1
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Misuraca L, Demé B, Oger P, Peters J. Alkanes increase the stability of early life membrane models under extreme pressure and temperature conditions. Commun Chem 2021; 4:24. [PMID: 36697785 PMCID: PMC9814696 DOI: 10.1038/s42004-021-00467-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/14/2021] [Indexed: 01/31/2023] Open
Abstract
Terrestrial life appeared on our planet within a time window of [4.4-3.5] billion years ago. During that time, it is suggested that the first proto-cellular forms developed in the surrounding of deep-sea hydrothermal vents, oceanic crust fractures that are still present nowadays. However, these environments are characterized by extreme temperature and pressure conditions that question the early membrane compartment's capability to endure a stable structural state. Recent studies proposed an adaptive strategy employed by present-day extremophiles: the use of apolar molecules as structural membrane components in order to tune the bilayer dynamic response when needed. Here we extend this hypothesis on early life protomembrane models, using linear and branched alkanes as apolar stabilizing molecules of prebiotic relevance. The structural ordering and chain dynamics of these systems have been investigated as a function of temperature and pressure. We found that both types of alkanes studied, even the simplest linear ones, impact highly the multilamellar vesicle ordering and chain dynamics. Our data show that alkane-enriched membranes have a lower multilamellar vesicle swelling induced by the temperature increase and are significantly less affected by pressure variation as compared to alkane-free samples, suggesting a possible survival strategy for the first living forms.
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Affiliation(s)
- Loreto Misuraca
- grid.4444.00000 0001 2112 9282Univ. Grenoble Alpes, CNRS, LIPhy, Grenoble, France ,grid.156520.50000 0004 0647 2236Institut Laue - Langevin, Grenoble, France
| | - Bruno Demé
- grid.156520.50000 0004 0647 2236Institut Laue - Langevin, Grenoble, France
| | - Philippe Oger
- grid.7849.20000 0001 2150 7757Univ Lyon, INSA Lyon, CNRS UMR5240, Villeurbanne, France
| | - Judith Peters
- grid.4444.00000 0001 2112 9282Univ. Grenoble Alpes, CNRS, LIPhy, Grenoble, France ,grid.156520.50000 0004 0647 2236Institut Laue - Langevin, Grenoble, France
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2
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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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3
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Dynamical properties of myoglobin in an ultraviscous water-glycerol solvent investigated with elastic neutron scattering and FTIR spectroscopy. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.07.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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4
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Saarman NP, Kober KM, Simison WB, Pogson GH. Sequence-Based Analysis of Thermal Adaptation and Protein Energy Landscapes in an Invasive Blue Mussel (Mytilus galloprovincialis). Genome Biol Evol 2018; 9:2739-2751. [PMID: 28985307 PMCID: PMC5647807 DOI: 10.1093/gbe/evx190] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2017] [Indexed: 12/12/2022] Open
Abstract
Adaptive responses to thermal stress in poikilotherms plays an important role in determining competitive ability and species distributions. Amino acid substitutions that affect protein stability and modify the thermal optima of orthologous proteins may be particularly important in this context. Here, we examine a set of 2,770 protein-coding genes to determine if proteins in a highly invasive heat tolerant blue mussel (Mytilus galloprovincialis) contain signals of adaptive increases in protein stability relative to orthologs in a more cold tolerant M. trossulus. Such thermal adaptations might help to explain, mechanistically, the success with which the invasive marine mussel M. galloprovincialis has displaced native species in contact zones in the eastern (California) and western (Japan) Pacific. We tested for stabilizing amino acid substitutions in warm tolerant M. galloprovincialis relative to cold tolerant M. trossulus with a generalized linear model that compares in silico estimates of recent changes in protein stability among closely related congeners. Fixed substitutions in M. galloprovincialis were 3,180.0 calories per mol per substitution more stabilizing at genes with both elevated dN/dS ratios and transcriptional responses to heat stress, and 705.8 calories per mol per substitution more stabilizing across all 2,770 loci investigated. Amino acid substitutions concentrated in a small number of genes were more stabilizing in M. galloprovincialis compared with cold tolerant M. trossulus. We also tested for, but did not find, enrichment of a priori GO terms in genes with elevated dN/dS ratios in M. galloprovincialis. This might indicate that selection for thermodynamic stability is generic across all lineages, and suggests that the high change in estimated protein stability that we observed in M. galloprovincialis is driven by selection for extra stabilizing substitutions, rather than by higher incidence of selection in a greater number of genes in this lineage. Nonetheless, our finding of more stabilizing amino acid changes in the warm adapted lineage is important because it suggests that adaption for thermal stability has contributed to M. galloprovincialis’ superior tolerance to heat stress, and that pairing tests for positive selection and tests for transcriptional response to heat stress can identify candidates of protein stability adaptation.
