Abstract
The Miyazawa-Jernigan (MJ) contact potential for globular proteins is a widely used knowledge-based potential. It is well known that MJ’s contact energies mainly come from one-body terms. Directly in the framework of the MJ energy for a protein, we derive the one-body term based on a probabilistic model, and compare the term with several hydrophobicity scales of amino acids. This derivation is based on a set of native structures, and the only information of structures manipulated in the analysis is the contact numbers of each residue. Contact numbers strongly correlate with layers of a protein when it is viewed as an ellipsoid. Using an entropic clustering approach, we obtain two coarse-grained states by maximizing the mutual information between coordination numbers and residue types, and find their differences in the two-body correction. A contact definition using sidechain centers roughly estimated from Cα atoms results in no significant changes.
Highlights
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Knowledge-based potentials for simplified models of protein are essential to understanding the protein structure and folding dynamics
It is not so obvious that many of them may be approximated with a simple function of individual residue properties such as hydrophobicity, demixing, and electrostatics [9]. (Note that the ‘one-body’ approximations of Ref. [9] may contain ‘two-body’ terms in the sense of interactions, and that the one-body term of the MJ contact energies is the contribution of each contact associated with a residue of a given type to the energy of a protein.)
Summary
Comprehending the nature of the physical interactions between different types of amino acids is crucial for understanding protein folding and structure prediction. The physics-based potential functions are based on full atomic models and require high computational cost. The number of different types of residue-residue contacts can be counted directly from the structure of proteins. By means of the approximation that the solvent and solute molecules are in quasi-chemical equilibrium and an approximate treatment of the effects of chain connectivity, Miyazawa and Jernigan estimated their interresidue contact energies from known crystal structures of globular proteins. Energy eab between residue types a and b may be decomposed into two components: the desolvation terms ea0. Among different types of contacts, the average difference of the desolvation terms is about 9 times larger than that of the mixing terms This means that contact energies eab are dominant by the ‘one-body’ desolvation.
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