Doyle ; G. Louie ; P. Dal Monte ; T. Sokoloski
Calorimetric Methods for Interpreting Protein-Ligand Interactions / H.F. Fisher ; N. Singh
Extracting Thermodynamic Data from Equilibrium Melting Curves for Oligonucleotide Order-Disorder Transitions / K.J. Breslauer
Thermodynamics and Mutations in RNA-Protein Interactions / K.B. Hall ; J.K. Kranz
Melting Studies of RNA Unfolding and RNA-Ligand Interactions / D.E. Draper ; T.C. Gluick
Structural-Perturbation Approaches to Thermodynamics of Site-Specific Protein-DNA Interactions / L. Jen-Jacobson
Thermodynamic Parameters from Hydrogen Exchange Measurements / Y. Bai ; J.J. Englander ; L. Mayne ; J.S. Milne ; S.W. Englander
Application of Pressure to Biochemical Equilibria: The Other Thermodynamic Variable / C.A. Royer
Molecular Volume / L.M. Rellick ; W.J. Becktel
Hydrostatic and Osmotic Pressure as Tools to Study Macromolecular Recognition / C.R. Robinson ; S.G. Sligar
Sedimentation Equilibrium as Thermodynamic Tool / T.M. Laue
Footprint Phenotypes: Structural Models of DNA-Binding Proteins from Chemical Modification Analysis of DNA / J. Yang ; J. Carey
Low-Temperature Electrophoresis Methods / M. Perrella ; I. Denisov
Use of Multiple Spectroscopic Methods to Monitor Equilibrium Unfolding of Proteins / M.R. Eftink
Probing Structural and Physical Basis of Protein Energetics Linked to Protons and Salt / B. Garcia-Moreno
Evaluating Contribution of Hydrogen Bonding and Hydrophobic Bonding to Protein Folding / C.N. Pace
Analyzing Solvent Reorganization and Hydrophobicity / B. Lee
Simple Force Field for Study of Peptide and Protein Conformational Properties / T.P. Creamer ; G.D. Rose
Probes for Analysis of Stability of Different Variants of Aspartate Aminotransferase / M. Martinez-Carrion ; A. Artigues ; A. Berezov ; M.L. Bianconi ; A.M. Reyes ; A. Iriarte
Gary K; Holt, Jo M.; Johnson, Michael L.; Ackers, Gary K. Ackers, Gary K. Ackers, Jo M. Holt, Michael L. Johnson, Gary K. Ackers, Michael L. Johnson, Jo M. Holt
Pathway of Allosteric Control as Revealed by Intermediate States of Hemoglobin / J.M. Holt ; G.K. Ackers
Probes of Energy Transduction in Enzyme Catalysis / Y. Huang ; D.W. Bolen
Macromolecules and Water: Probing with Osmotic Stress / V.A. Parsegian ; R.P. Rand ; D.C. Rau
Linkage of Protein Assembly to Protein-DNA Binding / I. Wong ; T.M. Lohman
Linkage at Steady State: Allosteric Transitions of Thrombin / E. Di Cera ; Q.D. Dang ; Y. Ayala ; A. Vindigni
Thermal Denaturation Methods in Study of Protein Folding / E. Freire
Kinetics of Lipid Membrane Phase Transitions: A Volume Perturbation Calorimeter Study / L. Chen ; R.L. Biltonen ; M.L. Johnson
Tight Binding Affinities Determined from the Thermodynamic Linkage to Protons by Titration Calorimetry / M.L. Doyle ; G. Louie ; P. Dal Monte ; T. Sokoloski
Calorimetric Methods for Interpreting Protein-Ligand Interactions / H.F. Fisher ; N. Singh
Extracting Thermodynamic Data from Equilibrium Melting Curves for Oligonucleotide Order-Disorder Transitions / K.J. Breslauer
Thermodynamics and Mutations in RNA-Protein Interactions / K.B. Hall ; J.K. Kranz
Melting Studies of RNA Unfolding and RNA-Ligand Interactions / D.E. Draper ; T.C. Gluick
Structural-Perturbation Approaches to Thermodynamics of Site-Specific Protein-DNA Interactions / L. Jen-Jacobson
Thermodynamic Parameters from Hydrogen Exchange Measurements / Y. Bai ; J.J. Englander ; L. Mayne ; J.S. Milne ; S.W. Englander
Application of Pressure to Biochemical Equilibria: The Other Thermodynamic Variable / C.A. Royer
Molecular Volume / L.M. Rellick ; W.J. Becktel
Hydrostatic and Osmotic Pressure as Tools to Study Macromolecular Recognition / C.R. Robinson ; S.G. Sligar
Sedimentation Equilibrium as Thermodynamic Tool / T.M. Laue
Footprint Phenotypes: Structural Models of DNA-Binding Proteins from Chemical Modification Analysis of DNA / J. Yang ; J. Carey
Low-Temperature Electrophoresis Methods / M. Perrella ; I. Denisov
Use of Multiple Spectroscopic Methods to Monitor Equilibrium Unfolding of Proteins / M.R. Eftink
Probing Structural and Physical Basis of Protein Energetics Linked to Protons and Salt / B. Garcia-Moreno
Evaluating Contribution of Hydrogen Bonding and Hydrophobic Bonding to Protein Folding / C.N. Pace
Analyzing Solvent Reorganization and Hydrophobicity / B. Lee
Simple Force Field for Study of Peptide and Protein Conformational Properties / T.P. Creamer ; G.D. Rose
Probes for Analysis of Stability of Different Variants of Aspartate Aminotransferase / M. Martinez-Carrion ; A. Artigues ; A. Berezov ; M.L. Bianconi ; A.M. Reyes ; A. Iriarte
Use of Least-Squares Techniques in Biochemistry / M.L. Johnson
Parameter Estimates from Nonlinear Models / D.G. Watts
Effects of Heteroscedasticity and Skewness on Prediction in Regression: Modeling Growth of the Human Heart / R.D. Abbott ; H.P. Gutgesell
Artifacts of Fourier Series Analysis / M. Lampl
Quantification of Evolution from Order to Randomness in Practical Time Series Analysis / S.M. Pincus
Sequential versus Simultaneous Analysis of Data: Differences in Reliability of Derived Quantitative Conclusions / M. Straume
Model-Independent Quantification of Measurement Error: Empirical Estimation of Discrete Variance Function Profiles Based on Standard Curves / J.D. Veldhuis
Impact of Variance Function Estimation in Regression and Calibration / L.-J. Hwang
Application of the Kalman Filter to Computational Problems in Statistics / E.N. Brown and ; C.H. Schmid
Modeling Chemical Reactions: Jacobian Paradigm and Related Issues / R.I. Shrager
The Mathematics of Biological Oscillators / G.B. Ermentrout
Diffusion-Modulated Energy Transfer and Quenching: Analysis by Numerical Integration of Diffusion Equation in Laplace Space / J. Kasba ; J.R. Lakowicz
Maximum Entropy Method of Data Analysis in Time-Resolved Spectroscopy / J.-C. Brochon
Analysis of Kinetic Data: Practical Applications of Computer Simulation and Fitting Programs / C. Frieden
Determination of Rate and Equilibrium Binding Constants for Macromolecular Interactions by Surface Plasmon Resonance / D.J. OShannessy ; M. Brigham-Burke ; K.K. Soneson ; P. Hensley ; I. Brooks
Analysis of Nonequilibrium Dynamics of Bound, Free, and Total Plasma Ligand Concentrations over Time Following Nonlinear Secretory Inputs: Kinetics of Two or More Hormones Pulsed into Compartments Containing Multiple Variable-Affinity Binding Proteins / L.M. Faunt
Testing Pulse Detection Algorithms with Simulations of Episodically Pulsatile Substrate, Metabolite, or Hormone Release
Error Analysis of Macromolecular Structures Determined with Nuclear MagneticResonance Data / J.W. Shriver ; S. Edmondson
Characterization of Enzyme-Complex Formation by Analysis of Nuclear Magnetic Resonance Line Shapes / C.B. Post
Computer Simulations of Nuclear Overhauser Effect Spectra of Complex Oligosaccharides / C.A. Bush
Determining Confidence Intervals for Parameters Derived from Analysis of Equilibrium Analytical Ultracentrifugation Data / D.G.Watts
Boundary Analysis in Sedimentation Velocity Experiments / W.F. Stafford, III
Statistical Thermodynamic Analysis of Differential Scanning Calorimetry Data: Structural Deconvolution of Heat Capacity Function of Proteins / E. Freire
Analysis of Two-Dimensional Differential Scanning Calorimetry Data: Elucidation of Complex Biomolecular Energetics
Monte Carlo Simulations of Membranes: Phase Transition of Small Unilamellar Dipalmitoylphosphatidylcholine Vesicles / I.P. Sugar ; R.L. Biltonen ; N. Mitchard
Analysis of Drug-DNA Binding Isotherms: A Monte Carlo Approach / J.J. Correia ; J.B. Chaires
Analysis of Multidimensional Spectroscopic Data to Monitor Unfolding of Proteins / G.D. Ramsay ; M.R. Eftink
Estimating Binding Constants for Site-Specific Interactions / B. Garcia-Moreno
Use of Least-Squares Techniques in Biochemistry / M.L. Johnson
Parameter Estimates from Nonlinear Models / D.G. Watts
Effects of Heteroscedasticity and Skewness on Prediction in Regression: Modeling Growth of the Human Heart / R.D. Abbott ; H.P. Gutgesell
Phase Response Curves: Elucidating the Dynamics of Coupled Oscillators / A. Granada ; R. M. Hennig ; B. Ronacher ; A. Kramer ; H. Herzel1：
Introduction
Estimation of Phase Response Curves / 2：
Specific Applications / 3：
Discussion / 4：
Acknowledgments / Appendix I：
References
Multiple Ion Binding Equilibria, Reaction Kinetics, and Thermodynamics in Dynamic Models of Biochemical Pathways / Kalyan C. Vinnakota ; Fan Wu ; Martin J. Kushmerick ; Daniel A. Beard
Biochemical Conventions and Calculations
Application to Physiological Systems
Acknowledgment
Analytical Methods for the Retrieval and Interpretation of Continuous Glucose Monitoring Data in Diabetes / Boris Kovatchev ; Marc Breton ; William Clarke
Decomposition of Sensor Errors
Measures of Average Glycemia and Deviation from Target
Risk and Variability Assessment
Measures and Plots of System Stability / 5：
Time-Series-Based Prediction of Future BG Values / 6：
Conclusions / 7：
Analysis of Heterogeneity in Molecular Weight and Shape by Analytical Ultracentrifugation Using Parallel Distributed Computing / Borries Demeler ; Emre Brookes ; Luitgard Nagel-Steger
Methodology
Job Submission
Results
Discrete Stochastic Simulation Methods for Chemically Reacting Systems / Yang Cao ; David C. Samuels
The Chemical Master Equation
The Stochastic Simulation Algorithm
The Tau-Leaping Method
Measurement of Simulation Error
Software and Two Numerical Experiments
Conclusion
Analyses for Physiological and Behavioral Rhythmicity / Harold B. Dowse
Types of Biological Data and Their Acquisition
Analysis in the Time Domain
Analysis in the Frequency Domain
Time/Frequency Analysis and the Wavelet Transform
Signal Conditioning
Strength and Regularity of a Signal
A Computational Approach for the Rational Design of Stable Proteins and Enzymes: Optimization of Surface Charge-Charge Interactions / Katrina L. Schweiker ; George I. Makhatadze8：
Computational Design of Surface Charge-Charge Interactions
Experimental Verification of Computational Predictions
Closing Remarks
Efficient Computation of Confidence Intervals for Bayesian Model Predictions Based on Multidimensional Parameter Space / Amber D. Smith ; Alan Genz ; David M. Freiberger ; Gregory Belenky ; Hans P. A. Van Dongen