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Affiliation(s)
- Norah P Saarman
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz.,Department of Ecology and Evolutionary Biology, Yale University
| | - Kord M Kober
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz.,Department of Physiological Nursing, University of California, San Francisco.,Institute for Computational Health Sciences, University of California, San Francisco
| | - W Brian Simison
- Center for Comparative Genomics, California Academy of Sciences, San Francisco, California
| | - Grant H Pogson
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz
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5
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Cinar S, Al-Ayoubi S, Sternemann C, Peters J, Winter R, Czeslik C. A high pressure study of calmodulin-ligand interactions using small-angle X-ray and elastic incoherent neutron scattering. Phys Chem Chem Phys 2018; 20:3514-3522. [PMID: 29336441 DOI: 10.1039/c7cp07399b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Calmodulin (CaM) is a Ca2+ sensor and mediates Ca2+ signaling through binding of numerous target ligands. The binding of ligands by Ca2+-saturated CaM (holo-CaM) is governed by attractive hydrophobic and electrostatic interactions that are weakened under high pressure in aqueous solutions. Moreover, the potential formation of void volumes upon ligand binding creates a further source of pressure sensitivity. Hence, high pressure is a suitable thermodynamic variable to probe protein-ligand interactions. In this study, we compare the binding of two different ligands to holo-CaM as a function of pressure by using X-ray and neutron scattering techniques. The two ligands are the farnesylated hypervariable region (HVR) of the K-Ras4B protein, which is a natural binding partner of holo-CaM, and the antagonist trifluoperazine (TFP), which is known to inhibit holo-CaM activity. From small-angle X-ray scattering experiments performed up to 3000 bar, we observe a pressure-induced partial unfolding of the free holo-CaM in the absence of ligands, where the two lobes of the dumbbell-shaped protein are slightly swelled. In contrast, upon binding TFP, holo-CaM forms a closed globular conformation, which is pressure stable at least up to 3000 bar. The HVR of K-Ras4B shows a different binding behavior, and the data suggest the dissociation of the holo-CaM/HVR complex under high pressure, probably due to a less dense protein contact of the HVR as compared to TFP. The elastic incoherent neutron scattering experiments corroborate these findings. Below 2000 bar, pressure induces enhanced atomic fluctuations in both holo-CaM/ligand complexes, but those of the holo-CaM/HVR complex seem to be larger. Thus, the inhibition of holo-CaM by TFP is supported by a low-volume ligand binding, albeit this is not associated with a rigidification of the complex structure on the sub-ns Å-scale.
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Affiliation(s)
- Süleyman Cinar
- Department of Chemistry and Chemical Biology, TU Dortmund University, D-44221 Dortmund, Germany.
