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Matsuo T, De Francesco A, Peters J. Molecular Dynamics of Lysozyme Amyloid Polymorphs Studied by Incoherent Neutron Scattering. Front Mol Biosci 2022; 8:812096. [PMID: 35111814 PMCID: PMC8801425 DOI: 10.3389/fmolb.2021.812096] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/03/2021] [Indexed: 11/22/2022] Open
Abstract
Lysozyme amyloidosis is a hereditary disease, which is characterized by the deposition of lysozyme amyloid fibrils in various internal organs. It is known that lysozyme fibrils show polymorphism and that polymorphs formed at near-neutral pH have the ability to promote more monomer binding than those formed at acidic pH, indicating that only specific polymorphs become dominant species in a given environment. This is likely due to the polymorph-specific configurational diffusion. Understanding the possible differences in dynamical behavior between the polymorphs is thus crucial to deepen our knowledge of amyloid polymorphism and eventually elucidate the molecular mechanism of lysozyme amyloidosis. In this study, molecular dynamics at sub-nanosecond timescale of two kinds of polymorphic fibrils of hen egg white lysozyme, which has long been used as a model of human lysozyme, formed at pH 2.7 (LP27) and pH 6.0 (LP60) was investigated using elastic incoherent neutron scattering (EINS) and quasi-elastic neutron scattering (QENS). Analysis of the EINS data showed that whereas the mean square displacement of atomic motions is similar for both LP27 and LP60, LP60 contains a larger fraction of atoms moving with larger amplitudes than LP27, indicating that the dynamical difference between the two polymorphs lies not in the averaged amplitude, but in the distribution of the amplitudes. Furthermore, analysis of the QENS data showed that the jump diffusion coefficient of atoms is larger for LP60, suggesting that the atoms of LP60 undergo faster diffusive motions than those of LP27. This study thus characterizes the dynamics of the two lysozyme polymorphs and reveals that the molecular dynamics of LP60 is enhanced compared with that of LP27. The higher molecular flexibility of the polymorph would permit to adjust its conformation more quickly than its counterpart, facilitating monomer binding.
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Affiliation(s)
- Tatsuhito Matsuo
- Univ. Grenoble Alpes, CNRS, LiPhy, Grenoble, France
- Institut Laue-Langevin, Grenoble, France
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Tokai, Japan
- *Correspondence: Tatsuhito Matsuo, ; Judith Peters,
| | - Alessio De Francesco
- Institut Laue-Langevin, Grenoble, France
- CNR-IOM and INSIDE@ILL C/O Operative Group in Grenoble (OGG), Grenoble, France
| | - Judith Peters
- Univ. Grenoble Alpes, CNRS, LiPhy, Grenoble, France
- Institut Laue-Langevin, Grenoble, France
- Institut Universitaire de France, Paris, France
- *Correspondence: Tatsuhito Matsuo, ; Judith Peters,
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2
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Roy P, Menon S, Sengupta N. Dynamical Manifestations of Supercooling in Amyloid Hydration. J Phys Chem B 2021; 126:44-53. [PMID: 34941279 DOI: 10.1021/acs.jpcb.1c07724] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effect of extreme temperature on amyloidogenic species remains sparsely explored. In a recent study (J. Phys. Chem. Lett., 2019, 10, (10)), we employed exhaustive molecular dynamics simulations to explore the cold thermal response of a putative small amyloid oligomer and to elicit the role of solvent modulation. Herein, we investigate the dynamical response of the hydration waters of the oligomer within the supercooled states. Using NMR-based formalism, we delineate the entropic response in terms of the side-chain conformational entropy that corroborates the weakening of the hydrophobic core with lowering of temperature. The translational dynamics of the protein and hydration waters reveal the coupling of protein dynamical fluctuations with solvent dynamics under supercooled conditions. Probing the translational motion as a space-time correlation indicates glassy dynamics exhibited by hydration waters in the supercooled regime. Caging of the water molecules with lowering of temperature and the resultant hopping dynamics are reflected in the longer β-relaxation timescales of translational motion. Furthermore, we utilized mode-coupling theory (MCT) and derived the ideal glass transition temperature from translational and rotational dynamics, around ∼196 and 209 K, respectively. Interestingly, rotational motion in the supercooled regime deviates from the MCT law, exhibits Arrhenius motion, and marks a fragile-to-strong crossover at 227 K. The low-frequency vibrational modes also coincide with the dynamical transition. This exposition lends dynamical insights into the hydration coupling of an amyloid aggregate under cryogenic conditions.
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Affiliation(s)
- Priti Roy
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India 741246
| | - Sneha Menon
- Tata Institute of Fundamental Research Hyderabad, Telangana 500046, India
| | - Neelanjana Sengupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India 741246
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3
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Pounot K, Grime GW, Longo A, Zamponi M, Noferini D, Cristiglio V, Seydel T, Garman EF, Weik M, Foderà V, Schirò G. Zinc determines dynamical properties and aggregation kinetics of human insulin. Biophys J 2021; 120:886-898. [PMID: 33545104 DOI: 10.1016/j.bpj.2020.11.2280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 11/08/2020] [Accepted: 11/30/2020] [Indexed: 12/26/2022] Open
Abstract
Protein aggregation is a widespread process leading to deleterious consequences in the organism, with amyloid aggregates being important not only in biology but also for drug design and biomaterial production. Insulin is a protein largely used in diabetes treatment, and its amyloid aggregation is at the basis of the so-called insulin-derived amyloidosis. Here, we uncover the major role of zinc in both insulin dynamics and aggregation kinetics at low pH, in which the formation of different amyloid superstructures (fibrils and spherulites) can be thermally induced. Amyloid aggregation is accompanied by zinc release and the suppression of water-sustained insulin dynamics, as shown by particle-induced x-ray emission and x-ray absorption spectroscopy and by neutron spectroscopy, respectively. Our study shows that zinc binding stabilizes the native form of insulin by facilitating hydration of this hydrophobic protein and suggests that introducing new binding sites for zinc can improve insulin stability and tune its aggregation propensity.
