<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Romo, T. D.</style></author><author><style face="normal" font="default" size="100%">Grossfield, A.</style></author><author><style face="normal" font="default" size="100%">Markelz, A. G.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Persistent Protein Motions in a Rugged Energy Landscape Revealed by Normal Mode Ensemble Analysis</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of Chemical Information and Modeling</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Chem Inf. Model.</style></alt-title><short-title><style face="normal" font="default" size="100%">J. Chem Inf. Model.J. Chem Inf. Model.</style></short-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Chemistry</style></keyword><keyword><style  face="normal" font="default" size="100%">Computer Science</style></keyword><keyword><style  face="normal" font="default" size="100%">molecular-dynamics</style></keyword><keyword><style  face="normal" font="default" size="100%">Pharmacology &amp; Pharmacy</style></keyword><keyword><style  face="normal" font="default" size="100%">photoactive yellow protein</style></keyword><keyword><style  face="normal" font="default" size="100%">spectroscopy</style></keyword><keyword><style  face="normal" font="default" size="100%">state</style></keyword><keyword><style  face="normal" font="default" size="100%">vibrational-modes</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2020</style></year><pub-dates><date><style  face="normal" font="default" size="100%">Dec</style></date></pub-dates></dates><number><style face="normal" font="default" size="100%">12</style></number><volume><style face="normal" font="default" size="100%">60</style></volume><pages><style face="normal" font="default" size="100%">6419-6426</style></pages><isbn><style face="normal" font="default" size="100%">1549-9596</style></isbn><language><style face="normal" font="default" size="100%">English</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;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.&lt;/p&gt;</style></abstract><work-type><style face="normal" font="default" size="100%">Article</style></work-type><accession-num><style face="normal" font="default" size="100%">WOS:000608875100076</style></accession-num><notes><style face="normal" font="default" size="100%">ISI Document Delivery No.: PT8QA&lt;br/&gt;Times Cited: 0&lt;br/&gt;Cited Reference Count: 47&lt;br/&gt;Cited References: &lt;br/&gt;     Acbas G, 2014, NAT COMMUN, V5, DOI 10.1038/ncomms4076&lt;br/&gt;     Bahar I, 2007, CURR OPIN STRUC BIOL, V17, P633, DOI 10.1016/j.sbi.2007.09.011&lt;br/&gt;     Balog E, 2011, J PHYS CHEM B, V115, P6811, DOI 10.1021/jp108493g&lt;br/&gt;     Castro-Camus E, 2008, CHEM PHYS LETT, V455, P289, DOI 10.1016/j.cplett.2008.02.084&lt;br/&gt;     Cerutti DS, 2008, BIOCHEMISTRY-US, V47, P12065, DOI 10.1021/bi800894u&lt;br/&gt;     Cerutti DS, 2019, WIRES COMPUT MOL SCI, V9, DOI 10.1002/wcms.1402&lt;br/&gt;     CHO M, 1994, J CHEM PHYS, V100, P6672, DOI 10.1063/1.467027&lt;br/&gt;     Choi JH, 2014, J PHYS CHEM B, V118, P12837, DOI 10.1021/jp508547y&lt;br/&gt;     Cote Y, 2017, BIOPHYS J, V112, P2575, DOI 10.1016/j.bpj.2017.05.018&lt;br/&gt;     Dong J, 1999, ACTA CRYSTALLOGR D, V55, P745, DOI 10.1107/S0907444998016047&lt;br/&gt;     ESSMANN U, 1995, J CHEM PHYS, V103, P8577, DOI 10.1063/1.470117&lt;br/&gt;     Falconer RJ, 2012, J INFRARED MILLIM TE, V33, P973, DOI 10.1007/s10762-012-9915-9&lt;br/&gt;     FELLER SE, 1995, J CHEM PHYS, V103, P4613, DOI 10.1063/1.470648&lt;br/&gt;     Gerek ZN, 2011, PLOS COMPUT BIOL, V7, DOI 10.1371/journal.pcbi.1002154&lt;br/&gt;     GO N, 1983, P NATL ACAD SCI-BIOL, V80, P3696, DOI 10.1073/pnas.80.12.3696&lt;br/&gt;     Grossfield A, 2019, LIVING J COMPUT