1
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Poudel H, Leitner DM. Locating dynamic contributions to allostery via determining rates of vibrational energy transfer. J Chem Phys 2023; 158:015101. [PMID: 36610954 DOI: 10.1063/5.0132089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Determining rates of energy transfer across non-covalent contacts for different states of a protein can provide information about dynamic and associated entropy changes during transitions between states. We investigate the relationship between rates of energy transfer across polar and nonpolar contacts and contact dynamics for the β2-adrenergic receptor, a rhodopsin-like G-protein coupled receptor, in an antagonist-bound inactive state and agonist-bound active state. From structures sampled during molecular dynamics (MD) simulations, we find the active state to have, on average, a lower packing density, corresponding to generally more flexibility and greater entropy than the inactive state. Energy exchange networks (EENs) are computed for the inactive and active states from the results of the MD simulations. From the EENs, changes in the rates of energy transfer across polar and nonpolar contacts are found for contacts that remain largely intact during activation. Change in dynamics of the contact, and entropy associated with the dynamics, can be estimated from the change in rates of energy transfer across the contacts. Measurement of change in the rates of energy transfer before and after the transition between states thereby provides information about dynamic contributions to activation and allostery.
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Affiliation(s)
- Humanath Poudel
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | - David M Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
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2
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Hu R, Ding X, Yu P, He X, Watts A, Zhao X, Wang J. Ultrafast Two-Dimensional Infrared Spectroscopy Resolved a Structured Lysine 159 on the Cytoplasmic Surface of the Microbial Photoreceptor Bacteriorhodopsin. J Am Chem Soc 2022; 144:22083-22092. [PMID: 36399663 DOI: 10.1021/jacs.2c09435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Bacteriorhodopsin (bR) is a light-driven microbial receptor, and lysine 159 (K159) is a charged residue on the cytoplasmic (CP) side of its E-F loop. However, its conformation and function remain unknown due to fast surface dynamics. By utilizing a 13C, 15N-labeled lysine (K) as an isotope probe, we created a network of site-specific amide-I vibrational signatures (backbone carbonyl stretch) to identify the frequency contribution of the labeled residues to the amide-I excitonic band structure. Thus, the red-shifted amide-I frequency in the 13C, 15N-lysine-labeled bR (uK-bR) to the unlabeled bR (WT-bR) could be differentiated and examined by ultrafast two-dimensional vibrational echo infrared (2D IR) spectroscopy. Our results showed that the backbone carbonyl of K159 is located at a high frequency of ca. 1693 cm-1 and has a vibrational excited-state relaxation time shorter than the bulk helical amide-I mode at the same frequency, suggesting that K159 may possess a hydrogen-bonded γ-turn structure with E161, one of the carboxylate residues on the CP surface of bR. The 2D solid-state NMR study of uK-bR also revealed conformational dependent lysine residues, from which K159 was found to involve the turn motif. This γ-turn structure maintained by K159 may help to stabilize the E-F loop and support E161 in attracting protons from the bulk during the late stage of the bR photocycle. The combined spectroscopic approach illustrated in this work may be applied to map residue-specific local structures and dynamics of other receptors and large proteins.
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Affiliation(s)
- Rong Hu
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Xiaoyan Ding
- Department of Physics, School of Physics and Electronic Science, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, P.R. China.,Department of Biochemistry, University of Oxford, South Park Road, Oxford OX1 3QU, U.K
| | - Pengyun Yu
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Xuemei He
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Anthony Watts
- Department of Biochemistry, University of Oxford, South Park Road, Oxford OX1 3QU, U.K
| | - Xin Zhao
- Department of Physics, School of Physics and Electronic Science, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, P.R. China
| | - Jianping Wang
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
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Yamashita S, Mizuno M, Mizutani Y. High suitability of tryptophan residues as a spectroscopic thermometer for local temperature in proteins under nonequilibrium conditions. J Chem Phys 2022; 156:075101. [DOI: 10.1063/5.0079797] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Satoshi Yamashita
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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Amadei A, Aschi M. Theoretical-Computational Modelling of the Vibrational Relaxation of Small Inorganic Species in Condensed Phase. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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5
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Fujisaki H. Multiscale aspects of molecular motions: From molecular vibrations, conformational changes of biomolecules to cellular dynamics. J NIPPON MED SCH 2021; 89:9-15. [PMID: 34526452 DOI: 10.1272/jnms.jnms.2022_89-116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Molecular aspects of living systems are important because it is the most basic aspects of life as exemplified in biochemistry and structural biology. Since molecules move due to interactive forces between atoms, physics plays an important role to understand the dynamic phenomena of living systems. Here we review our multiscale approaches for computationally treating different levels of molecular motions: vibrational dynamics of molecules, conformational change of biomolecules, and cellular dynamics using statistical-mechanics-based models.
