Document Detail


Ab initio folding simulation of Trpcage by replica exchange with hybrid Hamiltonian.
MedLine Citation:
PMID:  18775599     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Replica-exchange molecular dynamics simulations with hybrid Hamiltonian in explicit solvent were performed to study the folding of a designed 20-residue miniprotein, Trpcage, from a fully extended structure. During the simulations several folding/unfolding events happened. In the folded states the majority of experimentally observed NMR NOE restraints are satisfied. The folded structures have root mean squared deviation of 2.0 A with respect to the NMR structures considering all heavy atoms. The free-energy surface constructed by the hybrid Hamiltonian simulations is similar to the one built by a standard replica-exchange simulation which started from the native structure. Consistent with previous experimental observation, a pre-existing hydrophobic collapse in the unfolded state is detected by investigating the desolvation behavior of Trpcage. At room temperature, an intermediate state featured by a misfolded core, a nearly formed alpha-helix segment and an absence of 3(10)-helix is found. The replica exchange with hybrid Hamiltonian method is shown here to be capable of resolving the folding picture of the miniprotein.
Authors:
Weixin Xu; Yuguang Mu
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't     Date:  2008-08-13
Journal Detail:
Title:  Biophysical chemistry     Volume:  137     ISSN:  0301-4622     ISO Abbreviation:  Biophys. Chem.     Publication Date:  2008 Oct 
Date Detail:
Created Date:  2008-09-22     Completed Date:  2008-12-02     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  0403171     Medline TA:  Biophys Chem     Country:  Netherlands    
Other Details:
Languages:  eng     Pagination:  116-25     Citation Subset:  IM    
Affiliation:
School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
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MeSH Terms
Descriptor/Qualifier:
Circular Dichroism
Hydrophobicity
Models, Molecular*
Nuclear Magnetic Resonance, Biomolecular
Peptides / chemistry*
Protein Folding*
Protein Structure, Secondary
Static Electricity
Thermodynamics
Transition Temperature
Water / chemistry
Chemical
Reg. No./Substance:
0/Peptides; 7732-18-5/Water

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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