MOL, V1, P5067, DOI DOI 10.33011/LIVEC0MS.1.1.5067&lt;br/&gt;     Grossfield A, 2009, ANN REP COMP CHEM, V5, P23, DOI 10.1016/S1574-1400(09)00502-7&lt;br/&gt;     He YF, 2011, BIOPHYS J, V100, P1058, DOI 10.1016/j.bpj.2010.12.3731&lt;br/&gt;     HORIUCHI T, 1991, PROTEINS, V10, P106, DOI 10.1002/prot.340100204&lt;br/&gt;     Huang J, 2013, J COMPUT CHEM, V34, P2135, DOI 10.1002/jcc.23354&lt;br/&gt;     Katebi AR, 2014, PROTEIN SCI, V23, P213, DOI 10.1002/pro.2407&lt;br/&gt;     Kindt JT, 1997, J CHEM PHYS, V106, P4389, DOI 10.1063/1.473486&lt;br/&gt;     Kroll J, 2007, VIB SPECTROSC, V43, P324, DOI 10.1016/j.vibspec.2006.03.010&lt;br/&gt;     Leioatts N, 2012, J CHEM THEORY COMPUT, V8, P2424, DOI 10.1021/ct3000316&lt;br/&gt;     Lerbret A, 2009, J CHEM PHYS, V131, DOI 10.1063/1.3273218&lt;br/&gt;     Meinhold L, 2007, PHYS REV LETT, V99, DOI 10.1103/PhysRevLett.99.138101&lt;br/&gt;     Miller DW, 1999, J MOL BIOL, V286, P267, DOI 10.1006/jmbi.1998.2445&lt;br/&gt;     Niessen KA, 2019, NAT COMMUN, V10, DOI 10.1038/s41467-019-08926-3&lt;br/&gt;     Niessen KA, 2017, BIOPHYS J, V112, P933, DOI 10.1016/j.bpj.2016.12.049&lt;br/&gt;     Phillips JC, 2005, J COMPUT CHEM, V26, P1781, DOI 10.1002/jcc.20289&lt;br/&gt;     Porter JR, 2019, BIOPHYS J, V116, P818, DOI 10.1016/j.bpj.2018.11.3144&lt;br/&gt;     Romo TD, 2014, J COMPUT CHEM, V35, P2305, DOI 10.1002/jcc.23753&lt;br/&gt;     Romo TD, 2009, IEEE ENG MED BIO, P2332, DOI 10.1109/IEMBS.2009.5335065&lt;br/&gt;     Sassi P, 2013, J CHEM PHYS, V139, DOI 10.1063/1.4838355&lt;br/&gt;     Singh R, 2012, J PHYS CHEM A, V116, P10359, DOI 10.1021/jp307288r&lt;br/&gt;     Stehle CU, 2012, J CHEM PHYS, V136, DOI 10.1063/1.3686886&lt;br/&gt;     STRAUB JE, 1994, J PHYS CHEM-US, V98, P10978, DOI 10.1021/j100093a046&lt;br/&gt;     Tehver R, 2009, J MOL BIOL, V387, P390, DOI 10.1016/j.jmb.2008.12.032&lt;br/&gt;     Thirumuruganandham SP, 2009, J MOL MODEL, V15, P959, DOI 10.1007/s00894-008-0446-1&lt;br/&gt;     Whitmire SE, 2003, BIOPHYS J, V85, P1269, DOI 10.1016/S0006-3495(03)74562-7&lt;br/&gt;     Xie AH, 2000, PHYS REV LETT, V84, P5435, DOI 10.1103/PhysRevLett.84.5435&lt;br/&gt;     Xu D, 1996, J PHYS CHEM-US, V100, P12108, DOI 10.1021/jp960076a&lt;br/&gt;     Yu X, 2005, J CHEM PHYS, V122, DOI 10.1063/1.1830431&lt;br/&gt;     Yu X, 2004, CHEM PHYS LETT, V391, P181, DOI 10.1016/j.cplett.2004.04.100&lt;br/&gt;     Zakaria HA, 2011, APPL SPECTROSC, V65, P260, DOI 10.1366/10-06162&lt;br/&gt;     Zhang HL, 2009, J MOL GRAPH MODEL, V27, P655, DOI 10.1016/j.jmgm.2008.10.005&lt;br/&gt;     Zorba A, 2019, P NATL ACAD SCI USA, V116, P13937, DOI 10.1073/pnas.1906024116&lt;br/&gt;Romo, Tod D. Grossfield, Alan Markelz, Andrea G.&lt;br/&gt;Grossfield, Alan/0000-0002-5877-2789&lt;br/&gt;National Science FoundationNational Science Foundation (NSF) [MCB 1616529]; U.S. Department of EnergyUnited States Department of Energy (DOE) [DESC0016317]&lt;br/&gt;Funding was provided by the National Science Foundation (MCB 1616529) and the U.S. Department of Energy (DESC0016317).&lt;br/&gt;&lt;br/&gt;1&lt;br/&gt;Amer chemical soc&lt;br/&gt;Washington&lt;br/&gt;1549-960x</style></notes><auth-address><style face="normal" font="default" size="100%">[Romo, Tod D.|Grossfield, Alan] Univ Rochester, Dept Biochem &amp; Biophys, Med Ctr, Rochester, NY 14642 USA. [Markelz, Andrea G.] Univ Buffalo SUNY, Dept Phys, Buffalo, NY 14260 USA.&lt;br/&gt;Markelz, AG (corresponding author), Univ Buffalo SUNY, Dept Phys, Buffalo, NY 14260 USA.&lt;br/&gt;amarkelz@buffalo.edu</style></auth-address></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>47</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Deng, Y.</style></author><author><style face="normal" font="default" size="100%">McKinney, J.