Use of quantitative structure-property relationships to predict the folding ability of model proteins

• Published in: Proteins, structure, function, and bioinformatics Vol. 33; no. 2; pp. 177 - 203
• Main Authors: Dinner, Aaron R., So, Sung-Sau, Karplus, Martin
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 01.11.1998
• Subjects: Algorithms; genetic algorithm; Kinetics; lattice model; Models, Chemical; Monte Carlo; Monte Carlo Method; neural network; Protein Conformation; Protein Folding; QSPR; Structure-Activity Relationship
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/(SICI)1097-0134(19981101)33:2<177::AID-PROT4>3.0.CO;2-G

We investigate the folding of a 125‐bead heteropolymer model for proteins subject to Monte Carlo dynamics on a simple cubic lattice. Detailed study of a few sequences revealed a folding mechanism consisting of a rapid collapse followed by a slow search for a stable core that served as the transition state for folding to a near‐native intermediate. Rearrangement from the intermediate to the native state slowed folding further because it required breaking native‐like local structure between surface monomers so that those residues could condense onto the core. We demonstrate here the generality of this mechanism by a statistical analysis of a 200 sequence database using a method that employs a genetic algorithm to pick the sequence attributes that are most important for folding and an artificial neural network to derive the corresponding functional dependence of folding ability on the chosen sequence attributes [quantitative structure‐property relationships (QSPRs)]. QSPRs that use three sequence attributes yielded substantially more accurate predictions than those that use only one. The results suggest that efficient search for the core is dependent on both the native state's overall stability and its amount of kinetically accessible, cooperative structure, whereas rearrangement from the intermediate is facilitated by destabilization of contacts between surface monomers. Implications for folding and design are discussed. Proteins 33:177–203, 1998. © 1998 Wiley‐Liss, Inc.