Height of the Probability Density Function at the Boundary of the Smallest Multidimensional Confidence Region
Approximating a One-Dimensional Slice of the Probability Density Function by Means of Normal Curve Spline Pieces
Locating the Boundary of the Smallest Multidimensional Confidence Region
Finding the Minimum and Maximum of the Prediction Model over the Confidence Region
An Application: Bayesian Forecasting of Cognitive Performance Impairment during Sleep Deprivation
95% Confidence Intervals for Bayesian Predictions of Cognitive Performance Impairment during Sleep Deprivation
Appendix
Analyzing Enzymatic pH Activity Profiles and Protein Titration Curves Using Structure-Based pK<a/ Calculations and Titration Curve Fitting / Jens Erik Nielsen9：
Calculating the pH Dependence of Protein Characteristics
Least Squares in Calibration: Weights, Nonlinearity, and Other Nuisances / Joel Tellinghuisen10：
Review of Least Squares
Experiment Design Using Vprior/-Numerical Illustrations
Evaluation and Comparison of Computational Models / Jay I. Myung ; Yun Tang ; Mark A. Pitt11：
Conceptual Overview of Model Evaluation and Comparison
Model Comparison Methods
Model Comparison at Work: Choosing between Protein Folding Models
Desegregating Undergraduate Mathematics and Biology - Interdisciplinary Instruction with Emphasis on Ongoing Biomedical Research / Raina Robeva12：
Course Description
Mathematical Algorithms for High-Resolution DNA Melting Analysis / Robert Palais ; Carl T. Wittwer13：
Extracting Melting Curves from Raw Fluorescence
Methods Used for Clustering and Classifying Melting Curves by Genotype
Methods Used for Modeling Melting Curves
Biomathematical Modeling of Pulsatile Hormone Secretion: A Historical Perspective / William S. Evans ; Leon S. Farhy ; Michael L. Johnson14：
Early Attempts to Identify and Characterize Pulsatile Hormone Release
Impact of Sampling Protocol and Pulse Detection Algorithm on Hormone Pulse Detection
Application of Deconvolution Procedures for the Identification and Characterization of Hormone Secretory Bursts
Limitations and Subsequent Improvements in Deconvolution Procedures
Evaluation of Pulsatile and Basal Hormone Secretion Using a Stochastic Differential Equations Model
Characterization of Regulation of Signal and Response Elements: Estimation of Approximate Entropy
Evaluation of Coupled Systems
Evaluation of Hormonal Networks with Feedback Interactions
Future Directions
AutoDecon: A Robust Numerical Method for the Quantification of Pulsatile Events / Lenore Pipes ; Paula P. Veldhuis ; Ralf Nass ; Michael O. Thorner15：
Methods
Modeling Fatigue over Sleep Deprivation, Circadian Rhythm, and Caffeine with a Minimal Performance Inhibitor Model / Patrick L. Benitez ; Gary H. Kamimori ; Thomas J. Balkin ; Alexander Greene16：
A Method in Enzymology for Measuring Hydrolytic Activities in Live Cell Environments / Beverly Z. Packard ; Akira Komoriya1：
Protease Substrate Design
Protease Specificity / 2：
Cell-Permeable Fluorogenic Probes / 3：
Conclusions / 4：
References
Heterogeneity of Fluorescence Determined by the Method of Area-Normalized Time-Resolved Emission Spectroscopy / N. Periasamy
Introduction
TRES and TRANES Methods
TRES and TRANES Spectra of Simple Cases
Physical Significance of TRANES and Isoemissive Point
TRES and TRANES of Fluorophores in Microheterogeneous Media / 5：
Fluorescence in Microheterogeneous and Biological Media: Special Cases / 6：
Acknowledgment
Multiparametric Probing of Microenvironment with Solvatochromic Fluorescent Dyes / Andrey S. Klymchenko ; Alexander P. Demchenko
"Universal" and "Specific" Noncovalent Interactions
The Methodology of Multiparametric Approach with Application of 3-Hydroxyflavone Dyes
Correlations of Spectroscopic Data with Solvatochromic Variables
Algorithm for Multiparametric Probing Based on Parameters of Absorption and Dual Emission
Application of Multiparametric Probing
Limitations of the Multiparametric Approach
Concluding Remarks / 7：
Site-Selective Red-Edge Effects
Molecular Disorder and the Origin of Red-Edge Effects
The Principle of Photoselection
Ground-State Heterogeneity
The Magnitude of Red-Edge Excitation Fluorescence Shift and Its Connection with Dielectric Relaxations
Red-Edge Effect with High Resolution in Time
Red-Edge Effects in Excited-State Reactions
Fluorescent Probes for Optimal Observation of Red-Edge Effects / 8：
Peculiarities of the Red-Edge Effects of Indole and Tryptophan / 9：
Fluorescence Approaches to Quantifying Biomolecular Interactions / Catherine A. Royer ; Suzanne F. Scarlata10：
Fluorescence Observables
Designing a Fluorescence Experiment
Forster Resonance Energy Transfer Measurements of Transmembrane Helix Dimerization Energetics / Mikhail Merzlyakov ; Kalina Hristova
Challenges in Quantitative Measurements of Interactions Between TM Helices in Bilayers
Bilayer Platforms for Measuring TM Helix Interactions Using FRET
FRET Due to Random Colocalization of Donors and Acceptors (Proximity FRET)
FRET Efficiencies and Energetics of TM Helix Dimerization
Biological Insights from FRET Measurements
Conclusion
Application of Single-Molecule Spectroscopy in Studying Enzyme Kinetics and Mechanism / Jue Shi ; Joseph Dertouzos ; Ari Gafni ; Duncan Steel
Experimental Considerations
Sample Preparation
Instrumentation
Data Analysis of Single-Molecule Trajectories
Additional Considerations
Summary
Ultrafast Fluorescence Spectroscopy via Upconversion: Applications to Biophysics / Jianhua Xu ; Jay R. Knutson
Basic Concepts
Upconversion Spectrophotofluorometer and Experimental Considerations
Ultrafast Photophysics of Single Tryptophan, Peptides, Proteins, and Nucleic Acids
Summary and Future Directions
Use of Fluorescence Resonance Energy Transfer (FRET) in Studying Protein-induced DNA Bending / Anatoly I. Dragan ; Peter L. Privalov
Preparation of Labeled DNA Duplexes
Fluorescence Resonance Energy Transfer
FRET in Studying Large Protein-Induced DNA Bends
Dependence of the Protein-induced DNA Bend on the Forces Involved in Binding
FREt in Studying Small Protein-Induced DNA Bends
Fluorescent Pteridine Probes for Nucleic Acid Analysis / Mary E. Hawkins
Pteridine Analog Characteristics
Procedures for Oligonucleotide Synthesis with Pteridine Analogs
Characterization of Pteridine-Containing Sequences
Applications
Acknowledgments
Single-Molecule Fluorescence Methods for the Analysis of RNA Folding and Ribonucleoprotein Assembly / Goran Pljevaljcic ; David P. Millar11：
Labeling Methods
Single-Molecule Fluorescence Detection Methods
Diffusion Single-Pair FRET for RNA Based Systems
Total Internal Reflection Fluorescence (TIRF) for RNA Based Systems
Application 1: Folding of the Hairpin Ribozyme
Application 2: Assembly of the Rev-RRE Complex
Using Fluorophore-Labeled Oligonucleotides to Measure Affinities of Protein-DNA Interactions / Brian J. Anderson ; Chris Larkin ; Kip Guja ; Joel F. Schildbach12：
Definitions of Fluorescence Anisotropy and Intensity
Advantages of Fluorescence Measurements
Disadvantages of Fluorescence Measurements
Designing the Oligonucleotide
Designing the Experiment
Competition Assays for Determining Specificity
Identifying Small Pulsatile Signals within Noisy Data: A Fluorescence Application / Michael L. Johnson ; Leon S. Farhy ; Paula P. Veldhuis ; Joseph R. Lakowicz13：
Methods
Results
Discussion
Determination of Zinc Using Carbonic Anhydrase-Based Fluorescence Biosensors / Rebecca Bozym ; Tamiika K. Hurst ; Nissa Westerberg ; Andrea Stoddard ; Carol A. Fierke ; Christopher J. Frederickson ; Richard B. Thompson14：
Principles of CA-Based Zinc Sensing
Transducing Zinc Binding as a Fluorescence Change
"Free" Versus Bound Zinc Ion: Speciation
Metal Ion Buffers
Kinetics
Applications: Ratiometric Determination of Free Zinc in Solution
Preparation of Apocarbonic Anhydrase
Intracellular Sensing with TAT Tag
Intracellular Sensing with an Expressible CA Sensor
Instrumentation for Fluorescence-Based Fiber Optic Biosensors / Hui-Hui Zeng ; Daniel Ohnemus ; Bryan McCranor ; Michele Cramer ; James Moffett15：
Introduction and Rationale for Fluorescence-Based Fiber Optic Sensors
Basic Principles of Fiber Optics for Fluorescence Sensors
Optics and Mechanics of Fluorescence-Based Fiber Optic Sensors
Mounting and Alignment of the Instrument
Standards for Ratiometric and Lifetime-Based Fiber Optic Fluorescence Sensors
Construction of Fiber Optic Probes
Zn[superscript 2+] Probe
Cu[superscript 2+] Probe
Use of Fiber Optic Probes for Discrete Samples
Operating Issues: Noise, Background, Thermal Drift, and Mode Hopping
Practical Approaches to Protein Folding and Assembly: Spectroscopic Strategies in Thermodynamics and Kinetics / Jad Walters ; Sara L. Milam ; A. Clay Clark1：
Introduction
Equilibrium Unfolding / 2：
Measuring Folding Kinetics / 3：
References
Using Thermodynamics to Understand Progesterone Receptor Function: Method and Theory / Keith D. Connaghan-Jones ; David L. Bain
Assessing Protein Functional and Structural Homogeneity
Dissecting Linked Assembly Reactions
Analysis and Dissection of Natural Promoters / 4：
Measuring the Energetics of Coactivator Recruitment / 5：
Correlation to Biological Function / 6：
Conclusions and Future Directions / 7：
Acknowledgments
General Principles / Dan Grilley ; Ana Maria Soto ; David E. Draper
Ion-Binding Properties of HQS
Preparation of Solutions and Reagents
Instrumentation and Data Collection Protocols
Data Analysis
Controls and Further Considerations
Analysis of Repeat-Protein Folding Using Nearest-Neighbor Statistical Mechanical Models / Tural Aksel ; Doug Barrick
Historical Overview of Ising Models and Motivation for the Present Review
Linear Repeat Proteins and Their Connection to Linear Ising Models
Formulating a Homopolymer Partition Function and the Zipper Approximation
Matrix Approach: Homopolymers
Matrix Approach: Heteropolymers
Solvability Criteria for Ising Models Applied to Repeat-Protein Folding
Matrix Homopolymer Analysis of Consensus TPR Folding
Matrix Heteropolymer Analysis of Consensus Ankyrin Repeat Folding / 8：
Summary and Future Directions / 9：
Isothermal Titration Calorimetry: General Formalism Using Binding Polynomials / Ernesto Freire ; Arne Schön ; Adrian Velazquez-Campoy
The Binding Polynomial
Microscopic Constants and Cooperativity
Independent or Cooperative Binding?
