Literature DB >> 10506280

Folding funnels and binding mechanisms.

B Ma1, S Kumar, C J Tsai, R Nussinov.   

Abstract

The long-held views on lock-and-key versus induced fit in binding arose from the notion that a protein exists in a single, most stable conformation, dictated by its sequence. However, in solution proteins exist in a range of conformations, which may be described by statistical mechanical laws and their populations follow statistical distributions. Upon binding, the equilibrium will shift in favor of the bound conformation from the ensemble of conformations around the bottom of the folding funnel. Hence here we extend the implications and the usefulness of the folding funnel concept to explain fundamental binding mechanisms.

Mesh:

Substances:

Year:  1999        PMID: 10506280     DOI: 10.1093/protein/12.9.713

Source DB:  PubMed          Journal:  Protein Eng        ISSN: 0269-2139


  214 in total

Review 1.  Folding and binding cascades: dynamic landscapes and population shifts.

Authors:  S Kumar; B Ma; C J Tsai; N Sinha; R Nussinov
Journal:  Protein Sci       Date:  2000-01       Impact factor: 6.725

Review 2.  Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations.

Authors:  Buyong Ma; Maxim Shatsky; Haim J Wolfson; Ruth Nussinov
Journal:  Protein Sci       Date:  2002-02       Impact factor: 6.725

3.  Predicting flexible loop regions that interact with ligands: the challenge of accurate scoring.

Authors:  Matthew L Danielson; Markus A Lill
Journal:  Proteins       Date:  2011-11-09

4.  Protein topology determines binding mechanism.

Authors:  Yaakov Levy; Peter G Wolynes; José N Onuchic
Journal:  Proc Natl Acad Sci U S A       Date:  2003-12-23       Impact factor: 11.205

5.  Comparison of protein fragments identified by limited proteolysis and by computational cutting of proteins.

Authors:  Chung-Jung Tsai; Patrizia Polverino de Laureto; Angelo Fontana; Ruth Nussinov
Journal:  Protein Sci       Date:  2002-07       Impact factor: 6.725

6.  Polymorphic C-terminal beta-sheet interactions determine the formation of fibril or amyloid beta-derived diffusible ligand-like globulomer for the Alzheimer Abeta42 dodecamer.

Authors:  Buyong Ma; Ruth Nussinov
Journal:  J Biol Chem       Date:  2010-09-16       Impact factor: 5.157

7.  Vaccinia virus virulence factor N1L is a novel promising target for antiviral therapeutic intervention.

Authors:  Anton V Cheltsov; Mika Aoyagi; Alexander Aleshin; Eric Chi-Wang Yu; Taylor Gilliland; Dayong Zhai; Andrey A Bobkov; John C Reed; Robert C Liddington; Ruben Abagyan
Journal:  J Med Chem       Date:  2010-05-27       Impact factor: 7.446

8.  Entropic mechanism of large fluctuation in allosteric transition.

Authors:  Kazuhito Itoh; Masaki Sasai
Journal:  Proc Natl Acad Sci U S A       Date:  2010-04-12       Impact factor: 11.205

9.  Insights into the dynamics of specific telomeric single-stranded DNA recognition by Pot1pN.

Authors:  Johnny E Croy; Deborah S Wuttke
Journal:  J Mol Biol       Date:  2009-02-13       Impact factor: 5.469

10.  Enhancing Virtual Screening Performance of Protein Kinases with Molecular Dynamics Simulations.

Authors:  Tavina L Offutt; Robert V Swift; Rommie E Amaro
Journal:  J Chem Inf Model       Date:  2016-10-03       Impact factor: 4.956

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.