A minimal protein-like lattice model

Speaker(s)

Piotr Pokarowski

Affiliation

Uniwersytet Warszawski

Date

Nov. 3, 2010, 4:15 p.m.

Room

room 5820

Seminar

Seminar of Biomathematics and Game Theory Group

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I will summarize results of my papers with Andrzej Kolinski. We have designed a minimal model of protein folding that reproduces in a qualitative way the most pronounced features of globular proteins. Using Monte Carlo simulations we have estimated a set of parameters for which the native state is the global minimum of conformational energy. This implies the minimality of our force field. Then we have found such interaction parameters for which the model satisfies the thermodynamic hypothesis and folding transition is maximally cooperative. Contrary to H-P models, long range interactions are consistent with statistical contact potentials within an average protein environment and not with the transfer energies of residues from water. Cooperativity depends on protein architecture: it is the highest for the beta motif and the lowest for the alpha motif.

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