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Affiliation(s)
- Kevin Pounot
- Applied Physics, University of Tübingen, Tübingen, Baden-Würtemberg, Germany.
| | | | - Alessandro Longo
- Istituto per lo Studio dei Materiali Nanostrutturati, CNR, Palermo, Italy
| | - Michaela Zamponi
- Jülich Centre for Neutron Science JCNS, Forschungszentrum Jülich GmbH Outstation at MLZ, Garching, Germany
| | - Daria Noferini
- Jülich Centre for Neutron Science JCNS, Forschungszentrum Jülich GmbH Outstation at MLZ, Garching, Germany
| | | | - Tilo Seydel
- Science Division, Institut Max von Laue-Paul Langevin, Grenoble, France
| | | | - Martin Weik
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38000 Grenoble, France
| | - Vito Foderà
- Pharmacy, University of Copenhagen, Copenhagen, Denmark.
| | - Giorgio Schirò
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38000 Grenoble, France.
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4
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Krah A, Huber RG, Bond PJ. How Ligand Binding Affects the Dynamical Transition Temperature in Proteins. Chemphyschem 2020; 21:916-926. [DOI: 10.1002/cphc.201901221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 03/03/2020] [Indexed: 11/11/2022]
Affiliation(s)
- Alexander Krah
- School of Computational SciencesKorea Institute for Advanced Study 85 Hoegiro, Dongdaemun-gu Seoul 02455 Republic of Korea
- Bioinformatics InstituteAgency for Science Technology and Research (A*STAR) 30 Biopolis Str., #07-01 Matrix 138671 Singapore
| | - Roland G. Huber
- Bioinformatics InstituteAgency for Science Technology and Research (A*STAR) 30 Biopolis Str., #07-01 Matrix 138671 Singapore
| | - Peter J. Bond
- Bioinformatics InstituteAgency for Science Technology and Research (A*STAR) 30 Biopolis Str., #07-01 Matrix 138671 Singapore
- National University of SingaporeDepartment of Biological Sciences 14 Science Drive 4 Singapore 117543
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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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Atkinson SC, Dogovski C, Wood K, Griffin MDW, Gorman MA, Hor L, Reboul CF, Buckle AM, Wuttke J, Parker MW, Dobson RCJ, Perugini MA. Substrate Locking Promotes Dimer-Dimer Docking of an Enzyme Antibiotic Target. Structure 2018; 26:948-959.e5. [PMID: 29804823 DOI: 10.1016/j.str.2018.04.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 02/27/2018] [Accepted: 04/19/2018] [Indexed: 11/19/2022]
Abstract
Protein dynamics manifested through structural flexibility play a central role in the function of biological molecules. Here we explore the substrate-mediated change in protein flexibility of an antibiotic target enzyme, Clostridium botulinum dihydrodipicolinate synthase. We demonstrate that the substrate, pyruvate, stabilizes the more active dimer-of-dimers or tetrameric form. Surprisingly, there is little difference between the crystal structures of apo and substrate-bound enzyme, suggesting protein dynamics may be important. Neutron and small-angle X-ray scattering experiments were used to probe substrate-induced dynamics on the sub-second timescale, but no significant changes were observed. We therefore developed a simple technique, coined protein dynamics-mass spectrometry (ProD-MS), which enables measurement of time-dependent alkylation of cysteine residues. ProD-MS together with X-ray crystallography and analytical ultracentrifugation analyses indicates that pyruvate locks the conformation of the dimer that promotes docking to the more active tetrameric form, offering insight into ligand-mediated stabilization of multimeric enzymes.
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Affiliation(s)
- Sarah C Atkinson
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia
| | - Con Dogovski
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia
| | - Kathleen Wood
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW 2234, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael A Gorman
- ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Lilian Hor
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia; Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, La Trobe University, Melbourne, VIC 3086, Australia
| | - Cyril F Reboul
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Ashley M Buckle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Joachim Wuttke
- Juelich Centre for Neutron Science (JCNS), at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Juelich GmbH, Lichtenstrasse 1, Garching 85 747, Germany
| | - Michael W Parker
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia; ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Renwick C J Dobson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia; Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Private Bag, Christchurch 4800, New Zealand
| | - Matthew A Perugini
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, University of Melbourne, Parkville, VIC 3010, Australia; Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia.
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7
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Abstract
Dynamic neutron scattering directly probes motions in biological systems on femtosecond to microsecond timescales. When combined with molecular dynamics simulation and normal mode analysis, detailed descriptions of the forms and frequencies of motions can be derived. We examine vibrations in proteins, the temperature dependence of protein motions, and concepts describing the rich variety of motions detectable using neutrons in biological systems at physiological temperatures. New techniques for deriving information on collective motions using coherent scattering are also reviewed.
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Affiliation(s)
- Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, USA; .,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Pan Tan
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Loukas Petridis
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, USA; .,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Liang Hong
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
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8
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Abstract
Microbial rhodopsins (MRs) are a large family of photoactive membrane proteins, found in microorganisms belonging to all kingdoms of life, with new members being constantly discovered. Among the MRs are light-driven proton, cation and anion pumps, light-gated cation and anion channels, and various photoreceptors. Due to their abundance and amenability to studies, MRs served as model systems for a great variety of biophysical techniques, and recently found a great application as optogenetic tools. While the basic aspects of microbial rhodopsins functioning have been known for some time, there is still a plenty of unanswered questions. This chapter presents and summarizes the available knowledge, focusing on the functional and structural studies.
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Affiliation(s)
- Ivan Gushchin
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.
| | - Valentin Gordeliy
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.
- University of Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France.
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany.
