Kink Characterization and Modeling in Transmembrane Protein Structures

Abstract

Kinks have been observed to provide important functional and structural features for membrane proteins. Despite their ubiquity in membrane proteins, and their perceived importance, no protein modeling methods explicitly considers kinks. In spite of the limited data for transmembrane proteins, we were able to develop a knowledge-based modeling method for introducing kinks, which we demonstrate can be exploited in modeling approaches to improve the quality of models. The work entailed a thorough analysis of the available high resolution membrane protein structures, concomitantly demonstrating the complexity of the structural considerations for kink prediction. Furthermore, our results indicate that there are systematic and significant differences in the sequence as well as the structural environment between kinked and nonkinked transmembrane helices. To the best of our knowledge, we are reporting a method for modeling kinks for the first time.