Analysis of ITC Data Using Binding Polynomials
A Typical Case: Macromolecule with Two Ligand-Binding Sites
Data Interpretation
An Experimental Example
Experimental Situations from the Literature / 10：
Macromolecule with Three Ligand-Binding Sites / 11：
Conclusions / 12：
Appendix
Acknowledgment
Kinetic and Equilibrium Analysis of the Myosin ATPase / Enrique M. De La Cruz ; E. Michael Ostap
Reagents and Equipment Used for all Assays
Steady-State ATPase Activity of Myosin
Steady-State Measurement of Actomyosin Binding Affinities
Transient Kinetic Analysis of the Individuals ATPase Cycle Transitions
Kinetic Simulations
The Hill Coefficient: Inadequate Resolution of Cooperativity in Human Hemoglobin / Jo M. Holt ; Gary K. Ackers
Cooperativity and Intrinsic Binding
The Macroscopic Binding Isotherm
The Hill Coefficient
Microscopic Cooperativity in Hemoglobin
Summary
Methods for Measuring the Thermodynamic Stability of Membrane Proteins / Heedeok Hong ; Nathan H. Joh ; James U. Bowie ; Lukas K. Tamm
Two Classes of Membrane Proteins
Methods for Measuring Transmembrane Domain Oligomer Stability
Methods for Measuring Multipass ?-helical Membrane Protein Stability
Methods to Study the Stability of ?-barrel Membrane Proteins
A Few Salient Results on Forces that Stabilize Membrane Proteins
Conclusion and Outlook
NMR Analysis of Dynein Light Chain Dimerization and Interactions With Diverse Ligands / Gregory Benison ; Elisar Barbar
NMR Methodology
Monomer-dimer Equilibrium Coupled to Electrostatics
Dimerization is Coupled to Ligand Binding
Folding is Coupled to Binding
Allostery in LC8
Characterization of Parvalbumin and Polcalcin Divalent Ion Binding by Isothermal Titration Calorimetry / Michael T. Henzl
Practical Aspects of Data Collection
Illustrative Global ITC Analyses of Divalent Ion Binding
Conclusion
Energetic Profiling of Protein Folds / Jason Vertrees ; James O. Wrabl ; Vincent J. Hilser
Modeling the Native State Ensemble of Proteins using Statistical Thermodynamics
Energetic Profiles of Proteins Derived from Thermodynamics of the Native State Ensemble
Principal Components Analysis of Energetic Profile Space
Energetic Profiles are Conserved Between Homologous Proteins
Direct Alignment of Energetic Profiles Based on a Variant of the CE Algorithm
CE Algorithm Described for Structure Coordinates
Necessary Deviations from the CE Algorithm to Accommodate Energetic Profiles
Towards a Thermodynamic Homology of Fold Space: Clustering Energetic Profiles using STEPH
Energetic Profiles Provide a Vehicle to Discover Conserved Substructures in the Absence of Known Homology
Model Membrane Thermodynamics and Lateral Distribution of Cholesterol: From Experimental Data To Monte Carlo Simulation / Juyang Huang
Materials and Methods
Result and Discussion
Concluding Remarks
Thinking Inside the Box: Designing, Implementing, and Interpreting Thermodynamic Cycles to Dissect Cooperativity in RNA and DNA Folding / Nathan A. Siegfried ; Philip C. Bevilacqua13：
Folding Cooperativity Defined
Thermodynamic Boxes: Design, Implementation, and Interpretation
Thermodynamic Cubes: Design, Implementation, and Interpretation
Examples of Cooperativity in RNA
Measuring Thermodynamic Parameters by UV Melting
The Thermodynamics of Virus Capsid Assembly / Sarah Katen ; Adam Zlotnick14：
The Structural Basis of Capsid Stability
Analysis of Capsid Stability
Applications of Thermodynamic Evaluation of Virus Capsid Stability
Extracting Equilibrium Constants from Kinetically Limited Reacting Systems / John J. Correia ; Walter F. Stafford15：
NMR-based approaches for assessing effects of macromolecular crowding on globular proteins / Gary Pielak ; Andrew Miklos ; Lisa Charlton ; Conggang Li1：
Fluorescence spectroscopy in thermodynamic and kinetic analysis of membrane protein insertion / Alexey S. Ladokhin2：
Evaluating the energy-dependent "binding" in the early stage of protein import into chloroplasts / Mitsuru Akita ; Hitoshi Inoue3：
DNA length-dependent periodic properties of cooperative protein-DNA complexes / Michael Fried4：
Applying thermodynamic linkage to the study of pyruvate kinase / Aron Fenton5：
Conformational Stability of Cytochrome C / Reinhard Schweitzer-Stenner6：
Metadynamics methods applied to ion channel gating / Carmen Domene7：
Measuring Co-translational Conformations of Nascent Polypeptide Chains / Patricia L. Clark ; Krastyu G. Ugrinov8：
Taking an energetic approach to assess and explain cooperative gating phenomena in voltage-dependent potassium channels / Yifrach Ofer ; Zandany Nitzan ; Tzilhav Shem-Ad9：
Energetics of the collagen triple helix / Yujia Xu10：
Use of pressure perturbation calorimetry to characterize the volumetric properties of proteins / Katrina L. Schweiker ; George Makhatadze11：
Thermodynamic approaches to nucleosome-histone interactions / Andrew Andrews ; Karolin Luger12：
Thermodynamic approaches to carbohydrate binding by the agrin-G3 domain / Andrei T. Alexandrescu13：
Energetic methods applied to allostery in thrombin / Enrico Di Cera14：
Thermodynamics of protein translocation / Arnold J.M Driessen ; Alexej Kedrov15：
Solvent denaturation of proteins and the interpretation of the m-value / J. Martin Scholtz ; Nick Pace16：
Energetic approaches to the characterization of the E. coli PriA helicase / Wlodek Bujalowski17：
Protein-protein interactions and macromolecular stability / Lisa Gloss18：
Methods for assessing T cell receptor recognition / Brian M Baker19：
Thermodynamic analysis applied to bromodomain-histone interactions / Martin Thompson20：
Small molecule-membrane interactions / Anne Hinderliter22：
Constant pH molecular dynamics simulations / Jana Khandogin Shen23：
NMR-based approaches for assessing effects of macromolecular crowding on globular proteins / Gary Pielak ; Andrew Miklos ; Lisa Charlton ; Conggang Li1：
Fluorescence spectroscopy in thermodynamic and kinetic analysis of membrane protein insertion / Alexey S. Ladokhin2：
Evaluating the energy-dependent "binding" in the early stage of protein import into chloroplasts / Mitsuru Akita ; Hitoshi Inoue3：
Correlation Analysis: A Tool for Comparing Relaxation-Type Models to Experimental Data / Maurizio Tomaiuolo ; Joel Tabak ; Richard Bertram1：
Introduction
Scatter Plots and Correlation Analysis / 2：
Example 1: Relaxation Oscillations / 3：
Example 2: Square Wave Bursting / 4：
Example 3: Elliptic Bursting / 5：
Example 4: Using Correlation Analysis on Experimental Data / 6：
Summary / 7：
Acknowledgments
References
Trait Variability of Cancer Cells Quantified by High-Content Automated Microscopy of Single Cells / Vito Quaranta ; Darren R. Tyson ; Shawn P. Garbett ; Brandy Weidow ; Mark P. Harris ; Walter Georgescu
Background
Experimental and Computational Workflow
Application to Traits Relevant to Cancer Progression
Conclusions
Matrix Factorization for Recovery of Biological Processes from Microarray Data / Andrew V. Kossenkov ; Michael F. Ochs
Overview of Methods
Application to the Rosetta Compendium
Results of Analyses
Discussion
Modeling and Simulation of the Immune System as a Self-Regulating Network / Peter S. Kim ; Doron Levy ; Peter P. Lee
Mathematical Modeling of the Immune Network
Two Examples of Models to Understand T Cell Regulation
How to Implement Mathematical Models in Computer Simulations
Concluding Remarks
Acknowledgmentss
Entropy Demystified: The ôThermoö-dynamics of Stochastically Fluctuating Systems / Hong Qian
Energy
Entropy and ôThermoö-dynamics of Markov Processes
A Three-State Two-Cycle Motor Protein
Phosphorylation-Dephosphorylation Cycle1 Kinetics
Summary and Challenges
Effect of Kinetics on Sedimentation Velocity Profiles and the Role of Intermediates / John J. Correia ; P. Holland Alday ; Peter Sherwood ; Walter F. Stafford
Methods
ABCD Systems
Monomer-Tetramer Model
Algebraic Models of Biochemical Networks / Reinhard Laubenbacher ; Abdul Salam Jarrah
Computational Systems Biology
Network Inference
Reverse-Engineering of Discrete Models: An Example
High-Through put Computing in the Sciences / Mark Morgan ; Andrew Grimshaw8：
What is an HTC Application?
HTC Technologies
High-Throughput Computing Examples
Advanced Topics
Large Scale Transcriptome Data Integration Across Multiple Tissues to Decipher Stem Cell Signatures / Ghislain Bidaut ; Christian J. Stoeckert9：
Systems and Data Sources
Data Integration
Artificial Neural Network Training and Validation
Future Development and Enhancement Plans
DynaFit-A Software Package for Enzymology / Petr Kuzmiĉ10：
Equilibrium Binding Studies
Initial Rates of Enzyme Reactions
Time Course of Enzyme Reactions
General Methods and Algorithms
Discrete Dynamic Modeling of Cellular Signaling Networks / Réka Albert ; Rui-Sheng Wang11：
Cellular Signaling Networks
Boolean Dynamic Modeling
Variants of Boolean Network Models
Application Examples
Conclusion and Discussion
The Basic Concepts of Molecular Modeling / Akansha Saxena ; Diana Wong ; Karthikeyan Diraviyam ; David Sept12：
Homology Modeling
Molecular Dynamics
Molecular Docking
Deterministic and Stochastic Models of Genetic Regulatory Networks / Ilya Shmulevich ; John D. Aitchison13：
Boolean Networks
Differential Equation Models
Probabilistic Boolean Networks
Stochastic Differential Equation Models
Bayesian Probability Approach to ADHD Appraisal / Raina Robeva ; Jennifer Kim Penberthy14：
Bayesian Probability Algorithm
The Value of Bayesian Probability Approach as a Meta-Analysis Tool
Discussion and Future Directions
Simple Stochastic Simulation / Maria J. Schilstra ; Stephen R. Martin15：
Understanding Reaction Dynamics
Graphical Notation
Reactions
Reaction Kinetics
Transition Firing Rules
Notes
Monte Carlo Simulation in Establishing Analytical Quality Requirements for Clinical Laboratory Tests: Meeting Clinical Needs / James C. Boyd ; David E. Bruns16：
Modeling Approach
Methods for Simulation Study
Results
Nonlinear Dynamical Analysis and Optimization for Biological/Biomedical Systems / Amos Ben-Zvi ; Jong Mm Lee17：
Hypothalamic-Pituitary-Adrenal Axis System
Development of a Clinically Relevant Performance-Assessment Tools
Dynamic Programming
Computation of Optimal Treatments for HPA Axis System
Modeling of Growth Factor-Receptor Systems: From Molecular-Level Protein Interaction Networks to Whole-Body Compartment Models / Florence T. H. Wu ; Marianne O. Stefanini ; Feilim Mac Gabhann ; Aleksander S. Popel18：
Molecular-Level Kinetics Models: Simulation of In Vitro Experiments
Mesoscale Single-Tissue 3D Models: Simulation of In Vivo Tissue Regions
Single-Tissue Compartmental Models: Simulation at In Vivo Tissue
Multitissue Compartmental Models: Simulation of Whole Body
The Least-Squares Analysis of Data from Binding and Enzyme Kinetics Studies: Weights, Bias, and Confidence Intervals in Usual and Unusual Situations / Joel Tellinghuisen19：
Least Squares Review
Statistics of Reciprocals
Weights When y is a True Dependent Variable
Unusual Weighting: When x is the Dependent Variable
Assessing Data Uncertainty: Variance Function Estimation
Conclusion
Nonparametric Entropy Estimation Using Kernel Densities / Douglas E. Lake20：
Connection Between Template Matches and Kernel Densities
Summary and Future Work
Pancreatic Network Control of Glucagon Secretion and Counterregulation / Leon S. Farhy ; Anthony L. McCall21：
Mechanisms of Glucagon Counterregulation (GCR) Dysregulation in Diabetes
Interdisciplinary Approach to Investigating the Defects in the GCR
Initial Qualitative Analysis of the GCR Control Axis
Mathematical Models of the GCR Control Mechanisms in STZ-Treated Rats