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9
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Vugmeyster L, Ostrovsky D, Hoatson GL, Qiang W, Falconer IB. Solvent-Driven Dynamical Crossover in the Phenylalanine Side-Chain from the Hydrophobic Core of Amyloid Fibrils Detected by 2H NMR Relaxation. J Phys Chem B 2017; 121:7267-7275. [PMID: 28699757 PMCID: PMC5567839 DOI: 10.1021/acs.jpcb.7b04726] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aromatic residues are important markers of dynamical changes in proteins' hydrophobic cores. In this work we investigated the dynamics of the F19 side-chain in the core of amyloid fibrils across a wide temperature range of 300 to 140 K. We utilized solid-state 2H NMR relaxation to demonstrate the presence of a solvent-driven dynamical crossover between different motional regimes, often also referred to as the dynamical transition. In particular, the dynamics are dominated by small-angle fluctuations at low temperatures and by π-flips of the aromatic ring at high temperatures. The crossover temperature is more than 43 degrees lower for the hydrated state of the fibrils compared to the dry state, indicating that interactions with water facilitate π-flips. Further, crossover temperatures are shown to be very sensitive to polymorphic states of the fibrils, such as the 2-fold and 3-fold symmetric morphologies of the wild-type protein as well as D23N mutant protofibrils. We speculate that these differences can be attributed, at least partially, to enhanced interactions with water in the 3-fold polymorph, which has been shown to have a water-accessible cavity. Combined with previous studies of methyl group dynamics, the results highlight the presence of multiple dynamics modes in the core of the fibrils, which was originally believed to be quite rigid.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado at Denver, Denver, CO 80204
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado at Denver, Denver, CO 80204
| | - Gina L. Hoatson
- Department of Physics, College of William and Mary, Williamsburg, Virginia, 23187
| | - Wei Qiang
- Department of Chemistry, Binghamton University, Binghamton, NY 13902
| | - Isaac B. Falconer
- Department of Chemistry, University of Colorado at Denver, Denver, CO 80204
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10
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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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11
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Syryamina VN, Dzuba SA. Dynamical Transitions at Low Temperatures in the Nearest Hydration Shell of Phospholipid Bilayers. J Phys Chem B 2017; 121:1026-1032. [DOI: 10.1021/acs.jpcb.6b10133] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- V. N. Syryamina
- Institute
of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
- Physics
Department, Novosibirsk State University, Novosibirsk 630090, Russian Federation
| | - S. A. Dzuba
- Institute
of Chemical Kinetics and Combustion, Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
- Physics
Department, Novosibirsk State University, Novosibirsk 630090, Russian Federation
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12
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Misuraca L, Natali F, da Silva L, Peters J, Demé B, Ollivier J, Seydel T, Laux-Lesourd V, Haertlein M, Zaccai G, Deamer D, Maurel MC. Mobility of a Mononucleotide within a Lipid Matrix: A Neutron Scattering Study. Life (Basel) 2017; 7:life7010002. [PMID: 28054992 PMCID: PMC5370402 DOI: 10.3390/life7010002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/23/2016] [Accepted: 12/29/2016] [Indexed: 11/16/2022] Open
Abstract
An essential question in studies on the origins of life is how nucleic acids were first synthesized and then incorporated into compartments about 4 billion years ago. A recent discovery is that guided polymerization within organizing matrices could promote a non-enzymatic condensation reaction allowing the formation of RNA-like polymers, followed by encapsulation in lipid membranes. Here, we used neutron scattering and deuterium labelling to investigate 5′-adenosine monophosphate (AMP) molecules captured in a multilamellar phospholipid matrix. The aim of the research was to determine and compare how mononucleotides are captured and differently organized within matrices and multilamellar phospholipid structures and to explore the role of water in organizing the system to determine at which level the system becomes sufficiently anhydrous to lock the AMP molecules into an organized structure and initiate ester bond synthesis. Elastic incoherent neutron scattering experiments were thus employed to investigate the changes of the dynamic properties of AMP induced by embedding the molecules within the lipid matrix. The influence of AMP addition to the lipid membrane organization was determined through diffraction measurement, which also helped us to define the best working Q range for dynamical data analysis with respect to specific hydration. The use of different complementary instruments allowed coverage of a wide time-scale domain, from ns to ps, of atomic mean square fluctuations, providing evidence of a well-defined dependence of the AMP dynamics on the hydration level.
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Affiliation(s)
- Loreto Misuraca
- Institut Laue Langevin (ILL), 71, Avenue des Martyrs, 38000 Grenoble, France.
- Dipartimento di Fisica e Chimica, Università degli Studi di Palermo, Viale delle Scienze, Ed. 17, 90128 Palermo, Italy.
| | - Francesca Natali
- Institut Laue Langevin (ILL), 71, Avenue des Martyrs, 38000 Grenoble, France.
- Consiglio Nazionale delle Ricerche, Istituto Officina dei Materiali (CNR-IOM), Research Unit in Grenoble, 71 Avenue des Martyrs, 38000 Grenoble, France.
| | - Laura da Silva
- Institut de Systematique, Évolution, Biodiversité, (ISYEB) UMR 7205 CNRS-MNHN-UPMC-EPHE Sorbonne Universités, CP50, 57 rue Cuvier, 75005 Paris, France.
| | - Judith Peters
- Institut Laue Langevin (ILL), 71, Avenue des Martyrs, 38000 Grenoble, France.
- Université Grenoble Alpes (UGA), UFR PhITEM, 621 Avenue Centrale, 38000 Grenoble, France.
| | - Bruno Demé
- Institut Laue Langevin (ILL), 71, Avenue des Martyrs, 38000 Grenoble, France.
| | - Jacques Ollivier
- Institut Laue Langevin (ILL), 71, Avenue des Martyrs, 38000 Grenoble, France.
| | - Tilo Seydel
- Institut Laue Langevin (ILL), 71, Avenue des Martyrs, 38000 Grenoble, France.
| | | | - Michael Haertlein
- Institut Laue Langevin (ILL), 71, Avenue des Martyrs, 38000 Grenoble, France.
| | - Giuseppe Zaccai
- Institut Laue Langevin (ILL), 71, Avenue des Martyrs, 38000 Grenoble, France.
- Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, 38000 Grenoble, France.
- Commissariat à l'énergie atomique et aux énergies alternatives (CEA), 17 Avenue des Martyrs, 38054 Grenoble, France.
- Centre National de la Recherche Scientifique (CNRS), 25 Avenue des Martyrs, 38000 Grenoble, France.
| | - David Deamer
- University of California, Santa Cruz, CA 95060, USA.
| | - Marie Christine Maurel
- Institut de Systematique, Évolution, Biodiversité, (ISYEB) UMR 7205 CNRS-MNHN-UPMC-EPHE Sorbonne Universités, CP50, 57 rue Cuvier, 75005 Paris, France.
