Literature DB >> 11959498

Biomolecular diffusional association.

Razif R Gabdoulline1, Rebecca C Wade.   

Abstract

The primary method for the computational study of biomolecular diffusional association is Brownian dynamics. Recent work has seen advances in the efficiency of computing association rates and in the accuracy of simulation models. New areas to which Brownian dynamics has been applied include protein polymerisation and protein adsorption to a surface. There has recently been particularly intense study of protein-protein association, and Brownian dynamics, together with other theoretical and experimental approaches, has led to new insights into the determinants of protein-protein binding kinetics.

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Year:  2002        PMID: 11959498     DOI: 10.1016/s0959-440x(02)00311-1

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  62 in total

1.  Atomic-level observation of macromolecular crowding effects: escape of a protein from the GroEL cage.

Authors:  Adrian H Elcock
Journal:  Proc Natl Acad Sci U S A       Date:  2003-02-24       Impact factor: 11.205

2.  Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness.

Authors:  Maximilian Schlosshauer; David Baker
Journal:  Protein Sci       Date:  2004-05-07       Impact factor: 6.725

3.  A computational approach to increase time scales in Brownian dynamics-based reaction-diffusion modeling.

Authors:  Zachary Frazier; Frank Alber
Journal:  J Comput Biol       Date:  2012-06       Impact factor: 1.479

4.  Transition state and encounter complex for fast association of cytochrome c2 with bacterial reaction center.

Authors:  Osamu Miyashita; José N Onuchic; Melvin Y Okamura
Journal:  Proc Natl Acad Sci U S A       Date:  2004-11-01       Impact factor: 11.205

Review 5.  The structure and function of the cytochrome c2: reaction center electron transfer complex from Rhodobacter sphaeroides.

Authors:  Herbert L Axelrod; Melvin Y Okamura
Journal:  Photosynth Res       Date:  2005       Impact factor: 3.573

6.  Complexes of photosynthetic redox proteins studied by NMR.

Authors:  Marcellus Ubbink
Journal:  Photosynth Res       Date:  2004       Impact factor: 3.573

7.  Investigating the local flexibility of functional residues in hemoproteins.

Authors:  Sophie Sacquin-Mora; Richard Lavery
Journal:  Biophys J       Date:  2006-01-20       Impact factor: 4.033

8.  Computational methods for biomolecular electrostatics.

Authors:  Feng Dong; Brett Olsen; Nathan A Baker
Journal:  Methods Cell Biol       Date:  2008       Impact factor: 1.441

9.  Mechanistic details of a protein-protein association pathway revealed by paramagnetic relaxation enhancement titration measurements.

Authors:  Nicolas L Fawzi; Michaeleen Doucleff; Jeong-Yong Suh; G Marius Clore
Journal:  Proc Natl Acad Sci U S A       Date:  2010-01-07       Impact factor: 11.205

10.  Protein charge and mass contribute to the spatio-temporal dynamics of protein-protein interactions in a minimal proteome.

Authors:  Yu Xu; Hong Wang; Ruth Nussinov; Buyong Ma
Journal:  Proteomics       Date:  2013-03-18       Impact factor: 3.984

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