@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
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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.} } @conference {306, title = {Protein Intramolecular Motions with Deuteration and Inhibitor Binding Dependence}, booktitle = {APS R63.003}, year = {2019}, month = {03/2019}, url = {https://meetings.aps.org/Meeting/MAR19/Session/R63.3}, author = {Deng, Y. and McKinney, J. and Romo, T. and Grossfield, A. and Markelz, A. G.} } @article {249, title = {Spectral Assignment of Lysozyme Collective Vibrations}, journal = {Biophysical Journal}, volume = {116}, number = {3}, year = {2019}, note = {ISI Document Delivery No.: HO2XG
Times Cited: 0
Cited Reference Count: 1
Cited References:
Niessen KA, 2017, BIOPHYS J, V112, P933, DOI 10.1016/j.bpj.2016.12.049
Deng, Yanting Mckinney, Jeffrey Romo, Tod Grossfield, Alan Markelz, Andrea
63rd Annual Meeting of the Biophysical-Society
Mar 02-06, 2019
Baltimore, MD
Biophys Soc

8
Cell press
Cambridge
1542-0086
1}, month = {Feb}, pages = {564A-564A}, type = {Meeting Abstract}, abstract = {
Global structural vibrations at terahertz (THz) frequencies have been associated with protein function and allosteric control. A chief obstacle to utilizing this control mechanism has been measurement of specific motions. Recently it was shown that while the vibrational density of states, and isotropic absorption spectra are broad and featureless, collective vibrations can be isolated based on their directionality using aligned samples (realized with protein crystals) and anisotropic THz microscopy [1]. However the assignment of resonant bands to specific structural motions was complicated by the high symmetry of the tetragonal crystals used, and the slow experimental method. To structurally map the vibrations of the chicken egg white lysozyme (CEWL) we measure anisotropic absorption of triclinic crystals using our new technique: ideal polarization varying anisotropic THz microscopy (IPV-ATM). The low symmetry triclinic crystals provide absolute protein orientation, and the near field IPV-ATM rapidly measures broadband terahertz linear dichroism of the microcrystals. All measurements were performed at room temperature under 100\% humidity conditions. The unit cell parameters of triclinic lysozyme nitrate crystals, α = 28.5A{\textdegree}, b = 32.7A{\textdegree}, c = 35.1A{\textdegree}, α = 88.2{\textdegree}, β = 108.9{\textdegree}, γ = 111.9{\textdegree}, belonging to the P1 space group, were determined by X-ray diffraction before and after THz measurements. The intramolecular vibrational absorbance of the triclinic crystals has a more complex polarization dependence than the higher symmetry tetragonal crystals, as expected. While the tetragonal crystals have two strong bands at 45cm-1 and 55cm-1, the triclinic crystals have a series of narrow bands between 40 and 60cm-1 and a prominent band at 30cm-1. We compare the measured spectra to normal mode ensemble averaged calculations to assign the observed resonances, and isolating which collective motions impact the catalytic site.
}, keywords = {Biophysics}, isbn = {0006-3495}, doi = {10.1016/j.bpj.2018.11.3032}, author = {Deng, Y. T. and McKinney, J. and Romo, T. and Grossfield, A. and Markelz, A.} }