1
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Wang Z, Zhang S, Xu Q, Li Z, Gu X, Wood K, García Sakai V, Wan Q, Chu XQ. Experimental Evidence for the Role of Dynamics in pH-Dependent Enzymatic Activity. J Phys Chem B 2024; 128:5814-5822. [PMID: 38726956 DOI: 10.1021/acs.jpcb.4c00219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Enzymatic activity is heavily influenced by pH, but the rationale for the dynamical mechanism of pH-dependent enzymatic activity has not been fully understood. In this work, combined neutron scattering techniques, including quasielastic neutron scattering (QENS) and small angle neutron scattering (SANS), are used to study the structural and dynamic changes of a model enzyme, xylanase, under different pH and temperature environments. The QENS results reveal that xylanase at optimal pH exhibits faster relaxational dynamics and a lower energy barrier between conformational substates. The SANS results demonstrate that pH affects both xylanase's stability and monodispersity. Our findings indicate that enzymes have optimized stability and function under their optimal pH conditions, with both structure and dynamics being affected. The current study offers valuable insights into enzymatic functionality mechanisms, allowing for broad industrial applications.
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Affiliation(s)
- Zhixin Wang
- Graduate School of China Academy of Engineering Physics, Beijing 100193, China
| | - Shengkai Zhang
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
- Institute of Advanced Science Facilities, Shenzhen 518107, China
| | - Qin Xu
- College of Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhihong Li
- College of Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Xudong Gu
- Graduate School of China Academy of Engineering Physics, Beijing 100193, China
| | - Kathleen Wood
- Australian Nuclear Science and Technology Organization, Lucas Heights, NSW 2234, Australia
| | - Victoria García Sakai
- ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, United Kingdom
| | - Qun Wan
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizer, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Xiang-Qiang Chu
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
- Department of Physics, City University of Hong Kong, Hong Kong 999077, China
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2
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Acharya GR, Tyagi M, Mamontov E, Hoffmann PM. Diffusion Dynamics of Water and Ethanol in Graphene Oxide. J Phys Chem B 2023; 127:7384-7393. [PMID: 37556231 DOI: 10.1021/acs.jpcb.2c08960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
We utilized the momentum transfer (Q)-dependence of quasi-elastic neutron scattering (QENS) to measure the dynamics of water and ethanol confined in graphene oxide (GO) powder or membranes at different temperatures and in different orientations. We found reduced diffusivities (up to 30% in the case of water) and a depression of dynamic transition temperatures. While water showed near Arrhenius behavior with an almost bulk-like activation barrier in a temperature range of 280-310 K, the diffusivity of ethanol showed little temperature dependence. For both water and ethanol, we found evidence for immobile and mobile fractions of the confined liquid. The mobile fraction exhibited jump diffusion, with a jump length consistent with the expected average spacing of hydroxide groups in the GO surfaces. From anisotropy measurements, we found weak anisotropy in the diffusivity of the mobile species and in the fraction and geometry of immobile species.
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Affiliation(s)
- Gobin Raj Acharya
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
| | - Madhusudan Tyagi
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6102, United States
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Eugene Mamontov
- Neutron Scattering Division, Oak Ridge National Laboratory, P.O. Box 2008 MS6473, Oak Ridge, Tennessee 37831, United States
| | - Peter M Hoffmann
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
- Department of Physical Sciences, Embry-Riddle Aeronautical University, Daytona Beach, Florida 32114, United States
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3
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Unravelling the Adaptation Mechanisms to High Pressure in Proteins. Int J Mol Sci 2022; 23:ijms23158469. [PMID: 35955607 PMCID: PMC9369236 DOI: 10.3390/ijms23158469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 02/06/2023] Open
Abstract
Life is thought to have appeared in the depth of the sea under high hydrostatic pressure. Nowadays, it is known that the deep biosphere hosts a myriad of life forms thriving under high-pressure conditions. However, the evolutionary mechanisms leading to their adaptation are still not known. Here, we show the molecular bases of these mechanisms through a joint structural and dynamical study of two orthologous proteins. We observed that pressure adaptation involves the decoupling of protein–water dynamics and the elimination of cavities in the protein core. This is achieved by rearranging the charged residues on the protein surface and using bulkier hydrophobic residues in the core. These findings will be the starting point in the search for a complete genomic model explaining high-pressure adaptation.