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6
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Abstract
Protein dynamics is characterized by fluctuations among different conformational substates, i.e. the different minima of their energy landscape. At temperatures above ~200 K, these fluctuations lead to a steep increase in the thermal dependence of all dynamical properties, phenomenon known as Protein Dynamical Transition. In spite of the intense studies, little is known about the effects of pressure on these processes, investigated mostly near room temperature. We studied by neutron scattering the dynamics of myoglobin in a wide temperature and pressure range. Our results show that high pressure reduces protein motions, but does not affect the onset temperature for the Protein Dynamical Transition, indicating that the energy differences and barriers among conformational substates do not change with pressure. Instead, high pressure values strongly reduce the average structural differences between the accessible conformational substates, thus increasing the roughness of the free energy landscape of the system.
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7
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Aoun B, Pellegrini E, Trapp M, Natali F, Cantù L, Brocca P, Gerelli Y, Demé B, Marek Koza M, Johnson M, Peters J. Direct comparison of elastic incoherent neutron scattering experiments with molecular dynamics simulations of DMPC phase transitions. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2016; 39:48. [PMID: 27112937 DOI: 10.1140/epje/i2016-16048-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 03/24/2016] [Indexed: 06/05/2023]
Abstract
Neutron scattering techniques have been employed to investigate 1,2-dimyristoyl-sn -glycero-3-phosphocholine (DMPC) membranes in the form of multilamellar vesicles (MLVs) and deposited, stacked multilamellar-bilayers (MLBs), covering transitions from the gel to the liquid phase. Neutron diffraction was used to characterise the samples in terms of transition temperatures, whereas elastic incoherent neutron scattering (EINS) demonstrates that the dynamics on the sub-macromolecular length-scale and pico- to nano-second time-scale are correlated with the structural transitions through a discontinuity in the observed elastic intensities and the derived mean square displacements. Molecular dynamics simulations have been performed in parallel focussing on the length-, time- and temperature-scales of the neutron experiments. They correctly reproduce the structural features of the main gel-liquid phase transition. Particular emphasis is placed on the dynamical amplitudes derived from experiment and simulations. Two methods are used to analyse the experimental data and mean square displacements. They agree within a factor of 2 irrespective of the probed time-scale, i.e. the instrument utilized. Mean square displacements computed from simulations show a comparable level of agreement with the experimental values, albeit, the best match with the two methods varies for the two instruments. Consequently, experiments and simulations together give a consistent picture of the structural and dynamical aspects of the main lipid transition and provide a basis for future, theoretical modelling of dynamics and phase behaviour in membranes. The need for more detailed analytical models is pointed out by the remaining variation of the dynamical amplitudes derived in two different ways from experiments on the one hand and simulations on the other.
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Affiliation(s)
- Bachir Aoun
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
| | - Eric Pellegrini
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
| | - Marcus Trapp
- Angewandte Physikalische Chemie, Universität Heidelberg, Im Neuenheimer Feld 253, 69120, Heidelberg, Germany
- Helmholtz-Zentrum Berlin für Materialien und Energie, Lise-Meitner Campus, Hahn-Meitner-Platz 1, 14109, Berlin, Germany
| | - Francesca Natali
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
- CNR-IOM-OGG, c/o Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
| | - Laura Cantù
- University of Milan, via F. lli Cervi 93, 20090, Segrate, Italy
| | - Paola Brocca
- University of Milan, via F. lli Cervi 93, 20090, Segrate, Italy
| | - Yuri Gerelli
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
| | - Bruno Demé
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
| | - Michael Marek Koza
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
| | - Mark Johnson
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
| | - Judith Peters
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France.
- LiPhy, UFR PhITEM, Univ. Grenoble Alpes, 71 avenue des Martyrs, CS 10090, 38044, Grenoble, France.
