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Leighton RE, Frontiera RR. Quantifying Bacteriorhodopsin Activity as a Function of its Local Environment with a Raman-Based Assay. J Phys Chem B 2023; 127:8833-8841. [PMID: 37812499 DOI: 10.1021/acs.jpcb.3c04802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Bacteriorhodopsin (bR) is a transmembrane protein that functions as a light-driven proton pump in halophilic archaea. The bR photocycle has been well-characterized; however, these measurements almost exclusively measured purified bR, outside of its native membrane. To investigate what effect the cellular environment has on the bR photocycle, we have developed a Raman-based assay that can monitor the activity of the bR in a variety of conditions, including in its native membrane. The assay uses two continuous-wave lasers, one to initiate photochemistry and one to monitor bR activity. The excitation leads to the steady-state depletion of ground-state bR, which directly relates to the population of photocycle intermediate states. We have used this assay to monitor bR activity both in vitro and in vivo. Our in vitro measurements confirm that our assay is sensitive to bulk environmental changes reported in the literature. Our in vivo measurements show a decrease in bR activity with increasing extracellular pH for bR in its native membrane. The difference in activity with increasing pH indicates that the native membrane environment affects the function of bR. This assay opens the door to future measurements into understanding how the local environment of this transmembrane protein affects function.
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Affiliation(s)
- Ryan E Leighton
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Renee R Frontiera
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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2
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Tonel MZ, Abal JPK, Fagan SB, Barbosa MC. Ab initio study of water anchored in graphene pristine and vacancy-type defects. J Mol Model 2023; 29:198. [PMID: 37268861 DOI: 10.1007/s00894-023-05611-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/30/2023] [Indexed: 06/04/2023]
Abstract
CONTEXT In this paper, we have addressed two issues that are relevant to the interaction of water in pristine and vacant graphene through first-principles calculations based on the Density Functional Theory (DFT). The results showed that for the interaction of pristine graphene with water, the DOWN configuration (with the hydrogen atoms facing downwards) was the most stable, presenting binding energies in the order of -13.62 kJ/mol at a distance of 2.375 Å in the TOP position. We also evaluated the interaction of water with two vacancy models, removing one carbon atom (Vac-1C) and four atoms (Vac-4C). In the Vac-1C system, the most favourable system was the DOWN configuration, with binding energies ranging from -20.60 kJ/mol to -18.41 kJ/mol in the TOP and UP positions, respectively. A different behaviour was observed for the interaction of water with Vac-4C; regardless of the configuration of the water, it is always more favourable for the interaction to occur through the vacancy centre, with binding energies between -13.28 kJ/mol and -20.49 kJ/mol. Thus, the results presented open perspectives for the technological development of nanomembranes as well as providing a better understanding of the wettability effects of graphene sheets, whether pristine or with defects. METHOD We evaluated the interaction of pristine and vacant graphene with the water molecule, through calculations based on Density Functional Theory (DFT); implemented by the SIESTA program. The electronic, energetic, and structural properties were analyzed by solving self-consistent Kohn-Sham equations. In all calculations, a double ζ plus a polarized function (DZP) was used for the numerical baise set. Local Density Approximation (LDA) with the Perdew and Zunger (PZ) parameterisation along with a basis set superposition error (BSSE) correction were used to describe the exchange and correlation potential (Vxc). The water and isolated graphene structures were relaxed until the residual forces were less than 0.05 eV/Å-1 in all atomic coordinates.
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Affiliation(s)
- Mariana Zancan Tonel
- Universidade Franciscana-UFN, PPGNANO - Postgraduate Program in Nanoscience, Rua dos Andradas, 1614, ZIP, Santa Maria, RS, 97010-032, Brazil.
| | - João Pedro Kleinubing Abal
- Universidade Federal do Rio Grande do Sul- UFRGS, Institute of Physics, Av. Bento Gonçalves, 9500 - Agronomia, ZIP, Porto Alegre, RS, 91501-970, Brazil
| | - Solange Binotto Fagan
- Universidade Franciscana-UFN, PPGNANO - Postgraduate Program in Nanoscience, Rua dos Andradas, 1614, ZIP, Santa Maria, RS, 97010-032, Brazil
| | - Marcia Cristina Barbosa
- Universidade Federal do Rio Grande do Sul- UFRGS, Institute of Physics, Av. Bento Gonçalves, 9500 - Agronomia, ZIP, Porto Alegre, RS, 91501-970, Brazil
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3
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Nguan H, Ishak KA, Zahid NI, Martinez-Felipe A, Hashim R, Aripin NFK. Incommensurate lamellar phase from long chain Mannosides: Investigation by X-Ray scattering and replica exchange molecular dynamics (REMD). J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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4
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Cisse A, Schachner-Nedherer AL, Appel M, Beck C, Ollivier J, Leitinger G, Prassl R, Kornmueller K, Peters J. Dynamics of Apolipoprotein B-100 in Interaction with Detergent Probed by Incoherent Neutron Scattering. J Phys Chem Lett 2021; 12:12402-12410. [PMID: 34939807 DOI: 10.1021/acs.jpclett.1c03141] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Apolipoprotein B-100 (apo B-100) is the protein moiety of both low- and very-low-density lipoproteins, whose role is crucial to cholesterol and triglyceride transport. Aiming at the molecular dynamics' details of apo B-100, scarcely studied, we performed elastic and quasi-elastic incoherent neutron scattering (EINS, QENS) experiments combining different instruments and time scales. Similar to classical membrane proteins, the solubilization results in remaining detergent, here Nonidet P-40 (NP40). Therefore, we propose a framework for QENS studies of protein-detergent complexes, with the introduction of a combined model, including the experimental apo B-100/NP40 ratio. Relying on the simultaneous analysis of all QENS amplitudes, this approach is sensitive enough to separate both contributions. Its application identified two points: (i) apo B-100 slow dynamics and (ii) the acceleration of NP40 dynamics in the presence of apo B-100. Direct translation of the exposed methodology now makes the investigation of more membrane proteins by neutron spectroscopy achievable.
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Affiliation(s)
- Aline Cisse
- Université Grenoble Alpes, CNRS, LiPhy, 38000 Grenoble, France
- Institut Laue Langevin, 38042 Grenoble, France
| | | | | | - Christian Beck
- Institut Laue Langevin, 38042 Grenoble, France
- Institut of Applied Physics, University of Tübingen, 72076 Tübingen, Germany
| | | | | | | | | | - Judith Peters
- Université Grenoble Alpes, CNRS, LiPhy, 38000 Grenoble, France
- Institut Laue Langevin, 38042 Grenoble, France
- Institut Universitaire de France, 75231 Paris, France
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5
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Schirò G, Weik M. Role of hydration water in the onset of protein structural dynamics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:463002. [PMID: 31382251 DOI: 10.1088/1361-648x/ab388a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Proteins are the molecular workhorses in a living organism. Their 3D structures are animated by a multitude of equilibrium fluctuations and specific out-of-equilibrium motions that are required for proteins to be biologically active. When studied as a function of temperature, functionally relevant dynamics are observed at and above the so-called protein dynamical transition (~240 K) in hydrated, but not in dry proteins. In this review we present and discuss the main experimental and computational results that provided evidence for the dynamical transition, with a focus on the role of hydration water dynamics in sustaining functional protein dynamics. The coupling and mutual influence of hydration water dynamics and protein dynamics are discussed and the hypotheses illustrated that have been put forward to explain the physical origin of their onsets.
