Principles of Protein Structural Organization - H. Schultz 1982
Editor's Preface to the Translation
Amino acids
Amino Acids
Why These Particular Amino Acids?
Colinear relationship between nucleic acids and polypeptides
Empirical Analogies Among Amino Acid Residues
The Structural Role of the Peptide Bond
The structural role of the peptide bond
Structural Role of the Peptide Bond
The structural role of the peptide bond
Interactions Determining Protein Structure
Dispersion Forces and Electron Shell Repulsion
Covalent Protein Structure
Chain Assemblies
Functional and Structural Domains
Covalent Structure of Proteins
Covalent Protein Structure
Chain Ensembles
Three Main Physiological Types of Protein Molecules
Chain Assemblies
Immunoglobulins and HL-A Proteins
The Role of S-S Bridges in Extracellular and Intracellular Proteins
Disulfide bridges as structural components of proteins
Enzyme-Controlled Modifications of the Main Chain
Specific Cleavage of the Polypeptide Chain
Covalent Structure of Proteins
Covalent Protein Structure
Enzyme-Controlled Modifications of Side Chains
Cross-Links Based on Modified Lys Residues
Other Types of Modification Reactions
Covalent Structure of Proteins
Mechanisms of Polypeptide Chain Folding and Association
Mechanisms of polypeptide chain folding and association
Secondary structure
Mechanisms of Polypeptide Chain Folding and Association
Secondary Structure
Reverse Turns of the Peptide Chain
Mechanisms of polypeptide chain folding and association
Supersecondary structures
Modes of polypeptide chain folding and association
Mechanisms of polypeptide chain folding and association
β-Zigzags and other features of β-structures
Methods of polypeptide chain folding and association
Structural domains
Correlation between closely situated residues in the sequence
Mechanisms of polypeptide chain folding and association
Methods of polypeptide chain folding and association
Mechanisms of polypeptide chain folding and association
Aggregates of globular proteins
Methods of folding and association of polypeptide chains
Methods of folding and association of polypeptide chains
Mechanisms of polypeptide chain folding and association
Subunit contacts in dehydrogenases
Specificity of protein-protein interactions
Modes of folding and association of polypeptide chains
Mechanisms of polypeptide chain folding and association
Prediction of secondary structure from amino acid sequence
Probabilistic methods
Residue propensity for secondary structure
Propensity of two residues to simultaneously adopt a secondary structure
Propensity of three residues to incorporate into secondary structure
Physicochemical methods
Methods based on statistical mechanics
Methods based on stereochemical data
Application of predictive methods
Secondary structure prediction from amino acid sequence
Evaluation of predictive methods
Arbitrariness of parameter selection
Criteria for method evaluation
Prediction of secondary structure from amino acid sequence
General remarks
Prediction quality and local interactions
Prediction of Secondary Structure from Amino Acid Sequence
General Remarks
Prediction Success and Nucleation Centers
Secondary structure prediction from amino acid sequence
General remarks
Prediction as an analytical method
Prediction of secondary structure from amino acid sequence
Models, Depiction, and Documentation of Protein Structures
Protein Structure Data
Representation of Complete Structure
Two-Dimensional Representations
Abstract Concepts of Chain Folding
Ramachandran Plots for Main-Chain Angles
Distance Maps Between Cα-atoms
Thermodynamics and Kinetics of Polypeptide Chain Folding
Thermodynamic Aspects
Transition Between Two Thermodynamic States of the Chain
Balance of Energetic Contributions in a Globular Protein
Thermal Fluctuations in Protein Structures
Native State: Global or Local Energy Minima?
Speed, Fidelity, and Limitations of Folding In Vitro
Structural Elements in Unfolded Chains
Thermodynamics and kinetics of polypeptide chain folding
Thermodynamics and Kinetics of Polypeptide Chain Folding
Modeling of the Folding Process
Protein Specialization Frequency of Permissible Mutations
Protein Specialization
Frequency of Tolerated Mutations
Criteria for the Fixation of Amino Acid Substitutions in Proteins
Probability of Amino Acid Residue Mutations
Effect of Amino Acid Substitutions on Folding Dynamics
Amino Acid Substitutions as Experiments Conducted by Nature
Phylogeny Based on Protein Structures
Proteins Suitable for Phylogenetic Studies
Evolution of Behavior and Morphology in Comparison with Protein Evolution
Protein Differentiation
Construction of a phylogenetic tree for vasotocin, oxytocin, and vasopressin
Immunoglobulins, Transplantation Antigens, and Superoxide Dismutase
Morphological Similarity of Globins and Cytochromes b
Gene Fusion
Detection of Distant Evolutionary Relationships
Comparison of Amino Acid Sequences
Comparison of Layer Topologies
Protein–ligand interactions
Ligand-binding sites of immunoglobulins
Binding model in the immunoglobulin–ligand system
Protein-Ligand Interactions
Ligand-Binding Sites of Immunoglobulins
Immunoglobulin-Ligand Systems as Models for Other Protein-Ligand Interactions
Protein-ligand interactions
Substrate-binding sites of serine proteases
Formation of the chymotrypsin-substrate complex
Substrate-binding site in trypsin
Protein–ligand interactions
Heme binding sites
Bonds between heme and apoprotein
Protein-ligand interactions
Heme-binding sites
Influence of the heme group on protein structure
Heme binding sites
Chemical transformations of the heme iron atom within the protein microenvironment
Heme-binding sites
Heme ligands as trigger systems for structural changes in mammalian hemoglobin
Nucleotide-binding sites
NAD-binding domains of dehydrogenases
Protein–ligand interactions
Nucleotide-binding sites in other proteins
Nucleotide binding sites
Induced fit in adenylate kinase
Phosphoryl group binding sites
Protein interactions with other macromolecules
Protein-ligand interactions
Protein-macromolecule interactions
Protein–ligand interactions
Protein interactions with other macromolecules
Protein-ligand interactions
Structural Basis of Protein Mechanism, Action, and Function
Structural Foundations of Protein Mechanism, Action, and Function
Structural Basis of Protein Mechanism, Action, and Function
Catalytic Mechanism of Chymotrypsin
Effects Contributing to High Reaction Rates
Structural basis of the mechanism, action, and function of proteins
Biological and medical aspects of protein action and function
Proteins as functional components of the organism
Structural basis of protein mechanism, action, and function
Evolution of novel functions from preexisting proteins
Structural Foundations of Protein Mechanism, Action, and Function
Structural basis of the mechanism, action, and function of proteins
Skeletal muscle: a system where protein action can be correlated with the overall activity of the organ
Structural and functional organization of contractile proteins
Structural Basis of Protein Mechanism, Action, and Function
Skeletal muscle: a system where protein action can be linked to the overall activity of the organ
Response to nerve impulses and hormonal action in the muscle cell
Structural Foundations of the Mechanism, Action, and Function of Proteins
Skeletal Muscle: A system in which protein action can be linked to the overall activity of the organ
Statistical Mechanics of the Helix-Coil Transition
Distribution Function
Probability of a given residue conformation
The Zimm-Bragg Model for the Helix-Coil Transition
Fraction of Helical Residues in a Homopolymer
Number and Length of Helical Segments
Relationship between s and Temperature
Comparison with Experimental Data: Helix-Coil Transition Curves and the Zimm-Bragg Model
Transition Temperature and Helix Propensity
Comparison with Experimental Data. Helix-Coil Transition Curves and the Zimm-Bragg Model