On the optimal contact potential of proteins

Abstract

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.

5 pages, text only

References in corpus (2)

• Recoverable One-dimensional Encoding of Three-dimensional Protein Structures
• Predicting Secondary Structures, Contact Numbers, and Residue-wise Contact Orders of Native Protein Structure from Amino Acid Sequence by Critical Random Networks

Cited by in corpus (1)

• Nature of protein family signatures: Insights from singular value analysis of position-specific scoring matrices