NMR Relaxation in Proteins with Fast Internal Motions and Slow Conformational Exchange: Model Free Framework and Markov State Simulations.
 

NMR Relaxation in Proteins with Fast Internal Motions and Slow Conformational Exchange: Model Free Framework and Markov State Simulations.

NMR Relaxation in Proteins with Fast Internal Motions and Slow Conformational Exchange: Model Free Framework and Markov State Simulations.

J Phys Chem B. 2013 May 2;

Authors: Xia J, Deng NJ, Levy RM

Abstract
Calculating NMR relaxation effects for proteins with dynamics on multiple timescales generally requires very long trajectories based on conventional molecular dynamics simulations. In this report, we have built Markov state models from multiple MD trajectories and used the resulting MSM to capture the very fast internal motions of the protein within a free energy basin on a time scale up to hundreds of picoseconds and the more than three orders of magnitude slower conformational exchange between macrostates. To interpret the relaxation data, we derive new equations using the model free framework which includes two slowly exchanging macrostates, each of which also exhibits fast local motions.. Using simulations of HIV-1 Protease as an example, we show how the populations of slowly exchanging conformational states as well as order parameters for the different states can be determined from the NMR relaxation data.


PMID: 23638941 [PubMed - as supplied by publisher]



More...