Protein folding: Complex potential for the driving force in a two-dimensional space of collective variables
نویسندگان
چکیده
منابع مشابه
Protein folding: complex potential for the driving force in a two-dimensional space of collective variables.
Using the Helmholtz decomposition of the vector field of folding fluxes in a two-dimensional space of collective variables, a potential of the driving force for protein folding is introduced. The potential has two components. One component is responsible for the source and sink of the folding flows, which represent respectively, the unfolded states and the native state of the protein, and the o...
متن کاملProtein Folding as a Complex Reaction: A Two-Component Potential for the Driving Force of Folding and Its Variation with Folding Scenario
The Helmholtz decomposition of the vector field of probability fluxes in a two-dimensional space of collective variables makes it possible to introduce a potential for the driving force of protein folding [Chekmarev, J. Chem. Phys. 139 (2013) 145103]. The potential has two components: one component (Φ) is responsible for the source and sink of the folding flow, which represent, respectively, th...
متن کاملNature of Driving Force for Protein Folding -- A Result From Analyzing the Statistical Potential
In a statistical approach to protein structure analysis, Miyazawa and Jernigan (MJ) derived a 20 × 20 matrix of inter-residue contact energies between different types of amino acids. Using the method of eigenvalue decomposition, we find that the MJ matrix can be accurately reconstructed from its first two principal component vectors as Mij = C0 + C1(qi + qj) + C2qiqj , with constant C’s, and 20...
متن کاملOrigin of the native driving force for protein folding.
We derive an expression with four adjustable parameters that reproduces well the 20x20 Miyazawa-Jernigan potential matrix extracted from known protein structures. The numerical values of the parameters can be approximately computed from the surface tension of water, water-screened dipole interactions between residues and water and among residues, and average exposures of residues in folded prot...
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ژورنال
عنوان ژورنال: The Journal of Chemical Physics
سال: 2013
ISSN: 0021-9606,1089-7690
DOI: 10.1063/1.4824133