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Affiliation(s)
- Hiroshi Fujisaki
- Department of Physics, Nippon Medical School.,AMED-CREST, Japan Agency for Medical Research and Development
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6
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Reid KM, Yamato T, Leitner DM. Variation of Energy Transfer Rates across Protein–Water Contacts with Equilibrium Structural Fluctuations of a Homodimeric Hemoglobin. J Phys Chem B 2020; 124:1148-1159. [DOI: 10.1021/acs.jpcb.9b11413] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada 89557, United States
| | - Takahisa Yamato
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada 89557, United States
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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Amadei A, Aschi M. Modelling vibrational relaxation in complex molecular systems. Phys Chem Chem Phys 2019; 21:20003-20017. [PMID: 31478042 DOI: 10.1039/c9cp03379c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper we show how it is possible to treat the quantum vibrational relaxation of a chromophore, embedded in a complex atomic-molecular environment, via the explicit solution of the time-dependent Schroedinger equation once using a proper separation between quantum and semiclassical degrees of freedom. The rigorous theoretical framework derived, based on first principles and making use of well defined approximations/assumptions, is utilized to construct a general model for the kinetics of the vibrational relaxation as obtained by the direct evaluation of the density matrix for all the relevant quantum state transitions. Application to (deuterated) N-methylacetamide (the typical benchmark used as a model for the amino acids) shows that the obtained theoretical-computational approach captures the essential features of the experimental process, unveiling the basic relaxation mechanism involving several vibrational state transitions.
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Affiliation(s)
- Andrea Amadei
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma "Tor Vergata", via della Ricerca Scientifica 1, 00133 Roma, Italy.
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Xu Y, Leitner DM. Vibrational Energy Flow through the Green Fluorescent Protein–Water Interface: Communication Maps and Thermal Boundary Conductance. J Phys Chem B 2014; 118:7818-26. [DOI: 10.1021/jp412141z] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yao Xu
- Department
of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557, United States
- Physikalische
Chemie II, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - David M. Leitner
- Department
of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557, United States
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Müller-Werkmeister HM, Bredenbeck J. A donor–acceptor pair for the real time study of vibrational energy transfer in proteins. Phys Chem Chem Phys 2014; 16:3261-6. [DOI: 10.1039/c3cp54760d] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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10
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Farag MH, Zúñiga J, Requena A, Bastida A. Instantaneous normal mode analysis of the vibrational relaxation of the amide I mode of alanine dipeptide in water. J Chem Phys 2013; 138:205102. [DOI: 10.1063/1.4805086] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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11
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Soler MA, Bastida A, Farag MH, Zúñiga J, Requena A. A method for analyzing the vibrational energy flow in biomolecules in solution. J Chem Phys 2011; 135:204106. [DOI: 10.1063/1.3663707] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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12
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Middleton CT, Buchanan LE, Dunkelberger EB, Zanni MT. Utilizing Lifetimes to Suppress Random Coil Features in 2D IR Spectra of Peptides. J Phys Chem Lett 2011; 2:2357-2361. [PMID: 21966585 PMCID: PMC3182477 DOI: 10.1021/jz201024m] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We report that the waiting time delay in 2D IR pulse sequences can be used to suppress signals from structurally disordered regions of amyloid fibrils. At a waiting time delay of 1.0 ps, the random coil vibrational modes of amylin fibrils are no longer detectable, leaving only the sharp excitonic vibrational features of the fibril β-sheets. Isotope labeling with (13)C(18)O reveals that structurally disordered residues decay faster than residues protected from solvent. Since structural disorder is usually accompanied by hydration, we conclude that the shorter lifetimes of random-coil residues is due to solvent exposure. These results indicate that 2D IR pulse sequences can utilize the waiting time to better resolve solvent-protected regions of peptides and that local mode lifetimes should be included in simulations of 2D IR spectra.
