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1.

図書

図書
edited by Andrew B. Hughes
出版情報: Weinheim : Wiley-VCH, c2011  xx, 583 p. ; 25 cm
シリーズ名: Amino acids, peptides and proteins in organic chemistry / edited by Andrew B. Hughes ; v. 3
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Amino Acids As Building Blocks
Alpha-Amino Acid Biosnythesis (Proteinogenic and Non-Proteinogenic)
Heterocycles from Amino Acids
Radical Synthetic Methods for Alpha-Amino Acids
Enzymatic or Microbial Beta-Lactam Synthesis
Amino Acid Coupling Chemistry
Solution Phase Peptide Synthesis
Solid Phase Peptide Synthesis: Historical Aspects
Solid Phase Peptide Synthesis: Linkers
Solid Phase Peptide Synthesis: The Fmoc Methodology 1
Solid Phase Peptide Synthesis: The Fmoc Methodology 2
Solid Phase Peptide Synthesis: SPPS Strategies
Coupling Reagents
Chemical Ligation
Automation of Peptide Synthesis
Peptide Purification
Difficult Peptides
Amino Acids As Building Blocks
Alpha-Amino Acid Biosnythesis (Proteinogenic and Non-Proteinogenic)
Heterocycles from Amino Acids
2.

図書

図書
edited by Andrew B. Hughes
出版情報: Weinheim : Wiley-VCH, c2012  xviii, 490 p. ; 25 cm
シリーズ名: Amino acids, peptides and proteins in organic chemistry / edited by Andrew B. Hughes ; v. 5
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3.