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4
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Mesophilic Pyrophosphatase Function at High Temperature: A Molecular Dynamics Simulation Study. Biophys J 2020; 119:142-150. [PMID: 32533942 DOI: 10.1016/j.bpj.2020.05.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/06/2020] [Accepted: 05/15/2020] [Indexed: 02/06/2023] Open
Abstract
The mesophilic inorganic pyrophosphatase from Escherichia coli (EcPPase) retains function at 353 K, the physiological temperature of hyperthermophilic Thermococcus thioreducens, whereas the homolog protein (TtPPase) from this hyperthermophilic organism cannot function at room temperature. To explain this asymmetric behavior, we examined structural and dynamical properties of the two proteins using molecular dynamics simulations. The global flexibility of TtPPase is significantly higher than its mesophilic homolog at all tested temperature/pressure conditions. However, at 353 K, EcPPase reduces its solvent-exposed surface area and increases subunit compaction while maintaining flexibility in its catalytic pocket. In contrast, TtPPase lacks this adaptability and has increased rigidity and reduced protein/water interactions in its catalytic pocket at room temperature, providing a plausible explanation for its inactivity near room temperature.
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5
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Molecular dynamics in cells: A neutron view. Biochim Biophys Acta Gen Subj 2020; 1864:129475. [DOI: 10.1016/j.bbagen.2019.129475] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/01/2019] [Accepted: 11/05/2019] [Indexed: 11/21/2022]
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6
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Abstract
AbstractThe dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.
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7
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Dhiman I, Shrestha U, Bhowmik D, Cole D, Gautam S. Influence of molecular shape on self-diffusion under severe confinement: A molecular dynamics study. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2018.08.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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8
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Ashkar R, Bilheux HZ, Bordallo H, Briber R, Callaway DJE, Cheng X, Chu XQ, Curtis JE, Dadmun M, Fenimore P, Fushman D, Gabel F, Gupta K, Herberle F, Heinrich F, Hong L, Katsaras J, Kelman Z, Kharlampieva E, Kneller GR, Kovalevsky A, Krueger S, Langan P, Lieberman R, Liu Y, Losche M, Lyman E, Mao Y, Marino J, Mattos C, Meilleur F, Moody P, Nickels JD, O'Dell WB, O'Neill H, Perez-Salas U, Peters J, Petridis L, Sokolov AP, Stanley C, Wagner N, Weinrich M, Weiss K, Wymore T, Zhang Y, Smith JC. Neutron scattering in the biological sciences: progress and prospects. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1129-1168. [PMID: 30605130 DOI: 10.1107/s2059798318017503] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/12/2018] [Indexed: 12/11/2022]
Abstract
The scattering of neutrons can be used to provide information on the structure and dynamics of biological systems on multiple length and time scales. Pursuant to a National Science Foundation-funded workshop in February 2018, recent developments in this field are reviewed here, as well as future prospects that can be expected given recent advances in sources, instrumentation and computational power and methods. Crystallography, solution scattering, dynamics, membranes, labeling and imaging are examined. For the extraction of maximum information, the incorporation of judicious specific deuterium labeling, the integration of several types of experiment, and interpretation using high-performance computer simulation models are often found to be particularly powerful.