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Affiliation(s)
- Giorgio Schirò
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
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6
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Stephens AD, Kaminski Schierle GS. The role of water in amyloid aggregation kinetics. Curr Opin Struct Biol 2019; 58:115-123. [DOI: 10.1016/j.sbi.2019.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 05/30/2019] [Accepted: 06/06/2019] [Indexed: 12/16/2022]
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7
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Nakagawa H, Joti Y, Kitao A, Yamamuro O, Kataoka M. Universality and Structural Implications of the Boson Peak in Proteins. Biophys J 2019; 117:229-238. [PMID: 31255295 DOI: 10.1016/j.bpj.2019.06.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 05/19/2019] [Accepted: 06/05/2019] [Indexed: 12/12/2022] Open
Abstract
The softness and rigidity of proteins are reflected in the structural dynamics, which are in turn affected by the environment. The characteristic low-frequency vibrational spectrum of a protein, known as boson peak, is an indication of the structural rigidity of the protein at a cryogenic temperature or dehydrated conditions. In this article, the effect of hydration, temperature, and pressure on the boson peak and volumetric properties of a globular protein are evaluated by using inelastic neutron scattering and molecular dynamics simulation. Hydration, pressurization, and cooling shift the boson peak position to higher energy and depress the peak intensity and decreases the protein and cavity volumes. We found the correlation between the boson peak and cavity volume in a protein. A decrease of cavity volume means the increase of rigidity, which is the origin of the boson peak shift. Boson peak is the universal property of a protein, which is rationalized by the correlation.
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Affiliation(s)
- Hiroshi Nakagawa
- Hierarchical Structure Research Group, Materials Science Research Center, Japan Atomic Energy Agency, Tokai, Ibaraki, Japan.
| | - Yasumasa Joti
- XFEL Utilization Division, Japan Synchrotron Radiation Research Institute, Sayo-cho, Sayo-gun, Hyogo, Japan
| | - Akio Kitao
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro, Tokyo, Japan
| | - Osamu Yamamuro
- Institute for Solid State Physics, University of Tokyo, Kashiwa, Chiba, Japan
| | - Mikio Kataoka
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan; Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society, Tokai, Naka, Ibaraki, Japan.
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8
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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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9
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Watanabe K, Kawai K, Nagoe A, Suzuki T, Oguni M. Multiple Glass-Transitions of Globular Protein BSA Aqueous Solutions Depending on the Hydration Degree. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20180295] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Keisuke Watanabe
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Kiyoshi Kawai
- Department of Biofunctional Science and Technology, Graduate School of Biosphere Science, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Atsushi Nagoe
- Department of Mathematics and Science, School of Science and Engineering, Kokushikan University, 4-28-1 Setagaya, Setagaya-ku, Tokyo 154-8515, Japan
| | - Toru Suzuki
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Masaharu Oguni
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan
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10
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Zeller D, Telling MTF, Zamponi M, García Sakai V, Peters J. Analysis of elastic incoherent neutron scattering data beyond the Gaussian approximation. J Chem Phys 2018; 149:234908. [PMID: 30579322 DOI: 10.1063/1.5049938] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
This work addresses the use of the Gaussian approximation as a common tool to extract atomic motions in proteins from elastic incoherent neutron scattering and whether improvements in data analysis and additional information can be obtained when going beyond that. We measured alpha-lactalbumin with different levels of hydration on three neutron backscattering spectrometers, to be able to resolve a wide temporal and spatial range for dynamics. We demonstrate that the Gaussian approximation gives qualitatively similar results to models that include heterogeneity, if one respects a certain procedure to treat the intercept of the elastic intensities with the momentum transfer axis. However, the inclusion of motional heterogeneity provides better fits to the data. Our analysis suggests an approach of limited heterogeneity, where including only two kinds of motions appears sufficient to obtain more quantitative results for the mean square displacement. Finally, we note that traditional backscattering spectrometers pose a limit on the lowest accessible momentum transfer. We therefore suggest that complementary information about the spatial evolution of the elastic intensity close to zero momentum transfer can be obtained using other neutron methods, in particular, neutron spin-echo together with polarization analysis.
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Affiliation(s)
- D Zeller
- Université Grenoble Alpes, CNRS, LiPhy, 140 av. de la Physique, 38000 Grenoble, France
| | - M T F Telling
- ISIS Pulsed Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Chilton, Oxfordshire OX11 0QX, United Kingdom
| | - M Zamponi
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Lichtenbergstr. 1, 85748 Garching, Germany
| | - V García Sakai
- ISIS Pulsed Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Chilton, Oxfordshire OX11 0QX, United Kingdom
| | - J Peters
- Université Grenoble Alpes, CNRS, LiPhy, 140 av. de la Physique, 38000 Grenoble, France
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11
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Zanatta M, Tavagnacco L, Buratti E, Bertoldo M, Natali F, Chiessi E, Orecchini A, Zaccarelli E. Evidence of a low-temperature dynamical transition in concentrated microgels. SCIENCE ADVANCES 2018; 4:eaat5895. [PMID: 30276264 PMCID: PMC6162076 DOI: 10.1126/sciadv.aat5895] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 08/21/2018] [Indexed: 05/07/2023]
Abstract
A low-temperature dynamical transition has been reported in several proteins. We provide the first observation of a "protein-like" dynamical transition in nonbiological aqueous environments. To this aim, we exploit the popular colloidal system of poly-N-isopropylacrylamide (PNIPAM) microgels, extending their investigation to unprecedentedly high concentrations. Owing to the heterogeneous architecture of the microgels, water crystallization is avoided in concentrated samples, allowing us to monitor atomic dynamics at low temperatures. By elastic incoherent neutron scattering and molecular dynamics simulations, we find that a dynamical transition occurs at a temperature T d ~ 250 K, independently from PNIPAM mass fraction. However, the transition is smeared out on approaching dry conditions. The quantitative agreement between experiments and simulations provides evidence that the transition occurs simultaneously for PNIPAM and water dynamics. The similarity of these results with hydrated protein powders suggests that the dynamical transition is a generic feature in complex macromolecular systems, independently from their biological function.
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Affiliation(s)
- Marco Zanatta
- Department of Computer Science, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Letizia Tavagnacco
- Consiglio Nazionale delle Ricerche (CNR)–Istituto dei Sistemi Complessi, Sede Sapienza, and Department of Physics, Sapienza University of Rome, Piazzale A. Moro 2, 00185 Rome, Italy
| | - Elena Buratti
- CNR–Istituto per i Processi Chimico-Fisici, Sede Secondaria di Pisa, Area della Ricerca, via G. Moruzzi 1, 56124 Pisa, Italy
| | - Monica Bertoldo
- CNR–Istituto per i Processi Chimico-Fisici, Sede Secondaria di Pisa, Area della Ricerca, via G. Moruzzi 1, 56124 Pisa, Italy
- Corresponding author. (M.B.); (A.O.); (E.Z.)
| | - Francesca Natali
- CNR–Istituto Officina dei Materiali (IOM), Operative Group in Grenoble, c/o Institut Laue Langevin, 6 rue Jules Horowitz, BP 156, 38042 Grenoble Cedex 9, France
| | - Ester Chiessi
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica I, 00133 Rome, Italy
| | - Andrea Orecchini
- Department of Physics and Geology, University of Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR-IOM c/o Department of Physics and Geology, University of Perugia, Via A. Pascoli, 06123 Perugia, Italy
- Corresponding author. (M.B.); (A.O.); (E.Z.)
| | - Emanuela Zaccarelli
- Consiglio Nazionale delle Ricerche (CNR)–Istituto dei Sistemi Complessi, Sede Sapienza, and Department of Physics, Sapienza University of Rome, Piazzale A. Moro 2, 00185 Rome, Italy
- Corresponding author. (M.B.); (A.O.); (E.Z.)
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12
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Vural D, Smith JC, Glyde HR. Determination of Dynamical Heterogeneity from Dynamic Neutron Scattering of Proteins. Biophys J 2018; 114:2397-2407. [PMID: 29580551 DOI: 10.1016/j.bpj.2018.02.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 01/26/2018] [Accepted: 02/12/2018] [Indexed: 02/04/2023] Open
Abstract
Motional displacements of hydrogen (H) in proteins can be measured using incoherent neutron-scattering methods. These displacements can also be calculated numerically using data from molecular dynamics simulations. An enormous amount of data on the average mean-square motional displacement (MSD) of H as a function of protein temperature, hydration, and other conditions has been collected. H resides in a wide spectrum of sites in a protein. Some H are tightly bound to molecular chains, and the H motion is dictated by that of the chain. Other H are quite independent. As a result, there is a distribution of motions and MSDs of H within a protein that is denoted dynamical heterogeneity. The goal of this paper is to incorporate a distribution of MSDs into models of the H incoherent intermediate scattering function, I(Q,t), that is calculated and observed. The aim is to contribute information on the distribution as well as on the average MSD from comparison of the models with simulations and experiment. For example, we find that simulations of I(Q,t) in lysozyme are well reproduced if the distribution of MSDs is bimodal with two broad peaks rather than a single broad peak.
