CyberinfraV1, Main, Exploration, bibRecord, 000507

Folding helical proteins in explicit solvent using dihedral-biased tempering

Identifieur interne : 000507 ( Main/Exploration ); précédent : 000506; suivant : 000508

Folding helical proteins in explicit solvent using dihedral-biased tempering

Auteurs : Cheng Zhang [États-Unis] ; Jianpeng Ma [États-Unis]

Source :

Proceedings of the National Academy of Sciences of the United States of America [ 0027-8424 ] ; 2012.

RBID : PMC:3361456

Abstract

Using a single-trajectory-based tempering method with a high-temperature dihedral bias, we repeatedly folded four helical proteins [α₃D (PDB ID: 2A3D, 73 residues), α₃W (1LQ7, 67 residues), Fap1-NR_α (2KUB, 81 residues) and S-836 (2JUA, 102 residues)] and some of the mutants in explicit solvent within several microseconds. The lowest root-mean-square deviations of backbone atoms from the experimentally determined structures were 1.9, 1.4, 1.0, and 2.1 Å, respectively. Cluster analyses of folding trajectories showed the native conformation usually occupied the most populated cluster. The simulation protocol can be applied to large-scale simulations of other helical proteins on commonly accessible computing platforms.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3361456

DOI: 10.1073/pnas.1112143109
PubMed: 22573819
PubMed Central: 3361456

Affiliations:

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<front><div type="abstract" xml:lang="en"><p>Using a single-trajectory-based tempering method with a high-temperature dihedral bias, we repeatedly folded four helical proteins [<italic>α</italic>
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Folding helical proteins in explicit solvent using dihedral-biased tempering

Folding helical proteins in explicit solvent using dihedral-biased tempering

Source :

Abstract

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