101
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Analysis of Water and Hydrogen Bond Dynamics at the Surface of an Antifreeze Protein. ACTA ACUST UNITED AC 2012. [DOI: 10.1155/2012/125071] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We examine dynamics of water molecules and hydrogen bonds at the water-protein interface of the wild-type antifreeze protein from spruce budworm Choristoneura fumiferana and a mutant that is not antifreeze active by all-atom molecular dynamics simulations. Water dynamics in the hydration layer around the protein is analyzed by calculation of velocity autocorrelation functions and their power spectra, and hydrogen bond time correlation functions are calculated for hydrogen bonds between water molecules and the protein. Both water and hydrogen bond dynamics from subpicosecond to hundred picosecond time scales are sensitive to location on the protein surface and appear correlated with protein function. In particular, hydrogen bond lifetimes are longest for water molecules hydrogen bonded to the ice-binding plane of the wild type, whereas hydrogen bond lifetimes between water and protein atoms on all three planes are similar for the mutant.
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102
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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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103
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104
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Segura JJ, Verdaguer A, Sacha GM, Fraxedas J. Dipolar origin of water etching of amino acid surfaces. Phys Chem Chem Phys 2011; 13:21446-50. [PMID: 22048449 DOI: 10.1039/c1cp22277e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The etching induced by water on hydrophobic (001) surfaces of enantiomeric L-, D- and racemic DL-valine crystals has been characterized by means of atomic force microscopy (AFM) at ambient conditions. Well-defined chiral parallelepipedic shallow patterns, one bilayer deep, are observed for the enantiomeric crystals with sides (steps) oriented along low index crystallographic directions. Hence, chirality can be readily identified by visual inspection of an AFM image after etching. The formation of such regular patterns can be rationalized using basic concepts of electrical dipolar interactions. The key factor that determines the relative etching rate for each step and thus defines the shape of the etching patterns is the orientation of the molecular dipoles with respect to the step edge. The simplicity of the approach allows the prediction of the effect of water etching on other amino acid crystals as well as the effect of the interaction of water with amino acid molecules forming part of more complex structures.
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Affiliation(s)
- J J Segura
- Centre d' Investigació en Nanociència i Nanotecnologia, Edifici CM-7, Campus UAB, Esfera UAB, E-08193 Bellaterra, Catalunya, Spain
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105
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Luong TQ, Verma PK, Mitra RK, Havenith M. Do hydration dynamics follow the structural perturbation during thermal denaturation of a protein: a terahertz absorption study. Biophys J 2011; 101:925-33. [PMID: 21843484 DOI: 10.1016/j.bpj.2011.05.011] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 03/26/2011] [Accepted: 05/03/2011] [Indexed: 01/28/2023] Open
Abstract
We investigate the thermal denaturation of human serum albumin and the associated solvation using terahertz (THz) spectroscopy in aqueous buffer solution. Far- and near-ultraviolet circular dichroism spectroscopy reveal that the protein undergoes a native (N) to extended (E) state transition at temperature ≤55°C with a marginal change in the secondary and tertiary structure. At 70°C, the protein transforms into an unfolded (U) state with significant irreversible disruption of its structures. We measure the concentration- and temperature-dependent THz absorption coefficient (α) of the protein solution using a p-Ge THz difference spectrometer (2.1-2.8 THz frequency range), thereby probing the collective protein-water network dynamics. When the solvated protein is heated up to 55°C and cooled down again, a reversible change in THz absorption is observed. When increasing the temperature up to 70°C, we find a dramatic irreversible change of THz absorption. The increase in THz absorption compared to bulk water is attributed to a blue shift in the spectrum of the solvated protein compared to bulk water. This is supported by measurements of THz absorption coefficients using THz time-domain spectroscopy (0.1-1.2 THz frequency range). We also use picosecond-resolved fluorescence spectroscopy of the tryptophan 214 moiety of human serum albumin. All experimental observations can be explained by a change in the hydration dynamics of the solvated protein due to the additional exposure of hydrophobic residues upon unfolding.
