Alpha helical crossovers favor right-handed supersecondary structures by kinetic trapping: the phone cord effect in protein folding.
The remarkable predominance of right-handedness in beta-alpha-beta helical crossovers has been previously explained in terms of thermodynamic stability and kinetic accessibility, but a different kinetic trapping mechanism may also play a role. If the beta-sheet contacts are made before the crossover helix is fully formed, and if the backbone angles of the folding helix follows the energetic pathway of least resistance, then the helix would impart a torque on the ends of the two strands. Such a torque would tear apart a left-handed conformation but hold together a right-handed one. Right-handed helical crossovers predominate even in all-alpha proteins, where previous explanations based on the preferred twist of the beta sheet do not apply. Using simple molecular simulations, we can reproduce the right-handed preference in beta-alpha-beta units, without imposing specific beta-strand geometry. The new kinetic trapping mechanism is dubbed the "phone cord effect" because it is reminiscent of the way a helical phone cord forms superhelices to relieve torsional stress. Kinetic trapping explains the presence of a right-handed superhelical preference in alpha helical crossovers and provides a possible folding mechanism for knotted proteins.
Cole
Benjamin J
BJ
Departments of Biology and Computer Science, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, USA.
Bystroff
Christopher
C
D003198:Computer Simulation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013816:Thermodynamics