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Affiliation(s)
- Derya Vural
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware; Department of Physics, Giresun University, Giresun, Turkey.
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Henry R Glyde
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware
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13
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Nandi PK, English NJ, Futera Z, Benedetto A. Hydrogen-bond dynamics at the bio-water interface in hydrated proteins: a molecular-dynamics study. Phys Chem Chem Phys 2018; 19:318-329. [PMID: 27905589 DOI: 10.1039/c6cp05601f] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Water is fundamental to the biochemistry of enzymes. It is well known that without a minimum amount of water, enzymes are not biologically active. Bare minimal solvation for biological function corresponds to about a single layer of water covering enzymes' surfaces. Many contradictory studies on protein-hydration-water-coupled dynamics have been published in recent decades. Following prevailing wisdom, a dynamical crossover in hydration water (at around 220 K for hydrated lysozymes) can trigger larger-amplitude motions of the protein, activating, in turn, biological functions. Here, we present a molecular-dynamics-simulation study on a solvated model protein (hen egg-white lysozyme), in which we determine, inter alia, the relaxation dynamics of the hydrogen-bond network between the protein and its hydration water molecules on a residue-per-residue basis. Hydrogen-bond breakage/formation kinetics is rather heterogeneous in temperature dependence (due to the heterogeneity of the free-energy surface), and is driven by the magnitude of thermal motions of various different protein residues which provide enough thermal energy to overcome energy barriers to rupture their respective hydrogen bonds with water. In particular, arginine residues exhibit the highest number of such hydrogen bonds at low temperatures, losing almost completely such bonding above 230 K. This suggests that hydration water's dynamical crossover, observed experimentally for hydrated lysozymes at ∼220 K, lies not at the origin of the protein residues' larger-amplitude motions, but rather arises as a consequence thereof. This highlights the need for new experimental investigations, and new interpretations to link protein dynamics to functions, in the context of key interrelationships with the solvation layer.
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Affiliation(s)
- Prithwish K Nandi
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Niall J English
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Zdenek Futera
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Antonio Benedetto
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland. and Neutron-Scattering and Imaging Laboratory, Paul Scherrer Institute, Villigen, Switzerland
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14
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Liu Z, Huang J, Tyagi M, O'Neill H, Zhang Q, Mamontov E, Jain N, Wang Y, Zhang J, Smith JC, Hong L. Dynamical Transition of Collective Motions in Dry Proteins. PHYSICAL REVIEW LETTERS 2017; 119:048101. [PMID: 29341744 DOI: 10.1103/physrevlett.119.048101] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Indexed: 06/07/2023]
Abstract
Water is widely assumed to be essential for protein dynamics and function. In particular, the well-documented "dynamical" transition at ∼200 K, at which the protein changes from a rigid, nonfunctional form to a flexible, functional state, as detected in hydrogenated protein by incoherent neutron scattering, requires hydration. Here, we report on coherent neutron scattering experiments on perdeuterated proteins and reveal that a transition occurs in dry proteins at the same temperature resulting primarily from the collective heavy-atom motions. The dynamical transition discovered is intrinsic to the energy landscape of dry proteins.
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Affiliation(s)
- Zhuo Liu
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Juan Huang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Madhusudan Tyagi
- NIST Center for Neutron Research, National Institute of Standards and Technology (NIST), Gaithersburg, Maryland 20899, USA and Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - Hugh O'Neill
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37931, USA
| | - Qiu Zhang
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37931, USA
| | - Eugene Mamontov
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Nitin Jain
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Yujie Wang
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jie Zhang
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jeremy C Smith
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Liang Hong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
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15
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Nandi PK, English NJ. Role of Hydration Layer in Dynamical Transition in Proteins: Insights from Translational Self-Diffusivity. J Phys Chem B 2016; 120:12031-12039. [PMID: 27933939 DOI: 10.1021/acs.jpcb.6b06683] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Elucidation of the role of hydration water underpinning dynamical crossover in proteins has proven challenging. Indeed, many contradictory findings in the literature seek to establish either causal or correlative links between water and protein behavior. Here, via molecular dynamics, we compute the temperature dependence of mean-square displacement and translational self-diffusivities for both hen egg white lysozyme and its hydration layer from 190 to 300 K. We find that the protein's mobility increases sharply at ∼230 K, indicating dynamical onset; concerted motion with hydration-water molecules is evident up to ∼285 K, confirming dynamical correlation between them. Exploring underlying mechanisms of such concerted motion, we scrutinize the water-protein hydrogen-bonding network as a function of temperature, noting sharp deviation from linearity of the hydrogen bond number's profile with temperature originating near the protein dynamical transition. Our studies reveal a common temperature profile/dependence of self-diffusivity values of the protein, hydration water, and the bulk solvent, originating from a common dependence on the bulk solvent viscosity, ηS. The key mechanistic role adopted by the protein-water hydrogen bond network in relation to the onset of proteins' dynamical transition is also discussed.
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Affiliation(s)
- Prithwish K Nandi
- School of Chemical and Bioprocess Engineering, University College Dublin , Belfield, Dublin 4, Ireland
| | - Niall J English
- School of Chemical and Bioprocess Engineering, University College Dublin , Belfield, Dublin 4, Ireland
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16
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Hong L, Jain N, Cheng X, Bernal A, Tyagi M, Smith JC. Determination of functional collective motions in a protein at atomic resolution using coherent neutron scattering. SCIENCE ADVANCES 2016; 2:e1600886. [PMID: 27757419 PMCID: PMC5065251 DOI: 10.1126/sciadv.1600886] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Accepted: 09/02/2016] [Indexed: 06/06/2023]
Abstract
Protein function often depends on global, collective internal motions. However, the simultaneous quantitative experimental determination of the forms, amplitudes, and time scales of these motions has remained elusive. We demonstrate that a complete description of these large-scale dynamic modes can be obtained using coherent neutron-scattering experiments on perdeuterated samples. With this approach, a microscopic relationship between the structure, dynamics, and function in a protein, cytochrome P450cam, is established. The approach developed here should be of general applicability to protein systems.
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Affiliation(s)
- Liang Hong
- Institute of Natural Sciences and Department of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Nitin Jain
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Xiaolin Cheng
- Center for Molecular Biophysics, Oak Ridge National Laboratory, TN 37831, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Ana Bernal
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Madhusudan Tyagi
- NIST Center for Neutron Research, National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA
- Department of Materials Science and Engineering, University of Maryland, College Park, MD 20742, USA
| | - Jeremy C. Smith
- Center for Molecular Biophysics, Oak Ridge National Laboratory, TN 37831, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
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17
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Neutrons describe ectoine effects on water H-bonding and hydration around a soluble protein and a cell membrane. Sci Rep 2016; 6:31434. [PMID: 27527336 PMCID: PMC4985633 DOI: 10.1038/srep31434] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 07/21/2016] [Indexed: 01/09/2023] Open
Abstract
Understanding adaptation to extreme environments remains a challenge of high biotechnological potential for fundamental molecular biology. The cytosol of many microorganisms, isolated from saline environments, reversibly accumulates molar concentrations of the osmolyte ectoine to counterbalance fluctuating external salt concentrations. Although they have been studied extensively by thermodynamic and spectroscopic methods, direct experimental structural data have, so far, been lacking on ectoine-water-protein interactions. In this paper, in vivo deuterium labeling, small angle neutron scattering, neutron membrane diffraction and inelastic scattering are combined with neutron liquids diffraction to characterize the extreme ectoine-containing solvent and its effects on purple membrane of H. salinarum and E. coli maltose binding protein. The data reveal that ectoine is excluded from the hydration layer at the membrane surface and does not affect membrane molecular dynamics, and prove a previous hypothesis that ectoine is excluded from a monolayer of dense hydration water around the soluble protein. Neutron liquids diffraction to atomic resolution shows how ectoine enhances the remarkable properties of H-bonds in water—properties that are essential for the proper organization, stabilization and dynamics of biological structures.