Approximation of the Normal Endocrine Pancreas by a Minimal Control Network (MCN) and Analysis of the GCR Abnormalities in the Insulin Deficient Pancreas
Advantages and Limitations of the Interdisciplinary Approach
Enzyme Kinetics and Computational Modeling for Systems Biology / Pedro Mendes ; Hanan Messiha ; Naglis Malys ; Stefan Hoops22：
Computational Modeling and Enzyme Kinetics
Yeast Triosephosphate Isomerase (EC 5.3.1.1)
Initial Rate Analysis
Progress Curve Analysis
Fitting Enzyme Kinetic Data with KinTek Global Kinetic Explorer / Kenneth A. Johnson23：
Measurement and Analysis of Equilibrium Binding Titrations: A beginner's guide / Dorothy Beckett
Macromolecular Competition Titration Method: Accessing Thermodynamics of the Unmodified Macromolecule - Ligand Interactions Through Spectroscopic Titrations of Fluorescent Analogs / Wlodzimierz Bujalowski ; Maria J. Jezewska
Analysis of PKR-RNA interactions by sedimentation velocity / C. Jason Wong ; Katherine Launer-Felty ; James L. Cole
Structural and Thermodynamic Analysis of PDZ/Ligand Interactions / Tyson R. Shepherd ; Ernesto J. Fuentes
Thermodynamic analysis of metal ion-induced protein assembly / Andrew B. Herr ; Deborah G. Conrady
Thermodynamic Dissection of Colicin Interactions / Nicholas G Housden ; Colin Kleanthous
Energetics of Src homology domain interactions in receptor tyrosine kinase-mediated signaling / John E. Ladbury ; Stefan T. Arold
Structural and Functional Energetic Linkages in Allosteric Regulation of Muscle Pyruvate Kinase / J. Ching Lee ; Petr Herman
Analysis of Free Energy versus Temperature Curves in Protein Folding and Macromolecular Interactions / Vince J. LiCata ; Chin-Chi Liu
Application of the Sequential n-Step Kinetic Mechanism to Polypeptide Translocases / Aaron L. Lucius ; Justin M. Miller ; Burki Rajendar
A Coupled Equilibrium Approach to Study Nucleosome Thermodynamics / Andrew J. Andrews ; Karolin Luger
Quantitative methods for measuring DNA flexibility in vitro and in vivo / Justin P. Peters ; Nicole Becker ; Emily M. Rueter ; Zeljko Bajzer ; Jason D. Kahna ; L. James Maher
A Thermodynamic Approach for the Targeting of Nucleic Acid Structures Using Their Complementary Single Strands / Hui-Ting Lee ; Caroline Carr ; Hollie Siebler ; Lela Waters ; Irine Khutsishvili ; Fany Iseka ; Brian Domack ; Chris M. Olsen ; Luis Marky
Thermodynamics of Biological Processes / Hernan G. Garcia ; Jane Kondev ; Nigel Orme ; Julie Theriot ; Rob Phillips
Protein stability in the presence of co-solutes / Luis Marcelo F. Holthauzen ; Matthew Auton ; Mikhail Sineva ; Jorg Rosgen
Small Angle X-ray Scattering Studies of Peptide-Lipid Interactions using the Mouse Paneth Cell a-Defensin Cryptdin-4 / Abhijit Mishra ; Kenneth P. Tai ; Nathan W. Schmidt ; André J. Ouellette ; Gerard C. L. Wong
Synergy of molecular dynamics and isothermal titration calorimetry in studies of allostery / Rebecca Strawn ; Thomas Stockner ; Milan Melichercik ; Lihua Jin ; Wei-Feng Xue ; Jannette Carey ; Rüdiger Ettrich
Using tryptophan fluorescence to measure the stability of membrane proteins folded in liposomes / C. Preston Moon1 ; Karen G. Fleming
Non-B Conformations of CAG Repeats Using 2-aminopurine / Natalya N. Degtyareva ; Jeffrey T. Petty
Disulfide bond-mediated passenger domain stalling as a structural probe of autotransporter outer membrane secretion in vivo / Jonathan P. Renn ; Patricia L. Clark
Strategies for the Thermodynamic Characterization of Linked Binding/Local Folding Reactions Within the Native State: Application to the LID Domain of Adenylate Kinase from Escherichia coli / Travis P. Schrank ; W. Austin Elam ; Jing Li ; Vincent J. Hilser
Measurement and Analysis of Equilibrium Binding Titrations: A beginner's guide / Dorothy Beckett
Macromolecular Competition Titration Method: Accessing Thermodynamics of the Unmodified Macromolecule - Ligand Interactions Through Spectroscopic Titrations of Fluorescent Analogs / Wlodzimierz Bujalowski ; Maria J. Jezewska
Analysis of PKR-RNA interactions by sedimentation velocity / C. Jason Wong ; Katherine Launer-Felty ; James L. Cole
Predicting Fluorescence Lifetimes and Spectra of Biopolymers / Patrik R. Callis
Modeling of Regulatory Networks: Theory and Applications in the study of the Drosophila Circadian Clock / Elizabeth Y. Scribner ; Hassan M. Fathallah-Shaykh
Strategies for articulated multibody-based adaptive coarse grain simulation of RNA / Mohammad Poursina ; Kishor D. Bhalerao ; Samuel C. Flores ; Kurt S. Anderson ; Alain Laederach
Modeling Loop Entropy / Gregory S. Chirikjian
Inferring Functional Relationships and Causal Network Structure from Gene Expression Profiles / Radhakrishnan Nagarajan
Numerical solution of the chemical master equation: uniqueness and stability of the stationary distribution for chemical networks, and mRNA bursting in a gene network with negative feedback regulation / E. S. Zeron ; M. Santill_an
How molecular should your molecular model be? On the level of molecular detail required to simulate biological networks in systems and synthetic biology / Didier Gonze ; Wassim Abou-Jaoud´e ; Adama Ouattara ; Jos´e Halloy
Computational modelling of biological pathways by executable biology / Maria Luisa Guerriero John K. Heath
Computing Molecular Fluctuations in Biochemical Reaction Systems Based on A Mechanistic, Statisitical Theory of Irreversible Processes / Don Kulasiri
Probing the input-output behaviour of biochemical and genetic systems: system identification methods from control theory / David McMillen ; Brian Ingalls ; Jordan Ang
Biochemical pathway modelling tools for drug target detection in cancer and other complex diseases / Alberto Marin-Sanguino ; Shailendra K. Gupta ; Eberhard O. Voit ; Julio Vera
Deterministic and Stochastic Simulation and Analysis of Biochemical Reaction Networks: The Lactose Operon Example / Necmettin Yildirim ; Caner Kazanci F.
Multivariate Neighborhood Sample Entropy: A method for data reduction and prediction of complex data / Joshua S. Richman MD, PhD
Scaling differences of heartbeat excursions between wake and sleep periods / L. Guzm´an-Vargas ; I. Reyes-Ram´irez ; R. Hern´andez-P´erez ; F. Angulo-Brown
Changepoint analysis for single-molecule polarized totalinternal reflection fluorescence microscopy experiments / John F. Beausang ; Yale E. Goldman ; Philip C. Nelson
Inferring mechanisms from dose-response curves / Carson C. Chow ; Karen M. Ong ; Edward J. Dougherty ; S. Stoney Simons, Jr
Spatial Aspects in Biological System Simulations / Haluk Resat ; Michelle N. Costa ; Harish Shankaran
Computational Approaches to Modeling Viral Structure and Assembly / Stephen C. Harvey ; Anton S. Petrov ; Batsal Devkota ; Mustafa Burak Boz
An Object-Oriented Software Suite for the Simulation and Design of Macromolecules / Andrew Leaver-Fay ; Michael Tyka ; Steven M. Lewis ; Oliver F. Lange ; James Thompson ; Ron Jacak ; Kristian Kaufman ; P. Douglas Renfrew ; Colin A. Smith ; Will Sheffler ; Ian W. Davis ; Seth Cooper ; Adrien Treuille ; Daniel J. Mandell ; Florian Richter ; Yih-En Andrew Ban ; Sarel J. Fleishman ; Jacob E. Corn ; David E. Kim ; Sergey Lyskov ; Monica Berrondo ; Stuart Mentzer ; Zoran Popovic ; James J. Havranek ; John Karanicolas ; Rhiju Das ; Jens Meiler ; Tanja Kortemme ; Jeffrey J. Gray ; Brian Kuhlman1 ; David Baker ; Philip Bradley
Computational Design of Intermolecular Stability and Specificity in Protein Self-Assembly / Vikas Nanda ; Sohail Zahid ; Fei Xu ; Daniel Levine
Predicting Fluorescence Lifetimes and Spectra of Biopolymers / Patrik R. Callis
Modeling of Regulatory Networks: Theory and Applications in the study of the Drosophila Circadian Clock / Elizabeth Y. Scribner ; Hassan M. Fathallah-Shaykh
Strategies for articulated multibody-based adaptive coarse grain simulation of RNA / Mohammad Poursina ; Kishor D. Bhalerao ; Samuel C. Flores ; Kurt S. Anderson ; Alain Laederach
A Thermodynamic Approach for the Targeting of Nucleic Acid Structures Using Their Complementary Single Strands / Hui-Ting Lee ; Caroline Carr ; Hollie Siebler ; Lela Waters ; Irine Khutsishvili ; Fany Iseka ; Brian Domack ; Chris M. Olsen ; Luis A. Marky1：
Introduction
Materials and Methods / 2：
Results and Discussion / 3：
Conclusions / 4：
Acknowledgments
References
Thermodynamics of Biological Processes / Hernan G. Garcia ; Jane Kondev ; Nigel Orme ; Julie A. Theriot ; Rob Phillips
Introduction: Thermodynamics is Not Just for Dead Stuff
States and Weights from the Boltzmann Rule
Binding Reactions and Biological Thermodynamics
The Unreasonable Effectiveness of Random-Walk Models
Protein Stability in the Presence of Cosolutes / Luis Marcelo F. Holthauzen ; Matthew Auton ; Mikhail Sinev ; Jörg Rösgen5：
Isothermal Folding/Unfolding of Protein in the Presence of Stabilizing/Denaturing Osmolyte
Isothermal Protein (Un)Folding in the Presence of Osmolyte Mixtures
Osmolyte-Induced Unfolding at Variable Temperature
X-Rays as Structural Probes of Biological Systems Under Biomimetic Conditions
Preparation of Peptide-Lipid Complexes for X-Ray Measurements
Summary
Synergy of Molecular Dynamics and Isothermal Titration Calorimetry in Studies of Allostery / Rebecca Strawn ; Thomas Stockner ; Milan Melichercik ; Lihua Jin ; Wei-Feng Xue ; Jannette Carey ; Rüdiger Ettrich
Allostery
Arginine Repressor
Preparation for Simulations
Sampling of States
Equilibration
Observing System Motions
Correlated Motions / 7：
Structural Features of Correlated Motions / 8：
Arg Residues Promote Rotation and Oscillation / 9：
Structural Correlates of Rotational Oscillation / 10：
Single-Arginine Simulations / 11：
Rotational Ensembles / 12：
Energetic Contributions / 13：
Reconciliation with Crystallographic Data / 14：
Complementarity and Synergy of MD and ITC / 15：
Prospects / 16：
Acknowledgement
Using Tryptophan Fluorescence to Measure the Stability of Membrane Proteins Folded in Liposomes / C. Preston Moon ; Karen G. Fleming
Issues with Managing Light Scattering from Liposomes
Using Tryptophan Spectral Properties to Monitor Membrane Protein Folding into Liposomes
Choosing an Appropriate Tryptophan Spectral Property to Measure the Thermodynamic Stabilities of Folded Membrane Proteins
Non-B Conformations of CAG Repeats Using 2-Aminopurine / Natalya N. Degtyareva ; Jeffrey T. Petty
Disulfide Bond-Mediated Passenger Domain Stalling as a Structural Probe of Autotransporter Outer Membrane Secretion In Vivo / Jonathan P. Renn ; Patricia L. Clark
Protein Secretion: An Essential Component of Bacterial Virulence
The Autotransporter Secretion Pathway
Overview of Cys-Loop Stalling
Architecture and Processing of AT Passenger Domains
Heterologous Passenger Domain Secretion
Selecting a Model Autotransporter for Cys-Loop Stalling
Disulfide Mediated Passenger Domain Stalling
Methods to Measure OM Secretion and Folding of the Stalled AT Passenger
Applications: Using Cys-Loop Stalling to Define the Mechanism of AT OM Secretion
Strategies for the Thermodynamic Characterization of Linked Binding/Local Folding Reactions Within the Native State: Application to the LID Domain of Adenylate Kinase from Escherichia coli / Travis P. Schrank ; W. Austin Elam ; Jing Li ; Vincent J. Hilser
A Mutation Strategy to Amplify Locally Unfolded States
Thermodynamic Properties of Linked Folding and Binding Reactions
Strategies for Quantitative Interpretation of Measured Enthalpies for a Linked Folding and Binding System
Interplay of Local Mutational Effects, Global Stability, and Binding Affinity
Success of the Strategy in Preserving Structure
Comparison of Interaction Versus Entropy Based Mutation Strategy
How Similar Are Local and Global Unfolding?
