An analytical study of the interplay between geometrical and energetic effects in protein folding

The Journal of Chemical Physics
Yoko SuzukiJosé N Onuchic

Abstract

Analytical studies have several advantages for an understanding of the mechanisms of protein folding such as the interplay between geometrical and energetic effects. In this paper, we introduce a Gaussian filament with a C(alpha) structure-based (Go) potential as a new theoretical scheme based on a Hamiltonian approach. This model takes into account geometrical information in a realistic fashion without the need of phenomenological descriptions. In order to make this model more appropriate for comparison with protein folding simulations and experiments, we introduce a many-body interaction into the potential term to enhance cooperativity. We apply our new analytical model to a beta-hairpin-type peptide and compare our results with a molecular dynamics simulation of a structure-based model.

References

Feb 27, 1975·Nature·M Levitt, A Warshel
Sep 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·P E LeopoldJ N Onuchic
Dec 20, 1991·Journal of Molecular Biology·M S FriedrichsP G Wolynes
Nov 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·J D Bryngelson, P G Wolynes
Apr 11, 1995·Proceedings of the National Academy of Sciences of the United States of America·J N OnuchicN D Socci
Mar 22, 1996·Journal of Molecular Biology·J G Saven, P G Wolynes
Feb 1, 1996·Current Opinion in Structural Biology·A D Miranker, C M Dobson
Feb 4, 1997·Proceedings of the National Academy of Sciences of the United States of America·B A ShoemakerP G Wolynes
Feb 1, 1997·Current Opinion in Structural Biology·A R Fersht
Feb 1, 1997·Current Opinion in Structural Biology·W A EatonJ Hofrichter
Jan 1, 1997·Annual Review of Physical Chemistry·J N OnuchicP G Wolynes
Aug 1, 1994·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·S Ramanathan, E Shakhnovich
Jun 1, 1996·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·S S PlotkinP G Wolynes
Nov 19, 1990·Physical Review Letters·M Sasai, P G Wolynes
Apr 7, 2000·Advances in Protein Chemistry·J N OnuchicN D Socci
May 17, 2000·Proceedings of the National Academy of Sciences of the United States of America·C ClementiJ N Onuchic
Jun 7, 2000·Proceedings of the National Academy of Sciences of the United States of America·S S Plotkin, J N Onuchic
Jul 26, 2000·Proceedings of the National Academy of Sciences of the United States of America·B A ShoemakerP G Wolynes
Dec 13, 2000·Proceedings of the National Academy of Sciences of the United States of America·C HardinP G Wolynes
Aug 29, 2001·Nature Structural Biology·S B OzkanK A Dill
Feb 28, 2002·Proceedings of the National Academy of Sciences of the United States of America·Angel E García, Kevin Y Sanbonmatsu
Mar 23, 2002·Cell·Alan R Fersht, Valerie Daggett
Jul 26, 2002·Proceedings of the National Academy of Sciences of the United States of America·Avijit GhoshHarold A Scheraga
Aug 29, 2002·Quarterly Reviews of Biophysics·Steven S Plotkin, José N Onuchic
Nov 8, 2002·Journal of Molecular Biology·Emanuelel PaciMartin Karplus
Nov 8, 2002·Nature·Christopher D SnowMartin Gruebele
Jan 30, 2003·Proceedings of the National Academy of Sciences of the United States of America·Corey HardinPeter G Wolynes
Feb 26, 2003·Quarterly Reviews of Biophysics·Steven S Plotkin, José N Onuchic
Feb 26, 2003·Biopolymers·Garegin A Papoian, Peter G Wolynes
Jun 5, 2003·Nature Reviews. Molecular Cell Biology·Valerie Daggett, Alan Fersht
Dec 25, 2003·Proceedings of the National Academy of Sciences of the United States of America·Yaakov LevyJosé N Onuchic
Mar 12, 2004·Annual Review of Physical Chemistry·M Gruebele
Jul 21, 2006·The Journal of Physical Chemistry. B·Yoko Suzuki, José N Onuchic

❮ Previous
Next ❯

Citations

Apr 28, 2012·The Journal of Physical Chemistry. B·Jeffrey K NoelJosé N Onuchic
Jul 5, 2011·The Journal of Chemical Physics·Yoko SuzukiJosé N Onuchic
Sep 11, 2018·The Journal of Physical Chemistry. B·Lavi S Bigman, Yaakov Levy

❮ Previous
Next ❯

Methods Mentioned

BETA
protein folding

Software Mentioned

Plotkin

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.