図書

図書
edited by Andrew B. Hughes
出版情報: Weinheim : Wiley-VCH, c2011  xx, 531 p. ; 25 cm
シリーズ名: Amino acids, peptides and proteins in organic chemistry / edited by Andrew B. Hughes ; v. 4
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Protection Reactions
General Considerations
Alpha-Amino Protection (Nalpha-Protection)
Carboxy Protection
Side Chain Protection
Photocleavable Protections
Conclusion
Experimental Section
The Huisgen Cycloaddition in Peptidomimetic Chemistry
Introduction
The Huisgen [2+3] Cycloaddition Between Azides and Acetylenes
Mechanistic Consideration for the Cu-Huisgen and Ru-Huisgen Cycloaddition
Building Blocks for the Synthesis of Triazole Modified Peptidomimetics
Cyclic Triazole Peptidomimetics
Acylic Triazole Peptidomimetics
Useful Experimental Procedures
Recent Advances in Beta-Strand Mimetics
Macrocyclic Peptidomimetics
Acyclic Compounds
Aliphatic and Aromatic Carbocycles
Ligands Containing One Ring or Multiple Rings with One Heteroatom (O, S)
Ligands Containing One Ring with Two Heteroatoms (N,N)
Ligands Containing One Ring with Two Heteroatoms (N,S) or Three Heteroatoms (N,N,S or N,N,N)
Ligands Containing Two Rings with One Heteroatom (N or O)
Ligands Containing Two Rings with Two or Three Heteroatoms (N,N or N,S or N,N,N)
Concluding Remarks
Medicinal Chemistry of Alpha-Amino Acids
Glutamic Acid
Conformational Restriction
Bioisosterism
Structure-Activity-Studies
Medicinal Chemistry of Alicyclic Beta-Amino Acids
Five-Membered Alicyclic Beta-Amino Acids
Six-Membered Alicyclic Beta-Amino Acids
medicinal Chemistry of Alpha-Hydroxy-Beta-Amino Acids
Alpha-Hydroxy-Beta-Amino Acids
Antibacterial Agents
Inhibitors of Aminopeptidases
Aspartyl Proteases Inhibitors
Paclitaxel and its Derivatives
Peptide Drugs
Lights and Shades of Peptide and Protein Drugs
Peptide Drugs Available on the Market
Approved Peptides in Oncology
Antimicrobial Peptides
Perspectives
Oral Bioavailability of Peptide and Peptidomimetic Drugs
Fundamental Considerations of Intestinal Absorption
Barriers Limiting Oral Peptide/Peptidomimetic Drugs Bioavailability
Strategies to Improve Peptide-Based Drugs Oral Bioavailability
Conclusions
Asymmetric Synthesis of Beta-Lactams Via the Staudinger Reaction
The Staudinger Reaction
Influence of the Geometry of the Imine on Stereoselectivity in the Reaction
Influence of the Polarity of the Solvent on Stereoselectivity of the Reaction
Influence of the Isomerization of the Imine Prior to its Nucleophilic Attack onto the Ketene Stereoselectivity in the Reaction
Influence of the Order of Addition of the Reactants to the Reaction
Influence of Chiral Substituents on the Stereoselectivity of the Reaction
Asymmetric Induction from the Imine Component
Asymmetric Induction from the Ketene Component
Double Asymmetric Cycloinduction
Influence of Catalysts on the Stereoselectivity of the Reaction
Advances in N- and O-Glycopeptide Synthesis - A Tool to Study Clycosylation and Develop New Therapeutics
O-Glycopeptide Synthesis
Synthesis of Mucin Type Glycopeptides
Synthesis of Tumor-Associated Glycopeptides and Glycopeptide Vaccines
Synthesis of Tn, T, sialyl Tn, sialyl T Glycosylated Amino Acid Building Blocks
Synthesis of Tn, T, sialyl Tn, sialyl T Glycopeptides and Vaccines
Synthesis of Glycopeptide Recognition Domain of P-Selectin Glycoprotein Ligand 1 (PSGL-1)
Synthesis of a Core 2 sLe AMino Acid Building Block Including a sLe Mimic
Synthesis of Unsulfated and Sulfated Core 2 sLe and Core 2 sLe Mimic PSGL-1 Glycopeptides
Chemoenzymatic Synthesis of Unsulphated and Sulphated Sialyl Lewis PSGL-1 Glycopeptide
Synthesis of Other Types of O-Glycopeptides
Synthesis of Fmoc-GlcNAc-Ser/Thr Amino Acids
Synthesis of Estrogene Receptor Peptides for Conformational Analysis
Synthesis of N-Glycopeptides
Synthesis of Ribonuclease C (RNase C) Glycoprotein
Synthesis of Erythropoietin N-Glycopeptide Fragment 1-28
Synthesis of Biantennary Dodecasaccharide
Synthesis of N-Glycopeptide Fragment 1-28
Chemoenzymatic Synthesis of a HIV GP120 V3 Domain N-Glycopeptide
Synthesis of the Oxazoline Tetrasaccharide Donor
Synthesis of Fmoc-GlcNAc-Asn Amino Acid Building Block
Synthesis of V3 Cyclic GlcNAc Peptide and Endo A Coupling with Man3GlcNAc Oxazoline Donor
Recent Developments in Neoglycopeptide Synthesis
Neoglycoside and Neoglycopeptide Synthesis
Protein Side-Chain Modifications
Cu-Catalyzed Azide-Alkyne "Click" Cycloaddition
Cross Metathesis
Application of Neoglycopeptides as Synthetic Vaccines
Enzymatic, Molecular and Cell Biological Techniques
Combinatorial/Library Peptide Synthesis
High Throughput Synthesis of Peptides
Peptide Libraries
Future of Peptide Libraries
Synthetic Protocols
Protection Reactions
General Considerations
Alpha-Amino Protection (Nalpha-Protection)
4.

図書

図書
Arthur M. Lesk
出版情報: Oxford : Oxford University Press, 2010  xix, 455 p. ; 27 cm
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Introduction: Proteins in their Biological Context / 1:
Fundamentals of Protein Structure / 2:
Protein Structure Determination / 3:
Structural Bioinformatics / 4:
Proteins as Catalysts: Enzyme Structure, Kinetics, and Mechanism / 5:
Protein Interactions and Assemblies / 6:
Evolution of Protein Structure and Function / 7:
Protein Folding, Engineering and Design / 8:
Proteomics and Systems Biology / 9:
Systems Biology of Proteins / 10:
Proteins in Disease / 11:
Introduction: Proteins in their Biological Context / 1:
Fundamentals of Protein Structure / 2:
Protein Structure Determination / 3:
5.