Fluorescence-Detected Sedimentation in Dilute and Highly Concentrated Solutions / Jonathan S. Kingsbury ; Thomas M. Laue
Phase Response Curves: Elucidating the Dynamics of Coupled Oscillators / A. Granada ; R. M. Hennig ; B. Ronacher ; A. Kramer ; H. Herzel1：
Introduction
Estimation of Phase Response Curves / 2：
Specific Applications / 3：
Discussion / 4：
Acknowledgments / Appendix I：
References
Multiple Ion Binding Equilibria, Reaction Kinetics, and Thermodynamics in Dynamic Models of Biochemical Pathways / Kalyan C. Vinnakota ; Fan Wu ; Martin J. Kushmerick ; Daniel A. Beard
Biochemical Conventions and Calculations
Application to Physiological Systems
Acknowledgment
Analytical Methods for the Retrieval and Interpretation of Continuous Glucose Monitoring Data in Diabetes / Boris Kovatchev ; Marc Breton ; William Clarke
Decomposition of Sensor Errors
Measures of Average Glycemia and Deviation from Target
Risk and Variability Assessment
Measures and Plots of System Stability / 5：
Time-Series-Based Prediction of Future BG Values / 6：
Conclusions / 7：
Analysis of Heterogeneity in Molecular Weight and Shape by Analytical Ultracentrifugation Using Parallel Distributed Computing / Borries Demeler ; Emre Brookes ; Luitgard Nagel-Steger
Methodology
Job Submission
Results
Discrete Stochastic Simulation Methods for Chemically Reacting Systems / Yang Cao ; David C. Samuels
The Chemical Master Equation
The Stochastic Simulation Algorithm
The Tau-Leaping Method
Measurement of Simulation Error
Software and Two Numerical Experiments
Conclusion
Analyses for Physiological and Behavioral Rhythmicity / Harold B. Dowse
Types of Biological Data and Their Acquisition
Analysis in the Time Domain
Analysis in the Frequency Domain
Time/Frequency Analysis and the Wavelet Transform
Signal Conditioning
Strength and Regularity of a Signal
A Computational Approach for the Rational Design of Stable Proteins and Enzymes: Optimization of Surface Charge-Charge Interactions / Katrina L. Schweiker ; George I. Makhatadze8：
Computational Design of Surface Charge-Charge Interactions
Experimental Verification of Computational Predictions
Closing Remarks
Efficient Computation of Confidence Intervals for Bayesian Model Predictions Based on Multidimensional Parameter Space / Amber D. Smith ; Alan Genz ; David M. Freiberger ; Gregory Belenky ; Hans P. A. Van Dongen
Height of the Probability Density Function at the Boundary of the Smallest Multidimensional Confidence Region
Approximating a One-Dimensional Slice of the Probability Density Function by Means of Normal Curve Spline Pieces
Locating the Boundary of the Smallest Multidimensional Confidence Region
Finding the Minimum and Maximum of the Prediction Model over the Confidence Region
An Application: Bayesian Forecasting of Cognitive Performance Impairment during Sleep Deprivation
95% Confidence Intervals for Bayesian Predictions of Cognitive Performance Impairment during Sleep Deprivation
Appendix
Analyzing Enzymatic pH Activity Profiles and Protein Titration Curves Using Structure-Based pK<a/ Calculations and Titration Curve Fitting / Jens Erik Nielsen9：
Calculating the pH Dependence of Protein Characteristics
Least Squares in Calibration: Weights, Nonlinearity, and Other Nuisances / Joel Tellinghuisen10：
Review of Least Squares
Experiment Design Using Vprior/-Numerical Illustrations
Evaluation and Comparison of Computational Models / Jay I. Myung ; Yun Tang ; Mark A. Pitt11：
Conceptual Overview of Model Evaluation and Comparison
Model Comparison Methods
Model Comparison at Work: Choosing between Protein Folding Models
Desegregating Undergraduate Mathematics and Biology - Interdisciplinary Instruction with Emphasis on Ongoing Biomedical Research / Raina Robeva12：
Course Description
Mathematical Algorithms for High-Resolution DNA Melting Analysis / Robert Palais ; Carl T. Wittwer13：
Extracting Melting Curves from Raw Fluorescence
Methods Used for Clustering and Classifying Melting Curves by Genotype
Methods Used for Modeling Melting Curves
Biomathematical Modeling of Pulsatile Hormone Secretion: A Historical Perspective / William S. Evans ; Leon S. Farhy ; Michael L. Johnson14：
Early Attempts to Identify and Characterize Pulsatile Hormone Release
Impact of Sampling Protocol and Pulse Detection Algorithm on Hormone Pulse Detection
Application of Deconvolution Procedures for the Identification and Characterization of Hormone Secretory Bursts
Limitations and Subsequent Improvements in Deconvolution Procedures
Evaluation of Pulsatile and Basal Hormone Secretion Using a Stochastic Differential Equations Model
Characterization of Regulation of Signal and Response Elements: Estimation of Approximate Entropy
Evaluation of Coupled Systems
Evaluation of Hormonal Networks with Feedback Interactions
Future Directions
AutoDecon: A Robust Numerical Method for the Quantification of Pulsatile Events / Lenore Pipes ; Paula P. Veldhuis ; Ralf Nass ; Michael O. Thorner15：
Methods
Modeling Fatigue over Sleep Deprivation, Circadian Rhythm, and Caffeine with a Minimal Performance Inhibitor Model / Patrick L. Benitez ; Gary H. Kamimori ; Thomas J. Balkin ; Alexander Greene16：
A Method in Enzymology for Measuring Hydrolytic Activities in Live Cell Environments / Beverly Z. Packard ; Akira Komoriya1：
Protease Substrate Design
Protease Specificity / 2：
Cell-Permeable Fluorogenic Probes / 3：
Conclusions / 4：
References
Heterogeneity of Fluorescence Determined by the Method of Area-Normalized Time-Resolved Emission Spectroscopy / N. Periasamy
Introduction
TRES and TRANES Methods
TRES and TRANES Spectra of Simple Cases
Physical Significance of TRANES and Isoemissive Point
TRES and TRANES of Fluorophores in Microheterogeneous Media / 5：
Fluorescence in Microheterogeneous and Biological Media: Special Cases / 6：
Acknowledgment
Multiparametric Probing of Microenvironment with Solvatochromic Fluorescent Dyes / Andrey S. Klymchenko ; Alexander P. Demchenko
"Universal" and "Specific" Noncovalent Interactions
The Methodology of Multiparametric Approach with Application of 3-Hydroxyflavone Dyes
Correlations of Spectroscopic Data with Solvatochromic Variables
Algorithm for Multiparametric Probing Based on Parameters of Absorption and Dual Emission
Application of Multiparametric Probing
Limitations of the Multiparametric Approach
Concluding Remarks / 7：
Site-Selective Red-Edge Effects
Molecular Disorder and the Origin of Red-Edge Effects
The Principle of Photoselection
Ground-State Heterogeneity
The Magnitude of Red-Edge Excitation Fluorescence Shift and Its Connection with Dielectric Relaxations
Red-Edge Effect with High Resolution in Time
Red-Edge Effects in Excited-State Reactions
Fluorescent Probes for Optimal Observation of Red-Edge Effects / 8：
Peculiarities of the Red-Edge Effects of Indole and Tryptophan / 9：
Fluorescence Approaches to Quantifying Biomolecular Interactions / Catherine A. Royer ; Suzanne F. Scarlata10：
Fluorescence Observables
Designing a Fluorescence Experiment
Forster Resonance Energy Transfer Measurements of Transmembrane Helix Dimerization Energetics / Mikhail Merzlyakov ; Kalina Hristova
Challenges in Quantitative Measurements of Interactions Between TM Helices in Bilayers
Bilayer Platforms for Measuring TM Helix Interactions Using FRET
FRET Due to Random Colocalization of Donors and Acceptors (Proximity FRET)
FRET Efficiencies and Energetics of TM Helix Dimerization
Biological Insights from FRET Measurements
Conclusion
Application of Single-Molecule Spectroscopy in Studying Enzyme Kinetics and Mechanism / Jue Shi ; Joseph Dertouzos ; Ari Gafni ; Duncan Steel
Experimental Considerations
Sample Preparation
Instrumentation
Data Analysis of Single-Molecule Trajectories
Additional Considerations
Summary
Ultrafast Fluorescence Spectroscopy via Upconversion: Applications to Biophysics / Jianhua Xu ; Jay R. Knutson
Basic Concepts
Upconversion Spectrophotofluorometer and Experimental Considerations
Ultrafast Photophysics of Single Tryptophan, Peptides, Proteins, and Nucleic Acids
Summary and Future Directions
Use of Fluorescence Resonance Energy Transfer (FRET) in Studying Protein-induced DNA Bending / Anatoly I. Dragan ; Peter L. Privalov
Preparation of Labeled DNA Duplexes
Fluorescence Resonance Energy Transfer
FRET in Studying Large Protein-Induced DNA Bends
Dependence of the Protein-induced DNA Bend on the Forces Involved in Binding
FREt in Studying Small Protein-Induced DNA Bends
Fluorescent Pteridine Probes for Nucleic Acid Analysis / Mary E. Hawkins
Pteridine Analog Characteristics
Procedures for Oligonucleotide Synthesis with Pteridine Analogs
Characterization of Pteridine-Containing Sequences
Applications
Acknowledgments
Single-Molecule Fluorescence Methods for the Analysis of RNA Folding and Ribonucleoprotein Assembly / Goran Pljevaljcic ; David P. Millar11：
Labeling Methods
Single-Molecule Fluorescence Detection Methods
Diffusion Single-Pair FRET for RNA Based Systems
Total Internal Reflection Fluorescence (TIRF) for RNA Based Systems
Application 1: Folding of the Hairpin Ribozyme
Application 2: Assembly of the Rev-RRE Complex
Using Fluorophore-Labeled Oligonucleotides to Measure Affinities of Protein-DNA Interactions / Brian J. Anderson ; Chris Larkin ; Kip Guja ; Joel F. Schildbach12：
Definitions of Fluorescence Anisotropy and Intensity
Advantages of Fluorescence Measurements
Disadvantages of Fluorescence Measurements
Designing the Oligonucleotide
Designing the Experiment
Competition Assays for Determining Specificity
Identifying Small Pulsatile Signals within Noisy Data: A Fluorescence Application / Michael L. Johnson ; Leon S. Farhy ; Paula P. Veldhuis ; Joseph R. Lakowicz13：
Methods
Results
Discussion
Determination of Zinc Using Carbonic Anhydrase-Based Fluorescence Biosensors / Rebecca Bozym ; Tamiika K. Hurst ; Nissa Westerberg ; Andrea Stoddard ; Carol A. Fierke ; Christopher J. Frederickson ; Richard B. Thompson14：
Principles of CA-Based Zinc Sensing
Transducing Zinc Binding as a Fluorescence Change
"Free" Versus Bound Zinc Ion: Speciation
Metal Ion Buffers
Kinetics
Applications: Ratiometric Determination of Free Zinc in Solution
Preparation of Apocarbonic Anhydrase
Intracellular Sensing with TAT Tag
Intracellular Sensing with an Expressible CA Sensor
Instrumentation for Fluorescence-Based Fiber Optic Biosensors / Hui-Hui Zeng ; Daniel Ohnemus ; Bryan McCranor ; Michele Cramer ; James Moffett15：
Introduction and Rationale for Fluorescence-Based Fiber Optic Sensors
Basic Principles of Fiber Optics for Fluorescence Sensors
Optics and Mechanics of Fluorescence-Based Fiber Optic Sensors
Mounting and Alignment of the Instrument
Standards for Ratiometric and Lifetime-Based Fiber Optic Fluorescence Sensors
Construction of Fiber Optic Probes
Zn[superscript 2+] Probe
Cu[superscript 2+] Probe
Use of Fiber Optic Probes for Discrete Samples
Operating Issues: Noise, Background, Thermal Drift, and Mode Hopping
Practical Approaches to Protein Folding and Assembly: Spectroscopic Strategies in Thermodynamics and Kinetics / Jad Walters ; Sara L. Milam ; A. Clay Clark1：
Introduction
Equilibrium Unfolding / 2：
Measuring Folding Kinetics / 3：
References
Using Thermodynamics to Understand Progesterone Receptor Function: Method and Theory / Keith D. Connaghan-Jones ; David L. Bain
Assessing Protein Functional and Structural Homogeneity
Dissecting Linked Assembly Reactions
Analysis and Dissection of Natural Promoters / 4：
Measuring the Energetics of Coactivator Recruitment / 5：
Correlation to Biological Function / 6：
Conclusions and Future Directions / 7：
Acknowledgments
General Principles / Dan Grilley ; Ana Maria Soto ; David E. Draper
Ion-Binding Properties of HQS
Preparation of Solutions and Reagents
Instrumentation and Data Collection Protocols
Data Analysis
Controls and Further Considerations
Analysis of Repeat-Protein Folding Using Nearest-Neighbor Statistical Mechanical Models / Tural Aksel ; Doug Barrick
Historical Overview of Ising Models and Motivation for the Present Review
Linear Repeat Proteins and Their Connection to Linear Ising Models
Formulating a Homopolymer Partition Function and the Zipper Approximation
Matrix Approach: Homopolymers
Matrix Approach: Heteropolymers
Solvability Criteria for Ising Models Applied to Repeat-Protein Folding
Matrix Homopolymer Analysis of Consensus TPR Folding
Matrix Heteropolymer Analysis of Consensus Ankyrin Repeat Folding / 8：
Summary and Future Directions / 9：
Isothermal Titration Calorimetry: General Formalism Using Binding Polynomials / Ernesto Freire ; Arne Schön ; Adrian Velazquez-Campoy
The Binding Polynomial
Microscopic Constants and Cooperativity
Independent or Cooperative Binding?
