@article {241, title = {Persistent Protein Motions in a Rugged Energy Landscape Revealed by Normal Mode Ensemble Analysis}, journal = {Journal of Chemical Information and Modeling}, volume = {60}, number = {12}, year = {2020}, note = {ISI Document Delivery No.: PT8QA
Times Cited: 0
Cited Reference Count: 47
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Romo, Tod D. Grossfield, Alan Markelz, Andrea G.
Grossfield, Alan/0000-0002-5877-2789
National Science FoundationNational Science Foundation (NSF) [MCB 1616529]; U.S. Department of EnergyUnited States Department of Energy (DOE) [DESC0016317]
Funding was provided by the National Science Foundation (MCB 1616529) and the U.S. Department of Energy (DESC0016317).

1
Amer chemical soc
Washington
1549-960x}, month = {Dec}, pages = {6419-6426}, type = {Article}, abstract = {

Proteins are allosteric machines that couple motions at distinct, often distant, sites to control biological function. Low-frequency structural vibrations are a mechanism of this long-distance connection and are often used computationally to predict correlations, but experimentally identifying the vibrations associated with specific motions has proved challenging. Spectroscopy is an ideal tool to explore these excitations, but measurements have been largely unable to identify important frequency bands. The result is at odds with some previous calculations and raises the question what methods could successfully characterize protein structural vibrations. Here we show the lack of spectral structure arises in part from the variations in protein structure as the protein samples the energy landscape. However, by averaging over the energy landscape as sampled using an aggregate 18.5 mu s of all-atom molecular dynamics simulation of hen egg white lysozyme and normal-mode analyses, we find vibrations with large overlap with functional displacements are surprisingly concentrated in narrow frequency bands. These bands are not apparent in either the ensemble averaged vibrational density of states or isotropic absorption. However, in the case of the ensemble averaged anisotropic absorption, there is persistent spectral structure and overlap between this structure and the functional displacement frequency bands. We systematically lay out heuristics for calculating the spectra robustly, including the need for statistical sampling of the protein and inclusion of adequate water in the spectral calculation. The results show the congested spectrum of these complex molecules obscures important frequency bands associated with function and reveal a method to overcome this congestion by combining structurally sensitive spectroscopy with robust normal mode ensemble analysis.

}, keywords = {Chemistry, Computer Science, molecular-dynamics, Pharmacology \& Pharmacy, photoactive yellow protein, spectroscopy, state, vibrational-modes}, isbn = {1549-9596}, doi = {10.1021/acs.jcim.0c00879}, author = {Romo, T. D. and Grossfield, A. and Markelz, A. G.} } @article {247, title = {Increase in Dynamical Collectivity and Directionality of Orange Carotenoid Protein in the Photo-Protective State}, journal = {Biophysical Journal}, volume = {114}, number = {3}, year = {2018}, note = {ISI Document Delivery No.: GD5RB
Times Cited: 1
Cited Reference Count: 0
Deng, Yanting Luck, Catherine H. Romo, Tod D. Grossfield, Alan M. Bandara, Sepalika Ren, Zhong Yang, Xiaojing Markelz, Andrea G.
62nd Annual Meeting of the Biophysical-Society
Feb 17-21, 2018
San Francisco, CA
Biophys Soc
1

7
Cell press
Cambridge
1542-0086}, month = {Feb}, pages = {522A-522A}, type = {Meeting Abstract}, keywords = {Biophysics}, isbn = {0006-3495}, doi = {10.1016/j.bpj.2017.11.2854}, author = {Deng, Y. T. and Luck, C. H. and Romo, T. D. and Grossfield, A. M. and Bandara, S. and Ren, Z. and Yang, X. J. and Markelz, A. G.} }