Experimental mapping of short-wavelength phonons in proteins

Shrestha, Utsab R.; Mamontov, Eugene; O'Neill, Hugh M.; Zhang, Qiu; Kolesnikov, Alexander I.; Chu, Xiangqiang

doi:10.1016/j.xinn.2021.100199

Title: Experimental mapping of short-wavelength phonons in proteins

Journal Article · 31 December 2021 · The Innovation

DOI: https://doi.org/10.1016/j.xinn.2021.100199 · OSTI ID:1836353

Shrestha, Utsab R.; Mamontov, Eugene; O'Neill, Hugh M.;

;

; Chu, Xiangqiang

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: NSAF; National Natural Science Foundation of China (NSFC); National Science Foundation (NSF); USDOE; USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities Division

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1836353

Journal Information:: The Innovation, Journal Name: The Innovation Journal Issue: 1 Vol. 3; ISSN 2666-6758

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (51)

Relationship of Femtosecond–Picosecond Dynamics to Enzyme-Catalyzed H-Transfer Cheatum, Christopher M.; Kohen, Amnon Dynamics in Enzyme Catalysis https://doi.org/10.1007/128_2012_407	book	January 2013
Water and globular proteins Rupley, John A.; Gratton, Enrico; Careri, Giorgio Trends in Biochemical Sciences, Vol. 8, Issue 1 https://doi.org/10.1016/0968-0004(83)90063-4	journal	January 1983
Low-frequency collective modes in dry and hydrated proteins Bellissent-Funel, M. C.; Teixeira, J.; Chen, S. H. Biophysical Journal, Vol. 56, Issue 4 https://doi.org/10.1016/S0006-3495(89)82718-3	journal	October 1989
Apparent sound velocity of lysozyme in aqueous solutions Pfeiffer, Helge; Heremans, Karel Chemical Physics Letters, Vol. 361, Issue 3-4 https://doi.org/10.1016/S0009-2614(02)00809-6	journal	July 2002
Structure and dynamics of green fluorescent protein Phillips, George N. Current Opinion in Structural Biology, Vol. 7, Issue 6 https://doi.org/10.1016/S0959-440X(97)80153-4	journal	December 1997
Dynamics of Protein and its Hydration Water: Neutron Scattering Studies on Fully Deuterated GFP Nickels, Jonathan D.; O’Neill, Hugh; Hong, Liang Biophysical Journal, Vol. 103, Issue 7 https://doi.org/10.1016/j.bpj.2012.08.046	journal	October 2012
Coherent Neutron Scattering and Collective Dynamics in the Protein, GFP Nickels, Jonathan D.; Perticaroli, Stefania; O’Neill, Hugh Biophysical Journal, Vol. 105, Issue 9 https://doi.org/10.1016/j.bpj.2013.09.029	journal	November 2013
Role of hydration water in dynamics of biological macromolecules Sokolov, A. P.; Roh, J. H.; Mamontov, E. Chemical Physics, Vol. 345, Issue 2-3 https://doi.org/10.1016/j.chemphys.2007.07.013	journal	April 2008
Temperature dependence of the internal dynamics of a protein in an aqueous solvent: Decoupling from the solvent viscosity Mamontov, E.; O’Neill, H.; Zhang, Q. Chemical Physics, Vol. 424 https://doi.org/10.1016/j.chemphys.2013.02.026	journal	October 2013
Acoustic phonons in chrysotile asbestos probed by high-resolution inelastic x-ray scattering Mamontov, E.; Vakhrushev, S. B.; Kumzerov, Yu. A. Solid State Communications, Vol. 149, Issue 15-16 https://doi.org/10.1016/j.ssc.2009.01.033	journal	April 2009
Protein dynamics studied by neutron scattering Gabel, Frank; Bicout, Dominique; Lehnert, Ursula Quarterly Reviews of Biophysics, Vol. 35, Issue 4 https://doi.org/10.1017/S0033583502003840	journal	November 2002
Water Determines the Structure and Dynamics of Proteins Bellissent-Funel, Marie-Claire; Hassanali, Ali; Havenith, Martina Chemical Reviews, Vol. 116, Issue 13 https://doi.org/10.1021/acs.chemrev.5b00664	journal	April 2016
Collective Excitations in Protein as a Measure of Balance Between its Softness and Rigidity Shrestha, Utsab R.; Bhowmik, Debsindhu; Van Delinder, Kurt W. The Journal of Physical Chemistry B, Vol. 121, Issue 5 https://doi.org/10.1021/acs.jpcb.6b10245	journal	January 2017
Free-Energy Landscape of Enzyme Catalysis ^† Benkovic, Stephen J.; Hammes, Gordon G.; Hammes-Schiffer, Sharon Biochemistry, Vol. 47, Issue 11 https://doi.org/10.1021/bi800049z	journal	March 2008
New Insights into the Role of Water in Biological Function: Studying Solvated Biomolecules Using Terahertz Absorption Spectroscopy in Conjunction with Molecular Dynamics Simulations Conti Nibali, Valeria; Havenith, Martina Journal of the American Chemical Society, Vol. 136, Issue 37 https://doi.org/10.1021/ja504441h	journal	September 2014
