Folding helical proteins in explicit solvent using dihedral-biased tempering
Identifieur interne : 000507 ( Main/Exploration ); précédent : 000506; suivant : 000508Folding 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.
Abstract
Using a single-trajectory-based tempering method with a high-temperature dihedral bias, we repeatedly folded four helical proteins [
Url:
DOI: 10.1073/pnas.1112143109
PubMed: 22573819
PubMed Central: 3361456
Affiliations:
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Le document en format XML
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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>
<sub>3</sub>
D (PDB ID: 2A3D, 73 residues), <italic>α</italic>
<sub>3</sub>
W (1LQ7, 67 residues), Fap1-NR<sub><italic>α</italic>
</sub>
(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.</p>
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