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18
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Thorneywork AL, Aarts DGAL, Horbach J, Dullens RPA. On the Gaussian approximation in colloidal hard sphere fluids. SOFT MATTER 2016; 12:4129-4134. [PMID: 27064930 DOI: 10.1039/c5sm03049h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We study the behaviour of the self-intermediate scattering function and self-van Hove correlation function for quasi-two-dimensional colloidal hard sphere fluids at a range of area fractions. We compute these functions first directly from the particle coordinates and secondly from the mean squared displacement via the Gaussian approximation. This allows us to test the validity of this approximation over a range of length and time scales, where we find that the Gaussian approximation holds if the hydrodynamic limits are appropriately probed. Surprisingly, only small deviations from Gaussian behaviour are seen at intermediate times, even for dense fluids. We next consider these deviations from Gaussian behaviour firstly via the non-Gaussian parameter and secondly by considering the relaxation times of the intermediate scattering function. From these measurements we develop a scaling relation in order to directly determine the combinations of wavevectors and times at which the non-Gaussian behavior is seen. This allows for the clear identification of the hydrodynamic regimes and thus provides new insight into the crossover between long- and short-time self-diffusion.
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Affiliation(s)
- Alice L Thorneywork
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
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19
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Grimaldo M, Roosen-Runge F, Hennig M, Zanini F, Zhang F, Jalarvo N, Zamponi M, Schreiber F, Seydel T. Hierarchical molecular dynamics of bovine serum albumin in concentrated aqueous solution below and above thermal denaturation. Phys Chem Chem Phys 2016; 17:4645-55. [PMID: 25587698 DOI: 10.1039/c4cp04944f] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dynamics of proteins in solution is a complex and hierarchical process, affected by the aqueous environment as well as temperature. We present a comprehensive study on nanosecond time and nanometer length scales below, at, and above the denaturation temperature Td. Our experimental data evidence dynamical processes in protein solutions on three distinct time scales. We suggest a consistent physical picture of hierarchical protein dynamics: (i) self-diffusion of the entire protein molecule is confirmed to agree with colloid theory for all temperatures where the protein is in its native conformational state. At higher temperatures T > Td, the self-diffusion is strongly obstructed by cross-linking or entanglement. (ii) The amplitude of backbone fluctuations grows with increasing T, and a transition in its dynamics is observed above Td. (iii) The number of mobile side-chains increases sharply at Td while their average dynamics exhibits only little variations. The combination of quasi-elastic neutron scattering and the presented analytical framework provides a detailed microscopic picture of the protein molecular dynamics in solution, thereby reflecting the changes of macroscopic properties such as cluster formation and gelation.
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Affiliation(s)
- Marco Grimaldo
- Institut Max von Laue - Paul Langevin (ILL), CS 20156, F-38042 Grenoble, France.
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20
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Knoll W, Peters J, Kursula P, Gerelli Y, Natali F. Influence of myelin proteins on the structure and dynamics of a model membrane with emphasis on the low temperature regime. J Chem Phys 2015; 141:205101. [PMID: 25429962 DOI: 10.1063/1.4901738] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Myelin is an insulating, multi-lamellar membrane structure wrapped around selected nerve axons. Increasing the speed of nerve impulses, it is crucial for the proper functioning of the vertebrate nervous system. Human neurodegenerative diseases, such as multiple sclerosis, are linked to damage to the myelin sheath through demyelination. Myelin exhibits a well defined subset of myelin-specific proteins, whose influence on membrane dynamics, i.e., myelin flexibility and stability, has not yet been explored in detail. In a first paper [W. Knoll, J. Peters, P. Kursula, Y. Gerelli, J. Ollivier, B. Demé, M. Telling, E. Kemner, and F. Natali, Soft Matter 10, 519 (2014)] we were able to spotlight, through neutron scattering experiments, the role of peripheral nervous system myelin proteins on membrane stability at room temperature. In particular, the myelin basic protein and peripheral myelin protein 2 were found to synergistically influence the membrane structure while keeping almost unchanged the membrane mobility. Further insight is provided by this work, in which we particularly address the investigation of the membrane flexibility in the low temperature regime. We evidence a different behavior suggesting that the proton dynamics is reduced by the addition of the myelin basic protein accompanied by negligible membrane structural changes. Moreover, we address the importance of correct sample preparation and characterization for the success of the experiment and for the reliability of the obtained results.
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Affiliation(s)
- W Knoll
- University Joseph Fourier, UFR PhiTEM, Grenoble, France
| | - J Peters
- University Joseph Fourier, UFR PhiTEM, Grenoble, France
| | | | - Y Gerelli
- Institut Laue-Langevin, Grenoble, France
| | - F Natali
- Institut Laue-Langevin, Grenoble, France
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21
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Sebastiani F, Longo M, Orecchini A, Comez L, De Francesco A, Muthmann M, Teixeira SCM, Petrillo C, Sacchetti F, Paciaroni A. Hydration-dependent dynamics of human telomeric oligonucleotides in the picosecond timescale: A neutron scattering study. J Chem Phys 2015; 143:015102. [DOI: 10.1063/1.4923213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- F. Sebastiani
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - M. Longo
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- Elettra—Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | - A. Orecchini
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - L. Comez
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - A. De Francesco
- CNR-IOM OGG c/o Institut Laue-Langevin, 71 Avenue des Martyrs, CS20156, 38042 Grenoble Cedex 9, France
| | - M. Muthmann
- Jülich Centre for Neutron Science, Forschungszentrum Jülich GmbH, Outstation at Heinz Maier-Leibnitz Zentrum, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - S. C. M. Teixeira
- EPSAM, Keele University, Staffordshire ST5 5BG, United Kingdom
- Institut Laue–Langevin, 71 Avenue des Martyrs, CS20156, 38042 Grenoble Cedex 9, France
| | - C. Petrillo
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - F. Sacchetti
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - A. Paciaroni
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
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22
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Vural D, Hong L, Smith JC, Glyde HR. Motional displacements in proteins: The origin of wave-vector-dependent values. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:052705. [PMID: 26066197 DOI: 10.1103/physreve.91.052705] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Indexed: 06/04/2023]
Abstract
The average mean-square displacement, 〈r(2)〉, of H atoms in a protein is frequently determined using incoherent neutron-scattering experiments. 〈r(2)〉 is obtained from the observed elastic incoherent dynamic structure factor, S(i)(Q,ω=0), assuming the form S(i)(Q,ω=0) =exp(-Q(2)〈r(2)〉/3). This is often referred to as the Gaussian approximation (GA) to S(i)(Q,ω=0). 〈r(2)〉 obtained in this way depends on the value of the wave vector, Q considered. Equivalently, the observed S(i)(Q,ω=0) deviates from the GA. We investigate the origin of the Q dependence of 〈r(2)〉 by evaluating the scattering functions in different approximations using molecular dynamics (MD) simulation of the protein lysozyme. We find that keeping only the Gaussian term in a cumulant expansion of S(Q,ω) is an accurate approximation and is not the origin of the Q dependence of 〈r(2)〉. This is demonstrated by showing that the term beyond the Gaussian is negligible and that the GA is valid for an individual atom in the protein. Rather, the Q dependence (deviation from the GA) arises from the dynamical heterogeneity of the H in the protein. Specifically it arises from representing, in the analysis of data, this diverse dynamics by a single average scattering center that has a single, average 〈r(2)〉. The observed Q dependence of 〈r(2)〉 can be used to provide information on the dynamical heterogeneity in proteins.