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Affiliation(s)
- Rana Ashkar
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - Hassina Z Bilheux
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Robert Briber
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - David J E Callaway
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Xiaolin Cheng
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
| | - Xiang Qiang Chu
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mark Dadmun
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Paul Fenimore
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Frank Gabel
- Institut Laue-Langevin, Université Grenoble Alpes, CEA, CNRS, IBS, 38042 Grenoble, France
| | - Kushol Gupta
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederick Herberle
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Frank Heinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Liang Hong
- Department of Physics and Astronomy, Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - John Katsaras
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Eugenia Kharlampieva
- Department of Chemistry, University of Alabama at Birmingham, 901 14th Street South, Birmingham, AL 35294, USA
| | - Gerald R Kneller
- Centre de Biophysique Moléculaire, CNRS, Université d'Orléans, Chateau de la Source, Avenue du Parc Floral, Orléans, France
| | - Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Susan Krueger
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Paul Langan
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Raquel Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Yun Liu
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mathias Losche
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Edward Lyman
- Department of Physics and Astrophysics, University of Delaware, Newark, DE 19716, USA
| | - Yimin Mao
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - John Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
| | - Flora Meilleur
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Peter Moody
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, England
| | - Jonathan D Nickels
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - William B O'Dell
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Hugh O'Neill
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Ursula Perez-Salas
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Loukas Petridis
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - Alexei P Sokolov
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Christopher Stanley
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Norman Wagner
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Michael Weinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Kevin Weiss
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Troy Wymore
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Yang Zhang
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Jeremy C Smith
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
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9
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Perera SMDC, Chawla U, Shrestha UR, Bhowmik D, Struts AV, Qian S, Chu XQ, Brown MF. Small-Angle Neutron Scattering Reveals Energy Landscape for Rhodopsin Photoactivation. J Phys Chem Lett 2018; 9:7064-7071. [PMID: 30489081 DOI: 10.1021/acs.jpclett.8b03048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Knowledge of the activation principles for G-protein-coupled receptors (GPCRs) is critical to development of new pharmaceuticals. Rhodopsin is the archetype for the largest GPCR family, yet the changes in protein dynamics that trigger signaling are not fully understood. Here we show that rhodopsin can be investigated by small-angle neutron scattering (SANS) in fully protiated detergent micelles under contrast matching to resolve light-induced changes in the protein structure. In SANS studies of membrane proteins, the zwitterionic detergent [(cholamidopropyl)dimethylammonio]-propanesulfonate (CHAPS) is advantageous because of the low contrast difference between the hydrophobic core and hydrophilic head groups as compared with alkyl glycoside detergents. Combining SANS results with quasielastic neutron scattering reveals how changes in volumetric protein shape are coupled (slaved) to the aqueous solvent. Upon light exposure, rhodopsin is swollen by the penetration of water into the protein core, allowing interactions with effector proteins in the visual signaling mechanism.
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Affiliation(s)
- Suchithranga M D C Perera
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
| | - Udeep Chawla
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
| | - Utsab R Shrestha
- Department of Physics and Astronomy , Wayne State University , Detroit , Michigan 48201 , United States
| | - Debsindhu Bhowmik
- Department of Physics and Astronomy , Wayne State University , Detroit , Michigan 48201 , United States
| | - Andrey V Struts
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
- Laboratory of Biomolecular NMR , St. Petersburg State University , St. Petersburg 199034 , Russia
| | - Shuo Qian
- Neutron Scattering Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
| | - Xiang-Qiang Chu
- Graduate School of China Academy of Engineering Physics , Beijing 100193 , China
| | - Michael F Brown
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
- Department of Physics , University of Arizona , Tucson , Arizona 85721 , United States
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10
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Abstract
Protein dynamics is characterized by fluctuations among different conformational substates, i.e. the different minima of their energy landscape. At temperatures above ~200 K, these fluctuations lead to a steep increase in the thermal dependence of all dynamical properties, phenomenon known as Protein Dynamical Transition. In spite of the intense studies, little is known about the effects of pressure on these processes, investigated mostly near room temperature. We studied by neutron scattering the dynamics of myoglobin in a wide temperature and pressure range. Our results show that high pressure reduces protein motions, but does not affect the onset temperature for the Protein Dynamical Transition, indicating that the energy differences and barriers among conformational substates do not change with pressure. Instead, high pressure values strongly reduce the average structural differences between the accessible conformational substates, thus increasing the roughness of the free energy landscape of the system.
