Information-theoretic dissection of pairwise contact potentials.
Pairwise contact potentials have a long, successful history in protein structure prediction. They provide an easily-estimated representation of many attributes of protein structures, such as the hydrophobic effect. In order to improve on existing potentials, one should develop a clear understanding of precisely what information they convey. Here, using mutual information, we quantified the information in amino acid potentials, and the importance of hydropathy, charge, disulfide bonding, and burial. Sampling error in mutual information was controlled for by estimating how much information cannot be attributed to sampling bias. We found the information in amino acid contacts to be modest: 0.04 bits per contact. Of that, only 0.01 bits of information could not be attributed to hydropathy, charge, disulfide bonding, or burial.
Cline
Melissa S
MS
Center for Biomolecular Science and Engineering, Baskin School of Engineering, University of California, Santa Cruz, California 95064, USA. cline@soe.ucsc.edu
Karplus
Kevin
K
Lathrop
Richard H
RH
Smith
Temple F
TF
Rogers
Robert G
RG
Haussler
David
D
D000596:Amino Acids / Q000737:chemistry*; D004220:Disulfides / Q000737:chemistry; D057927:Hydrophobic and Hydrophilic Interactions; D008954:Models, Biological; D015394:Molecular Structure; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity
D000596:Amino Acids; D004220:Disulfides; D011506:Proteins; D012997:Solvents