Protein Physics

Part I INTRODUCTIONLecture 1: Main functions of proteinsPart II ELEMENTARY INTERACTIONS IN AND AROUND PROTEINSLecture 2: Amino acid residues in proteinsLecture 3: Quantum mechanics, Pauli exclusion principle, and non-covalent interactionsLecture 4: Influence of water environmentLecture 5: Water, hydrophobicity and proteinsLecture 6: Influence of an aqueous environment on electrostatic interactionsPart III SECONDARY STRUCTURES OF POLYPEPTIDE CHAINSLecture 7: Secondary structure of polypeptidesLecture 8: Elements of statistical mechanicsLecture 9: Free energy of initiation and elongation of a-helices in a homopolypeptideLecture 10: 20 + 2 + 1 gene-coded amino acids in proteinsPart IV PROTEIN STRUCTURESLecture 11: Fibrous proteins, their functions, their regular primary and secondary structuresLecture 12: Membrane proteins; peculiarities of their structure and functionLecture 13: Globular proteinsLecture 14: Structure of a-proteinsLecture 15: Classification of protein foldsLecture 16: What secondary structure can be expected for random and quasi-random amino acid sequencesPart V COOPERATIVE TRANSITIONS IN PROTEIN MOLECULESLecture 17: "Well-folded" and "natively disordered" (or "intrinsically disordered") proteinsLecture 18: Denaturation of globular protein: why is it an "all-or-none" transitionLecture 19: Protein folding in vivo and in vitroLecture 20: Two-state folding of small proteins: kinetic analog of the thermodynamic "all-or-none" transitionLecture 21: Solution of "Levinthal paradox"Part VI PREDICTION AND DESIGN OF PROTEIN STRUCTURELecture 22: Protein structure prediction from amino acid sequencesLecture 23: Overview of approaches to prediction and recognition of tertiary structures of proteins from their amino acid sequencesPart VII PHYSICAL BACKGROUND OF PROTEIN FUNCTIONSLecture 24: Protein function and protein structureLecture 25: Combination of elementary functionsAppendix A.: Theory of coil-globule transitions in homopolymersAppendix B.: Theory of helix-coil transitions in homopolymers Appendix C.: Statistical physics of one-dimensional systems and dynamic programmingAppendix D.: Random energy model and energy gap in the random energy modelAppendix E.: How to use stereo drawingsProblems & Solutions