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Affiliation(s)
- Trung Quan Luong
- Department of Physical Chemistry II, Ruhr-University Bochum, Bochum, Germany
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106
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107
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Bhattacharjee N, Biswas P. Local order and mobility of water molecules around ambivalent helices. J Phys Chem B 2011; 115:12257-65. [PMID: 21916474 DOI: 10.1021/jp2066106] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Water on a protein surface plays a key role in determining the structure and dynamics of proteins. Compared to the properties of bulk water, many aspects of the structure and dynamics of the water surrounding the proteins are less understood. It is interesting therefore to explore how the properties of the water within the solvation shell around the peptide molecule depend on its specific secondary structure. In this work we investigate the orientational order and residence times of the water molecules to characterize the structure, energetics, and dynamics of the hydration shell water around ambivalent peptides. Ambivalent sequences are identical sequences which display multiple secondary structures in different proteins. Molecular dynamics simulations of representative proteins containing variable helix, variable nonhelix, and conserved helix are also used to explore the local structure and mobility of water molecules in their vicinity. The results, for the first time, depict a different water distribution pattern around the conserved and variable helices. The water molecules surrounding the helical segments in variable helices are found to possess a less locally ordered structure compared to those around their corresponding nonhelical counterparts and conserved helices. The long conserved helices exhibit extremely high local residence times compared to the helical conformations of the variable helices, whereas the residence times of the nonhelical conformations of the variable helices are comparable to those of the short conserved helices. This differential pattern of the structure and dynamics of water molecules in the vicinity of conserved/variable helices may lend valuable insights for understanding the role of solvent effects in determining sequence ambivalency and help in improving the accuracy of water models used in the simulations of proteins.
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108
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Bakulin AA, Pshenichnikov MS. Reduced coupling of water molecules near the surface of reverse micelles. Phys Chem Chem Phys 2011; 13:19355-61. [PMID: 21959913 DOI: 10.1039/c1cp22235j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report on vibrational dynamics of water near the surface of AOT reverse micelles studied by narrow-band excitation, mid-IR pump-probe spectroscopy. Evidence of OH-stretch frequency splitting into the symmetric and asymmetric modes is clearly observed for the interfacial H(2)O molecules. The polarization memory of interfacial waters is preserved over an exceptionally extended >10 ps timescale which is a factor of 100 longer than in bulk water. These observations point towards negligibly small intermolecular vibrational coupling between the water molecules as well as strongly reduced water rotational mobility within the interfacial water layer.
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Affiliation(s)
- Artem A Bakulin
- Department of Physical Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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109
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El Khoury Y, Hellwig P. A combined far-infrared spectroscopic and electrochemical approach for the study of iron-sulfur proteins. Chemphyschem 2011; 12:2669-74. [PMID: 21887734 DOI: 10.1002/cphc.201100165] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 06/15/2011] [Indexed: 11/11/2022]
Abstract
Herein, we present the development of a far-infrared spectroscopic approach for studying metalloenzyme active sites in a redox-dependent manner. An electrochemical cell with 5 mm path and based on silicon windows was found to be appropriate for the measurement of aqueous solutions down to 200 cm(-1) . The cell was probed with the infrared redox signature of the metal-ligand vibrations of different iron-sulfur proteins. Each Fe-S cluster type was found to show a specific spectral signature. As a common feature, a downshift of the frequency of the Fe-S vibrations was seen upon reduction, in line with the increase of the Fe-S bond. This downshift was found to be fully reversible. Electrochemically induced FTIR difference spectroscopy in the far infrared is now possible, opening new perspectives on the understanding of metalloproteins in function of the redox state.