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8
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Effects of pressure on the dynamics of an oligomeric protein from deep-sea hyperthermophile. Proc Natl Acad Sci U S A 2015; 112:13886-91. [PMID: 26504206 DOI: 10.1073/pnas.1514478112] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Inorganic pyrophosphatase (IPPase) from Thermococcus thioreducens is a large oligomeric protein derived from a hyperthermophilic microorganism that is found near hydrothermal vents deep under the sea, where the pressure is up to 100 MPa (1 kbar). It has attracted great interest in biophysical research because of its high activity under extreme conditions in the seabed. In this study, we use the quasielastic neutron scattering (QENS) technique to investigate the effects of pressure on the conformational flexibility and relaxation dynamics of IPPase over a wide temperature range. The β-relaxation dynamics of proteins was studied in the time ranges from 2 to 25 ps, and from 100 ps to 2 ns, using two spectrometers. Our results indicate that, under a pressure of 100 MPa, close to that of the native environment deep under the sea, IPPase displays much faster relaxation dynamics than a mesophilic model protein, hen egg white lysozyme (HEWL), at all measured temperatures, opposite to what we observed previously under ambient pressure. This contradictory observation provides evidence that the protein energy landscape is distorted by high pressure, which is significantly different for hyperthermophilic (IPPase) and mesophilic (HEWL) proteins. We further derive from our observations a schematic denaturation phase diagram together with energy landscapes for the two very different proteins, which can be used as a general picture to understand the dynamical properties of thermophilic proteins under pressure.
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9
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Erlkamp M, Marion J, Martinez N, Czeslik C, Peters J, Winter R. Influence of Pressure and Crowding on the Sub-Nanosecond Dynamics of Globular Proteins. J Phys Chem B 2015; 119:4842-8. [DOI: 10.1021/acs.jpcb.5b01017] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- M. Erlkamp
- Physical
Chemistry I − Biophysical Chemistry, Department of Chemistry and Chemical
Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - J. Marion
- Université
Grenoble Alpes, IBS, 71 avenue des
Martyrs, CS 10090, 38044 Grenoble, France
- Institut Laue-Langevin, 71 avenue
des Martyrs, CS 20156, 38042 CEDEX 9 Grenoble, France
| | - N. Martinez
- Université
Grenoble Alpes, IBS, 71 avenue des
Martyrs, CS 10090, 38044 Grenoble, France
- Institut Laue-Langevin, 71 avenue
des Martyrs, CS 20156, 38042 CEDEX 9 Grenoble, France
| | - C. Czeslik
- Physical
Chemistry I − Biophysical Chemistry, Department of Chemistry and Chemical
Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - J. Peters
- Université
Grenoble Alpes, IBS, 71 avenue des
Martyrs, CS 10090, 38044 Grenoble, France
- Institut Laue-Langevin, 71 avenue
des Martyrs, CS 20156, 38042 CEDEX 9 Grenoble, France
| | - R. Winter
- Physical
Chemistry I − Biophysical Chemistry, Department of Chemistry and Chemical
Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
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10
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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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11
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Trapp M, Trovaslet M, Nachon F, Koza MM, van Eijck L, Hill F, Weik M, Masson P, Tehei M, Peters J. Energy Landscapes of Human Acetylcholinesterase and Its Huperzine A-Inhibited Counterpart. J Phys Chem B 2012. [DOI: 10.1021/jp304704h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marcus Trapp
- Comissariat
à l’Energie
Atomique, Institut de Biologie Structurale, F-38054 Grenoble, France
- Centre National De La Recherche Scientifique, UMR5075, F-38027 Grenoble,
France
- Université Joseph Fourier, UFR PhITEM, F-38041 Grenoble Cédex
9, France
- Institut Laue Langevin, F-38042 Grenoble Cédex
9, France
| | - Marie Trovaslet
- Institut de Recherche Biomédicale des Armées, F-38700 La Tronche,
France
| | - Florian Nachon
- Institut de Recherche Biomédicale des Armées, F-38700 La Tronche,
France
| | - Marek M. Koza
- Institut Laue Langevin, F-38042 Grenoble Cédex
9, France
| | - Lambert van Eijck
- Delft University of Technology, Faculty of Applied Sciences, RST/NPM2
Mekelweg 15, 2629JB Delft Netherlands
| | - Flynn Hill
- School of Chemistry and
Centre for
Medical Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Martin Weik
- Comissariat
à l’Energie
Atomique, Institut de Biologie Structurale, F-38054 Grenoble, France
- Centre National De La Recherche Scientifique, UMR5075, F-38027 Grenoble,
France