図書

図書
Danton H. O'Day, Andrew Catalano, editors
出版情報: Dordrecht : Springer, c2013  vi, 371 p. ; 25 cm
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6.

図書

図書
volume editor, Stephan A. Sieber ; with contributions by R. Breinbauer ... [et al.]
出版情報: Heidelberg : Springer, c2012  xi, 165 p. ; 24 cm
シリーズ名: Topics in current chemistry = Fortschritte der chemischen Forschung ; 324
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7.

図書

図書
Arthur M. Lesk
出版情報: Oxford : Oxford University Press, 2016  xxii, 466 p. ; 27 cm
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Preface to the first edition
Preface to the second edition
Preface to the third edition
Introduction / 1:
Proteins in their biological context
The amino acids
Dogmas-central and peripheral
The relationship between ammo acid sequence and protein stricture is robust
Disorder in proteins
Regulation
The genetic code
With life so dependent on proteins, there is ample opportunity for things to go wrong
Genome sequences
Gene sequence determines amino acid sequence
Protein synthesis: the ribosome is the point of contact between genes and proteins-it is the fulcrum of genomics
Ribosomes were implicated in protein synthesis very early on
Structural studies of ribosomes by X-ray crystallography and electron microscopy
Protein stability, denaturation, aggregation, and turnover
Protein turnover
Description of protein structures
Primary structure
Secondary structure: helices and sheets are favourable conformations of the chain that recur in many proteins
Tertiary and quaternary structure
Folding patterns in native proteins-themes and variations
Modular proteins, and 'mixing and matching' as a mechanism of evolution
How do proteins develop new functions?
The study of proteins: in the laboratory, in the cell, in the computer
Spectroscopic methods of characterizing proteins in solution
Absorbance and fluorescence of proteins
Fluorescence is sensitive to the environment and dynamics of the chromophore
Fluorescence resonance energy transfer (FRET)
Circular dichroism
Protein expression patterns in space and time: Proteomics
Subcellular localization
The transcriptome
DNA microaaays
Mass spectrometry
Computing in protein science
Computer-instrument partnerships in the laboratory
Simulations, including molecular dynamics
Bioinformatics
Introduction to databanks for protein science
Information-retrieval tools
Web access to the scientific literature
Useful websites
Recommended reading
Exercises and Problems
Protein structure / 2:
Structures of the amino acids
Protein conformation
Conformational angles and the Sasisekharan-Ramakrishnan-Ramachandran plot
Sidechain conformation
Rotamer libraries
Stabilization of the naïve state
Conformational change
Protein folding patterns
Supersecondary structures
An album of small structures
Comparison of the folding patterns of acylphosphatase and a fungal toxin
Classification of protein structures
Databanks of protein structure classifications
SCOP
SCOP2
CATH
The DALI Database
A survey of protein structures and functions
Fibrous proteins
Enzymes-proteins that catalyse chemical reactions
Antibodies
Inhibitors
Carrier proteins
Membrane proteins
Receptors
Regulatory proteins
Motor proteins
Control of protein activity
Regulation of tyrosine hydroxylase illustrates several control mechanisms common to many proteins
Control cascades
Protein structure determination / 3:
X-ray crystallography
X-ray structure determination
X-ray crystallography of proteins
Interpretation of the electron density: model building and improvement
The endgame-refinement
How accurate are the structures?
X-ray crystallography-the theoretical background
Nuclear magnetic resonance spectroscopy in structural biology
NMR spectra of proteins
Measurement of NMR spectra
Protein structure determination by NMR
Assignment of the spectrum
Transverse relaxation optimized spectroscopy
From the data to the structure
Solid-state NMR: magic angle spinning
Near atomic-resolution low-temperature electron microscopy (cryo-EM)
Octameric pyruvate-ferredoxin oxidoreductase from Desulfovibrio vulgaris Hildenborough
Conformational change in activation of human integrin αVβ3
Trajectories of conformational change