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13
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Kim SB, Gupta DR, Debenedetti PG. Computational investigation of dynamical transitions in Trp-cage miniprotein powders. Sci Rep 2016; 6:25612. [PMID: 27151767 PMCID: PMC4858699 DOI: 10.1038/srep25612] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 04/20/2016] [Indexed: 12/02/2022] Open
Abstract
We investigate computationally the dynamical transitions in Trp-cage miniprotein powders, at three levels of hydration: 0.04, 0.26 and 0.4 g water/g protein. We identify two distinct temperatures where transitions in protein dynamics occur. Thermal motions are harmonic and independent of hydration level below Tlow ≈ 160 K, above which all powders exhibit harmonic behavior but with a different and enhanced temperature dependence. The second onset, which is often referred to as the protein dynamical transition, occurs at a higher temperature TD that decreases as the hydration level increases, and at the lowest hydration level investigated here (0.04 g/g) is absent in the temperature range we studied in this work (T ≤ 300 K). Protein motions become anharmonic at TD, and their amplitude increases with hydration level. Upon heating above TD, hydrophilic residues experience a pronounced enhancement in the amplitude of their characteristic motions in hydrated powders, whereas it is the hydrophobic residues that experience the more pronounced enhancement in the least hydrated system. The dynamical transition in Trp-cage is a collective phenomenon, with every residue experiencing a transition to anharmonic behavior at the same temperature.
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Affiliation(s)
- Sang Beom Kim
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Devansh R Gupta
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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14
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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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15
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Perticaroli S, Ehlers G, Jalarvo N, Katsaras J, Nickels JD. Elasticity and Inverse Temperature Transition in Elastin. J Phys Chem Lett 2015; 6:4018-4025. [PMID: 26722771 DOI: 10.1021/acs.jpclett.5b01890] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Elastin is a structural protein and biomaterial that provides elasticity and resilience to a range of tissues. This work provides insights into the elastic properties of elastin and its peculiar inverse temperature transition (ITT). These features are dependent on hydration of elastin and are driven by a similar mechanism of hydrophobic collapse to an entropically favorable state. Using neutron scattering, we quantify the changes in the geometry of molecular motions above and below the transition temperature, showing a reduction in the displacement of water-induced motions upon hydrophobic collapse at the ITT. We also measured the collective vibrations of elastin gels as a function of elongation, revealing no changes in the spectral features associated with local rigidity and secondary structure, in agreement with the entropic origin of elasticity.
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Affiliation(s)
- Stefania Perticaroli
- Joint Institute for Neutron Sciences, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
- Chemical and Materials Sciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
- Department of Chemistry, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Georg Ehlers
- Quantum Condensed Matter Division, Oak Ridge National Laboratory , P.O. Box 2008, Oak Ridge, Tennessee 37831, United States
| | - Niina Jalarvo
- Jülich Centre for Neutron Science (JCNS), Forschungszentrum Jülich , D-52425 Jülich, Germany
- Chemical and Engineering Materials Division, Neutron Sciences Directorate, and JCNS Outstation at the Spallation Neutron Source (SNS), Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - John Katsaras
- Joint Institute for Neutron Sciences, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
- Biology and Soft Matter Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Jonathan D Nickels
- Joint Institute for Neutron Sciences, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
- Biology and Soft Matter Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
- The Department of Physics and Astronomy, University of Tennessee, Knoxville , Knoxville, Tennessee 37996, United States
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16
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Fichou Y, Heyden M, Zaccai G, Weik M, Tobias DJ. Molecular Dynamics Simulations of a Powder Model of the Intrinsically Disordered Protein Tau. J Phys Chem B 2015; 119:12580-9. [PMID: 26351734 DOI: 10.1021/acs.jpcb.5b05849] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The tau protein, whose aggregates are involved in Alzheimer's disease, is an intrinsically disordered protein (IDP) that regulates microtubule activity in neurons. An IDP lacks a single, well-defined structure and, rather, constantly exchanges among multiple conformations. In order to study IDP dynamics, the combination of experimental techniques, such as neutron scattering, and computational techniques, such as molecular dynamics (MD) simulations, is a powerful approach. Amorphous hydrated powder samples have been very useful for studying protein internal dynamics experimentally, e.g., using neutron scattering. Thus, there is demand for realistic in silico models of hydrated protein powders. Here we present an MD simulation analysis of a powder hydrated at 0.4 g water/g protein of the IDP tau in the temperature range 20-300 K. By comparing with neutron scattering data, we identify the protein-water interface as the predominant feature determining IDP dynamics. The so-called protein dynamical transition is shown to be attenuated, but not suppressed, in the parts of the protein that are not exposed to the solvent. In addition, we find similarities in the mean-squared displacements of the core of a globular protein and "dry" clusters formed by the IDP in hydrated powders. Thus, the ps to ns dynamics of proteins in hydrated powders originate mainly from those residues in contact with solvent. We propose that by measuring the dynamics of protein assemblies, such as aggregates, one might assess qualitatively their state of hydration.
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Affiliation(s)
- Yann Fichou
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France.,CNRS, IBS, F-38044 Grenoble, France.,CEA, IBS, F-38044 Grenoble, France
| | - Matthias Heyden
- Max-Planck-Institut für Kohlenforschung , D-45470 Mülheim an der Ruhr, Germany
| | | | - Martin Weik
- Université Grenoble Alpes, IBS, F-38044 Grenoble, France.,CNRS, IBS, F-38044 Grenoble, France.,CEA, IBS, F-38044 Grenoble, France
| | - Douglas J Tobias
- Department of Chemistry, University of California , Irvine, California 92697-2025, United States
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17
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Khodadadi S, Sokolov AP. Protein dynamics: from rattling in a cage to structural relaxation. SOFT MATTER 2015; 11:4984-4998. [PMID: 26027652 DOI: 10.1039/c5sm00636h] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present an overview of protein dynamics based mostly on results of neutron scattering, dielectric relaxation spectroscopy and molecular dynamics simulations. We identify several major classes of protein motions on the time scale from faster than picoseconds to several microseconds, and discuss the coupling of these processes to solvent dynamics. Our analysis suggests that the microsecond backbone relaxation process might be the main structural relaxation of the protein that defines its glass transition temperature, while faster processes present some localized secondary relaxations. Based on the overview, we formulate a general picture of protein dynamics and discuss the challenges in this field.