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Affiliation(s)
- Youssef El Khoury
- Institut de Chimie, UMR, Laboratoire de spectroscopie vibrationnelle et électrochimie des biomolécules Université de Strasbourg, France
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110
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Laage D, Stirnemann G, Sterpone F, Rey R, Hynes JT. Reorientation and Allied Dynamics in Water and Aqueous Solutions. Annu Rev Phys Chem 2011; 62:395-416. [DOI: 10.1146/annurev.physchem.012809.103503] [Citation(s) in RCA: 271] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Damien Laage
- Department of Chemistry, Ecole Normale Supérieure, UMR ENS-CNRS-UPMC 8640, 75005 Paris, France;
| | - Guillaume Stirnemann
- Department of Chemistry, Ecole Normale Supérieure, UMR ENS-CNRS-UPMC 8640, 75005 Paris, France;
| | - Fabio Sterpone
- Department of Chemistry, Ecole Normale Supérieure, UMR ENS-CNRS-UPMC 8640, 75005 Paris, France;
| | - Rossend Rey
- Departament de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya, Barcelona 08034, Spain;
| | - James T. Hynes
- Department of Chemistry, Ecole Normale Supérieure, UMR ENS-CNRS-UPMC 8640, 75005 Paris, France;
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215;
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111
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Fleisher AJ, Young JW, Pratt DW, Cembran A, Gao J. Flickering dipoles in the gas phase: Structures, internal dynamics, and dipole moments of β-naphthol-H2O in its ground and excited electronic states. J Chem Phys 2011; 134:114304. [DOI: 10.1063/1.3562373] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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112
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Niehues G, Heyden M, Schmidt DA, Havenith M. Exploring hydrophobicity by THz absorption spectroscopy of solvated amino acids. Faraday Discuss 2011; 150:193-207; discussion 257-92. [DOI: 10.1039/c0fd00007h] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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113
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Yamaguchi S, Tominaga K, Saito S. Intermolecular vibrational mode of the benzoic acid dimer in solution observed by terahertz time-domain spectroscopy. Phys Chem Chem Phys 2011; 13:14742-9. [DOI: 10.1039/c1cp20912d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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114
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Ding T, Li R, Zeitler JA, Huber TL, Gladden LF, Middelberg APJ, Falconer RJ. Terahertz and far infrared spectroscopy of alanine-rich peptides having variable ellipticity. OPTICS EXPRESS 2010; 18:27431-44. [PMID: 21197019 DOI: 10.1364/oe.18.027431] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Terahertz spectra of four alanine-rich peptides with known secondary structures were studied by terahertz time domain spectroscopy (THz-TDS) and by Fourier transform infrared spectroscopy (FTIR) using a synchrotron light source and a liquid-helium cooled bolometer. At ambient temperatures the usable bandwidth was restricted to 0.2-1.5 THz by the absorbance of water. The existence of a solvation shell around the peptide in solution was observed and its size estimated to be between 11 and 17 Å. By cooling the peptide solution to 80 K in order to reduce the water absorbance the bandwidth was increased to 0.1-3.0 THz for both THz-TDS and FTIR. Spectra were consistent with monotonic absorbance of the peptide and the existence of a solid amorphous low density solvation shell.
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Affiliation(s)
- Tao Ding
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
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115
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Hielscher R, Friedrich T, Hellwig P. Far- and Mid-Infrared Spectroscopic Analysis of the Substrate-Induced Structural Dynamics of Respiratory Complex I. Chemphyschem 2010; 12:217-24. [DOI: 10.1002/cphc.201000688] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 10/22/2010] [Indexed: 11/07/2022]
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116
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Gnanasekaran R, Xu Y, Leitner DM. Dynamics of water clusters confined in proteins: a molecular dynamics simulation study of interfacial waters in a dimeric hemoglobin. J Phys Chem B 2010; 114:16989-96. [PMID: 21126033 DOI: 10.1021/jp109173t] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Water confined in proteins exhibits dynamics distinct from the dynamics of water in the bulk or near the surface of a biomolecule. We examine the water dynamics at the interface of the two globules of the homodimeric hemoglobin from Scapharca inaequivalvis (HbI) by molecular dynamics (MD) simulations, with focus on water-protein hydrogen bond lifetimes and rotational anisotropy of the interfacial waters. We find that relaxation of the waters at the interface of both deoxy- and oxy-HbI, which contain a cluster of 17 and 11 interfacial waters, respectively, is well described by stretched exponentials with exponents from 0.1 to 0.6 and relaxation times of tens to thousands of picoseconds. The interfacial water molecules of oxy-HbI exhibit slower rotational relaxation and hydrogen bond rearrangement than those of deoxy-HbI, consistent with an allosteric transition from unliganded to liganded conformers involving the expulsion of several water molecules from the interface. Though the interfacial waters are translationally and rotationally static on the picosecond time scale, they contribute to fast communication between the globules via vibrations. We find that the interfacial waters enhance vibrational energy transport across the interface by ≈10%.
