On the optimal contact potential of proteins

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Kinjo, Akira R.
Miyazawa, Sanzo
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We analytically derive the lower bound of the total conformational energy of a protein structure by assuming that the total conformational energy is well approximated by the sum of sequence-dependent pairwise contact energies. The condition for the native structure achieving the lower bound leads to the contact energy matrix that is a scalar multiple of the native contact matrix, i.e., the so-called Go potential. We also derive spectral relations between contact matrix and energy matrix, and approximations related to one-dimensional protein structures. Implications for protein structure prediction are discussed.
Comment: 5 pages, text only
Keywords
Quantitative Biology - Biomolecules, Physics - Biological Physics, Physics - Chemical Physics
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