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2005 | 52 | 4 | 741-748
Article title

Protein modeling with reduced representation: statistical potentials and protein folding mechanism

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EN
Abstracts
EN
A high resolution reduced model of proteins is used in Monte Carlo dynamics studies of the folding mechanism of a small globular protein, the B1 immunoglobulin-binding domain of streptococcal protein G. It is shown that in order to reproduce the physics of the folding transition, the united atom based model requires a set of knowledge-based potentials mimicking the short-range conformational propensities and protein-like chain stiffness, a model of directional and cooperative hydrogen bonds, and properly designed knowledge-based potentials of the long-range interactions between the side groups. The folding of the model protein is cooperative and very fast. In a single trajectory, a number of folding/unfolding cycles were observed. Typically, the folding process is initiated by assembly of a native-like structure of the C-terminal hairpin. In the next stage the rest of the four-ribbon β-sheet folds. The slowest step of this pathway is the assembly of the central helix on the scaffold of the β-sheet.
Publisher

Year
Volume
52
Issue
4
Pages
741-748
Physical description
Dates
published
2005
received
2005-01-14
revised
2005-03-30
accepted
2005-05-20
(unknown)
2005-05-31
Contributors
  • Faculty of Chemistry, Warsaw University, Warszawa, Poland
  • Faculty of Chemistry, Warsaw University, Warszawa, Poland
  • Faculty of Chemistry, Warsaw University, Warszawa, Poland
References
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Document Type
Publication order reference
Identifiers
YADDA identifier
bwmeta1.element.bwnjournal-article-abpv52p741kz
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