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Affiliation(s)
- S Khodadadi
- Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
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18
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Laulumaa S, Nieminen T, Lehtimäki M, Aggarwal S, Simons M, Koza MM, Vattulainen I, Kursula P, Natali F. Dynamics of the Peripheral Membrane Protein P2 from Human Myelin Measured by Neutron Scattering--A Comparison between Wild-Type Protein and a Hinge Mutant. PLoS One 2015; 10:e0128954. [PMID: 26068118 PMCID: PMC4466134 DOI: 10.1371/journal.pone.0128954] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 05/01/2015] [Indexed: 12/01/2022] Open
Abstract
Myelin protein P2 is a fatty acid-binding structural component of the myelin sheath in the peripheral nervous system, and its function is related to its membrane binding capacity. Here, the link between P2 protein dynamics and structure and function was studied using elastic incoherent neutron scattering (EINS). The P38G mutation, at the hinge between the β barrel and the α-helical lid, increased the lipid stacking capacity of human P2 in vitro, and the mutated protein was also functional in cultured cells. The P38G mutation did not change the overall structure of the protein. For a deeper insight into P2 structure-function relationships, information on protein dynamics in the 10 ps to 1 ns time scale was obtained using EINS. Values of mean square displacements mainly from protein H atoms were extracted for wild-type P2 and the P38G mutant and compared. Our results show that at physiological temperatures, the P38G mutant is more dynamic than the wild-type P2 protein, especially on a slow 1-ns time scale. Molecular dynamics simulations confirmed the enhanced dynamics of the mutant variant, especially within the portal region in the presence of bound fatty acid. The increased softness of the hinge mutant of human myelin P2 protein is likely related to an enhanced flexibility of the portal region of this fatty acid-binding protein, as well as to its interactions with the lipid bilayer surface requiring conformational adaptations.
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Affiliation(s)
- Saara Laulumaa
- Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
- German Electron Synchrotron (DESY), Hamburg, Germany
- European Spallation Source (ESS), Lund, Sweden
| | - Tuomo Nieminen
- Department of Physics, Tampere University of Technology, Tampere, Finland
| | - Mari Lehtimäki
- Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Shweta Aggarwal
- Max Planck Institute for Experimental Medicine, Göttingen, Germany
| | - Mikael Simons
- Max Planck Institute for Experimental Medicine, Göttingen, Germany
| | | | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, Tampere, Finland
| | - Petri Kursula
- Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
- German Electron Synchrotron (DESY), Hamburg, Germany
- Department of Biomedicine, University of Bergen, Bergen, Norway
- * E-mail: (PK); (FN)
| | - Francesca Natali
- Institut Laue-Langevin (ILL), Grenoble, France
- CNR-IOM, OGG, Grenoble, France
- * E-mail: (PK); (FN)
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19
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Lewandowski JR, Halse ME, Blackledge M, Emsley L. Direct observation of hierarchical protein dynamics. Science 2015; 348:578-81. [DOI: 10.1126/science.aaa6111] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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20
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Dhindsa GK, Tyagi M, Chu XQ. Temperature-dependent dynamics of dry and hydrated β-casein studied by quasielastic neutron scattering. J Phys Chem B 2014; 118:10821-9. [PMID: 25144497 DOI: 10.1021/jp504548w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
β-Casein is a component of casein micelle with amphillic nature and is recognized as a "natively disordered" protein that lacks secondary structures. In this study, the temperature and hydration effects on the dynamics of β-casein are explored by quasielastic neutron scattering (QENS). An upturn in the mean square displacement (MSD) of hydrated β-casein indicates an increase of protein flexibility at a temperature of ~225 K. Another increase in MSD at ~100 K, observed in both dry and hydrated β-casein, is ascribed to the methyl group rotations, which are not sensitive to hydration. QENS analysis in the energy domain reveals that the fraction of hydrogen atoms participating in motion in a sphere of diffusion is highly hydration dependent and increases with temperature. In the time domain analysis, a logarithmic-like decay is observed in the range of picosecond to nanosecond (β-relaxation time) in the dynamics of hydrated β-casein. This dynamical behavior has been observed in hydrated globular and oligomeric proteins. Our temperature-dependent QENS experiments provide evidence that lack of a secondary structure in β-casein results in higher flexibility in its dynamics and easier reversible thermal unfolding compared to other rigid biomolecules.
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Affiliation(s)
- Gurpreet K Dhindsa
- Department of Physics and Astronomy, Wayne State University , Detroit, Michigan 48201, United States
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21
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Surovtsev NV, Dzuba SA. Flexibility of phospholipids with saturated and unsaturated chains studied by Raman scattering: The effect of cholesterol on dynamical and phase transitions. J Chem Phys 2014; 140:235103. [DOI: 10.1063/1.4883237] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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22
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Schirò G, Vetri V, Andersen C, Natali F, Koza M, Leone M, Cupane A. The Boson Peak of Amyloid Fibrils: Probing the Softness of Protein Aggregates by Inelastic Neutron Scattering. J Phys Chem B 2014; 118:2913-23. [DOI: 10.1021/jp412277y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- G. Schirò
- Dipartimento
di Fisica e Chimica, Università di Palermo, 90136 Palermo, Italy
| | - V. Vetri
- Dipartimento
di Fisica e Chimica, Università di Palermo, 90136 Palermo, Italy
| | - C.B. Andersen
- Department
of Diabetes Biophysics, Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Måløv, Denmark
| | - F. Natali
- CNR-IOM, c/o Institut Laue Langevin, Grenoble, France
| | - M.M. Koza
- Institut Laue Langevin, Grenoble, France
| | - M. Leone
- Dipartimento
di Fisica e Chimica, Università di Palermo, 90136 Palermo, Italy
| | - A. Cupane
- Dipartimento
di Fisica e Chimica, Università di Palermo, 90136 Palermo, Italy
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23
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Martínez JI, Alonso PJ, García-Rubio I, Medina M. Methyl rotors in flavoproteins. Phys Chem Chem Phys 2014; 16:26203-12. [DOI: 10.1039/c4cp03115f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ENDOR evidence shows that methyl groups in flavin behave as quantum locked rotors.