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11
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Daskalakis V, Papadatos S. The Photosystem II Subunit S under Stress. Biophys J 2018; 113:2364-2372. [PMID: 29211990 DOI: 10.1016/j.bpj.2017.09.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/29/2017] [Accepted: 09/29/2017] [Indexed: 01/08/2023] Open
Abstract
Nonphotochemical quenching is the protective mechanism against overexcitation of photosystem II, triggered by excess ΔpH in photosynthetic membranes. The light-harvesting complexes (LHCs), the de-epoxidation of violaxanthin to zeaxanthin, and the photosystem II subunit S (PsbS) work in synergy for an optimized multilevel response. Understanding the fine details of this synergy has proven challenging to scientific research. Here, we employ large-scale, all-atom molecular simulations and beyond experimental insight, we proceed a step further in identifying the PsbS dynamics that could possibly be associated with this synergy. For the first time, to our knowledge, we probe the distinct behavior of PsbS under ΔpH that probes the details of the potential dimer-to-monomer transition, and in a violaxanthin/zeaxanthin-rich membrane, at an all-atom resolution. We propose that the lumen-exposed residues, threonine 162 and glutamic acid 173, form stabilizing hydrogen bonds between the PsbS monomers only at high lumen pH, whereas at low pH (excess ΔpH) this interaction is lost, and leads to higher flexibility of the protein and potentially to the dimer-to-monomer transition. Lastly, we discuss how conformational changes under the presence of ΔpH/zeaxanthin are related to the PsbS role in the current nonphotochemical quenching model in the literature. For the latter, we probe a PsbS-monomeric LHCII association. The association is proposed to potentially alter the monomeric LHCII sensitivity to ΔpH by changing the pKa values of interacting LHCII residues. This serves as an example where protonation-ligation events enhance protein-protein interactions fundamental to many life processes.
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Affiliation(s)
- Vangelis Daskalakis
- Department of Environmental Science and Technology, Cyprus University of Technology, Limassol, Cyprus.
| | - Sotiris Papadatos
- Department of Environmental Science and Technology, Cyprus University of Technology, Limassol, Cyprus
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12
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Shrestha UR, Bhowmik D, Van Delinder KW, Mamontov E, O’Neill H, Zhang Q, Alatas A, Chu XQ. Collective Excitations in Protein as a Measure of Balance Between its Softness and Rigidity. J Phys Chem B 2017; 121:923-930. [DOI: 10.1021/acs.jpcb.6b10245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Utsab R. Shrestha
- Department
of Physics and Astronomy, Wayne State University, Detroit, MI 48201, United States
| | - Debsindhu Bhowmik
- Computational
Science and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Kurt W. Van Delinder
- Department
of Physics and Astronomy, Wayne State University, Detroit, MI 48201, United States
| | - Eugene Mamontov
- Chemical
and Engineering Materials Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Hugh O’Neill
- Biology
and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Qiu Zhang
- Biology
and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Ahmet Alatas
- Advanced
Photon Source, Argonne National laboratory, Argonne, IL 60439, United States
| | - Xiang-Qiang Chu
- Department
of Physics and Astronomy, Wayne State University, Detroit, MI 48201, United States
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13
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Shrestha UR, Perera SMDC, Bhowmik D, Chawla U, Mamontov E, Brown MF, Chu XQ. Quasi-elastic Neutron Scattering Reveals Ligand-Induced Protein Dynamics of a G-Protein-Coupled Receptor. J Phys Chem Lett 2016; 7:4130-4136. [PMID: 27628201 PMCID: PMC5378701 DOI: 10.1021/acs.jpclett.6b01632] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Light activation of the visual G-protein-coupled receptor (GPCR) rhodopsin leads to significant structural fluctuations of the protein embedded within the membrane yielding the activation of cognate G-protein (transducin), which initiates biological signaling. Here, we report a quasi-elastic neutron scattering study of the activation of rhodopsin as a GPCR prototype. Our results reveal a broadly distributed relaxation of hydrogen atom dynamics of rhodopsin on a picosecond-nanosecond time scale, crucial for protein function, as only observed for globular proteins previously. Interestingly, the results suggest significant differences in the intrinsic protein dynamics of the dark-state rhodopsin versus the ligand-free apoprotein, opsin. These differences can be attributed to the influence of the covalently bound retinal ligand. Furthermore, an idea of the generic free-energy landscape is used to explain the GPCR dynamics of ligand-binding and ligand-free protein conformations, which can be further applied to other GPCR systems.
