Homology modeling of the Abl-SH3 domain

Research output: Contribution to journalResearch articleContributedpeer-review

Contributors

  • M T Pisabarro - , Structural Bioinformatics (Research Group), Biotechnology Center, European Molecular Biology Laboratory (EMBL) Heidelberg, Structures & Biocomputing (First author)
  • A R Ortiz - , European Molecular Biology Laboratory (EMBL) Heidelberg, University of Alcalá (Author)
  • L Serrano - , European Molecular Biology Laboratory (EMBL) Heidelberg, Structures & Biocomputing (Author)
  • R C Wade - , European Molecular Biology Laboratory (EMBL) Heidelberg, Structures & Biocomputing (Author)

Abstract

A tertiary structure model of the Abl-SH3 domain is predicted by using homology modeling techniques coupled to molecular dynamics simulations. Two template proteins were used, Fyn-SH3 and Spc-SH3. The refined model was extensively checked for errors using criteria based on stereochemistry, packing, solvation free-energy, accessible surface areas, and contact analyses. The different checking methods do not totally agree, as each one evaluates a different characteristic of protein structures. Several zones of the protein are more susceptible to incorporating errors. These include residues 13, 15, 35, 39, 45, 46, 50, and 60. An interesting finding is that the measurement of the C alpha chirality correlated well with the rest of the criteria, suggesting that this parameter might be a good indicator of correct local conformation. Deviations of more than 4 degrees may be indicative of poor local structure.

Details

Original languageEnglish
Pages (from-to)203-215
Number of pages13
JournalProteins
Volume20
Issue number3
Publication statusPublished - Nov 1994
Peer-reviewedYes

External IDs

Scopus 0028063255

Keywords

Keywords

  • Computer Simulation, Humans, Models, Molecular, Monte Carlo Method, Protein Structure, Tertiary, Proto-Oncogene Proteins/chemistry, Proto-Oncogene Proteins c-abl/chemistry, Proto-Oncogene Proteins c-fyn, Sequence Alignment, Sequence Homology, Amino Acid, Spectrin/chemistry, Stereoisomerism, Templates, Genetic

Library keywords