Paper Citing NAMD - Abstract
Lu, Wenzhe; Negi, Surendra S.; Oberhauser, Andres F.; Braun, Werner
Engineering proteins with enhanced mechanical stability by force-specific sequence motifs
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:1308-1315, MAR 2012
Use of atomic force microscopy (AFM) has recently led to a better understanding of the molecular mechanisms of the unfolding process by mechanical forces; however, the rational design of novel proteins with specific mechanical strength remains challenging. We have approached this problem from a new perspective that generates linear physicalchemical properties (PCP) motifs from a limited AFM data set. Guided by our linear sequence analysis, we designed and analyzed four new mutants of the titin I1 domain with the goal of increasing the domain's mechanical strength. All four mutants could be cloned and expressed as soluble proteins. AFM data indicate that at least two of the mutants have increased molecular mechanical strength. This observation suggests that the PCP method is useful to graft sequences specific for high mechanical stability to weak proteins to increase their mechanical stability, and represents an additional tool in the design of novel proteins besides steered molecular dynamics calculations, coarse grained simulations, and ?-value analysis of the transition state. Proteins 2012; (c) 2011 Wiley Periodicals, Inc.
