title: [When and how can homologs overcome errors in the energy estimates and make the 3D structure prediction possible].
abstract: One still cannot predict the 3D fold of a protein from its amino acid sequence, mainly because of errors in the energy estimates underlying the prediction. However, a recently developed theory [1] shows that having a set of homologs (i.e., the chains with equal, in despite of numerous mutations, 3D folds) one can average the potential of each interaction over the homologs and thus predict the common 3D fold of protein family even when a correct fold prediction for an individual sequence is impossible because the energies are known only approximately. This theoretical conclusion has been verified by simulation of the energy spectra of simplified models of protein chains [2], and the further investigation of these simplified models shows that their true "native" fold can be found by folding of the chain where each interaction potential is averaged over the homologs. In conclusion, the applicability of the "homolog-averaging" approach is tested by recognition of real protein 3D structures. Both the gapless threading of sequences onto the known protein folds [3] and the more practically important gapped threading (which allows to consider not only the known 3D structures, but the more or less similar to them folds as well) shows a significant increase in selectivity of the native chain fold recognition.
authors.affiliation: Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
authors.forename: A V
authors.initials: AV
authors.lastname: Finkel'shteĭn
authors.forename: D S
authors.initials: DS
authors.lastname: Rykunov
authors.forename: M Iu
authors.initials: MIu
authors.lastname: Lobanov
authors.forename: F Ia
authors.initials: FIa
authors.lastname: Badretdinov
authors.forename: B A
authors.initials: BA
authors.lastname: Reva
authors.forename: J
authors.initials: J
authors.lastname: Skolnick
authors.forename: L A
authors.initials: LA
authors.lastname: Mirnyĭ
authors.forename: E I
authors.initials: EI
authors.lastname: Shakhnovich
mesh_terms: D003198:Computer Simulation; D008958:Models, Molecular; D020836:Protein Structure, Quaternary; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D011506:Proteins