On the origin of the cooperativity of protein folding: implications from model simulations

Proteins
A KolinskiJ Skolnick

Abstract

There is considerable experimental evidence that the cooperativity of protein folding resides in the transition from the molten globule to the native state. The objective of this study is to examine whether simplified models can reproduce this cooperativity and if so, to identify its origin. In particular, the thermodynamics of the conformational transition of a previously designed sequence (A. Kolinski, W. Galazka, and J. Skolnick, J. Chem. Phys. 103: 10286-10297, 1995), which adopts a very stable Greek-key beta-barrel fold has been investigated using the entropy Monte Carlo sampling (ESMC) technique of Hao and Scheraga (M.-H. Hao and H.A. Scheraga, J. Phys. Chem. 98: 9882-9883, 1994). Here, in addition to the original potential, which includes one body and pair interactions between side chains, the force field has been supplemented by two types of multi-body potentials describing side chain interactions. These potentials facilitate the protein-like pattern of side chain packing and consequently increase the cooperativity of the folding process. Those models that include an explicit cooperative side chain packing term exhibit a well-defined all-or-none transition from a denatured, random coil state to a high-density, well-defi...Continue Reading

References

Jan 1, 1975·Advances in Protein Chemistry·C B Anfinsen, H A Scheraga
May 25, 1977·Journal of Molecular Biology·F C BernsteinM Tasumi
Jan 1, 1989·Annual Review of Biophysics and Biophysical Chemistry·W L Mattice
Apr 1, 1995·Protein Science : a Publication of the Protein Society·K A DillH S Chan
Feb 1, 1995·Current Opinion in Structural Biology·M Karplus, A Sali
Apr 8, 1994·Journal of Molecular Biology·M ViethJ Skolnick
Aug 1, 1993·Proceedings of the National Academy of Sciences of the United States of America·E I Shakhnovich, A M Gutin
Aug 1, 1995·Current Opinion in Structural Biology·S F BetzW F DeGrado
Dec 1, 1996·Journal of Computer-aided Molecular Design·Y IwataS Miyamoto
Jan 6, 1992·Physical Review Letters·B A Berg, T Neuhaus
Jul 12, 1993·Physical Review Letters·J Lee

❮ Previous
Next ❯

Citations

Aug 21, 2009·The Journal of Chemical Physics·L WuW Wang
Aug 24, 2005·Proceedings of the National Academy of Sciences of the United States of America·Patrick WeinkamPeter G Wolynes
May 25, 2005·Proceedings of the National Academy of Sciences of the United States of America·Edyta MałolepszaLucjan Piela
Sep 2, 1998·Proceedings of the National Academy of Sciences of the United States of America·E D Nelson, J N Onuchic
Oct 8, 2004·Proceedings of the National Academy of Sciences of the United States of America·M R EjtehadiS S Plotkin
Oct 6, 1997·Proceedings of the National Academy of Sciences of the United States of America·U H HansmannY Okamoto
May 30, 1998·Protein Science : a Publication of the Protein Society·L Zhang, J Skolnick
Mar 1, 1997·Protein Science : a Publication of the Protein Society·J SkolnickA Godzik
Dec 7, 2000·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·J M Sorenson, T Head-Gordon
Feb 4, 2016·Chemical Reviews·A Subha Mahadevi, G Narahari Sastry
May 30, 1998·Journal of Molecular Biology·M H Hao, H A Scheraga
Mar 10, 2006·Current Opinion in Structural Biology·Jeffrey Skolnick
Jan 13, 2006·Biochemical and Biophysical Research Communications·Yawen Bai
Jul 2, 1999·Biophysical Journal·D MohantyJ Skolnick
Nov 19, 2015·Journal of Chemical Theory and Computation·Joseph F Rudzinski, William G Noid
Mar 27, 2002·Journal of Computational Chemistry·D K Klimov, D Thirumalai
Nov 10, 2005·Journal of Bioinformatics and Computational Biology·Hongzhi Li, Yaoqi Zhou
Nov 2, 1999·Journal of Molecular Biology·Y Zhou, M Karplus
Nov 18, 2000·Physical Review Letters·H Kaya, H S Chan
Dec 2, 1998·Journal of Biomolecular Structure & Dynamics·J SkolnickA R Ortiz
Jan 28, 2020·Biophysics and Physicobiology·Yuko Okamoto
Feb 9, 2005·Physical Review Letters·Mai Suan LiD Thirumalai
Feb 11, 2010·Accounts of Chemical Research·Patrick WeinkamPeter G Wolynes
Nov 1, 2020·Current Opinion in Structural Biology·Jeffrey Skolnick, Mu Gao
Dec 21, 2013·Journal of Chemical Information and Modeling·María Larriva, Antonio Rey

❮ Previous
Next ❯

Related Concepts

Related Feeds

Cajal Bodies & Gems

Cajal bodies or coiled bodies are dense foci of coilin protein. Gemini of Cajal bodies, or gems, are microscopically similar to Cajal bodies. It is believed that Cajal bodies play important roles in RNA processing while gems assist the Cajal bodies. Find the latest research on Cajal bodies and gems here.