On the optimal contact potential of proteins

Details On the optimal contact potential of proteins On the optimal contact potential of proteins

2007-09-04

arxiv.org/abs/0709.0346v2

Chemical Physics Letters, Vol. 451 pp. 132-135 (2008)

Biology

Quantitative Biology

Biomolecules

5 pages, text only

Scientific paper

10.1016/j.cplett.2007.12.005

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.

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