- Université Joseph Fourier, UFR PhITEM, F-38041 Grenoble Cédex
9, France
| | - Patrick Masson
- Comissariat
à l’Energie
Atomique, Institut de Biologie Structurale, F-38054 Grenoble, France
- Centre National De La Recherche Scientifique, UMR5075, F-38027 Grenoble,
France
- Université Joseph Fourier, UFR PhITEM, F-38041 Grenoble Cédex
9, France
- Institut de Recherche Biomédicale des Armées, F-38700 La Tronche,
France
| | - Moeava Tehei
- School of Chemistry and
Centre for
Medical Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
- Australian Institute of Nuclear Science and Engineering (AINSE), Menai, NSW,
Australia
| | - Judith Peters
- Comissariat
à l’Energie
Atomique, Institut de Biologie Structurale, F-38054 Grenoble, France
- Centre National De La Recherche Scientifique, UMR5075, F-38027 Grenoble,
France
- Université Joseph Fourier, UFR PhITEM, F-38041 Grenoble Cédex
9, France
- Institut Laue Langevin, F-38042 Grenoble Cédex
9, France
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13
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Tatke SS, Loong CK, D'Souza N, Schoephoerster RT, Prabhakaran M. Large scale motions in a biosensor protein glucose oxidase: a combined approach by QENS, normal mode analysis, and molecular dynamics studies. Biopolymers 2008; 89:582-94. [PMID: 18273893 DOI: 10.1002/bip.20956] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The characteristics of the glucose oxidase were studied using a combination of experimental and theoretical techniques. Quasi elastic neutron scattering experiments were used to obtain the vibrational frequencies of the protein. These were compared to theoretical results obtained by normal mode analysis. Results indicate a good match between the experimental and theoretical values. Molecular dynamic simulation with covariant analysis was used to study the structure and dynamics of glucose oxidase. Various parameters like the radius of gyration, root mean square fluctuations, solvent accessibility were studied for evaluating the structural stability of the protein. The frequency of vibration calculated from the three methods is used to derive the large scale motions. Theses studies were used to predict the suitable lysine residues for linkage with carbon nanotubes.
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Affiliation(s)
- Sujit S Tatke
- Biomedical Engineering Department, FL International University, Miami, FL, USA
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14
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Jasnin M, Tehei M, Moulin M, Haertlein M, Zaccai G. Solvent isotope effect on macromolecular dynamics in E. coli. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 37:613-7. [DOI: 10.1007/s00249-008-0281-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Revised: 12/20/2007] [Accepted: 01/30/2008] [Indexed: 10/22/2022]
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15
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Doster W. The dynamical transition of proteins, concepts and misconceptions. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 37:591-602. [PMID: 18270694 DOI: 10.1007/s00249-008-0274-3] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2007] [Revised: 01/10/2008] [Accepted: 01/17/2008] [Indexed: 10/22/2022]
Abstract
The dynamics of hydrated proteins and of protein crystals can be studied within a wide temperature range, since the water of hydration does not crystallize at low temperature. Instead it turns into an amorphous glassy state below 200 K. Extending the temperature range facilitates the spectral separation of different molecular processes. The conformational motions of proteins show an abrupt enhancement near 180 K, which has been called a "dynamical transition". In this contribution various aspects of the transition are critically reviewed: the role of the instrumental resolution function in extracting displacements from neutron elastic scattering data and the question of the appropriate dynamic model, discrete transitions between states of different energy versus continuous diffusion inside a harmonic well, are discussed. A decomposition of the transition involving two motional components is performed: rotational transitions of methyl groups and small scale librations of side-chains, induced by water at the protein surface. Both processes create an enhancement of the observed amplitude. The onset occurs, when their time scale becomes compatible with the resolution of the spectrometer. The reorientational rate of hydration water follows a super-Arrhenius temperature dependence, a characteristic feature of a dynamical transition. It occurs only with hydrated proteins, while the torsional motion of methyl groups takes place also in the dehydrated or solvent-vitrified system. Finally, the role of fast hydrogen bond fluctuations contributing to the amplitude enhancement is discussed.