</style></author><author><style face="normal" font="default" size="100%">Romo, T.</style></author><author><style face="normal" font="default" size="100%">Grossfield, A.</style></author><author><style face="normal" font="default" size="100%">Markelz, A. G.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Protein Intramolecular Motions with Deuteration and Inhibitor Binding Dependence</style></title><secondary-title><style face="normal" font="default" size="100%">APS R63.003</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2019</style></year><pub-dates><date><style  face="normal" font="default" size="100%">03/2019</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">https://meetings.aps.org/Meeting/MAR19/Session/R63.3</style></url></web-urls></urls><language><style face="normal" font="default" size="100%">eng</style></language></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Deng, Y. T.</style></author><author><style face="normal" font="default" size="100%">McKinney, J.</style></author><author><style face="normal" font="default" size="100%">Romo, T.</style></author><author><style face="normal" font="default" size="100%">Grossfield, A.</style></author><author><style face="normal" font="default" size="100%">Markelz, A.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Spectral Assignment of Lysozyme Collective Vibrations</style></title><secondary-title><style face="normal" font="default" size="100%">Biophysical Journal</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Biophys. J.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biophysics</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2019</style></year><pub-dates><date><style  face="normal" font="default" size="100%">Feb</style></date></pub-dates></dates><number><style face="normal" font="default" size="100%">3</style></number><volume><style face="normal" font="default" size="100%">116</style></volume><pages><style face="normal" font="default" size="100%">564A-564A</style></pages><isbn><style face="normal" font="default" size="100%">0006-3495</style></isbn><language><style face="normal" font="default" size="100%">English</style></language><abstract><style face="normal" font="default" size="100%">&lt;div class=&quot;section-paragraph&quot;&gt;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°, b = 32.7A°, c = 35.1A°, α = 88.2°, β = 108.9°, γ = 111.9°, 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&lt;sup&gt;−1&lt;/sup&gt; and 55cm&lt;sup&gt;−1&lt;/sup&gt;, the triclinic crystals have a series of narrow bands between 40 and 60cm&lt;sup&gt;−1&lt;/sup&gt; and a prominent band at 30cm&lt;sup&gt;−1&lt;/sup&gt;. 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.&lt;/div&gt;</style></abstract><work-type><style face="normal" font="default" size="100%">Meeting Abstract</style></work-type><accession-num><style face="normal" font="default" size="100%">WOS:000460779802832</style></accession-num><notes><style face="normal" font="default" size="100%">ISI Document Delivery No.: HO2XG&lt;br/&gt;Times Cited: 0&lt;br/&gt;Cited Reference Count: 1&lt;br/&gt;Cited References: &lt;br/&gt;     Niessen KA, 2017, BIOPHYS J, V112, P933, DOI 10.1016/j.bpj.2016.12.049&lt;br/&gt;Deng, Yanting Mckinney, Jeffrey Romo, Tod Grossfield, Alan Markelz, Andrea&lt;br/&gt;63rd Annual Meeting of the Biophysical-Society&lt;br/&gt;Mar 02-06, 2019&lt;br/&gt;Baltimore, MD&lt;br/&gt;Biophys Soc&lt;br/&gt;&lt;br/&gt;8&lt;br/&gt;Cell press&lt;br/&gt;Cambridge&lt;br/&gt;1542-0086&lt;br/&gt;1</style></notes><auth-address><style face="normal" font="default" size="100%">[Deng, Yanting|Mckinney, Jeffrey|Markelz, Andrea] SUNY Buffalo, Phys, Buffalo, NY USA. [Romo, Tod|Grossfield, Alan] Univ Rochester, Med Ctr, Dept Biochem &amp; Biophys, Rochester, NY 14642 USA.</style></auth-address></record></records></xml>