Analysis of ITC Data Using Binding Polynomials
A Typical Case: Macromolecule with Two Ligand-Binding Sites
Data Interpretation
An Experimental Example
Experimental Situations from the Literature / 10：
Macromolecule with Three Ligand-Binding Sites / 11：
Conclusions / 12：
Appendix
Acknowledgment
Kinetic and Equilibrium Analysis of the Myosin ATPase / Enrique M. De La Cruz ; E. Michael Ostap
Reagents and Equipment Used for all Assays
Steady-State ATPase Activity of Myosin
Steady-State Measurement of Actomyosin Binding Affinities
Transient Kinetic Analysis of the Individuals ATPase Cycle Transitions
Kinetic Simulations
The Hill Coefficient: Inadequate Resolution of Cooperativity in Human Hemoglobin / Jo M. Holt ; Gary K. Ackers
Cooperativity and Intrinsic Binding
The Macroscopic Binding Isotherm
The Hill Coefficient
Microscopic Cooperativity in Hemoglobin
Summary
Methods for Measuring the Thermodynamic Stability of Membrane Proteins / Heedeok Hong ; Nathan H. Joh ; James U. Bowie ; Lukas K. Tamm
Two Classes of Membrane Proteins
Methods for Measuring Transmembrane Domain Oligomer Stability
Methods for Measuring Multipass ?-helical Membrane Protein Stability
Methods to Study the Stability of ?-barrel Membrane Proteins
A Few Salient Results on Forces that Stabilize Membrane Proteins
Conclusion and Outlook
NMR Analysis of Dynein Light Chain Dimerization and Interactions With Diverse Ligands / Gregory Benison ; Elisar Barbar
NMR Methodology
Monomer-dimer Equilibrium Coupled to Electrostatics
Dimerization is Coupled to Ligand Binding
Folding is Coupled to Binding
Allostery in LC8
Characterization of Parvalbumin and Polcalcin Divalent Ion Binding by Isothermal Titration Calorimetry / Michael T. Henzl
Practical Aspects of Data Collection
Illustrative Global ITC Analyses of Divalent Ion Binding
Conclusion
Energetic Profiling of Protein Folds / Jason Vertrees ; James O. Wrabl ; Vincent J. Hilser
Modeling the Native State Ensemble of Proteins using Statistical Thermodynamics
Energetic Profiles of Proteins Derived from Thermodynamics of the Native State Ensemble
Principal Components Analysis of Energetic Profile Space
Energetic Profiles are Conserved Between Homologous Proteins
Direct Alignment of Energetic Profiles Based on a Variant of the CE Algorithm
CE Algorithm Described for Structure Coordinates
Necessary Deviations from the CE Algorithm to Accommodate Energetic Profiles
Towards a Thermodynamic Homology of Fold Space: Clustering Energetic Profiles using STEPH
Energetic Profiles Provide a Vehicle to Discover Conserved Substructures in the Absence of Known Homology
Model Membrane Thermodynamics and Lateral Distribution of Cholesterol: From Experimental Data To Monte Carlo Simulation / Juyang Huang
Materials and Methods
Result and Discussion
Concluding Remarks
Thinking Inside the Box: Designing, Implementing, and Interpreting Thermodynamic Cycles to Dissect Cooperativity in RNA and DNA Folding / Nathan A. Siegfried ; Philip C. Bevilacqua13：
Folding Cooperativity Defined
Thermodynamic Boxes: Design, Implementation, and Interpretation
Thermodynamic Cubes: Design, Implementation, and Interpretation
Examples of Cooperativity in RNA
Measuring Thermodynamic Parameters by UV Melting
The Thermodynamics of Virus Capsid Assembly / Sarah Katen ; Adam Zlotnick14：
The Structural Basis of Capsid Stability
Analysis of Capsid Stability
Applications of Thermodynamic Evaluation of Virus Capsid Stability
Extracting Equilibrium Constants from Kinetically Limited Reacting Systems / John J. Correia ; Walter F. Stafford15：
NMR-based approaches for assessing effects of macromolecular crowding on globular proteins / Gary Pielak ; Andrew Miklos ; Lisa Charlton ; Conggang Li1：
Fluorescence spectroscopy in thermodynamic and kinetic analysis of membrane protein insertion / Alexey S. Ladokhin2：
Evaluating the energy-dependent "binding" in the early stage of protein import into chloroplasts / Mitsuru Akita ; Hitoshi Inoue3：
DNA length-dependent periodic properties of cooperative protein-DNA complexes / Michael Fried4：
Applying thermodynamic linkage to the study of pyruvate kinase / Aron Fenton5：
Conformational Stability of Cytochrome C / Reinhard Schweitzer-Stenner6：
Metadynamics methods applied to ion channel gating / Carmen Domene7：
Measuring Co-translational Conformations of Nascent Polypeptide Chains / Patricia L. Clark ; Krastyu G. Ugrinov8：
Taking an energetic approach to assess and explain cooperative gating phenomena in voltage-dependent potassium channels / Yifrach Ofer ; Zandany Nitzan ; Tzilhav Shem-Ad9：
Energetics of the collagen triple helix / Yujia Xu10：
Use of pressure perturbation calorimetry to characterize the volumetric properties of proteins / Katrina L. Schweiker ; George Makhatadze11：
Thermodynamic approaches to nucleosome-histone interactions / Andrew Andrews ; Karolin Luger12：
Thermodynamic approaches to carbohydrate binding by the agrin-G3 domain / Andrei T. Alexandrescu13：
Energetic methods applied to allostery in thrombin / Enrico Di Cera14：
Thermodynamics of protein translocation / Arnold J.M Driessen ; Alexej Kedrov15：
Solvent denaturation of proteins and the interpretation of the m-value / J. Martin Scholtz ; Nick Pace16：
Energetic approaches to the characterization of the E. coli PriA helicase / Wlodek Bujalowski17：
Protein-protein interactions and macromolecular stability / Lisa Gloss18：
Methods for assessing T cell receptor recognition / Brian M Baker19：
Thermodynamic analysis applied to bromodomain-histone interactions / Martin Thompson20：
Small molecule-membrane interactions / Anne Hinderliter22：
Constant pH molecular dynamics simulations / Jana Khandogin Shen23：
NMR-based approaches for assessing effects of macromolecular crowding on globular proteins / Gary Pielak ; Andrew Miklos ; Lisa Charlton ; Conggang Li1：
Fluorescence spectroscopy in thermodynamic and kinetic analysis of membrane protein insertion / Alexey S. Ladokhin2：
Evaluating the energy-dependent "binding" in the early stage of protein import into chloroplasts / Mitsuru Akita ; Hitoshi Inoue3：
Correlation Analysis: A Tool for Comparing Relaxation-Type Models to Experimental Data / Maurizio Tomaiuolo ; Joel Tabak ; Richard Bertram1：
Introduction
Scatter Plots and Correlation Analysis / 2：
Example 1: Relaxation Oscillations / 3：
Example 2: Square Wave Bursting / 4：
Example 3: Elliptic Bursting / 5：
Example 4: Using Correlation Analysis on Experimental Data / 6：
Summary / 7：
Acknowledgments
References
Trait Variability of Cancer Cells Quantified by High-Content Automated Microscopy of Single Cells / Vito Quaranta ; Darren R. Tyson ; Shawn P. Garbett ; Brandy Weidow ; Mark P. Harris ; Walter Georgescu
Background
Experimental and Computational Workflow
Application to Traits Relevant to Cancer Progression
Conclusions
Matrix Factorization for Recovery of Biological Processes from Microarray Data / Andrew V. Kossenkov ; Michael F. Ochs
Overview of Methods
Application to the Rosetta Compendium
Results of Analyses
Discussion
Modeling and Simulation of the Immune System as a Self-Regulating Network / Peter S. Kim ; Doron Levy ; Peter P. Lee
Mathematical Modeling of the Immune Network
Two Examples of Models to Understand T Cell Regulation
How to Implement Mathematical Models in Computer Simulations
Concluding Remarks
Acknowledgmentss
Entropy Demystified: The ôThermoö-dynamics of Stochastically Fluctuating Systems / Hong Qian
Energy
Entropy and ôThermoö-dynamics of Markov Processes
A Three-State Two-Cycle Motor Protein
Phosphorylation-Dephosphorylation Cycle1 Kinetics
Summary and Challenges
Effect of Kinetics on Sedimentation Velocity Profiles and the Role of Intermediates / John J. Correia ; P. Holland Alday ; Peter Sherwood ; Walter F. Stafford
Methods
ABCD Systems
Monomer-Tetramer Model
Algebraic Models of Biochemical Networks / Reinhard Laubenbacher ; Abdul Salam Jarrah
Computational Systems Biology
Network Inference
Reverse-Engineering of Discrete Models: An Example
High-Through put Computing in the Sciences / Mark Morgan ; Andrew Grimshaw8：
What is an HTC Application?
HTC Technologies
High-Throughput Computing Examples
Advanced Topics
Large Scale Transcriptome Data Integration Across Multiple Tissues to Decipher Stem Cell Signatures / Ghislain Bidaut ; Christian J. Stoeckert9：
Systems and Data Sources
Data Integration
Artificial Neural Network Training and Validation
Future Development and Enhancement Plans
DynaFit-A Software Package for Enzymology / Petr Kuzmiĉ10：
Equilibrium Binding Studies
Initial Rates of Enzyme Reactions
Time Course of Enzyme Reactions
General Methods and Algorithms
Discrete Dynamic Modeling of Cellular Signaling Networks / Réka Albert ; Rui-Sheng Wang11：
Cellular Signaling Networks
Boolean Dynamic Modeling
Variants of Boolean Network Models
Application Examples
Conclusion and Discussion
The Basic Concepts of Molecular Modeling / Akansha Saxena ; Diana Wong ; Karthikeyan Diraviyam ; David Sept12：
Homology Modeling
Molecular Dynamics
Molecular Docking
Deterministic and Stochastic Models of Genetic Regulatory Networks / Ilya Shmulevich ; John D. Aitchison13：
Boolean Networks
Differential Equation Models
Probabilistic Boolean Networks
Stochastic Differential Equation Models
Bayesian Probability Approach to ADHD Appraisal / Raina Robeva ; Jennifer Kim Penberthy14：
Bayesian Probability Algorithm
The Value of Bayesian Probability Approach as a Meta-Analysis Tool
Discussion and Future Directions
Simple Stochastic Simulation / Maria J. Schilstra ; Stephen R. Martin15：
Understanding Reaction Dynamics
Graphical Notation
Reactions
Reaction Kinetics
Transition Firing Rules
Notes
Monte Carlo Simulation in Establishing Analytical Quality Requirements for Clinical Laboratory Tests: Meeting Clinical Needs / James C. Boyd ; David E. Bruns16：
Modeling Approach
Methods for Simulation Study
Results
Nonlinear Dynamical Analysis and Optimization for Biological/Biomedical Systems / Amos Ben-Zvi ; Jong Mm Lee17：
Hypothalamic-Pituitary-Adrenal Axis System
Development of a Clinically Relevant Performance-Assessment Tools
Dynamic Programming
Computation of Optimal Treatments for HPA Axis System
Modeling of Growth Factor-Receptor Systems: From Molecular-Level Protein Interaction Networks to Whole-Body Compartment Models / Florence T. H. Wu ; Marianne O. Stefanini ; Feilim Mac Gabhann ; Aleksander S. Popel18：
Molecular-Level Kinetics Models: Simulation of In Vitro Experiments
Mesoscale Single-Tissue 3D Models: Simulation of In Vivo Tissue Regions
Single-Tissue Compartmental Models: Simulation at In Vivo Tissue
Multitissue Compartmental Models: Simulation of Whole Body
The Least-Squares Analysis of Data from Binding and Enzyme Kinetics Studies: Weights, Bias, and Confidence Intervals in Usual and Unusual Situations / Joel Tellinghuisen19：
Least Squares Review
Statistics of Reciprocals
Weights When y is a True Dependent Variable
Unusual Weighting: When x is the Dependent Variable
Assessing Data Uncertainty: Variance Function Estimation
Conclusion
Nonparametric Entropy Estimation Using Kernel Densities / Douglas E. Lake20：
Connection Between Template Matches and Kernel Densities
Summary and Future Work
Pancreatic Network Control of Glucagon Secretion and Counterregulation / Leon S. Farhy ; Anthony L. McCall21：
Mechanisms of Glucagon Counterregulation (GCR) Dysregulation in Diabetes
Interdisciplinary Approach to Investigating the Defects in the GCR
Initial Qualitative Analysis of the GCR Control Axis
Mathematical Models of the GCR Control Mechanisms in STZ-Treated Rats