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Affiliation(s)
- Utsab R. Shrestha
- Department of Physics and Astronomy, Wayne State University, Detroit, MI 48201, USA
| | | | - Debsindhu Bhowmik
- Department of Physics and Astronomy, Wayne State University, Detroit, MI 48201, USA
| | - Udeep Chawla
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Eugene Mamontov
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Michael F. Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
- Department of Physics, University of Arizona, Tucson, AZ 85721, USA
| | - Xiang-qiang Chu
- Department of Physics and Astronomy, Wayne State University, Detroit, MI 48201, USA
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14
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Ingr M, Kutálková E, Hrnčiřík J, Lange R. Equilibria of oligomeric proteins under high pressure - A theoretical description. J Theor Biol 2016; 411:16-26. [PMID: 27717844 DOI: 10.1016/j.jtbi.2016.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 09/14/2016] [Accepted: 10/03/2016] [Indexed: 01/18/2023]
Abstract
High pressure methods have become a useful tool for studying protein structure and stability. Using them, various physico-chemical processes including protein unfolding, aggregation, oligomer dissociation or enzyme-activity decrease were studied on many different proteins. Oligomeric protein dissociation is a process that can perfectly utilize the potential of high-pressure techniques, as the high pressure shifts the equilibria to higher concentrations making them better observable by spectroscopic methods. This can be especially useful when the oligomeric form is highly stable at atmospheric pressure. These applications may be, however, hindered by less intensive experimental response as well as interference of the oligomerization equilibria with unfolding or aggregation of the subunits, but also by more complex theoretical description. In this study we develop mathematical models describing different kinds of oligomerization equilibria, both closed (equilibrium of monomer and the highest possible oligomer without any intermediates) and consecutive. Closed homooligomer equilibria are discussed for any oligomerization degree, while the more complex heterooligomer equilibria and the consecutive equilibria in both homo- and heterooligomers are taken into account only for dimers and trimers. In all the cases, fractions of all the relevant forms are evaluated as functions of pressure and concentration. Significant points (inflection points and extremes) of the resulting transition curves, that can be determined experimentally, are evaluated as functions of pressure and/or concentration. These functions can be further used in order to evaluate the thermodynamic parameters of the system, i.e. atmospheric-pressure equilibrium constants and volume changes of the individual steps of the oligomer-dissociation processes.
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Affiliation(s)
- Marek Ingr
- Tomas Bata University in Zlín, Faculty of Technology, Department of Physics and Materials Engineering, nám. T. G. Masaryka 5555, 76001 Zlín, Czechia; Charles University in Prague, Faculty of Science, Department of Biochemistry, Hlavova 2030, 12843 Prague 2, Czechia.
| | - Eva Kutálková
- Tomas Bata University in Zlín, Faculty of Technology, Department of Physics and Materials Engineering, nám. T. G. Masaryka 5555, 76001 Zlín, Czechia
| | - Josef Hrnčiřík
- Tomas Bata University in Zlín, Faculty of Technology, Department of Physics and Materials Engineering, nám. T. G. Masaryka 5555, 76001 Zlín, Czechia
| | - Reinhard Lange
- Université Montpellier, INRA UMR IATE, Biochimie et Technologie Alimentaires, cc023, Place Eugene Bataillon, 34095 Montpellier Cedex 05, France
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15
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Dhindsa GK, Bhowmik D, Goswami M, O’Neill H, Mamontov E, Sumpter BG, Hong L, Ganesh P, Chu XQ. Enhanced Dynamics of Hydrated tRNA on Nanodiamond Surfaces: A Combined Neutron Scattering and MD Simulation Study. J Phys Chem B 2016; 120:10059-10068. [DOI: 10.1021/acs.jpcb.6b07511] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Gurpreet K. Dhindsa
- Department
of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
| | - Debsindhu Bhowmik
- Department
of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
| | - Monojoy Goswami
- Center
for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Computer
Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Hugh O’Neill
- Biology and
Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Eugene Mamontov
- Chemical
and Engineering Materials Division, Oak Ridge National Laboratory, Oak
Ridge, Tennessee 37831, United States
| | - Bobby G. Sumpter
- Center
for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Computer
Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Liang Hong
- Institute of Natural Science & Department of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Panchapakesan Ganesh
- Center
for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Xiang-qiang Chu
- Department
of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
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16
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Britton J, Meneghini LM, Raston CL, Weiss GA. Accelerating Enzymatic Catalysis Using Vortex Fluidics. Angew Chem Int Ed Engl 2016; 55:11387-91. [PMID: 27493015 PMCID: PMC5524626 DOI: 10.1002/anie.201604014] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Indexed: 11/09/2022]
Abstract
Enzymes catalyze chemical transformations with outstanding stereo- and regio-specificities, but many enzymes are limited by their long reaction times. A general method to accelerate enzymes using pressure waves contained within thin films is described. Each enzyme responds best to specific frequencies of pressure waves, and an acceleration landscape for each protein is reported. A vortex fluidic device introduces pressure waves that drive increased rate constants (kcat ) and enzymatic efficiency (kcat /Km ). Four enzymes displayed an average seven-fold acceleration, with deoxyribose-5-phosphate aldolase (DERA) achieving an average 15-fold enhancement using this approach. In solving a common problem in enzyme catalysis, a powerful, generalizable tool for enzyme acceleration has been uncovered. This research provides new insights into previously uncontrolled factors affecting enzyme function.