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Affiliation(s)
- Jesús I. Martínez
- Instituto de Ciencia de Materiales de Aragón
- Universidad de Zaragoza-Consejo Superior de Investigaciones Científicas
- Facultad de Ciencias
- 50009 Zaragoza, Spain
| | - Pablo J. Alonso
- Instituto de Ciencia de Materiales de Aragón
- Universidad de Zaragoza-Consejo Superior de Investigaciones Científicas
- Facultad de Ciencias
- 50009 Zaragoza, Spain
| | - Inés García-Rubio
- Laboratory of Physical Chemistry
- ETH Zurich
- 8093 Zürich, Switzerland
- Centro Universitario de la Defensa
- 50090 Zaragoza, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular and Instituto de Biocomputación y Física de Sistemas Complejos (BIFI)
- Universidad de Zaragoza
- 50009 Zaragoza, Spain
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24
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25
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Ngai K, Capaccioli S, Paciaroni A. Nature of the water specific relaxation in hydrated proteins and aqueous mixtures. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.05.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Schiró G. Anharmonic onsets in polypeptides revealed by neutron scattering: Experimental evidences and quantitative description of energy resolution dependence. Biophys Chem 2013; 180-181:29-36. [DOI: 10.1016/j.bpc.2013.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 05/26/2013] [Accepted: 05/26/2013] [Indexed: 10/26/2022]
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27
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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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28
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Ngai KL, Capaccioli S, Paciaroni A. Change of caged dynamics at Tg in hydrated proteins: Trend of mean squared displacements after correcting for the methyl-group rotation contribution. J Chem Phys 2013; 138:235102. [DOI: 10.1063/1.4810752] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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29
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Vugmeyster L, Ostrovsky D, Lipton AS. Origin of abrupt rise in deuteron NMR longitudinal relaxation times of protein methyl groups below 90 K. J Phys Chem B 2013; 117:6129-37. [PMID: 23627365 DOI: 10.1021/jp4021596] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In order to examine the origin of the abrupt change in the temperature dependence of (2)H NMR longitudinal relaxation times observed previously for methyl groups of L69 in the hydrophobic core of villin headpiece protein at around 90 K (Vugmeyster et al. J. Am. Chem. Soc. 2010, 132, 4038-4039), we extended the measurements to several other methyl groups in the hydrophobic core. We show that, for all methyl groups, relaxation times experience a dramatic jump several orders of magnitude around this temperature. Theoretical modeling supports the conclusion that the origin of the apparent transition in the relaxation times is due to the existence of the distribution of conformers distinguished by their activation energy for methyl three-site hops. It is also crucial to take into account the differential contribution of individual conformers into overall signal intensity. When a particular conformer approaches the regime at which its three-site hop rate constant is on the order of the quadrupolar coupling interaction constant, the intensity of the signal due to this conformer experiences a sharp drop, thus changing the balance of the contributions of different conformers into the overall signal. As a result, the observed apparent transition in the relaxation rates can be explained without the assumption of an underlying transition in the rate constants. This work in combination with earlier results also shows that the model based on the distribution of conformers explains the relaxation behavior in the entire temperature range between 300 and 70 K.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, Alaska 99508, United States.
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30
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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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31
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Bastos M, Alves N, Maia S, Gomes P, Inaba A, Miyazaki Y, Zanotti JM. Hydration water and peptide dynamics – two sides of a coin. A neutron scattering and adiabatic calorimetry study at low hydration and cryogenic temperatures. Phys Chem Chem Phys 2013; 15:16693-703. [DOI: 10.1039/c3cp51937f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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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 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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33
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Nickels JD, O'Neill H, Hong L, Tyagi M, Ehlers G, Weiss KL, Zhang Q, Yi Z, Mamontov E, Smith JC, Sokolov AP. Dynamics of protein and its hydration water: neutron scattering studies on fully deuterated GFP. Biophys J 2012; 103:1566-75. [PMID: 23062349 DOI: 10.1016/j.bpj.2012.08.046] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 08/22/2012] [Accepted: 08/23/2012] [Indexed: 11/15/2022] Open
Abstract
We present a detailed analysis of the picosecond-to-nanosecond motions of green fluorescent protein (GFP) and its hydration water using neutron scattering spectroscopy and hydrogen/deuterium contrast. The analysis reveals that hydration water suppresses protein motions at lower temperatures (<~ 200 K), and facilitates protein dynamics at high temperatures. Experimental data demonstrate that the hydration water is harmonic at temperatures <~ 180-190 K and is not affected by the proteins' methyl group rotations. The dynamics of the hydration water exhibits changes at ~ 180-190 K that we ascribe to the glass transition in the hydrated protein. Our results confirm significant differences in the dynamics of protein and its hydration water at high temperatures: on the picosecond-to-nanosecond timescale, the hydration water exhibits diffusive dynamics, while the protein motions are localized to <~3 Å. The diffusion of the GFP hydration water is similar to the behavior of hydration water previously observed for other proteins. Comparison with other globular proteins (e.g., lysozyme) reveals that on the timescale of 1 ns and at equivalent hydration level, GFP dynamics (mean-square displacements and quasielastic intensity) are of much smaller amplitude. Moreover, the suppression of the protein dynamics by the hydration water at low temperatures appears to be stronger in GFP than in other globular proteins. We ascribe this observation to the barrellike structure of GFP.
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Affiliation(s)
- Jonathan D Nickels
- Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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34
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Schiró G, Natali F, Cupane A. Physical origin of anharmonic dynamics in proteins: new insights from resolution-dependent neutron scattering on homomeric polypeptides. PHYSICAL REVIEW LETTERS 2012; 109:128102. [PMID: 23005991 DOI: 10.1103/physrevlett.109.128102] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Indexed: 06/01/2023]
Abstract
Neutron scattering reveals a complex dynamics in polypeptide chains, with two main onsets of anharmonicity whose physical origin and biological role are still debated. In this study the dynamics of strategically selected homomeric polypeptides is investigated with elastic neutron scattering using different energy resolutions and compared with that of a real protein. Our data spotlight the dependence of anharmonic transition temperatures and fluctuation amplitudes on energy resolution, which we quantitatively explain in terms of a two-site model for the protein-hydration water energy landscape. Experimental data strongly suggest that the protein dynamical transition is not a mere resolution effect but is due to a real physical effect. Activation barriers and free energy values obtained for the protein dynamical transition allow us to make a connection with the two-well interaction potential of supercooled-confined water proposed to explain a low-density→high-density liquid-liquid transition.
