title: Modeling membrane proteins utilizing information from silent amino acid substitutions.
abstract: This unit describes predicting the structure of simple transmembrane alpha-helical bundles. The protocol is based on a global molecular dynamics search (GMDS) of the configuration space of the helical bundle, yielding several candidates structures. The correct structure amongst these candidates is selected using information from silent amino acid substitutions, employing the following premise: Only the correct structure must (by definition) accept all of the silent amino acid substitutions. Thus, the correct structure is found by repeating the GMDS for several close homologues and selecting the structure that persists in all of the trials.
authors.affiliation: The Hebrew University, Jerusalem, Israel.
authors.forename: Uzi
authors.initials: U
authors.lastname: Kochva
authors.forename: Hadas
authors.initials: H
authors.lastname: Leonov
authors.forename: Isaiah T
authors.initials: IT
authors.lastname: Arkin
authors.forename: Paul D
authors.initials: PD
authors.lastname: Adams
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D003198:Computer Simulation; D008565:Membrane Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D008565:Membrane Proteins