Atomistic Picture of Conformational Exchange in a T4 Lysozyme Cavity Mutant: An Experiment-Guided Molecular Dynamics Study. Vallurupalli, P., Chakrabarti, N., Pomes, R., & Kay, L. Chemical Science, 3:3602-3613, 2016.
Atomistic Picture of Conformational Exchange in a T4 Lysozyme Cavity Mutant: An Experiment-Guided Molecular Dynamics Study [pdf]Paper  abstract   bibtex   
Despite the importance of dynamics to protein function there is little information about the states that are formed as the protein explores its conformational landscape or about the mechanism by which transitions between the different states occur. Here we used a combined NMR spin relaxation and unbiased molecular dynamics (MD) approach to investigate the exchange process by which a cavity in an L99A mutant of T4 lysozyme (T4L 99A) interconverts between an empty and occupied form that involves repositioning of an aromatic residue, Phe114. Although structures of the end-states of the exchange process are available, insight into the mechanism by which the transition takes place cannot be obtained from experiment and the timescales involved are too slow to address using brute force MD. Using spin relaxation NMR methods, we have identified a triple-mutant of T4L that undergoes the same exchange process as T4L L99A but where the minor state lifetime has decreased significantly so that the spontaneous conformational transition to the major state can be studied using all-atom MD simulations. The simulation trajectories were analyzed using Markov state models and the energy landscape so obtained is in good agreement with expectations based on NMR studies. Notably there is no large-scale perturbation of the structure during the transition, multiple intermediates are formed between the two similar exchanging conformations and the free energy barrier between these two well-folded, compact forms is small (6 kBT), only slightly larger than for processes considered to be barrierless.

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