Transitional Trajectories Between Minimum Energy Conformations of Flexible Biomolecules
Smith-Palmer, Michael McWilliams
MetadataShow full item record
This paper describes conformational transitions of flexible biomolecules, especially proteins. Molecules tend to naturally occur in stable (or minimum energy) conformations. Dynamics methods can be used to model a molecule through use of computer simulation. Within a generated trajectory, we expect the molecule to exist and make transitions between minimum energy conformations. High activation energy barriers prevent frequent transitions. Generalized density dynamics techniques will be utilized to increase the sampling of molecules in different stable molecular conformations. Paths within the trajectory that contain transitions can then be isolated. Once isolated, a transitional trajectory can be optimized to a minimum energy path (MEP) between two minimum energy conformations. The MEP will help discover the activation energy of the molecule according to the min-max principle (taking the lowest path over a barrier). The CHARMM package, along with MATLAB and gOpenMol, will be used to analyze the physical conformations of alanine dipeptide (as a test case). Further, we describe work on larger helical model protein systems.