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35
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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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36
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Stadler AM, Garvey CJ, Bocahut A, Sacquin-Mora S, Digel I, Schneider GJ, Natali F, Artmann GM, Zaccai G. Thermal fluctuations of haemoglobin from different species: adaptation to temperature via conformational dynamics. J R Soc Interface 2012; 9:2845-55. [PMID: 22696485 PMCID: PMC3479923 DOI: 10.1098/rsif.2012.0364] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Thermodynamic stability, configurational motions and internal forces of haemoglobin (Hb) of three endotherms (platypus, Ornithorhynchus anatinus; domestic chicken, Gallus gallus domesticus and human, Homo sapiens) and an ectotherm (salt water crocodile, Crocodylus porosus) were investigated using circular dichroism, incoherent elastic neutron scattering and coarse-grained Brownian dynamics simulations. The experimental results from Hb solutions revealed a direct correlation between protein resilience, melting temperature and average body temperature of the different species on the 0.1 ns time scale. Molecular forces appeared to be adapted to permit conformational fluctuations with a root mean square displacement close to 1.2 Å at the corresponding average body temperature of the endotherms. Strong forces within crocodile Hb maintain the amplitudes of motion within a narrow limit over the entire temperature range in which the animal lives. In fully hydrated powder samples of human and chicken, Hb mean square displacements and effective force constants on the 1 ns time scale showed no differences over the whole temperature range from 10 to 300 K, in contrast to the solution case. A complementary result of the study, therefore, is that one hydration layer is not sufficient to activate all conformational fluctuations of Hb in the pico- to nanosecond time scale which might be relevant for biological function. Coarse-grained Brownian dynamics simulations permitted to explore residue-specific effects. They indicated that temperature sensing of human and chicken Hb occurs mainly at residues lining internal cavities in the β-subunits.
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Affiliation(s)
- A M Stadler
- Institute for Complex Systems (ICS-5: Molecular Biophysics), Forschungszentrum Jülich, Jülich, Germany.
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37
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Lima TA, Sato ET, Martins ET, Homem-de-Mello P, Lago AF, Coutinho-Neto MD, Ferreira FF, Giles C, Pires MOC, Martinho H. Anharmonic transitions in nearly dry L-cysteine I. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:195104. [PMID: 22499214 DOI: 10.1088/0953-8984/24/19/195104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Two special dynamical transitions of universal character have recently been observed in macromolecules (lysozyme, myoglobin, bacteriorhodopsin, DNA and RNA) at T* ~100-150 K and T(D) ~180-220 K. The underlying mechanisms governing these transitions have been the subject of debate. In the present work, a survey is reported on the temperature dependence of structural, vibrational and thermodynamical properties of a nearly anhydrous amino acid (orthorhombic polymorph of the amino acid l-cysteine at a hydration level of 3.5%). The temperature dependence of x-ray powder diffraction patterns, Raman spectra and specific heat revealed these two transitions at T* = 70 K and T(D) = 230 K for this sample. The data were analyzed considering amino acid-amino acid, amino acid-water, water-water phonon-phonon interactions and molecular rotor activation. Our results indicated that the two referred temperatures define the triggering of very simple and particular events that govern all the interactions of the biomolecular: activation of CH(2) rigid rotors (T < T* ), phonon-phonon interactions between specific amino acid and water dimer vibrational modes (T* < T < T(D)), and water rotational barriers surpassing (T > T(D)).
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Affiliation(s)
- T A Lima
- Centro de Ciências Naturais e Humanas, UFABC, Rua Santa Adélia 166, Santo André, São Paulo, Brazil
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38
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Role of methyl groups in dynamics and evolution of biomolecules. J Biol Phys 2012; 38:497-505. [PMID: 23729910 DOI: 10.1007/s10867-012-9268-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 03/19/2012] [Indexed: 10/28/2022] Open
Abstract
Recent studies have discovered strong differences between the dynamics of nucleic acids (RNA and DNA) and proteins, especially at low hydration and low temperatures. This difference is caused primarily by dynamics of methyl groups that are abundant in proteins, but are absent or very rare in RNA and DNA. In this paper, we present a hypothesis regarding the role of methyl groups as intrinsic plasticizers in proteins and their evolutionary selection to facilitate protein dynamics and activity. We demonstrate the profound effect methyl groups have on protein dynamics relative to nucleic acid dynamics, and note the apparent correlation of methyl group content in protein classes and their need for molecular flexibility. Moreover, we note the fastest methyl groups of some enzymes appear around dynamical centers such as hinges or active sites. Methyl groups are also of tremendous importance from a hydrophobicity/folding/entropy perspective. These significant roles, however, complement our hypothesis rather than preclude the recognition of methyl groups in the dynamics and evolution of biomolecules.Electronic supplementary material The online version of this article (doi:10.1007/s10867-012-9268-6) contains supplementary material, which is available to authorized users.
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39
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Yi Z, Miao Y, Baudry J, Jain N, Smith JC. Derivation of mean-square displacements for protein dynamics from elastic incoherent neutron scattering. J Phys Chem B 2012; 116:5028-36. [PMID: 22471396 DOI: 10.1021/jp2102868] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The derivation of mean-square displacements from elastic incoherent neutron scattering (EINS) of proteins is examined, with the aid of experiments on camphor-bound cytochrome P450cam and complementary molecular dynamics simulations. It is shown that a q(4) correction to the elastic incoherent structure factor (where q is the scattering vector) can be simply used to reliably estimate from the experiment both the average mean-square atomic displacement, <Δr(2)> of the nonexchanged hydrogen atoms in the protein and its variance, σ(2). The molecular dynamics simulation results are in broad agreement with the experimentally derived <Δr(2)> and σ(2) derived from EINS on instruments at two different energy resolutions, corresponding to dynamics on the ∼100 ps and ∼1 ns time scales. Significant dynamical heterogeneity is found to arise from methyl-group rotations. The easy-to-apply q(4) correction extends the information extracted from elastic incoherent neutron scattering experiments and should be of wide applicability.
