Polymer principles and protein folding
- 1 January 1999
- journal article
- review article
- Published by Wiley in Protein Science
- Vol. 8 (6), 1166-1180
- https://doi.org/10.1110/ps.8.6.1166
Abstract
This paper surveys the emerging role of statistical mechanics and polymer theory in protein folding. In the polymer perspective, the folding code is more a solvation code than a code of local ØΨ propensities. The polymer perspective resolves two classic puzzles: (1) the Blind Watchmaker' Paradox that biological proteins could not have originated from random sequences, and (2) Levinthal' Paradox that the folded state of a protein cannot be found by random search. Both paradoxes are traditionally framed in terms of random unguided searches through vast spaces, and vastness is equated with impossibility. But both processes are partly guided. The searches are more akin to balls rolling down funnels than balls rolling aimlessly on flat surfaces. In both cases, the vastness of the search is largely irrelevant to the search time and success. These ideas are captured by energy and fitness landscapes. Energy landscapes give a language for bridging between microscopics and macroscopics, for relating folding kinetics to equilibrium fluctuations, and for developing new and faster computational search strategies.Keywords
This publication has 99 references indexed in Scilit:
- A Protein Designed by Binary Patterning of Polar and Nonpolar Amino Acids Displays Native-like PropertiesJournal of the American Chemical Society, 1997
- Protein Structure and Energy Landscape Dependence on Sequence Using a Continuous Energy FunctionJournal of Computational Biology, 1997
- Protein Folding Triggered by Electron TransferScience, 1996
- Trifluoroethanol-induced Stabilization of the α-Helical Structure of β-Lactoglobulin: Implication for Non-hierarchical Protein FoldingJournal of Molecular Biology, 1995
- ‘‘Sequence space soup’’ of proteins and copolymersThe Journal of Chemical Physics, 1991
- The role of internal packing interactions in determining the structure and stability of a proteinJournal of Molecular Biology, 1991
- Protein-folding dynamicsNature, 1976
- Nucleation, Rapid Folding, and Globular Intrachain Regions in ProteinsProceedings of the National Academy of Sciences, 1973
- Polypeptides. IV. The Molecular Weight, Configuration and Association of Poly-γ-benzyl-L-glutamate in Various SolventsJournal of the American Chemical Society, 1956
- POLYPEPTIDES. VII. POLY-γ-BENZYL-L-GLUTAMATE: THE HELIX-COIL TRANSITION IN SOLUTION1Journal of the American Chemical Society, 1956