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1.

電子ブック
ＥＢ
1. Numerical Computer Methods, Part C
Ludwig Brand, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books , Academic Press, 2000
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2.

電子ブック
ＥＢ
2. Energetics of Biological Macromolecules, Part C
John N. Abelson, Gary K. Ackers, Jo M. Holt, Michael L. Johnson, Melvin I. Simon
出版情報: Elsevier ScienceDirect Books , Burlington : Academic Press, 2000
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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
Predicting Thermodynamic Properties of RNA / M.J. Serra ; D.H. Turner
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
Thermodynamic Approaches to Understanding Aspartate Transcarbamylase / N.M. Allewell ; V.J. LiCata
On the Interpretation of Data from Isothermal Processes / R. Lumry
Author Index
Subject Index
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
3.

電子ブック
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3. Energetics of Biological Macromolecules, Part D
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
出版情報: Elsevier ScienceDirect Books , Burlington : Academic Press, 2004
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目次情報: 続きを見る
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
Predicting Thermodynamic Properties of RNA / M.J. Serra ; D.H. Turner
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
Thermodynamic Approaches to Understanding Aspartate Transcarbamylase / N.M. Allewell ; V.J. LiCata
On the Interpretation of Data from Isothermal Processes / R. Lumry
Author Index
Subject Index
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
4.

電子ブック
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4. Energetics of Biological Macromolecules, Part E
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
出版情報: Elsevier ScienceDirect Books , Burlington : Academic Press, 2004
所蔵情報: loading…
目次情報: 続きを見る
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
Predicting Thermodynamic Properties of RNA / M.J. Serra ; D.H. Turner
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
Thermodynamic Approaches to Understanding Aspartate Transcarbamylase / N.M. Allewell ; V.J. LiCata
On the Interpretation of Data from Isothermal Processes / R. Lumry
Author Index
Subject Index
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
5.

電子ブック
ＥＢ
5. Numerical Computer Methods, Part D
Ludwig; Johnson, Michael L. Brand, Ludwig Brand, Michael L. Johnson, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books , Burlington : Academic Press, 2004
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6.

電子ブック
ＥＢ
6. Numerical Computer Methods, Part E
Michael L.; Brand, Ludwig Johnson, Ludwig Brand, Michael L. Johnson, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books , Burlington : Academic Press, 2004
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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
7.

電子ブック
ＥＢ
7. Computer Methods Part A
Ludwig; Johnson, Michael L.; Brand, Ludwig Brand, Ludwig Brand, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books , Academic Press, 2009
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Contributors
Preface
Volumes in Series
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
Setting up and Running a pKa/ Calculation
Analyzing the Results of a pKa/ Calculation
How Reliable Are Calculated pKa/ Values?
Predicting pH Activity Profiles
Decomposition Analysis
Predicting Protein Stability Profiles
Fitting pH Titration Curves, pH Activity Profiles, and pH Stability Profiles
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：
Author Index
Subject Index
Contributors
Preface
Volumes in Series
8.

電子ブック
ＥＢ
8. Fluorescence Spectroscopy
Michael L; Brand, Ludwig; Johnson, Michael L. Johnson, Ludwig Brand, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books , Academic Press, 2008
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Contributors
Preface
Volumes in Series
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
Field and Shipboard Use
Author Index
Subject Index
Contributors
Preface
Volumes in Series
9.

電子ブック
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9. Biothermodynamics Part A
Michael L.; Holt, Jo M.; Ackers, Gary K.; Johnson, Michael L Johnson, Gary K. Ackers, Jo M. Holt, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books , Academic Press, 2009
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Contributors
Preface
Volumes in Series
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：
Methods
Simulation and Analysis of Dimerization
Kinetically Mediated Dimerization
A Stepwise Approach
Final Thoughts
Author Index
Subject Index
Contributors
Preface
Volumes in Series
10.

電子ブック
ＥＢ
10. Biothermodynamics, Part B
Michael L.; Holt, Jo M.; Ackers, Gary K.; Ackers, Gary K Johnson, Gary K. Ackers, Jo M. Holt, Michael L. Johnson
出版情報: Elsevier ScienceDirect Books , Academic Press, 2009
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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：
Thermodynamic parameters fo dimer-dimer interaction in 2-cys peroxiredoxin / Karl-Josef Dietz21：
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：
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