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Affiliation(s)
- Derya Vural
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716-2570, USA
| | - Liang Hong
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, P. O. Box 2008, Tennessee 37831, USA
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, P. O. Box 2008, Tennessee 37831, USA
| | - Henry R Glyde
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716-2570, USA
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23
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Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins. Nat Commun 2015; 6:6490. [PMID: 25774711 PMCID: PMC4382692 DOI: 10.1038/ncomms7490] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 02/02/2015] [Indexed: 12/12/2022] Open
Abstract
Hydration water is the natural matrix of biological macromolecules and is essential for their activity in cells. The coupling between water and protein dynamics has been intensively studied, yet it remains controversial. Here we combine protein perdeuteration, neutron scattering and molecular dynamics simulations to explore the nature of hydration water motions at temperatures between 200 and 300 K, across the so-called protein dynamical transition, in the intrinsically disordered human protein tau and the globular maltose binding protein. Quasi-elastic broadening is fitted with a model of translating, rotating and immobile water molecules. In both experiment and simulation, the translational component markedly increases at the protein dynamical transition (around 240 K), regardless of whether the protein is intrinsically disordered or folded. Thus, we generalize the notion that the translational diffusion of water molecules on a protein surface promotes the large-amplitude motions of proteins that are required for their biological activity. Hydration water plasticizes protein structures and is essential for their biological functions, such as enzymatic catalysis. Here, the authors use neutron scattering and molecular dynamics simulations to study hydration water at the dynamical transition of folded and disordered proteins.
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24
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Picosecond dynamics in haemoglobin from different species: A quasielastic neutron scattering study. Biochim Biophys Acta Gen Subj 2014; 1840:2989-99. [DOI: 10.1016/j.bbagen.2014.06.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 06/10/2014] [Accepted: 06/11/2014] [Indexed: 11/22/2022]
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25
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Mukhopadhyay S, Cohen SR, Marchak D, Friedman N, Pecht I, Sheves M, Cahen D. Nanoscale electron transport and photodynamics enhancement in lipid-depleted bacteriorhodopsin monomers. ACS NANO 2014; 8:7714-7722. [PMID: 25003581 DOI: 10.1021/nn500202k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Potential future use of bacteriorhodopsin (bR) as a solid-state electron transport (ETp) material requires the highest possible active protein concentration. To that end we prepared stable monolayers of protein-enriched bR on a conducting HOPG substrate by lipid depletion of the native bR. The ETp properties of this construct were then investigated using conducting probe atomic force microscopy at low bias, both in the ground dark state and in the M-like intermediate configuration, formed upon excitation by green light. Photoconductance modulation was observed upon green and blue light excitation, demonstrating the potential of these monolayers as optoelectronic building blocks. To correlate protein structural changes with the observed behavior, measurements were made as a function of pressure under the AFM tip, as well as humidity. The junction conductance is reversible under pressure changes up to ∼300 MPa, but above this pressure the conductance drops irreversibly. ETp efficiency is enhanced significantly at >60% relative humidity, without changing the relative photoactivity significantly. These observations are ascribed to changes in protein conformation and flexibility and suggest that improved electron transport pathways can be generated through formation of a hydrogen-bonding network.
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26
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Hofmeister ions control protein dynamics. Biochim Biophys Acta Gen Subj 2013; 1830:4564-72. [DOI: 10.1016/j.bbagen.2013.05.036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 05/24/2013] [Accepted: 05/28/2013] [Indexed: 11/19/2022]
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27
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Rakshit S, Saha R, Pal SK. Modulation of Environmental Dynamics at the Active Site and Activity of an Enzyme under Nanoscopic Confinement: Subtilisin Carlsberg in Anionic AOT Reverse Micelle. J Phys Chem B 2013; 117:11565-74. [DOI: 10.1021/jp4061494] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Surajit Rakshit
- Department of Chemical, Biological,
and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences, Block JD,
Sector III, Salt Lake, Kolkata 700098, India
| | - Ranajay Saha
- Department of Chemical, Biological,
and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences, Block JD,
Sector III, Salt Lake, Kolkata 700098, India
| | - Samir Kumar Pal
- Department of Chemical, Biological,
and Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences, Block JD,
Sector III, Salt Lake, Kolkata 700098, India
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28
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Gerwert K, Freier E, Wolf S. The role of protein-bound water molecules in microbial rhodopsins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:606-13. [PMID: 24055285 DOI: 10.1016/j.bbabio.2013.09.006] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 09/08/2013] [Accepted: 09/10/2013] [Indexed: 02/06/2023]
Abstract
Protein-bound internal water molecules are essential features of the structure and function of microbial rhodopsins. Besides structural stabilization, they act as proton conductors and even proton storage sites. Currently, the most understood model system exhibiting such features is bacteriorhodopsin (bR). During the last 20 years, the importance of water molecules for proton transport has been revealed through this protein. It has been shown that water molecules are as essential as amino acids for proton transport and biological function. In this review, we present an overview of the historical development of this research on bR. We furthermore summarize the recently discovered protein-bound water features associated with proton transport. Specifically, we discuss a pentameric water/amino acid arrangement close to the protonated Schiff base as central proton-binding site, a protonated water cluster as proton storage site at the proton-release site, and a transient linear water chain at the proton uptake site. We highlight how protein conformational changes reposition or reorient internal water molecules, thereby guiding proton transport. Last, we compare the water positions in bR with those in other microbial rhodopsins to elucidate how protein-bound water molecules guide the function of microbial rhodopsins. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
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Affiliation(s)
- Klaus Gerwert
- Department of Biophysics, University of Bochum, ND 04 North, 44780 Bochum, Germany; Department of Biophysics, Chinese Academy of Sciences-Max-Planck Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences (SIBS), 320 Yue Yang Lu, 200031 Shanghai, PR China.
| | - Erik Freier
- Department of Biophysics, University of Bochum, ND 04 North, 44780 Bochum, Germany
| | - Steffen Wolf
- Department of Biophysics, Chinese Academy of Sciences-Max-Planck Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences (SIBS), 320 Yue Yang Lu, 200031 Shanghai, PR China
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29
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Peters J, Giudici-Orticoni MT, Zaccai G, Guiral M. Dynamics measured by neutron scattering correlates with the organization of bioenergetics complexes in natural membranes from hyperthermophile and mesophile bacteria. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2013; 36:78. [PMID: 23880731 DOI: 10.1140/epje/i2013-13078-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 02/01/2013] [Accepted: 02/26/2013] [Indexed: 06/02/2023]
Abstract
Various models on membrane structure and organization of proteins and complexes in natural membranes emerged during the last years. However, the lack of systematic dynamical studies to complement structural investigations hindered the establishment of a more complete picture of these systems. Elastic incoherent neutron scattering gives access to the dynamics on a molecular level and was applied to natural membranes extracted from the hyperthermophile Aquifex aeolicus and the mesophile Wolinella succinogenes bacteria. The results permitted to extract a hierarchy of dynamic flexibility and atomic resilience within the samples, which correlated with the organization of proteins in bioenergetics complexes and the functionality of the membranes.
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Affiliation(s)
- J Peters
- Institut Laue Langevin, 6 rue J. Horowitz, BP 156, F-38042 Grenoble Cedex 9, France.
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30
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Marty V, Jasnin M, Fabiani E, Vauclare P, Gabel F, Trapp M, Peters J, Zaccai G, Franzetti B. Neutron scattering: a tool to detect in vivo thermal stress effects at the molecular dynamics level in micro-organisms. J R Soc Interface 2013; 10:20130003. [PMID: 23446053 DOI: 10.1098/rsif.2013.0003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In vivo molecular dynamics in Halobacterium salinarum cells under stress conditions was measured by neutron scattering experiments coupled with microbiological characterization. Molecular dynamics alterations were detected with respect to unstressed cells, reflecting a softening of protein structures consistent with denaturation. The experiments indicated that the neutron scattering method provides a promising tool to study molecular dynamics modifications in the proteome of living cells induced by factors altering protein folds.
