The Physical Foundation of Protein Architecture

by Saito, Nobuhiko; Kobayashi, Yukio

• ISBN13: 9789810247102
• ISBN10: 9810247109
• Format: Hardcover
• Copyright: 2001-12-01
• Publisher: WORLD SCIENTIFIC PUB CO INC

Summary

Intended to solve the mystery from the physiochemical basis by elucidating the mechanism of various processes in protein folding. The main features of protein folding are shown to be described by the island model with long range hydrophobic interaction which is capable of finding the specific residue, and the lampshade criterion for disulfide bonding.

Table of Contents

Preface	v
Generalities	1	(46)
Introduction	1	(5)
Helix-Coil Transition in Polypeptide	6	(14)
α- and β-keratins	6	(2)
Helix-coil transition	8	(2)
Theory of the formation of α-helices and β-strands in protein	10	(4)
Prediction of α-helices and β-strands in a protein	14	(1)
Some preliminary results for the secondary structure prediction	15	(3)
Stability of α-helix	18	(2)
Some Aspects of Protein Folding	20	(27)
Reversible denaturation and renaturation: Anfinsen's dogma	20	(4)
Hydrophobic core	24	(3)
Folding pathway	27	(2)
Molten globule state	29	(5)
Graphical representations of protein structures	34	(2)
Statistical mechanical simulation of protein conformation	36	(7)
Driving force for packing the secondary structures	43	(4)
Mechanism of Protein Folding	47	(48)
Island Model	47	(1)
α-Helical Proteins	48	(14)
Sperm whale myoglobin	48	(8)
Cytochrome b562	56	(2)
Sea hare myoglobin	58	(4)
Lysozyme and Phospholipase	62	(13)
Disulfide bonding and lampshade	63	(2)
Lysozyme	65	(6)
Phospholipase	71	(4)
Bovine Pancreatic Trypsin Inhibitor	75	(9)
Flavodoxin and Thioredoxin	84	(5)
Ferredoxin	89	(6)
Folding of a Protein of Unknown Structure	95	(12)
Ab Initio Method of Prediction of Protein Structure	95	(9)
General principles	95	(3)
Packing order and Anfinsen's dogma	98	(2)
Application to parathyroid-hormone-related protein (residues 1-34), abbreviated as PTHrP (1-34)	100	(4)
Search for the Conformation of Minimum Energy	104	(3)
Validity of Anfinsen's dogma	104	(1)
Simulated annealing	104	(3)
Topics Related to Protein Structures	107	(10)
Phase Transition	107	(1)
Module	108	(1)
Exons, introns, and modules	108	(1)
Stability of modules	108	(1)
Molecular Chaperones	109	(2)
Membrane Proteins	111	(1)
Structure Prediction Based on Protein Data	112	(2)
Secondary structure	113	(1)
Tertiary structure	114	(1)
Concluding Remarks	114	(3)
Appendix A Helix-Coil Transition in Homopolypeptide	117	(4)
A.1 Lifson-Roig Theory	117	(1)
A.2 Interaction of Side Chains	118	(1)
A.3 Conformation in the Helix-Coil Transition Region	119	(2)
Appendix B Levinthal Paradox	121	(4)
B.1 Phase Space of a Protein	121	(1)
B.2 Ideal Gas	122	(3)
Appendix C Method of Bremermann for Searching the Conformation of Minimum Energy	125	(6)
C.1 Outline of the Method	125	(3)
C.2 An Example	128	(3)
Appendix D Formation of β-Sheets	131	(4)
D.1 Antiparallel β-Structure	131	(4)
References	135	(8)
Index	143