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Affiliation(s)
- Wolfgang Doster
- Physics Department E13, Technical University Munich, 85748 Garching, Germany.
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16
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Hilmer JK, Zlotnick A, Bothner B. Conformational equilibria and rates of localized motion within hepatitis B virus capsids. J Mol Biol 2007; 375:581-94. [PMID: 18022640 DOI: 10.1016/j.jmb.2007.10.044] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2007] [Revised: 10/08/2007] [Accepted: 10/09/2007] [Indexed: 10/22/2022]
Abstract
Functional analysis of hepatitis B virus (HBV) core particles has associated a number of biological roles with the C terminus of the capsid protein. One set of functions require the C terminus to be on the exterior of the capsid, while others place this domain on the interior. According to the crystal structure of the capsid, this segment is strictly internal to the capsid shell and buried at a protein-protein interface. Using kinetic hydrolysis, a form of protease digestion assayed by SDS-PAGE and mass spectrometry, the structurally and biologically important C-terminal region of HBV capsid protein assembly domain (Cp149, residues 1-149) has been shown to be dynamic in both dimer and capsid forms. HBV is an enveloped virus with a T=4 icosahedral core that is composed of 120 copies of a homodimer capsid protein. Free dimer and assembled capsid forms of the protein are readily hydrolyzed by trypsin and thermolysin, around residues 127-128, indicating that this region is dynamic and exposed to the capsid surface. The measured conformational equilibria have an opposite temperature dependence between free dimer and assembled capsid. This work helps to explain the previously described allosteric regulation of assembly and functional properties of a buried domain. These observations make a critical connection between structure, dynamics, and function: made possible by the first quantitative measurements of conformational equilibria and rates of conversion between protein conformers for a megaDalton complex.
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Affiliation(s)
- Jonathan K Hilmer
- Montana State University, Department of Chemistry and Biochemistry, Chemistry and Biochemistry Building, Bozeman, MT 59717, USA
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17
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Abstract
Work on the relationship between hyperthermophile protein dynamics, stability and activity is reviewed. Neutron spectroscopy has been applied to measure and compare the macromolecular dynamics of various hyperthermophilic and mesophilic proteins, under different conditions. First, molecular dynamics have been analyzed for the hyperthermophile malate dehydrogenase from Methanococcus jannaschii and a mesophilic homologue, the lactate dehydrogenase from Oryctolagus cunniculus (rabbit) muscle. The neutron scattering approach has provided independent measurements of the global flexibility and structural resilience of each protein, and it has been demonstrated that macromolecular dynamics represents one of the molecular mechanisms of thermoadaptation. The resilience was found to be higher for the hyperthermophilic protein, thus ensuring similar flexibilities in both enzymes at their optimal activity temperature. Second, the neutron method has been developed to quantify the average macromolecular flexibility and resilience within the natural crowded environment of the cell, and mean macromolecular motions have been measured in vivo in psychrophile, mesophile, thermophile and hyperthermophile bacteria. The macromolecular resilience in bacteria was found to increase with adaptation to high temperatures, whereas flexibility was maintained within narrow limits, independent of physiological temperature for all cells in their active state. Third, macromolecular motions have been measured in free and immobilized dihydrofolate reductase from Escherichia coli. The immobilized mesophilic enzyme has increased stability and decreased activity, so that its properties are changed to resemble those of a thermophilic enzyme. Quasi-elastic neutron scattering measurements have also been performed to probe the protein motions. Compared to the free enzyme, the average height of the activation free energy barrier to local motions was found to be increased by 0.54 kcal.mol(-1) in the immobilized dihydrofolate reductase, a value that is of the same order as expected from the theoretical rate equation.
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