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31
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Choi DH, Son H, Jung S, Park J, Park WY, Kwon OS, Park GS. Dielectric relaxation change of water upon phase transition of a lipid bilayer probed by terahertz time domain spectroscopy. J Chem Phys 2013; 137:175101. [PMID: 23145747 DOI: 10.1063/1.4764304] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We investigate the influence of the 1, 2-ditetradecanoyl-sn-glycero-3-phosphocholine lipid bilayer phases on the water reorientation dynamics with terahertz time domain spectroscopy. The phase of the lipids was controlled by the temperature in the range of 14-35 °C. During the gel-to-fluid phase transition, the hydration water ratio drastically changed from 0.3 to 0.6. The absorption coefficient of the hydration water increased with the temperature in the gel phase and then decreased in the fluid phase. The dielectric relaxation time of the lipid solution decreased initially but then increased after the phase transition. This indicates that the hydration water reorientation dynamics are restricted by lipids and that this phenomenon is pronounced in a biologically relevant fluid phase.
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Affiliation(s)
- Da-Hye Choi
- Center for THz-Bio Application Systems, Department of Physics and Astronomy, Seoul National University, Seoul 151-747, South Korea
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32
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Wood K, Gallat FX, Otten R, van Heel AJ, Lethier M, van Eijck L, Moulin M, Haertlein M, Weik M, Mulder FAA. Protein Surface and Core Dynamics Show Concerted Hydration-Dependent Activation. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201205898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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33
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Gallat FX, Laganowsky A, Wood K, Gabel F, van Eijck L, Wuttke J, Moulin M, Härtlein M, Eisenberg D, Colletier JP, Zaccai G, Weik M. Dynamical coupling of intrinsically disordered proteins and their hydration water: comparison with folded soluble and membrane proteins. Biophys J 2012; 103:129-36. [PMID: 22828339 DOI: 10.1016/j.bpj.2012.05.027] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 05/03/2012] [Accepted: 05/18/2012] [Indexed: 11/16/2022] Open
Abstract
Hydration water is vital for various macromolecular biological activities, such as specific ligand recognition, enzyme activity, response to receptor binding, and energy transduction. Without hydration water, proteins would not fold correctly and would lack the conformational flexibility that animates their three-dimensional structures. Motions in globular, soluble proteins are thought to be governed to a certain extent by hydration-water dynamics, yet it is not known whether this relationship holds true for other protein classes in general and whether, in turn, the structural nature of a protein also influences water motions. Here, we provide insight into the coupling between hydration-water dynamics and atomic motions in intrinsically disordered proteins (IDP), a largely unexplored class of proteins that, in contrast to folded proteins, lack a well-defined three-dimensional structure. We investigated the human IDP tau, which is involved in the pathogenic processes accompanying Alzheimer disease. Combining neutron scattering and protein perdeuteration, we found similar atomic mean-square displacements over a large temperature range for the tau protein and its hydration water, indicating intimate coupling between them. This is in contrast to the behavior of folded proteins of similar molecular weight, such as the globular, soluble maltose-binding protein and the membrane protein bacteriorhodopsin, which display moderate to weak coupling, respectively. The extracted mean square displacements also reveal a greater motional flexibility of IDP compared with globular, folded proteins and more restricted water motions on the IDP surface. The results provide evidence that protein and hydration-water motions mutually affect and shape each other, and that there is a gradient of coupling across different protein classes that may play a functional role in macromolecular activity in a cellular context.
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Affiliation(s)
- F-X Gallat
- Comissariat à l'Energie Atomique, Institut de Biologie Structurale, Grenoble, France
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34
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Wood K, Gallat FX, Otten R, van Heel AJ, Lethier M, van Eijck L, Moulin M, Haertlein M, Weik M, Mulder FAA. Protein surface and core dynamics show concerted hydration-dependent activation. Angew Chem Int Ed Engl 2012; 52:665-8. [PMID: 23154872 DOI: 10.1002/anie.201205898] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 10/29/2012] [Indexed: 11/09/2022]
Abstract
By specifically labeling leucine/valine methyl groups and lysine side chains "inside" and "outside" dynamics of proteins on the nanosecond timescale are compared using neutron scattering. Surprisingly, both groups display similar dynamics as a function of temperature, and the buried hydrophobic core is sensitive to hydration and undergoes a dynamical transition.
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Affiliation(s)
- Kathleen Wood
- Australian Nuclear Science and Technology Organisation Bragg Institute, Menai NSW, Australia
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35
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Delgado-García M, Valdivia-Urdiales B, Aguilar-González CN, Contreras-Esquivel JC, Rodríguez-Herrera R. Halophilic hydrolases as a new tool for the biotechnological industries. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2012; 92:2575-2580. [PMID: 22926924 DOI: 10.1002/jsfa.5860] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 07/05/2012] [Accepted: 07/18/2012] [Indexed: 06/01/2023]
Abstract
Halophilic micro-organisms are able to survive in high salt concentrations because they have developed diverse biochemical, structural and physiological modifications, allowing the catalytic synthesis of proteins with interesting physicochemical and structural properties. The main characteristic of halophilic enzymes that allows them to be considered as a novel alternative for use in the biotechnological industries is their polyextremophilicity, i.e. they have the capacity to be thermostable, tolerate a wide range of pH, withstand denaturation and tolerate high salt concentrations. However, there have been relatively few studies on halophilic enzymes, with some being based on their isolation and others on their characterisation. These enzymes are scarcely researched because attention has been focused on other extremophile micro-organisms. Only a few industrial applications of halophilic enzymes, principally in the fermented food, textile, pharmaceutical and leather industries, have been reported. However, it is important to investigate applications of these enzymes in more biotechnological processes at both the chemical and the molecular level. This review discusses the modifications of these enzymes, their industrial applications and research perspectives in different biotechnological areas.
