Tertiary structure prediction of mixed α/β proteins via energy minimization

✍ Scribed by Daron M. Standley; John R. Gunn; Richard A. Friesner; Ann E. McDermott

• Publisher: John Wiley and Sons
• Year: 1998
• Tongue: English
• Weight: 257 KB
• Volume: 33
• Category: Article
• ISSN: 0887-3585
• DOI: 10.1002/(sici)1097-0134(19981101)33:2<240::aid-prot8>3.0.co;2-m

✦ Synopsis

We describe an improved algorithm for protein structure prediction, assuming that the location of secondary structural elements is known, with particular focus on prediction for proteins containing ␤-strands. Hydrogen bonding terms are incorporated into the potential function, supplementing our previously developed residue-residue potential which is based on a combination of database statistics and an excluded volume term. Two small mixed ␣/␤ proteins, 1-CTF and BPTI, are studied. In order to obtain native-like structures, it is necessary to allow the ␤-strands in BPTI to distort substantially from an ideal geometry, and an automated algorithm to carry this out efficiently is presented. Simulated annealing Monte Carlo methods, which contain a genetic algorithm component as well, are used to produce an ensemble of low-energy structures. For both proteins, a cluster of structures with low RMS deviation from the native structure is generated and the energetic ranking of this cluster is in the top 2 or 3 clusters obtained from simulations. These results are encouraging with regard to the possibility of constructing a robust procedure for tertiary folding which is applicable to ␤-strand containing proteins. Proteins 33:240-252, 1998.