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14
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Kobus M, Nguyen PH, Stock G. Coherent vibrational energy transfer along a peptide helix. J Chem Phys 2011; 134:124518. [DOI: 10.1063/1.3574395] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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15
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Bastida A, Soler MA, Zúñiga J, Requena A, Kalstein A, Fernández-Alberti S. Instantaneous normal modes, resonances, and decay channels in the vibrational relaxation of the amide I mode of N-methylacetamide-D in liquid deuterated water. J Chem Phys 2010; 132:224501. [DOI: 10.1063/1.3435212] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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16
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Nguyen PH, Park SM, Stock G. Nonequilibrium molecular dynamics simulation of the energy transport through a peptide helix. J Chem Phys 2010; 132:025102. [DOI: 10.1063/1.3284742] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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Park SM, Nguyen PH, Stock G. Molecular dynamics simulation of cooling: Heat transfer from a photoexcited peptide to the solvent. J Chem Phys 2009; 131:184503. [DOI: 10.1063/1.3259971] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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18
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Nguyen PH, Derreumaux P, Stock G. Energy Flow and Long-Range Correlations in Guanine-Binding Riboswitch: A Nonequilibrium Molecular Dynamics Study. J Phys Chem B 2009; 113:9340-7. [DOI: 10.1021/jp902013s] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Phuong H. Nguyen
- Institute of Physical and Theoretical Chemistry, Goethe University, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany, and Laboratoire de Biochimie Theorique, UPR 9080 CNRS, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Philippe Derreumaux
- Institute of Physical and Theoretical Chemistry, Goethe University, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany, and Laboratoire de Biochimie Theorique, UPR 9080 CNRS, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Gerhard Stock
- Institute of Physical and Theoretical Chemistry, Goethe University, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany, and Laboratoire de Biochimie Theorique, UPR 9080 CNRS, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France
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Zhang Y, Fujisaki H, Straub JE. Mode-Specific Vibrational Energy Relaxation of Amide I′ and II′ Modes in N-Methylacetamide/Water Clusters: Intra- and Intermolecular Energy Transfer Mechanisms. J Phys Chem A 2009; 113:3051-60. [DOI: 10.1021/jp8109995] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yong Zhang
- Department of Chemistry, Boston University, Boston, Massachusetts 02215
| | - Hiroshi Fujisaki
- Department of Chemistry, Boston University, Boston, Massachusetts 02215
| | - John E. Straub
- Department of Chemistry, Boston University, Boston, Massachusetts 02215
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20
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Zhang Y, Fujisaki H, Straub JE. Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. I. Five-coordinate ferrous iron porphyrin model. J Chem Phys 2009; 130:025102. [DOI: 10.1063/1.3055277] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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21
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Fang Y, Shigeto S, Seong NH, Dlott DD. Vibrational Energy Dynamics of Glycine, N-Methylacetamide, and Benzoate Anion in Aqueous (D2O) Solution. J Phys Chem A 2008; 113:75-84. [DOI: 10.1021/jp8062228] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Ying Fang
- School of Chemical Sciences, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Shinsuke Shigeto
- School of Chemical Sciences, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Nak-Hyun Seong
- School of Chemical Sciences, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
| | - Dana D. Dlott
- School of Chemical Sciences, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801
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22
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Fujisaki H, Stock G. Dynamic treatment of vibrational energy relaxation in a heterogeneous and fluctuating environment. J Chem Phys 2008; 129:134110. [DOI: 10.1063/1.2985606] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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23
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Nagata Y, Lennartz C. Atomistic simulation on charge mobility of amorphous tris(8-hydroxyquinoline) aluminum (Alq3): Origin of Poole–Frenkel–type behavior. J Chem Phys 2008; 129:034709. [DOI: 10.1063/1.2949506] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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