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Affiliation(s)
- Mariana Delgado-García
- Food Research Department, School of Chemistry, Universidad Autónoma de Coahuila, Saltillo, Coahuila, Mexico
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36
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Gallat FX, Brogan APS, Fichou Y, McGrath N, Moulin M, Härtlein M, Combet J, Wuttke J, Mann S, Zaccai G, Jackson CJ, Perriman AW, Weik M. A Polymer Surfactant Corona Dynamically Replaces Water in Solvent-Free Protein Liquids and Ensures Macromolecular Flexibility and Activity. J Am Chem Soc 2012; 134:13168-71. [DOI: 10.1021/ja303894g] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- François-Xavier Gallat
- Institut de
Biologie Structurale, Comissariat à l’Energie Atomique, F-38054
Grenoble, France
- CNRS, UMR5075, F-38027 Grenoble, France
- Université Joseph Fourier, F-38000 Grenoble, France
- Institut Laue-Langevin, 6 rue Jules Horowitz, B.P. 156, 38042 Grenoble Cedex 9, France
| | - Alex P. S. Brogan
- Center for Organized Matter
Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Yann Fichou
- Institut de
Biologie Structurale, Comissariat à l’Energie Atomique, F-38054
Grenoble, France
- CNRS, UMR5075, F-38027 Grenoble, France
- Université Joseph Fourier, F-38000 Grenoble, France
| | - Nina McGrath
- Center for Organized Matter
Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Martine Moulin
- Institut Laue-Langevin, 6 rue Jules Horowitz, B.P. 156, 38042 Grenoble Cedex 9, France
- ILL-EMBL Deuteration Laboratory, Partnership for Structural
Biology, 38042 Grenoble Cedex 9, France
| | - Michael Härtlein
- Institut Laue-Langevin, 6 rue Jules Horowitz, B.P. 156, 38042 Grenoble Cedex 9, France
- ILL-EMBL Deuteration Laboratory, Partnership for Structural
Biology, 38042 Grenoble Cedex 9, France
| | - Jérôme Combet
- Institut Laue-Langevin, 6 rue Jules Horowitz, B.P. 156, 38042 Grenoble Cedex 9, France
| | - Joachim Wuttke
- Forschungszentrum Jülich, JCNS at FRM II, Lichtenbergstrasse 1,
85747 Garching, Germany
| | - Stephen Mann
- Center for Organized Matter
Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Giuseppe Zaccai
- Institut de
Biologie Structurale, Comissariat à l’Energie Atomique, F-38054
Grenoble, France
- CNRS, UMR5075, F-38027 Grenoble, France
- Université Joseph Fourier, F-38000 Grenoble, France
- Institut Laue-Langevin, 6 rue Jules Horowitz, B.P. 156, 38042 Grenoble Cedex 9, France
| | - Colin J. Jackson
- Research School of Chemistry, Australian National University, ACT, 0200, Australia
| | - Adam W. Perriman
- Center for Organized Matter
Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Martin Weik
- Institut de
Biologie Structurale, Comissariat à l’Energie Atomique, F-38054
Grenoble, France
- CNRS, UMR5075, F-38027 Grenoble, France
- Université Joseph Fourier, F-38000 Grenoble, France
- ESRF, 6 rue Jules Horowitz, BP 220, 38043 Grenoble
Cedex, France
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Pieper J, Trapp M, Skomorokhov A, Natkaniec I, Peters J, Renger G. Temperature-dependent vibrational and conformational dynamics of photosystem II membrane fragments from spinach investigated by elastic and inelastic neutron scattering. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1213-9. [PMID: 22465855 DOI: 10.1016/j.bbabio.2012.03.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/07/2012] [Accepted: 03/16/2012] [Indexed: 11/27/2022]
Abstract
Vibrational and conformational protein dynamics of photosystem II (PS II) membrane fragments from spinach were investigated by elastic and inelastic incoherent neutron scattering (EINS and IINS). As to the EINS experiments, the average atomic mean square displacement values of PS II membrane fragments hydrated at a relative humidity of 57% exhibit a dynamical transition at ~230K. In contrast, the dynamical transition was absent at a relative humidity of 44%. These findings are in agreement with previous studies which reported a "freezing" of protein mobility due to dehydration (Pieper et al. (2008) Eur. Biophys. J. 37: 657-663) and its correlation with an inhibition of electron transfer from Q(A)(-) to Q(B) (Kaminskaya et al. (2003) Biochemistry 42, 8119-8132). IINS spectra of a sample hydrated at a relative humidity of 57% show a distinct Boson peak at ~7.5meV at 20K, which shifts towards lower energy values upon temperature increase to 250K. This unexpected effect is interpreted in terms of a "softening" of the protein matrix along with the onset of conformational protein dynamics as revealed by the EINS experiments. Information on the density of vibrational states of pigment-protein complexes is important for a realistic calculation of excitation energy transfer kinetics and spectral lineshapes and is often routinely obtained by optical line-narrowing spectroscopy at liquid helium temperature. The data presented here demonstrate that IINS is a valuable experimental tool in determining the density of vibrational states not only at cryogenic, but also at nearly physiological temperatures up to 250K. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.
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Affiliation(s)
- Jörg Pieper
- Institute of Physics, University of Tartu, Tartu, Estonia.
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Satarić MV, Zdravković S, Tuszyński JA. Modeling of relay helix functional dynamics and feasibility of experimental verification by neutron scattering. CHAOS (WOODBURY, N.Y.) 2011; 21:043135. [PMID: 22225372 DOI: 10.1063/1.3665091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Cellular long-range transport involves motor proteins (MPs) (especially, kinesin and myosin) which contain a so-called relay helix. Its motion is of crucial importance to the conversion of chemical energy released in ATP hydrolysis into the coordinated mechanical movement of the entire motor protein. In this paper, we propose two combined nonlinear mechanisms for this particular functional activity and suggest the application of neutron scattering assays to experimentally determine the incoherent dynamic structure factor S(q,ω). We argue that this type of experiment is not only feasible but it could offer significant insights into the mechanism of MP function at a molecular level.
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Affiliation(s)
- Miljko V Satarić
- Fakultet Tehničkih Nauka, Univerzitet u Novom Sadu, 21000 Novi Sad, Serbia.
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Polymer and Water Dynamics in Poly(vinyl alcohol)/Poly(methacrylate) Networks. A Molecular Dynamics Simulation and Incoherent Neutron Scattering Investigation. Polymers (Basel) 2011. [DOI: 10.3390/polym3041805] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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41
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Goyal P, Ghosh N, Phatak P, Clemens M, Gaus M, Elstner M, Cui Q. Proton storage site in bacteriorhodopsin: new insights from quantum mechanics/molecular mechanics simulations of microscopic pK(a) and infrared spectra. J Am Chem Soc 2011; 133:14981-97. [PMID: 21761868 PMCID: PMC3178665 DOI: 10.1021/ja201568s] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Identifying the group that acts as the proton storage/loading site is a challenging but important problem for understanding the mechanism of proton pumping in biomolecular proton pumps, such as bacteriorhodopsin (bR) and cytochrome c oxidase. Recent experimental studies of bR propelled the idea that the proton storage/release group (PRG) in bR is not an amino acid but a water cluster embedded in the protein. We argue that this idea is at odds with our knowledge of protein electrostatics, since invoking the water cluster as the PRG would require the protein to raise the pK(a) of a hydronium by almost 11 pK(a) units, which is difficult considering known cases of pK(a) shifts in proteins. Our recent quantum mechanics/molecular mechanics (QM/MM) simulations suggested an alternative "intermolecular proton bond" model in which the stored proton is shared between two conserved Glu residues (194 and 204). Here we show that this model leads to microscopic pK(a) values consistent with available experimental data and the functional requirement of a PRG. Extensive QM/MM simulations also show that, independent of a number of technical issues, such as the influence of QM region size, starting X-ray structure, and nuclear quantum effects, the "intermolecular proton bond" model is qualitatively consistent with available spectroscopic data. Potential of mean force calculations show explicitly that the stored proton strongly prefers the pair of Glu residues over the water cluster. The results and analyses help highlight the importance of considering protein electrostatics and provide arguments for why the "intermolecular proton bond" model is likely applicable to the PRG in biomolecular proton pumps in general.
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Affiliation(s)
- Puja Goyal
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Ave, Madison, WI 53706
| | - Nilanjan Ghosh
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Ave, Madison, WI 53706
| | - Prasad Phatak
- Department of Physical and Theoretical Chemistry, TU Braunschweig, Hans-Sommer-Straβe 10, D-38106 Braunschweig, Germany
| | - Maike Clemens
- Department of Physical and Theoretical Chemistry, TU Braunschweig, Hans-Sommer-Straβe 10, D-38106 Braunschweig, Germany
| | - Michael Gaus
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131 Karlsruhe, Germany
| | - Marcus Elstner
- Department of Physical and Theoretical Chemistry, TU Braunschweig, Hans-Sommer-Straβe 10, D-38106 Braunschweig, Germany
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131 Karlsruhe, Germany
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Ave, Madison, WI 53706
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Wang SC, Mirarefi P, Faraone A, Lee CT. Light-controlled protein dynamics observed with neutron spin echo measurements. Biochemistry 2011; 50:8150-62. [PMID: 21809812 DOI: 10.1021/bi200206z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A photoresponsive surfactant has been used as a means to control protein structure and dynamics with light illumination. This cationic azobenzene surfactant, azoTAB, which undergoes a reversible photoisomerization upon exposure to the appropriate wavelength of light, adopts a relatively hydrophobic, trans structure under visible light illumination and a relatively hydrophilic cis structure under UV light illumination. Small-angle neutron scattering (SANS) and neutron spin echo (NSE) spectroscopy were used to measure the tertiary structure and internal dynamics of lysozyme in the presence of the photosurfactant, respectively. The SANS-based in vitro structures indicate that under visible light the photosurfactant induces partial unfolding that principally occurs away from the active site near the hinge region connecting the α and β domains. Upon UV exposure, however, the protein refolds to a nativelike structure. At the same time, enhanced internal dynamics of lysozyme were detected with the surfactant in the trans form through NSE measurements of the Q-dependent effective diffusion coefficient (D(eff)) of the protein. In contrast, the D(eff) values of lysozyme in the presence of cis azoTAB largely agree with the rigid-body calculation as well as those measured for pure lysozyme, suggesting that the native protein is dormant on the nanosecond time and nanometer length scales. Lysozyme internal motions were modeled by assuming a protein of two (α and β domains) or three (α and β domains and the hinge region) domains connects by either soft linkers or rigid, freely rotating bonds. Protein dynamics were also tracked with Fourier transform infrared spectroscopy through hydrogen-deuterium exchange kinetics, which further demonstrated enhanced protein flexibility induced by the trans form of the surfactant relative to the native protein. Ensemble-averaged intramolecular fluorescent resonance energy transfer measurements similarly demonstrated the enhanced dynamics of lysozyme with the trans form of the photosurfactant. Previous results have shown a significant increase in protein activity in the presence of azoTAB in the trans conformation. Combined, these results provide insight into a unique light-based method of controlling protein structure, dynamics, and function and strongly support the relevance of large domain motions for the activity of proteins.
