NDLI: All-atom replica exchange molecular simulation of protein BBL.

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All-atom replica exchange molecular simulation of protein BBL.

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All-atom replica exchange molecular simulation of protein BBL.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Zhang, Jian Li, Wenfei Wang, Jun Qin, Meng Wang, Wei
Description	Country affiliation: China Author Affiliation: Zhang J ( Department of Physics, National Laboratory of Solid State Microstructure, Institute of Biophysics, Nanjing University, Nanjing, China.)
Abstract	Downhill folding is one of the most important predictions of energy landscape theory. Recently, the Escherichia coli 2-oxoglutarate dehydrogenase PSBD was described as a first example of global downhill folding (Garcia-Mira et al., Science 2002;298:2191), classification that has been later subject of significant controversy. To help resolve this problem, by using intensive all-atom simulation with explicit water model and the replica exchange method, we sample the phase space of protein BBL and depict the free energy landscape. We give an estimate of the free energy barrier height of 1-2 k(B)T, dependent on the way the energy landscape is projected. We also study the conformational distribution of the transition region and find that the three helices generally take the similar positions as that in the native states whereas their spatial orientations show large variability. We further detect the inconsistency between different signals by individually fitting the thermal denaturation curves of five structural features using two-state model, which gives a wide spread melting temperature of 19 K. All of these features are consistent with a picture of folding with very low cooperativities. Compared with the experimental data (Sadqi et al., Nature 2006; 442:317), our results indicate that the Naf-BBL (pH5.3) may have an even lower barrier height and cooperativity.
File Format	HTM / HTML
ISSN	08873585
Issue Number	3
Volume Number	72
e-ISSN	10970134
Journal	Proteins: Structure, Function, and Bioinformatics
Language	English
Publisher	Wiley-Liss
Publisher Date	2008-08-15
Publisher Place	United States
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Research Support, Non-u.s. Gov't Temperature Discipline Biochemistry Models, Molecular Ketoglutarate Dehydrogenase Complex Metabolism Protein Folding Journal Article Proteins Thermodynamics Chemistry Escherichia Coli Computer Simulation Protein Denaturation Protein Conformation Enzymology
Content Type	Text
Resource Type	Article
Subject	Structural Biology Biochemistry Molecular Biology

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