Principles of Protein Structure: (Springer Advanced Texts in Chemistry)

There has been an explosion in the information available about protein structure. Principles of Protein Structure provides a comprehensive overview of this massive set of information. The authors use the known structures to illustrate the forces which determine protein structures, the rationale behind many of the features of organization of proteins, and the mechanisms by which proteins perform biological functions. This textbook surveys not only what is known, but also how the structural data can be organized and systematized and what it can be used for in chemical and biomedical research. The book includes what is probably the most comprehensive published bibliography on protein structure.

Table of Contents:
1 Amino Acids.- 1.1 The 20 Standard Amino Acids.- 1.2 Why Were Just These Amino Acids Selected?.- 1.3 Colinear Relation Between Nucleic Acids and Polypeptides.- 1.4 Side Chain Properties.- 1.5 Empirical Similarities Between Amino Acid Residues.- Summary.- 2 Structural Implications of the Peptide Bond.- 2.1 Synthesis on Ribosomes.- 2.2 Peptide Bond Dimensions.- 2.3 Steric Hindrance.- 2.4 Conformational Energy.- 2.5 cis versus trans Configuration.- Summary.- 3 Noncovalent Forces Determining Protein Structure.- 3.1 Dispersion Forces and Electron Shell Repulsion.- 3.2 Electrostatic Interactions.- 3.3 Van der Waals Potentials.- 3.4 Hydrogen Bonds.- 3.5 Entropic Forces.- 3.6 Molecular Packing.- Summary.- 4 The Covalent Structure of Proteins.- 4.1 Chain Assemblies.- 4.2 Disulfide Bonds.- 4.3 Enzyme-Controlled Modifications of the Main Chain.- 4.4 Enzyme-Controlled Side Chain Modifications.- Summary.- 5 Patterns of Folding and Association of Polypeptide Chains.- 5.1 Secondary Structure.- 5.2 Supersecondary Structures.- 5.3 Structural Domains.- 5.4 Globular Proteins.- 5.5 Aggregates of Globular Proteins.- 5.6 Hierarchy of Levels.- Summary.- 6 Prediction of Secondary Structure from the Amino Acid Sequence.- 6.1 Probabilistic Methods.- 6.2 Physico-Chemical Methods.- 6.3 Application of Prediction Methods.- 6.4 Evaluation of Prediction Methods.- 6.5 Emerging General Results.- Summary.- 7 Models, Display, and Documentation of Protein Structures.- 7.1 Structural Ingredients.- 7.2 Representations of Complete Structures.- 7.3 Abstract Chain Fold Representations.- Summary.- 8 Thermodynamics and Kinetics of Polypeptide Chain Folding.- 8.1 Thermodynamic Aspects.- 8.2 Speed, Precision, and Limitations of Folding in vitro.- 8.3 Structural Elements in Unfolded Chains.- 8.4 Folding Pathway.- 8.5 The Influence of Ligands.- 8.6 Simulations of the Folding Process.- Summary.- 9 Protein Evolution.- 9.1 Protein Speciation.- 9.2 Phylogeny on the Basis of Protein Structures.- 9.3 Protein Differentiation.- 9.4 Gene Fusion.- 9.5 Convergent Evolution in Proteins.- 9.6 Recognition of Distant Relationships.- Summary.- 10 Protein-Ligand Interactions.- 10.1 Ligand-Binding Sites of Immunoglobulins.- 10.2 Substrate-Binding Sites of Serine Proteases.- 10.3 Haem-Binding Sites.- 10.4 Nucleotide-Binding Sites.- 10.5 Binding Sites for Phosphoryl Groups.- 10.6 Interactions of Proteins With Other Macromolecules.- Summary.- 11 The Structural Basis of Protein Mechanism, Action, and Function.- 11.1 Definitions.- 11.2 Enzyme Catalysis.- 11.3 Biological and Medical Aspects of Protein Action and Function.- 11.4 Skeletal Muscle, a System in Which Protein Action Can be Related to the Overall Performance of an Organ.- Summary.- Appendix Statistical Mechanics of the Helix-Coil Transition.- A.1 Partition Function.- A.2 Probability of a Residue Being in a Certain Conformation.- A.3 Ising Model.- A.4 Zimm-Bragg Model for Helix-Coil Transition.- A.5 Comparision With Experimental Data.- References.