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

• Autorzy: Ekonomiuk D. , Kielbasinski M. , Kolinski A.
• Języki publikacji: EN

Abstrakty

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.

Słowa kluczowe

EN

protein modelling; folding mechanism; protein folding; protein G; statistical potential; high resolution lattice protein; computer simulation; Monte Carlo simulation

• Wydawca: -
• Czasopismo: Acta Biochimica Polonica
• Rocznik: 2005
• Tom: 52
• Numer: 4
• Opis fizyczny: p.741-748,fig.,ref.

Twórcy

autor

Ekonomiuk D.

• Warsaw University, Warsaw, Poland

autor

Kielbasinski M.

autor

Kolinski A.

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