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Affiliation(s)
- Shao-Chun Wang
- Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA
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43
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Internal motions of actin characterized by quasielastic neutron scattering. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:661-71. [DOI: 10.1007/s00249-011-0669-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 12/28/2010] [Accepted: 01/03/2011] [Indexed: 10/18/2022]
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44
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Combet S, Zanotti JM, Bellissent-Funel MC. Temperature- and hydration-dependent internal dynamics of stripped human erythrocyte vesicles studied by incoherent neutron scattering. Biochim Biophys Acta Gen Subj 2010; 1810:202-10. [PMID: 21059380 DOI: 10.1016/j.bbagen.2010.10.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 10/08/2010] [Accepted: 10/26/2010] [Indexed: 11/29/2022]
Abstract
BACKGROUND We focus on temperature- and hydration-dependence of internal molecular motions in stripped human red blood cell (RBC) vesicles, widely used as a model system for more complex biomembranes. METHODS We singled out picosecond local motions of the non-exchangeable hydrogen atoms of RBC vesicles by performing elastic and quasielastic incoherent neutron scattering measurements in dry and heavy water (D₂O)-hydrated RBC powders. RESULTS In dry stripped RBCs, hydrogen motions remained harmonic all along the measured temperature range (100-310K) and mean-square displacements (MSDs) exhibited no temperature transition up to 310K. In contrast, MSDs of hydrated stripped RBCs (h ≈ 0.38g D₂O/g dry powder) exhibited a pronounced transition near 260K, with the sharp rise of anharmonic diffusive motions of hydrogen atoms. This transition at ~260K was correlated with both the onset of nonvibrational (harmonic and nonharmonic) motions and the melting of crystallized hydration water. GENERAL SIGNIFICANCE In conclusion, we have shown that MSDs in human RBC vesicles are temperature-and hydration-dependent. These results provide insight into biomembrane internal dynamics at picosecond timescale and nanometer length scale. Such motions have been shown to act as the "lubricant" of larger conformational changes on a slower, millisecond timescale that are necessary for important biological processes.
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Affiliation(s)
- S Combet
- Laboratoire Léon-Brillouin, UMR 12 CEA/CNRS, Gif-sur-Yvette Cedex, France.
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Trapp M, Gutberlet T, Juranyi F, Unruh T, Demé B, Tehei M, Peters J. Hydration dependent studies of highly aligned multilayer lipid membranes by neutron scattering. J Chem Phys 2010; 133:164505. [DOI: 10.1063/1.3495973] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Wood K, Tobias DJ, Kessler B, Gabel F, Oesterhelt D, Mulder FAA, Zaccai G, Weik M. The low-temperature inflection observed in neutron scattering measurements of proteins is due to methyl rotation: direct evidence using isotope labeling and molecular dynamics simulations. J Am Chem Soc 2010; 132:4990-1. [PMID: 20302295 DOI: 10.1021/ja910502g] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There is increasing interest in the contribution of methyl groups to the overall dynamics measured by neutron scattering experiments of proteins. In particular an inflection observed in atomic mean square displacements measured as a function of temperature on high resolution spectrometers (approximately 1 microeV) was explained by the onset of methyl group rotations. By specifically labeling a non-methyl-containing side-chain in a native protein system, the purple membrane, and performing neutron scattering measurements, we here provide direct experimental evidence that the observed inflection is indeed due to methyl group rotations. Molecular dynamics simulations reproduce the experimental data, and their analysis suggests that the apparent transition is due to methyl group rotation entering the finite instrumental resolution of the spectrometer. Methyl group correlation times measured by solid state NMR in the purple membrane, taken from previous work, support the interpretation.
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Nakagawa H, Kamikubo H, Kataoka M. Effect of conformational states on protein dynamical transition. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:27-33. [DOI: 10.1016/j.bbapap.2009.06.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Revised: 06/10/2009] [Accepted: 06/29/2009] [Indexed: 10/20/2022]
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From powder to solution: hydration dependence of human hemoglobin dynamics correlated to body temperature. Biophys J 2009; 96:5073-81. [PMID: 19527667 DOI: 10.1016/j.bpj.2009.03.043] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Revised: 02/25/2009] [Accepted: 03/30/2009] [Indexed: 11/23/2022] Open
Abstract
A transition in hemoglobin (Hb), involving partial unfolding and aggregation, has been shown previously by various biophysical methods. The correlation between the transition temperature and body temperature for Hb from different species, suggested that it might be significant for biological function. To focus on such biologically relevant human Hb dynamics, we studied the protein internal picosecond motions as a response to hydration, by elastic and quasielastic neutron scattering. Rates of fast diffusive motions were found to be significantly enhanced with increasing hydration from fully hydrated powder to concentrated Hb solution. In concentrated protein solution, the data showed that amino acid side chains can explore larger volumes above body temperature than expected from normal temperature dependence. The body temperature transition in protein dynamics was absent in fully hydrated powder, indicating that picosecond protein dynamics responsible for the transition is activated only at a sufficient level of hydration. A collateral result from the study is that fully hydrated protein powder samples do not accurately describe all aspects of protein picosecond dynamics that might be necessary for biological function.
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Stadler AM, Digel I, Artmann GM, Embs JP, Zaccai G, Büldt G. Hemoglobin dynamics in red blood cells: correlation to body temperature. Biophys J 2008; 95:5449-61. [PMID: 18708462 PMCID: PMC2586580 DOI: 10.1529/biophysj.108.138040] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A transition in hemoglobin behavior at close to body temperature has been discovered recently by micropipette aspiration experiments on single red blood cells (RBCs) and circular dichroism spectroscopy on hemoglobin solutions. The transition temperature was directly correlated to the body temperatures of a variety of species. In an exploration of the molecular basis for the transition, we present neutron scattering measurements of the temperature dependence of hemoglobin dynamics in whole human RBCs in vivo. The data reveal a change in the geometry of internal protein motions at 36.9 degrees C, at human body temperature. Above that temperature, amino acid side-chain motions occupy larger volumes than expected from normal temperature dependence, indicating partial unfolding of the protein. Global protein diffusion in RBCs was also measured and the findings compared favorably with theoretical predictions for short-time self-diffusion of noncharged hard-sphere colloids. The results demonstrated that changes in molecular dynamics in the picosecond time range and angstrom length scale might well be connected to a macroscopic effect on whole RBCs that occurs at body temperature.
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50
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Fabiani E, Stadler AM, Madern D, Koza MM, Tehei M, Hirai M, Zaccai G. Dynamics of apomyoglobin in the α-to-β transition and of partially unfolded aggregated protein. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 38:237-44. [DOI: 10.1007/s00249-008-0375-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Revised: 09/17/2008] [Accepted: 09/22/2008] [Indexed: 10/21/2022]
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