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Affiliation(s)
- Joshua Britton
- Chemical and Physical Sciences, Flinders University, Bedford Park, Adelaide, 5001, Australia
- Department of Chemistry, University of California, Irvine, Irvine, CA, 92697-2025, USA
| | - Luz M Meneghini
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, 92697-2025, USA
| | - Colin L Raston
- Chemical and Physical Sciences, Flinders University, Bedford Park, Adelaide, 5001, Australia.
| | - Gregory A Weiss
- Department of Chemistry, University of California, Irvine, Irvine, CA, 92697-2025, USA.
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, 92697-2025, USA.
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17
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High protein flexibility and reduced hydration water dynamics are key pressure adaptive strategies in prokaryotes. Sci Rep 2016; 6:32816. [PMID: 27595789 PMCID: PMC5011708 DOI: 10.1038/srep32816] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/12/2016] [Indexed: 12/12/2022] Open
Abstract
Water and protein dynamics on a nanometer scale were measured by quasi-elastic neutron scattering in the piezophile archaeon Thermococcus barophilus and the closely related pressure-sensitive Thermococcus kodakarensis, at 0.1 and 40 MPa. We show that cells of the pressure sensitive organism exhibit higher intrinsic stability. Both the hydration water dynamics and the fast protein and lipid dynamics are reduced under pressure. In contrast, the proteome of T. barophilus is more pressure sensitive than that of T. kodakarensis. The diffusion coefficient of hydration water is reduced, while the fast protein and lipid dynamics are slightly enhanced with increasing pressure. These findings show that the coupling between hydration water and cellular constituents might not be simply a master-slave relationship. We propose that the high flexibility of the T. barophilus proteome associated with reduced hydration water may be the keys to the molecular adaptation of the cells to high hydrostatic pressure.
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18
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Britton J, Meneghini LM, Raston CL, Weiss GA. Accelerating Enzymatic Catalysis Using Vortex Fluidics. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Joshua Britton
- Chemical and Physical Sciences Flinders University Bedford Park Adelaide 5001 Australia
- Department of Chemistry University of California, Irvine Irvine CA 92697-2025 USA
| | - Luz M. Meneghini
- Department of Molecular Biology and Biochemistry University of California, Irvine Irvine CA 92697-2025 USA
| | - Colin L. Raston
- Chemical and Physical Sciences Flinders University Bedford Park Adelaide 5001 Australia
| | - Gregory A. Weiss
- Department of Chemistry University of California, Irvine Irvine CA 92697-2025 USA
- Department of Molecular Biology and Biochemistry University of California, Irvine Irvine CA 92697-2025 USA
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19
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Chen H, Wang XL. China's first pulsed neutron source. NATURE MATERIALS 2016; 15:689-691. [PMID: 27329454 DOI: 10.1038/nmat4655] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Hesheng Chen
- China Spallation Neutron Source, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 10049, China
| | - Xun-Li Wang
- Department of Physics and Materials Science, City University of Hong Kong, Kowloon, Hong Kong SAR, China and at the CityU Shenzhen Research Institute, Shenzhen, China
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