Homology modeling of the Abl-SH3 domain

• Published in: Proteins, structure, function, and bioinformatics Vol. 20; no. 3; p. 203
• Main Authors: Pisabarro, M T, Ortiz, A R, Serrano, L, Wade, R C
• Format: Journal Article
• Language: English
• Published: United States 01-11-1994
• Subjects: 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
• ISSN: 0887-3585
• DOI: 10.1002/prot.340200302

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.