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Affiliation(s)
- Zheng Yi
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics , P.O. Box 2008, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
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40
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Combet S, Zanotti JM. Further evidence that interfacial water is the main "driving force" of protein dynamics: a neutron scattering study on perdeuterated C-phycocyanin. Phys Chem Chem Phys 2012; 14:4927-34. [PMID: 22388956 DOI: 10.1039/c2cp23725c] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fundamental role of hydration water (also called interfacial water) is widely recognized in protein flexibility, especially in the existence of the so-called protein "dynamical transition" at around 220 K. In the present study, we take advantage of perdeuterated C-phycocyanin (CPC) and elastic incoherent neutron scattering (EINS) to distinguish between protein dynamics and interfacial water dynamics. Powders of hydrogenated (hCPC) and perdeuterated (dCPC) CPC protein have been hydrated, respectively, with D(2)O or H(2)O and measured by EINS to separately probe protein dynamics (hCPC/D(2)O) and water dynamics (dCPC/H(2)O) at different time- and length-scales. We find that "fast" (<20 ps) local mean-square displacements (MSD) of both protein and interfacial water coincide all along the temperature range, with the same dynamical transition temperature at ~220 K. On higher resolution (<400 ps), two different types of motions can be separated: (i) localized motions with the same amplitude for CPC and hydration water and two transitions at ~170 and ~240 K for both; (ii) large scale fluctuations exhibiting for both water molecules and CPC protein a single transition at ~240 K, with a significantly higher amplitude for the interfacial water than for CPC. Moreover, by comparing these motions with bulk water MSD measured under the same conditions, we show no coupling between bulk water dynamics and protein dynamics all along the temperature range. These results show that interfacial water is the main "driving force" governing both local and large scale motions in proteins.
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Affiliation(s)
- Sophie Combet
- Laboratoire Léon-Brillouin, UMR 12 CEA/CNRS, bât. 563, CEA-Saclay, F-91191 Gif-sur-Yvette, France.
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41
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Li H, Barsan MM, Butler IS. Low-temperature (293-60 K) Raman spectra of the crystalline tert-butylisocyanide complexes, Cr(CO) 5(CNBu- t) and cis-Cr(CO) 4(CNBu- t) 2. CAN J CHEM 2012. [DOI: 10.1139/v11-125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Low-temperature (293–60 K) Raman spectra have been recorded in the 3500–50 cm–1 region for the crystalline tert-butylisocyanide (CNBu-t) complexes, Cr(CO)5(CNBu-t) (I) and cis-Cr(CO)4(CNBu-t)2 (II). Several of the factor group splittings that are predicted for the νCO, νCN, νCrC, νCrCN and δCrCO modes on the basis of the P21/a (C2h5) (I) and Pccn (D2h10) (II) crystallographic symmetries can be detected at very low temperatures. No phase transitions are observed for either complex throughout the temperature range investigated.
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Affiliation(s)
- Honqi Li
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 2K6, Canada
| | - Mirela M. Barsan
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 2K6, Canada
| | - Ian S. Butler
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 2K6, Canada
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42
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Marcos E, Mestres P, Crehuet R. Crowding induces differences in the diffusion of thermophilic and mesophilic proteins: a new look at neutron scattering results. Biophys J 2011; 101:2782-9. [PMID: 22261067 PMCID: PMC3297780 DOI: 10.1016/j.bpj.2011.09.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 09/20/2011] [Accepted: 09/23/2011] [Indexed: 10/14/2022] Open
Abstract
The dynamical basis underlying the increased thermal stability of thermophilic proteins remains uncertain. Here, we challenge the new paradigm established by neutron scattering experiments in solution, in which the adaptation of thermophilic proteins to high temperatures lies in the lower sensitivity of their flexibility to temperature changes. By means of a combination of molecular dynamics and Brownian dynamics simulations, we report a reinterpretation of those experiments and show evidence that under crowding conditions, such as in vivo, thermophilic and homolog mesophilic proteins have diffusional properties with different thermal behavior.
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Affiliation(s)
| | | | - Ramon Crehuet
- Department of Biological Chemistry and Molecular Modeling, Institute of Advanced Chemistry of Catalonia (IQAC – CSIC), Barcelona, Spain
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43
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Borreguero JM, He J, Meilleur F, Weiss KL, Brown CM, Myles DA, Herwig KW, Agarwal PK. Redox-promoting protein motions in rubredoxin. J Phys Chem B 2011; 115:8925-36. [PMID: 21608980 DOI: 10.1021/jp201346x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteins are dynamic objects, constantly undergoing conformational fluctuations, yet the linkage between internal protein motion and function is widely debated. This study reports on the characterization of temperature-activated collective and individual atomic motions of oxidized rubredoxin, a small 53 residue protein from thermophilic Pyrococcus furiosus (RdPf). Computational modeling allows detailed investigations of protein motions as a function of temperature, and neutron scattering experiments are used to compare to computational results. Just above the dynamical transition temperature which marks the onset of significant anharmonic motions of the protein, the computational simulations show both a significant reorientation of the average electrostatic force experienced by the coordinated Fe(3+) ion and a dramatic rise in its strength. At higher temperatures, additional anharmonic modes become activated and dominate the electrostatic fluctuations experienced by the ion. At 360 K, close to the optimal growth temperature of P. furiosus, simulations show that three anharmonic modes including motions of two conserved residues located at the protein active site (Ile7 and Ile40) give rise to the majority of the electrostatic fluctuations experienced by the Fe(3+) ion. The motions of these residues undergo displacements which may facilitate solvent access to the ion.
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Affiliation(s)
- Jose M Borreguero
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States.
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44
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Vugmeyster L, Ostrovsky D, Moses M, Ford JJ, Lipton AS, Hoatson GL, Vold RL. Comparative dynamics of leucine methyl groups in FMOC-leucine and in a protein hydrophobic core probed by solid-state deuteron nuclear magnetic resonance over 7-324 K temperature range. J Phys Chem B 2010; 114:15799-807. [PMID: 21077644 DOI: 10.1021/jp1082467] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quantitative dynamics of methyl groups in 9-fluorenylmethyloxycarbonyl-leucine (FMOC-leu) have been analyzed and compared with earlier studies of methyl dynamics in chicken villin headpiece subdomain protein (HP36) labeled at L69, a key hydrophobic core position. A combination of deuteron solid-state nuclear magnetic resonance experiments over the temperature range of 7-324 K and computational modeling indicated that while the two compounds show the same modes of motions, there are marked differences in the best-fit parameters of these motions. One of the main results is that the crossover observed in the dynamics of the methyl groups in the HP36 sample at 170 K is absent in FMOC-leu. A second crossover at around 95-88 K is present in both samples. The differences in the behavior of the two compounds suggest that some of the features of methyl dynamics reflect the complexity of the protein hydrophobic core and are not determined solely by local interactions.
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45
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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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