The elastic network model accounts for conformational change in Mycobacterium tuberculosis thioredoxin reductase
The relationship between structure determinations of Isolated proteins, and protein structure and function in vivo
Protein structure prediction and modeling
A priori methods of protein structure prediction
Empirical, or 'knowledge-based', methods of protein structure prediction
Secondary structure prediction
Homology modelling
Fold recognition
Antibody modeling
Prediction of special categories of structures
Conformational energy calculations and molecular dynamics
ROSETTA
Protein structure prediction from contact maps derived from correlated mutations in multiple sequence alignments
Critical Assessment of Structure Prediction (CASP)
CAPRI
Bioinformatics of protein sequence and structure / 4:
Databases and information retrieval
Amino acid sequence databases
Protein databases at the U.S. National Center for Biotechnology Information
Specialized, or 'boutique', databases
Nucleic acid sequence databases
Genome databases and genome browsers
Ensembl
Expression and proteomics databases
Debases of macromolecular structure
Organization of wwPDB entries
Retrieval of sequences and structures
Retrieval of amino acid sequences by keyword
The Protein Information Resource (PIR) and associated databases
Retrieval of structures by keyword
Probing databanks with sequence information
Sequence alignment
The dotplot
Dotplots and alignments
BLAST and PSI-BLAST
Significance of alignments
Multiple sequence alignment
A multiple sequence alignment of thioredoxins shows the importance of conservation patterns
Analysis of structures
Superposition of structures
Structural alignment
Multiple structure alignment
Database searching for structures or fragments
Databases of protein families
Classifications of protein structures
Classification and assignment of protein function
The Enzyme Commission
The Gene Ontology™ Consortium protein function classification
The ENZYME database and PROSITE
Databases of metabolic networks
Proteins as catalysts: enzyme structure, kinetics, and mechanism / 5:
What are the crucial features of enzymes?
Reaction rates and transition states
The activated complex
Measurement of reaction rates
Slow the reaction down
Fast methods of data collection
Active sites
Cofactors
Protein-ligand binding equilibria
The Scatchard plot
Catalysis by enzymes
Enzyme kinetics
Derivation of KM and Vmax from rate data
Measures of effectiveness of enzymes
Irreversible inhibitor binding
Multisubstrate reactions
Enzyme mechanisms
The mechanism of action of thymidylate synthase
Computational approaches to enzyme mechanisms
The mechanism of action of chymotrypsin
The evidence from kinetics
The evidence from crystallography
Blood coagulation
Thrombosis
Serpins: serine proteinase inhibitors-conformational disease
Several conformational states of serpins are known
Mechanism of proteinase inhibition by serpins
Evolutionary divergence of enzymes
The mechanism of action of malate and lactate dehydrogenases
Enolase, mandelate racemase, and muconate lactonizing enzyme catalyse different reactions but have related mechanisms
The structure and mechanism of E. coli topoisomerase III
The sliding filament mechanism of muscle contraction
ATP synthase
Membrane transport
Specificity of the potassium channel from Streptomyces lividans-room to swing a cation?
Allosteric regulation of protein activity
The allosteric structural change of haemoglobin
Proteins with partners / 6:
General properties of protein-protein interfaces
Burial of protein surface
The composition of the interface
Complementarity
Specific interactions at protein-protein interfaces
Phage M13 gene III protein and E. coli TolA
Multisubunit proteins
Diseases of protein aggregation
Amyloidoses
Alzheimer's disease
Prion diseases-spongiform encephalopathies
The immune system
Antibody structure
Antibody maturation
Catalytic antibodies-'abzymes'
Proteins of the major histocompatibility complex
T-cell receptors
Virus structures
Tomato bushy stunt virus
Bacteriophage HK97: protein chain-mail
Photosynthetic reaction centres
Protein-DNA interactions
Structural themes in protein-DNA binding and sequence recognition
Bacteriophage T7 DNA polymerase
