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Abstract: Theory of multi-dimensional representation of free energy surface of proteinfolding is developed by adopting structural order parameters of multipleregions in protein as multiple coordinates. Various scenarios of folding areclassified in terms of cooperativity within individual regions and interactionsamong multiple regions and thus obtained classification is used to analyze thefolding process of several example proteins. Ribosomal protein S6, src-SH3domain, CheY, barnase, and BBL domain are analyzed with the two-dimensionalrepresentation by using a structure-based Hamiltonian model. Extension to thehigher dimensional representation leads to the finer description of the foldingprocess. Barnase, NtrC, and an ankyrin repeat protein are examined with thethree-dimensional representation. The multi-dimensional representation allowsus to directly address questions on folding pathways, intermediates, andtransition states.



Author: Kazuhito Itoh, Masaki Sasai

Source: https://arxiv.org/







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