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Effects of salt bridges on protein structure and design
Author(s) -
Sindelar Charles V.,
Hendsch Zachary S.,
Tidor Bruce
Publication year - 1998
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.5560070906
Subject(s) - chemistry , chemical physics , crystal structure , crystallography , lattice energy , protein folding , lattice (music) , electrostatics , salt bridge , computational chemistry , physics , mutant , biochemistry , gene , acoustics
Abstract Theoretical calculations (Hendsch ZS & Tidor B, 1994, Protein Sci 3 :211‐226) and experiments (Waldburger CD et al., 1995, Nut Struct Biol 2 :122‐128; Wimley WC et al., 1996, Proc Natl Acud Sci USA 93 :2985‐2990) suggest that hydrophobic interactions are more stabilizing than salt bridges in protein folding. The lack of apparent stability benefit for many salt bridges requires an alternative explanation for their occurrence within proteins. To examine the effect of salt bridges on protein structure and stability in more detail, we have developed an energy function for simple cubic lattice polymers based on continuum electrostatic calculations of a representative selection of salt bridges found in known protein crystal structures. There are only three types of residues in the model, with charges of ‐1, 0, or +1. We have exhaustively enumerated conformational space and significant regions of sequence space for three‐dimensional cubic lattice polymers of length 16. The results demonstrate that, while the more highly charged sequences are less stable, the loss of stability is accompanied by a substantial reduction in the degeneracy of the lowest‐energy state. Moreover, the reduction in degeneracy is greater due to charges that pair than for lone charges that remain relatively exposed to solvent. We have also explored and illustrated the use of ion‐pairing strategies for rational structural design using model lattice studies.