Approximation of the Normal Endocrine Pancreas by a Minimal Control Network (MCN) and Analysis of the GCR Abnormalities in the Insulin Deficient Pancreas
Advantages and Limitations of the Interdisciplinary Approach
Enzyme Kinetics and Computational Modeling for Systems Biology / Pedro Mendes ; Hanan Messiha ; Naglis Malys ; Stefan Hoops22：
Computational Modeling and Enzyme Kinetics
Yeast Triosephosphate Isomerase (EC 5.3.1.1)
Initial Rate Analysis
Progress Curve Analysis
Fitting Enzyme Kinetic Data with KinTek Global Kinetic Explorer / Kenneth A. Johnson23：
Measurement and Analysis of Equilibrium Binding Titrations: A beginner's guide / Dorothy Beckett
Macromolecular Competition Titration Method: Accessing Thermodynamics of the Unmodified Macromolecule - Ligand Interactions Through Spectroscopic Titrations of Fluorescent Analogs / Wlodzimierz Bujalowski ; Maria J. Jezewska
Analysis of PKR-RNA interactions by sedimentation velocity / C. Jason Wong ; Katherine Launer-Felty ; James L. Cole
Structural and Thermodynamic Analysis of PDZ/Ligand Interactions / Tyson R. Shepherd ; Ernesto J. Fuentes
Thermodynamic analysis of metal ion-induced protein assembly / Andrew B. Herr ; Deborah G. Conrady
Thermodynamic Dissection of Colicin Interactions / Nicholas G Housden ; Colin Kleanthous
Energetics of Src homology domain interactions in receptor tyrosine kinase-mediated signaling / John E. Ladbury ; Stefan T. Arold
Structural and Functional Energetic Linkages in Allosteric Regulation of Muscle Pyruvate Kinase / J. Ching Lee ; Petr Herman
Analysis of Free Energy versus Temperature Curves in Protein Folding and Macromolecular Interactions / Vince J. LiCata ; Chin-Chi Liu
Application of the Sequential n-Step Kinetic Mechanism to Polypeptide Translocases / Aaron L. Lucius ; Justin M. Miller ; Burki Rajendar
A Coupled Equilibrium Approach to Study Nucleosome Thermodynamics / Andrew J. Andrews ; Karolin Luger
Quantitative methods for measuring DNA flexibility in vitro and in vivo / Justin P. Peters ; Nicole Becker ; Emily M. Rueter ; Zeljko Bajzer ; Jason D. Kahna ; L. James Maher
A Thermodynamic Approach for the Targeting of Nucleic Acid Structures Using Their Complementary Single Strands / Hui-Ting Lee ; Caroline Carr ; Hollie Siebler ; Lela Waters ; Irine Khutsishvili ; Fany Iseka ; Brian Domack ; Chris M. Olsen ; Luis Marky
Thermodynamics of Biological Processes / Hernan G. Garcia ; Jane Kondev ; Nigel Orme ; Julie Theriot ; Rob Phillips
Protein stability in the presence of co-solutes / Luis Marcelo F. Holthauzen ; Matthew Auton ; Mikhail Sineva ; Jorg Rosgen
Small Angle X-ray Scattering Studies of Peptide-Lipid Interactions using the Mouse Paneth Cell a-Defensin Cryptdin-4 / Abhijit Mishra ; Kenneth P. Tai ; Nathan W. Schmidt ; André J. Ouellette ; Gerard C. L. Wong
Synergy of molecular dynamics and isothermal titration calorimetry in studies of allostery / Rebecca Strawn ; Thomas Stockner ; Milan Melichercik ; Lihua Jin ; Wei-Feng Xue ; Jannette Carey ; Rüdiger Ettrich
Using tryptophan fluorescence to measure the stability of membrane proteins folded in liposomes / C. Preston Moon1 ; Karen G. Fleming
Non-B Conformations of CAG Repeats Using 2-aminopurine / Natalya N. Degtyareva ; Jeffrey T. Petty
Disulfide bond-mediated passenger domain stalling as a structural probe of autotransporter outer membrane secretion in vivo / Jonathan P. Renn ; Patricia L. Clark
Strategies for the Thermodynamic Characterization of Linked Binding/Local Folding Reactions Within the Native State: Application to the LID Domain of Adenylate Kinase from Escherichia coli / Travis P. Schrank ; W. Austin Elam ; Jing Li ; Vincent J. Hilser
Measurement and Analysis of Equilibrium Binding Titrations: A beginner's guide / Dorothy Beckett
Macromolecular Competition Titration Method: Accessing Thermodynamics of the Unmodified Macromolecule - Ligand Interactions Through Spectroscopic Titrations of Fluorescent Analogs / Wlodzimierz Bujalowski ; Maria J. Jezewska
Analysis of PKR-RNA interactions by sedimentation velocity / C. Jason Wong ; Katherine Launer-Felty ; James L. Cole
Predicting Fluorescence Lifetimes and Spectra of Biopolymers / Patrik R. Callis
Modeling of Regulatory Networks: Theory and Applications in the study of the Drosophila Circadian Clock / Elizabeth Y. Scribner ; Hassan M. Fathallah-Shaykh
Strategies for articulated multibody-based adaptive coarse grain simulation of RNA / Mohammad Poursina ; Kishor D. Bhalerao ; Samuel C. Flores ; Kurt S. Anderson ; Alain Laederach
Modeling Loop Entropy / Gregory S. Chirikjian
Inferring Functional Relationships and Causal Network Structure from Gene Expression Profiles / Radhakrishnan Nagarajan
Numerical solution of the chemical master equation: uniqueness and stability of the stationary distribution for chemical networks, and mRNA bursting in a gene network with negative feedback regulation / E. S. Zeron ; M. Santill_an
How molecular should your molecular model be? On the level of molecular detail required to simulate biological networks in systems and synthetic biology / Didier Gonze ; Wassim Abou-Jaoud´e ; Adama Ouattara ; Jos´e Halloy
Computational modelling of biological pathways by executable biology / Maria Luisa Guerriero John K. Heath
Computing Molecular Fluctuations in Biochemical Reaction Systems Based on A Mechanistic, Statisitical Theory of Irreversible Processes / Don Kulasiri
Probing the input-output behaviour of biochemical and genetic systems: system identification methods from control theory / David McMillen ; Brian Ingalls ; Jordan Ang
Biochemical pathway modelling tools for drug target detection in cancer and other complex diseases / Alberto Marin-Sanguino ; Shailendra K. Gupta ; Eberhard O. Voit ; Julio Vera
Deterministic and Stochastic Simulation and Analysis of Biochemical Reaction Networks: The Lactose Operon Example / Necmettin Yildirim ; Caner Kazanci F.
Multivariate Neighborhood Sample Entropy: A method for data reduction and prediction of complex data / Joshua S. Richman MD, PhD
Scaling differences of heartbeat excursions between wake and sleep periods / L. Guzm´an-Vargas ; I. Reyes-Ram´irez ; R. Hern´andez-P´erez ; F. Angulo-Brown
Changepoint analysis for single-molecule polarized totalinternal reflection fluorescence microscopy experiments / John F. Beausang ; Yale E. Goldman ; Philip C. Nelson
Inferring mechanisms from dose-response curves / Carson C. Chow ; Karen M. Ong ; Edward J. Dougherty ; S. Stoney Simons, Jr
Spatial Aspects in Biological System Simulations / Haluk Resat ; Michelle N. Costa ; Harish Shankaran
Computational Approaches to Modeling Viral Structure and Assembly / Stephen C. Harvey ; Anton S. Petrov ; Batsal Devkota ; Mustafa Burak Boz
An Object-Oriented Software Suite for the Simulation and Design of Macromolecules / Andrew Leaver-Fay ; Michael Tyka ; Steven M. Lewis ; Oliver F. Lange ; James Thompson ; Ron Jacak ; Kristian Kaufman ; P. Douglas Renfrew ; Colin A. Smith ; Will Sheffler ; Ian W. Davis ; Seth Cooper ; Adrien Treuille ; Daniel J. Mandell ; Florian Richter ; Yih-En Andrew Ban ; Sarel J. Fleishman ; Jacob E. Corn ; David E. Kim ; Sergey Lyskov ; Monica Berrondo ; Stuart Mentzer ; Zoran Popovic ; James J. Havranek ; John Karanicolas ; Rhiju Das ; Jens Meiler ; Tanja Kortemme ; Jeffrey J. Gray ; Brian Kuhlman1 ; David Baker ; Philip Bradley
Computational Design of Intermolecular Stability and Specificity in Protein Self-Assembly / Vikas Nanda ; Sohail Zahid ; Fei Xu ; Daniel Levine
Predicting Fluorescence Lifetimes and Spectra of Biopolymers / Patrik R. Callis
Modeling of Regulatory Networks: Theory and Applications in the study of the Drosophila Circadian Clock / Elizabeth Y. Scribner ; Hassan M. Fathallah-Shaykh
Strategies for articulated multibody-based adaptive coarse grain simulation of RNA / Mohammad Poursina ; Kishor D. Bhalerao ; Samuel C. Flores ; Kurt S. Anderson ; Alain Laederach
A Thermodynamic Approach for the Targeting of Nucleic Acid Structures Using Their Complementary Single Strands / Hui-Ting Lee ; Caroline Carr ; Hollie Siebler ; Lela Waters ; Irine Khutsishvili ; Fany Iseka ; Brian Domack ; Chris M. Olsen ; Luis A. Marky1：
Introduction
Materials and Methods / 2：
Results and Discussion / 3：
Conclusions / 4：
Acknowledgments
References
Thermodynamics of Biological Processes / Hernan G. Garcia ; Jane Kondev ; Nigel Orme ; Julie A. Theriot ; Rob Phillips
Introduction: Thermodynamics is Not Just for Dead Stuff
States and Weights from the Boltzmann Rule
Binding Reactions and Biological Thermodynamics
The Unreasonable Effectiveness of Random-Walk Models
Protein Stability in the Presence of Cosolutes / Luis Marcelo F. Holthauzen ; Matthew Auton ; Mikhail Sinev ; Jörg Rösgen5：
Isothermal Folding/Unfolding of Protein in the Presence of Stabilizing/Denaturing Osmolyte
Isothermal Protein (Un)Folding in the Presence of Osmolyte Mixtures
Osmolyte-Induced Unfolding at Variable Temperature
X-Rays as Structural Probes of Biological Systems Under Biomimetic Conditions
Preparation of Peptide-Lipid Complexes for X-Ray Measurements
Summary
Synergy of Molecular Dynamics and Isothermal Titration Calorimetry in Studies of Allostery / Rebecca Strawn ; Thomas Stockner ; Milan Melichercik ; Lihua Jin ; Wei-Feng Xue ; Jannette Carey ; Rüdiger Ettrich
Allostery
Arginine Repressor
Preparation for Simulations
Sampling of States
Equilibration
Observing System Motions
Correlated Motions / 7：
Structural Features of Correlated Motions / 8：
Arg Residues Promote Rotation and Oscillation / 9：
Structural Correlates of Rotational Oscillation / 10：
Single-Arginine Simulations / 11：
Rotational Ensembles / 12：
Energetic Contributions / 13：
Reconciliation with Crystallographic Data / 14：
Complementarity and Synergy of MD and ITC / 15：
Prospects / 16：
Acknowledgement
Using Tryptophan Fluorescence to Measure the Stability of Membrane Proteins Folded in Liposomes / C. Preston Moon ; Karen G. Fleming
Issues with Managing Light Scattering from Liposomes
Using Tryptophan Spectral Properties to Monitor Membrane Protein Folding into Liposomes
Choosing an Appropriate Tryptophan Spectral Property to Measure the Thermodynamic Stabilities of Folded Membrane Proteins
Non-B Conformations of CAG Repeats Using 2-Aminopurine / Natalya N. Degtyareva ; Jeffrey T. Petty
Disulfide Bond-Mediated Passenger Domain Stalling as a Structural Probe of Autotransporter Outer Membrane Secretion In Vivo / Jonathan P. Renn ; Patricia L. Clark
Protein Secretion: An Essential Component of Bacterial Virulence
The Autotransporter Secretion Pathway
Overview of Cys-Loop Stalling
Architecture and Processing of AT Passenger Domains
Heterologous Passenger Domain Secretion
Selecting a Model Autotransporter for Cys-Loop Stalling
Disulfide Mediated Passenger Domain Stalling
Methods to Measure OM Secretion and Folding of the Stalled AT Passenger
Applications: Using Cys-Loop Stalling to Define the Mechanism of AT OM Secretion
Strategies for the Thermodynamic Characterization of Linked Binding/Local Folding Reactions Within the Native State: Application to the LID Domain of Adenylate Kinase from Escherichia coli / Travis P. Schrank ; W. Austin Elam ; Jing Li ; Vincent J. Hilser
A Mutation Strategy to Amplify Locally Unfolded States
Thermodynamic Properties of Linked Folding and Binding Reactions
Strategies for Quantitative Interpretation of Measured Enthalpies for a Linked Folding and Binding System
Interplay of Local Mutational Effects, Global Stability, and Binding Affinity
Success of the Strategy in Preserving Structure
Comparison of Interaction Versus Entropy Based Mutation Strategy
How Similar Are Local and Global Unfolding?
