hide
Free keywords:
membrane proteins
CD3-zeta
glycophorin
molecular dynamics
proteomics
molecular modeling
transmembrane alpha-helices
zeta-chain dimerization
cell antigen
receptor
structure prediction
homologous proteins
secondary
structure
phospholamban
sequences
domain
association
Biochemistry & Molecular Biology
Biophysics
Abstract:
The importance of accurately modeling membrane proteins cannot be overstated, in lieu of the difficulties in solving their structures experimentally. Often, however, modeling procedures (e.g., global searching molecular dynamics) generate several possible candidates rather then pointing to a single model. Herein we present a new approach to select among candidate models based on the general hypothesis that silent amino acid substitutions, present in variants identified from evolutionary conservation data or mutagenesis analysis, do not affect the stability of a native structure but may destabilize the non-native structures also found. The proof of this hypothesis has been tested on the alpha -helical transmembrane domains of two homodimers, human glycophorin A and human CD3-zeta, a component of the T-cell receptor. For both proteins, only one structure was identified using all the variants. For glycophorin A, this structure is virtually identical to the structure determined experimentally by NAM. We present a model for the transmembrane domain of CD3-zeta that is consistent with predictions based on mutagenesis, homology modeling, and the presence of a disulfide bond. Our experiments suggest that this method allows the prediction of transmembrane domain structure based only on widely available evolutionary conservation data. (C) 2001 Wiley-Liss, Inc.
