New textbooks at all levels of chemistry appear with great regularity. Some fields like basic biochemistry, organic reaction mechanisms, and chemical thermodynamics are well represented by many excellent texts, and new or revised editions are published sufficiently often to keep up with progress in research. However, some areas of chemistry, especially many of those taught at the graduate level, suffer from a real lack of up-to-date textbooks. The most serious needs occur in fields that are rapidly changing. Textbooks in these subjects usually have to be written by scientists actually involved…mehr
New textbooks at all levels of chemistry appear with great regularity. Some fields like basic biochemistry, organic reaction mechanisms, and chemical thermodynamics are well represented by many excellent texts, and new or revised editions are published sufficiently often to keep up with progress in research. However, some areas of chemistry, especially many of those taught at the graduate level, suffer from a real lack of up-to-date textbooks. The most serious needs occur in fields that are rapidly changing. Textbooks in these subjects usually have to be written by scientists actually involved in the research which is advancing the field. It is not often easy to persuade such individuals to set time aside to help spread the knowledge they have accumulated. Our goal, in this series, is to pinpoint areas of chemistry where recent progress has outpaced what is covered in any available textbooks, and then seek out and persuade experts in these fields to produce relatively concise butinstructive introductions to their fields. These should serve the needs of one semester or one quarter graduate courses in chemistry and biochemistry. In some cases the availability of texts in active research areas should help stimulate the creation of new courses.
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.
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.
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