Fluorescence-Detected Sedimentation in Dilute and Highly Concentrated Solutions / Jonathan S. Kingsbury ; Thomas M. Laue
Pathway of Allosteric Control as Revealed by Intermediate States of Hemoglobin / J.M. Holt ; G.K. Ackers
Probes of Energy Transduction in Enzyme Catalysis / Y. Huang ; D.W. Bolen
Macromolecules and Water: Probing with Osmotic Stress / V.A. Parsegian ; R.P. Rand ; D.C. Rau
Linkage of Protein Assembly to Protein-DNA Binding / I. Wong ; T.M. Lohman
Linkage at Steady State: Allosteric Transitions of Thrombin / E. Di Cera ; Q.D. Dang ; Y. Ayala ; A. Vindigni
Thermal Denaturation Methods in Study of Protein Folding / E. Freire
Kinetics of Lipid Membrane Phase Transitions: A Volume Perturbation Calorimeter Study / L. Chen ; R.L. Biltonen ; M.L. Johnson
Tight Binding Affinities Determined from the Thermodynamic Linkage to Protons by Titration Calorimetry / M.L. Doyle ; G. Louie ; P. Dal Monte ; T. Sokoloski
Calorimetric Methods for Interpreting Protein-Ligand Interactions / H.F. Fisher ; N. Singh
Extracting Thermodynamic Data from Equilibrium Melting Curves for Oligonucleotide Order-Disorder Transitions / K.J. Breslauer
Thermodynamics and Mutations in RNA-Protein Interactions / K.B. Hall ; J.K. Kranz
Melting Studies of RNA Unfolding and RNA-Ligand Interactions / D.E. Draper ; T.C. Gluick
Structural-Perturbation Approaches to Thermodynamics of Site-Specific Protein-DNA Interactions / L. Jen-Jacobson
Thermodynamic Parameters from Hydrogen Exchange Measurements / Y. Bai ; J.J. Englander ; L. Mayne ; J.S. Milne ; S.W. Englander
Application of Pressure to Biochemical Equilibria: The Other Thermodynamic Variable / C.A. Royer
Molecular Volume / L.M. Rellick ; W.J. Becktel
Hydrostatic and Osmotic Pressure as Tools to Study Macromolecular Recognition / C.R. Robinson ; S.G. Sligar
Sedimentation Equilibrium as Thermodynamic Tool / T.M. Laue
Footprint Phenotypes: Structural Models of DNA-Binding Proteins from Chemical Modification Analysis of DNA / J. Yang ; J. Carey
Low-Temperature Electrophoresis Methods / M. Perrella ; I. Denisov
Use of Multiple Spectroscopic Methods to Monitor Equilibrium Unfolding of Proteins / M.R. Eftink
Probing Structural and Physical Basis of Protein Energetics Linked to Protons and Salt / B. Garcia-Moreno
Evaluating Contribution of Hydrogen Bonding and Hydrophobic Bonding to Protein Folding / C.N. Pace
Analyzing Solvent Reorganization and Hydrophobicity / B. Lee
Simple Force Field for Study of Peptide and Protein Conformational Properties / T.P. Creamer ; G.D. Rose
Probes for Analysis of Stability of Different Variants of Aspartate Aminotransferase / M. Martinez-Carrion ; A. Artigues ; A. Berezov ; M.L. Bianconi ; A.M. Reyes ; A. Iriarte
Jo M.; Johnson, Michael L.; Ackers, Gary K.; Ackers, Gary K Holt, Gary K. Ackers, Jo M. Holt, Michael L. Johnson, Gary K. Ackers, Michael L. Johnson, Jo M. Holt
Pathway of Allosteric Control as Revealed by Intermediate States of Hemoglobin / J.M. Holt ; G.K. Ackers
Probes of Energy Transduction in Enzyme Catalysis / Y. Huang ; D.W. Bolen
Macromolecules and Water: Probing with Osmotic Stress / V.A. Parsegian ; R.P. Rand ; D.C. Rau
Linkage of Protein Assembly to Protein-DNA Binding / I. Wong ; T.M. Lohman
Linkage at Steady State: Allosteric Transitions of Thrombin / E. Di Cera ; Q.D. Dang ; Y. Ayala ; A. Vindigni
Thermal Denaturation Methods in Study of Protein Folding / E. Freire
Kinetics of Lipid Membrane Phase Transitions: A Volume Perturbation Calorimeter Study / L. Chen ; R.L. Biltonen ; M.L. Johnson
Tight Binding Affinities Determined from the Thermodynamic Linkage to Protons by Titration Calorimetry / M.L. Doyle ; G. Louie ; P. Dal Monte ; T. Sokoloski
Calorimetric Methods for Interpreting Protein-Ligand Interactions / H.F. Fisher ; N. Singh
Extracting Thermodynamic Data from Equilibrium Melting Curves for Oligonucleotide Order-Disorder Transitions / K.J. Breslauer
Thermodynamics and Mutations in RNA-Protein Interactions / K.B. Hall ; J.K. Kranz
Melting Studies of RNA Unfolding and RNA-Ligand Interactions / D.E. Draper ; T.C. Gluick
Structural-Perturbation Approaches to Thermodynamics of Site-Specific Protein-DNA Interactions / L. Jen-Jacobson
Thermodynamic Parameters from Hydrogen Exchange Measurements / Y. Bai ; J.J. Englander ; L. Mayne ; J.S. Milne ; S.W. Englander
Application of Pressure to Biochemical Equilibria: The Other Thermodynamic Variable / C.A. Royer
Molecular Volume / L.M. Rellick ; W.J. Becktel
Hydrostatic and Osmotic Pressure as Tools to Study Macromolecular Recognition / C.R. Robinson ; S.G. Sligar
Sedimentation Equilibrium as Thermodynamic Tool / T.M. Laue
Footprint Phenotypes: Structural Models of DNA-Binding Proteins from Chemical Modification Analysis of DNA / J. Yang ; J. Carey
Low-Temperature Electrophoresis Methods / M. Perrella ; I. Denisov
Use of Multiple Spectroscopic Methods to Monitor Equilibrium Unfolding of Proteins / M.R. Eftink
Probing Structural and Physical Basis of Protein Energetics Linked to Protons and Salt / B. Garcia-Moreno
Evaluating Contribution of Hydrogen Bonding and Hydrophobic Bonding to Protein Folding / C.N. Pace
Analyzing Solvent Reorganization and Hydrophobicity / B. Lee
Simple Force Field for Study of Peptide and Protein Conformational Properties / T.P. Creamer ; G.D. Rose
Probes for Analysis of Stability of Different Variants of Aspartate Aminotransferase / M. Martinez-Carrion ; A. Artigues ; A. Berezov ; M.L. Bianconi ; A.M. Reyes ; A. Iriarte
Gary K; Holt, Jo M.; Johnson, Michael L.; Ackers, Gary K. Ackers, Gary K. Ackers, Jo M. Holt, Michael L. Johnson, Gary K. Ackers, Michael L. Johnson, Jo M. Holt
Pathway of Allosteric Control as Revealed by Intermediate States of Hemoglobin / J.M. Holt ; G.K. Ackers
Probes of Energy Transduction in Enzyme Catalysis / Y. Huang ; D.W. Bolen
Macromolecules and Water: Probing with Osmotic Stress / V.A. Parsegian ; R.P. Rand ; D.C. Rau
Linkage of Protein Assembly to Protein-DNA Binding / I. Wong ; T.M. Lohman
Linkage at Steady State: Allosteric Transitions of Thrombin / E. Di Cera ; Q.D. Dang ; Y. Ayala ; A. Vindigni
Thermal Denaturation Methods in Study of Protein Folding / E. Freire
Kinetics of Lipid Membrane Phase Transitions: A Volume Perturbation Calorimeter Study / L. Chen ; R.L. Biltonen ; M.L. Johnson
Tight Binding Affinities Determined from the Thermodynamic Linkage to Protons by Titration Calorimetry / M.L. Doyle ; G. Louie ; P. Dal Monte ; T. Sokoloski
Calorimetric Methods for Interpreting Protein-Ligand Interactions / H.F. Fisher ; N. Singh
Extracting Thermodynamic Data from Equilibrium Melting Curves for Oligonucleotide Order-Disorder Transitions / K.J. Breslauer
Thermodynamics and Mutations in RNA-Protein Interactions / K.B. Hall ; J.K. Kranz
Melting Studies of RNA Unfolding and RNA-Ligand Interactions / D.E. Draper ; T.C. Gluick
Structural-Perturbation Approaches to Thermodynamics of Site-Specific Protein-DNA Interactions / L. Jen-Jacobson
Thermodynamic Parameters from Hydrogen Exchange Measurements / Y. Bai ; J.J. Englander ; L. Mayne ; J.S. Milne ; S.W. Englander
Application of Pressure to Biochemical Equilibria: The Other Thermodynamic Variable / C.A. Royer
Molecular Volume / L.M. Rellick ; W.J. Becktel
Hydrostatic and Osmotic Pressure as Tools to Study Macromolecular Recognition / C.R. Robinson ; S.G. Sligar
Sedimentation Equilibrium as Thermodynamic Tool / T.M. Laue
Footprint Phenotypes: Structural Models of DNA-Binding Proteins from Chemical Modification Analysis of DNA / J. Yang ; J. Carey
Low-Temperature Electrophoresis Methods / M. Perrella ; I. Denisov
Use of Multiple Spectroscopic Methods to Monitor Equilibrium Unfolding of Proteins / M.R. Eftink
Probing Structural and Physical Basis of Protein Energetics Linked to Protons and Salt / B. Garcia-Moreno
Evaluating Contribution of Hydrogen Bonding and Hydrophobic Bonding to Protein Folding / C.N. Pace
Analyzing Solvent Reorganization and Hydrophobicity / B. Lee
Simple Force Field for Study of Peptide and Protein Conformational Properties / T.P. Creamer ; G.D. Rose
Probes for Analysis of Stability of Different Variants of Aspartate Aminotransferase / M. Martinez-Carrion ; A. Artigues ; A. Berezov ; M.L. Bianconi ; A.M. Reyes ; A. Iriarte
Use of Least-Squares Techniques in Biochemistry / M.L. Johnson
Parameter Estimates from Nonlinear Models / D.G. Watts
Effects of Heteroscedasticity and Skewness on Prediction in Regression: Modeling Growth of the Human Heart / R.D. Abbott ; H.P. Gutgesell
Artifacts of Fourier Series Analysis / M. Lampl
Quantification of Evolution from Order to Randomness in Practical Time Series Analysis / S.M. Pincus
Sequential versus Simultaneous Analysis of Data: Differences in Reliability of Derived Quantitative Conclusions / M. Straume
Model-Independent Quantification of Measurement Error: Empirical Estimation of Discrete Variance Function Profiles Based on Standard Curves / J.D. Veldhuis
Impact of Variance Function Estimation in Regression and Calibration / L.-J. Hwang
Application of the Kalman Filter to Computational Problems in Statistics / E.N. Brown and ; C.H. Schmid
Modeling Chemical Reactions: Jacobian Paradigm and Related Issues / R.I. Shrager
The Mathematics of Biological Oscillators / G.B. Ermentrout
Diffusion-Modulated Energy Transfer and Quenching: Analysis by Numerical Integration of Diffusion Equation in Laplace Space / J. Kasba ; J.R. Lakowicz
Maximum Entropy Method of Data Analysis in Time-Resolved Spectroscopy / J.-C. Brochon
Analysis of Kinetic Data: Practical Applications of Computer Simulation and Fitting Programs / C. Frieden
Determination of Rate and Equilibrium Binding Constants for Macromolecular Interactions by Surface Plasmon Resonance / D.J. OShannessy ; M. Brigham-Burke ; K.K. Soneson ; P. Hensley ; I. Brooks
Analysis of Nonequilibrium Dynamics of Bound, Free, and Total Plasma Ligand Concentrations over Time Following Nonlinear Secretory Inputs: Kinetics of Two or More Hormones Pulsed into Compartments Containing Multiple Variable-Affinity Binding Proteins / L.M. Faunt
Testing Pulse Detection Algorithms with Simulations of Episodically Pulsatile Substrate, Metabolite, or Hormone Release
Error Analysis of Macromolecular Structures Determined with Nuclear MagneticResonance Data / J.W. Shriver ; S. Edmondson
Characterization of Enzyme-Complex Formation by Analysis of Nuclear Magnetic Resonance Line Shapes / C.B. Post
Computer Simulations of Nuclear Overhauser Effect Spectra of Complex Oligosaccharides / C.A. Bush
Determining Confidence Intervals for Parameters Derived from Analysis of Equilibrium Analytical Ultracentrifugation Data / D.G.Watts
Boundary Analysis in Sedimentation Velocity Experiments / W.F. Stafford, III
Statistical Thermodynamic Analysis of Differential Scanning Calorimetry Data: Structural Deconvolution of Heat Capacity Function of Proteins / E. Freire
Analysis of Two-Dimensional Differential Scanning Calorimetry Data: Elucidation of Complex Biomolecular Energetics
Monte Carlo Simulations of Membranes: Phase Transition of Small Unilamellar Dipalmitoylphosphatidylcholine Vesicles / I.P. Sugar ; R.L. Biltonen ; N. Mitchard
Analysis of Drug-DNA Binding Isotherms: A Monte Carlo Approach / J.J. Correia ; J.B. Chaires
Analysis of Multidimensional Spectroscopic Data to Monitor Unfolding of Proteins / G.D. Ramsay ; M.R. Eftink
Estimating Binding Constants for Site-Specific Interactions / B. Garcia-Moreno
Use of Least-Squares Techniques in Biochemistry / M.L. Johnson
Parameter Estimates from Nonlinear Models / D.G. Watts
Effects of Heteroscedasticity and Skewness on Prediction in Regression: Modeling Growth of the Human Heart / R.D. Abbott ; H.P. Gutgesell
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