Collective Dynamics of Protein Hydration Water by Brillouin Neutron Spectroscopy Orecchini, Andrea; Paciaroni, Alessandro; Francesco, Alessio De Journal of the American Chemical Society, Vol. 131, Issue 13 https://doi.org/10.1021/ja807957p	journal	April 2009
Bulk Modulus of a Protein Active-Site Mimic Leu, Bogdan M.; Sage, J. Timothy; Silvernail, Nathan J. The Journal of Physical Chemistry B, Vol. 115, Issue 15 https://doi.org/10.1021/jp112007z	journal	March 2011
Vibrational Collective Dynamics of Dry Proteins in the Terahertz Region Paciaroni, Alessandro; Orecchini, Andrea; Haertlein, Michael The Journal of Physical Chemistry B, Vol. 116, Issue 12 https://doi.org/10.1021/jp211190q	journal	March 2012
Inelastic X-ray Scattering Studies of the Short-Time Collective Vibrational Motions in Hydrated Lysozyme Powders and Their Possible Relation to Enzymatic Function Wang, Zhe; Bertrand, Christopher E.; Chiang, Wei-Shan The Journal of Physical Chemistry B, Vol. 117, Issue 4 https://doi.org/10.1021/jp312842m	journal	January 2013
Apparent Decoupling of the Dynamics of a Protein from the Dynamics of its Aqueous Solvent Chu, Xiang-qiang; Mamontov, Eugene; O’Neill, Hugh The Journal of Physical Chemistry Letters, Vol. 3, Issue 3 https://doi.org/10.1021/jz201435q	journal	January 2012
On the Coupling between the Collective Dynamics of Proteins and Their Hydration Water Conti Nibali, Valeria; D’Angelo, Giovanna; Paciaroni, Alessandro The Journal of Physical Chemistry Letters, Vol. 5, Issue 7 https://doi.org/10.1021/jz500023e	journal	March 2014
Dynamic personalities of proteins Henzler-Wildman, Katherine; Kern, Dorothee Nature, Vol. 450, Issue 7172 https://doi.org/10.1038/nature06522	journal	December 2007
The molecular structure of green fluorescent protein Yang, Fan; Moss, Larry G.; Phillips, George N. Nature Biotechnology, Vol. 14, Issue 10 https://doi.org/10.1038/nbt1096-1246	journal	October 1996
Good vibrations in enzyme-catalysed reactions Hay, Sam; Scrutton, Nigel S. Nature Chemistry, Vol. 4, Issue 3 https://doi.org/10.1038/nchem.1223	journal	January 2012
Enzymatic transition states and dynamic motion in barrier crossing Schwartz, Steven D.; Schramm, Vern L. Nature Chemical Biology, Vol. 5, Issue 8 https://doi.org/10.1038/nchembio.202	journal	July 2009
Acoustic-like dynamics of amorphous drugs in the THz regime Pogna, E. A. A.; Rodríguez-Tinoco, C.; Krisch, M. Scientific Reports, Vol. 3, Issue 1 https://doi.org/10.1038/srep02518	journal	August 2013
One role of hydration water in proteins: key to the “softening” of short time intraprotein collective vibrations of a specific length scale Wang, Zhe; Chiang, Wei-Shan; Le, Peisi Soft Matter, Vol. 10, Issue 24 https://doi.org/10.1039/C4SM00257A	journal	January 2014
Protein dynamics: from rattling in a cage to structural relaxation Khodadadi, S.; Sokolov, A. P. Soft Matter, Vol. 11, Issue 25 https://doi.org/10.1039/C5SM00636H	journal	January 2015
Experimental evidence of logarithmic relaxation in single-particle dynamics of hydrated protein molecules Chu, Xiang-qiang; Lagi, Marco; Mamontov, Eugene Soft Matter, Vol. 6, Issue 12 https://doi.org/10.1039/c002602f	journal	January 2010
Phonon-like excitation in secondary and tertiary structure of hydrated protein powders Li, Mingda; Chu, Xiang-qiang; Fratini, Emiliano Soft Matter, Vol. 7, Issue 21 https://doi.org/10.1039/c1sm05954h	journal	January 2011
Water–protein dynamic coupling and new opportunities for probing it at low to physiological temperatures in aqueous solutions Mamontov, Eugene; Chu, Xiang-qiang Physical Chemistry Chemical Physics, Vol. 14, Issue 33 https://doi.org/10.1039/c2cp41443k	journal	January 2012
Coupling of protein and hydration-water dynamics in biological membranes Wood, K.; Plazanet, M.; Gabel, F. Proceedings of the National Academy of Sciences, Vol. 104, Issue 46 https://doi.org/10.1073/pnas.0706566104	journal	November 2007
Dynamics and mechanism of ultrafast water–protein interactions Qin, Yangzhong; Wang, Lijuan; Zhong, Dongping Proceedings of the National Academy of Sciences, Vol. 113, Issue 30 https://doi.org/10.1073/pnas.1602916113	journal	June 2016