Some protein-DNA complexes that regulate gene transcription
Evolution of protein structure and function / 7:
Protein structure classification
A case study: superpositions and alignments of pairs of proteins with increasingly more-distant relationships
Structural relationships among homologous domains
Changes in proteins during evolution give clues to the roles of residues at different positions
To what constraint are pathways of protein evolution subject?
Closed β-barrel structures
The TIM barrel
Evolution of the globins
Mammalian globins
What determines the globin folding pattern?
Truncated globins
Expansion of the globin family
Classification of the globins
Globin functions
Phycocyanins and the globins
Evolution of NAD-binding domains of dehydrogenases
Comparison of NAD-binding domains of dehydrogenases
The sequence motif G*G**G
Structure and evolution of serine proteinases of the chymotrypsin family
Structures of individual domains
The domain/domain interface
The specificity pocket
The β-barrels in serine proteinase domains and the packing of residues in their interiors
Evolution of visual pigments and related molecules
Selection has tuned vertebrate opsins so that the absorption maximum varies with the light environment
How do proteins evolve new functions?
Pathways and limits in the divergence of sequence, structure and function
Evolution of functional change in the enolase superfamily
Protein evolution at the level of domain assembly
Domain swapping is a general mechanism for forming an oligomer from a multidomain protein
Directed evolution
Directed evolution of subtilisin E
Enhancement of thermal stability
Activity in organic solvents
Affinity selectivity by phage display
Protein folding and design / 8:
Why is protein folding so fast?
Thermodynamics-key concepts
Entropy
Spontaneity and equilibrium
Kinetics
Thermodynamics, protein folding
Thermodynamics of mutated proteins
Experimental character nation of events in protein folding
The molten globule
Folding funnels
The effect of denaturants on rates of folding and unfolding: chevron plots
The kinetics of folding of mutated proteins gives clues to the structure of the transition state for folding
Comparison of folding pathways of a natural protein and a circular permutant
Relationship between native structure and folding
The hierarchical model of protein folding
How fast could a protein fold?
Protein misfolding and the GroEL-GroES chaperone protein
The GroEL-GroES conformational change
Protein design
ab initio design of a hyperstable variant of Streptococcal protein G, β1 domain
Expanding and contracting the genetic code
Expansion of the genetic code
Contraction of the genetic code
Understanding the contents and layout of the common genetic code
Proteomics and systems biology / 9:
Separation and analysis of proteins
Polyacrylamide gel electrophoresis
Two-dimensional polyacrylamide gel electrophoresis
Difference gel electrophoresis
Identification of components of a complex mixture
Protein sequencing by mass spectrometry
Quantitative analysis of relative abundance
Measuring deuterium exchange in proteins
'Ome, 'ome, on the range-environmental genomics and proteomics
Metagenomics
Metaproteomics
Dynamic proteomics of the response to cadmium challenge
Microarrays
Microarray data are semiquantitative
Applications of DNA microarrays
Analysis of microarray data
Expression patterns in different physiological states
Expression pattern changes in development: the life cycle of Drosophila melanogaster
RNAseq
RNAseq v. microarrays
Systems biology
Two parallel networks: physical and logical
Networks and graphs
Robustness and redundancy
Connectivity in networks
Dynamics, stability, and robustness
Protein complexes and aggregates
Protein interaction networks
Regulatory networks
Structures of regulatory networks
Structural biology of regulatory networks
Gene regulation
The transcriptional regulatory network of E. coli
Regulation of the lactose operon in E. coli
The genetic regulatory network of Saccharomyces cerevisiae
Adaptability of the yeast regulatory network
Epilogue
List of Abbreviations
Glossary
Index
Preface to the first edition
Preface to the second edition
Preface to the third edition
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