Simplified model for hierarchical protein folding with self-consistent energy of contacts
Abstract
Simplified protein folding model is considered. The protein is represented as a homopolymer, which is subject to hierarchical compactization. It is assumed that the first stage of folding is a formation of local first-level clusters, which later aggregate to form the clusters of higher hierarchical levels. Formation of the higher level clusters is assumed to be much slower than the dynamics of the lower-level cluster and is considered in adiabatic approximation. Formation of clusters cause the "freezing" of individual monomers, which lead to dramatic narrowing of the conformation space of the chain and to the steady motion toward the native energy minimum. The energy of contacts is considered to be dependent on the large-scale generalized structural coordinate, which determine the state of the folding chain. This coordinate, in turn, depends on the number of the formed contacts, which makes the system self-organized. It is shown that such a system can have two discrete steady states - unfolded and native. Probabilities of the states
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References
Dobson CM, Sail A, Karplus M. Protein Folding: A Perspective from Theory and Experiment. Angew. Chem. Int. Ed. 1998;37:868-93.
Mirny L, Shakhnovich E. Protein folding theory: from lattice to all-atom models. Annu. Rev. Biophys. Biomol. Struct. 2001;30:361-96.
Yesylevskyy SO, Demchenko AP. Modeling the hierarchical protein folding using clustering Monte-Carlo algorithm. Protein and Peptide Letters. 2001;6:437-42.
Michalet X, Weiss S. Single-molecule spectroscopy and microscopy. C. R. Physique. 2002;3:619-44.
Yesylevskyy SO, Demchenko AP. Towards realistic description of collective motions in the lattice protein folding models. J. Biophys. Chem. 2003.
Goushcha AO, Kharkyanen VN, Scott GW, Holzwarth AR. Self-Regulation Phenomena in Baacterial Reaction Centers. I. Gneral Theory. Byophys. J. 2000;79:1237-52.
Yesylevskyy SO, Kharkyanen VN. Hierarchy of motions and quasi-particles in the simplified model of potassium channel selectivity filter. J. Biological Physics. 2003.
Demchenko AP, Ustinov AA, Kharkianen VN. Analiticheskaia teoriia ligand-indutcirovannykh konformatcionnykh perekhodov v belkakh. Biofizicheskii vestnik. 2001;1(8):7-17. (in Russian)
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