Phonon spectroscopy by inelastic x-ray scattering Burkel, Eberhard Reports on Progress in Physics, Vol. 63, Issue 2 https://doi.org/10.1088/0034-4885/63/2/203	journal	January 2000
Protein dynamics: determination of anisotropic vibrations at the haem iron of myoglobin Achterhold, Klaus; Parak, Fritz G. Journal of Physics: Condensed Matter, Vol. 15, Issue 18 https://doi.org/10.1088/0953-8984/15/18/302	journal	April 2003
Water dynamics in a lithium chloride aqueous solution probed by Brillouin neutron and x-ray scattering Mamontov, E.; De Francesco, A.; Formisano, F. Journal of Physics: Condensed Matter, Vol. 24, Issue 6 https://doi.org/10.1088/0953-8984/24/6/064102	journal	January 2012
SEQUOIA: A Newly Operating Chopper Spectrometer at the SNS Granroth, G. E.; Kolesnikov, A. I.; Sherline, T. E. Journal of Physics: Conference Series, Vol. 251 https://doi.org/10.1088/1742-6596/251/1/012058	journal	November 2010
Transverse dynamics of water across the melting point: A parallel neutron and x-ray inelastic scattering study Cunsolo, A.; Kodituwakku, C. N.; Bencivenga, F. Physical Review B, Vol. 85, Issue 17 https://doi.org/10.1103/PhysRevB.85.174305	journal	May 2012
Studies of Phononlike Low-Energy Excitations of Protein Molecules by Inelastic X-Ray Scattering Liu, Dazhi; Chu, Xiang-qiang; Lagi, Marco Physical Review Letters, Vol. 101, Issue 13 https://doi.org/10.1103/PhysRevLett.101.135501	journal	September 2008
Three Classes of Motion in the Dynamic Neutron-Scattering Susceptibility of a Globular Protein Hong, Liang; Smolin, Nikolai; Lindner, Benjamin Physical Review Letters, Vol. 107, Issue 14 https://doi.org/10.1103/PhysRevLett.107.148102	journal	September 2011
Observation of High-Frequency Transverse Phonons in Metallic Glasses Li, X. Y.; Zhang, H. P.; Lan, S. Physical Review Letters, Vol. 124, Issue 22 https://doi.org/10.1103/PhysRevLett.124.225902	journal	June 2020
Observation of New Short-Wavelength Collective Excitations in Heavy Water by Coherent Inelastic Neutron Scattering Teixeira, J.; Bellissent-Funel, M. C.; Chen, S. H. Physical Review Letters, Vol. 54, Issue 25 https://doi.org/10.1103/PhysRevLett.54.2681	journal	June 1985
Role of Protein-Water Hydrogen Bond Dynamics in the Protein Dynamical Transition Tarek, M.; Tobias, D. J. Physical Review Letters, Vol. 88, Issue 13 https://doi.org/10.1103/PhysRevLett.88.138101	journal	March 2002
The energy landscapes and motions of proteins Frauenfelder, H.; Sligar, S.; Wolynes, P. Science, Vol. 254, Issue 5038 https://doi.org/10.1126/science.1749933	journal	December 1991
Formation of Glasses from Liquids and Biopolymers Angell, C. A. Science, Vol. 267, Issue 5206 https://doi.org/10.1126/science.267.5206.1924	journal	March 1995
Dynamics of Glasses and Glass-Forming Liquids Studied by Inelastic X-ray Scattering Sette, F. Science, Vol. 280, Issue 5369 https://doi.org/10.1126/science.280.5369.1550	journal	June 1998
How Soft Is a Protein? A Protein Dynamics Force Constant Measured by Neutron Scattering Zaccai, G. Science, Vol. 288, Issue 5471 https://doi.org/10.1126/science.288.5471.1604	journal	June 2000
Hydrogen Tunneling Links Protein Dynamics to Enzyme Catalysis Klinman, Judith P.; Kohen, Amnon Annual Review of Biochemistry, Vol. 82, Issue 1 https://doi.org/10.1146/annurev-biochem-051710-133623	journal	June 2013
Conformational Substates in Proteins Frauenfelder, H.; Parak, F.; Young, R. D. Annual Review of Biophysics and Biophysical Chemistry, Vol. 17, Issue 1 https://doi.org/10.1146/annurev.bb.17.060188.002315	journal	June 1988
Water Mediation in Protein Folding and Molecular Recognition Levy, Yaakov; Onuchic, José N. Annual Review of Biophysics and Biomolecular Structure, Vol. 35, Issue 1 https://doi.org/10.1146/annurev.biophys.35.040405.102134	journal	June 2006
Protein Surface Softness Is the Origin of Enzyme Cold-Adaptation of Trypsin Isaksen, Geir Villy; Åqvist, Johan; Brandsdal, Bjørn Olav PLoS Computational Biology, Vol. 10, Issue 8 https://doi.org/10.1371/journal.pcbi.1003813	journal	August 2014

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Title: Experimental mapping of short-wavelength phonons in proteins

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