Computational estimation of specific side chain interaction energies in alpha helices

Citation
S. Fisinger et al., Computational estimation of specific side chain interaction energies in alpha helices, PROTEIN SCI, 10(4), 2001, pp. 809-818
Citations number
32
Language
INGLESE
art.tipo
Article
Categorie Soggetti
Biochemistry & Biophysics
Journal title
PROTEIN SCIENCE
ISSN journal
0961-8368 → ACNP
Volume
10
Issue
4
Year of publication
2001
Pages
809 - 818
Database
ISI
SICI code
0961-8368(200104)10:4<809:CEOSSC>2.0.ZU;2-5
Abstract
We have used a structure energy-based computer program developed for protei n design, Perla, to provide theoretical estimates of all specific side chai n-side chain interaction energies occurring in cr helices. The computed sid e chain-side chain interaction energies were used as substitutes for the co rresponding values used by the helix/coil transition algorithm, AGADIR. Pre dictions of peptide helical contents were nearly as successful as those obt ained with the originally calibrated set of parameters; a correlation to ex perimentally observed a-helical populations of 0.91 proved that our theoret ical estimates are reasonably correct for amino acid pairs that are frequen t in our database of peptides. Furthermore, we have determined experimental ly the previously uncharacterized interaction energies for Lys-Ile, Thr-Ile , and Phe-Ile amino acid pairs at i,i + 4 positions. The experimental value s compare favorably with the computed theoretical estimates. Importantly, t he computed values for Thr-Ile and Phe-Ile interactions are better than the energies based on chemical similarity, whereas for Lys-Ile they are simila r. Thus, computational techniques can be used to provide precise energies f or amino acid pairwise interactions, a fact that supports the development o f structure energy-based computational tools for structure predictions and sequence design.