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117
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Willenbring D, Xu Y, Tang P. The role of structured water in mediating general anesthetic action on alpha4beta2 nAChR. Phys Chem Chem Phys 2010; 12:10263-9. [PMID: 20661501 PMCID: PMC3265171 DOI: 10.1039/c003573d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Water is an essential component for many biological processes. Pauling proposed that water might play a critical role in general anesthesia by forming water clathrates around anesthetic molecules. To examine potential involvement of water in general anesthesia, we analyzed water within alpha4beta2 nAChR, a putative protein target hypersensitive to volatile anesthetics. Experimental structure-derived closed- and open-channel nAChR systems in a fully hydrated lipid bilayer were examined using all-atom molecular dynamics simulations. At the majority of binding sites in alpha4beta2 nAChR, halothane replaced the slow-exchanging water molecules and caused a regional water population decrease. Only two binding sites had an increased quantity of water in the presence of halothane, where water arrangements resemble clathrate-like structures. The small number of such clathrate-like water clusters suggests that the formation of water clathrates is unlikely to be a primary cause for anesthesia. Despite the decrease in water population at most of the halothane binding sites, the number of sites that can be occupied transiently by water is actually increased in the presence of halothane. Many of these water sites were located between two subunits or in regions containing agonist binding sites or critical structural elements for transducing agonist binding to channel gating. Changes in water sites in the presence of halothane affected water-mediated protein-protein interactions and the protein dynamics, which can have direct impact on protein function. Collectively, water contributes to the action of anesthetics in proteins by mediating interactions between protein subunits and altering protein dynamics, instead of forming water clathrates around anesthetics.
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Affiliation(s)
- Dan Willenbring
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Yan Xu
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Pei Tang
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
- Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
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118
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Kohn JE, Afonine PV, Ruscio JZ, Adams PD, Head-Gordon T. Evidence of functional protein dynamics from X-ray crystallographic ensembles. PLoS Comput Biol 2010; 6. [PMID: 20865158 PMCID: PMC2928775 DOI: 10.1371/journal.pcbi.1000911] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2010] [Accepted: 07/28/2010] [Indexed: 11/21/2022] Open
Abstract
It is widely recognized that representing a protein as a single static conformation is inadequate to describe the dynamics essential to the performance of its biological function. We contrast the amino acid displacements below and above the protein dynamical transition temperature, TD∼215K, of hen egg white lysozyme using X-ray crystallography ensembles that are analyzed by molecular dynamics simulations as a function of temperature. We show that measuring structural variations across an ensemble of X-ray derived models captures the activation of conformational states that are of functional importance just above TD, and they remain virtually identical to structural motions measured at 300K. Our results highlight the ability to observe functional structural variations across an ensemble of X-ray crystallographic data, and that residue fluctuations measured in MD simulations at room temperature are in quantitative agreement with the experimental observable. There is a well-recognized gap between the dynamical motions of proteins required to execute function and the experimental techniques capable of capturing that motion at the atomic level. We show that much experimental detail of dynamical motion is already present in X-ray crystallographic data, which arises from being solved by different research groups using different methodologies under different crystallization conditions, which then capture an ensemble of structures whose variations can be quantified on a residue-by-residue level using local density correlations. We contrast the amino acid displacements below and above the protein dynamical transition temperature, TD∼215K, of hen egg white lysozyme by comparing the X-ray ensemble to MD ensembles as a function of temperature. We show that measuring structural variations across an ensemble of X-ray derived models captures the activation of conformational states that are of functional importance just above TD and they remain virtually identical to structural motions measured at 300K. It provides a novel analysis of large X-ray ensemble data that is useful for the broader structural biology community.
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Affiliation(s)
- Jonathan E. Kohn
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
| | - Pavel V. Afonine
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Jory Z. Ruscio
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
| | - Paul D. Adams
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Teresa Head-Gordon
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail:
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119
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El Khoury Y, Trivella A, Gross J, Hellwig P. Probing the Hydrogen Bonding Structure in the Rieske Protein. Chemphyschem 2010; 11:3313-9. [DOI: 10.1002/cphc.201000331] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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120
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LeBard DN, Matyushov DV. Ferroelectric Hydration Shells around Proteins: Electrostatics of the Protein−Water Interface. J Phys Chem B 2010; 114:9246-58. [DOI: 10.1021/jp1006999] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- David N. LeBard
- Center for Biological Physics, Arizona State University, PO Box 871604, Tempe, Arizona 85287-1604
| | - Dmitry V. Matyushov
- Center for Biological Physics, Arizona State University, PO Box 871604, Tempe, Arizona 85287-1604
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121
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Heyden M, Havenith M. Combining THz spectroscopy and MD simulations to study protein-hydration coupling. Methods 2010; 52:74-83. [PMID: 20685393 DOI: 10.1016/j.ymeth.2010.05.007] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 05/17/2010] [Accepted: 05/20/2010] [Indexed: 10/19/2022] Open
Abstract
THz spectroscopy is combined with MD simulations to study the dynamical properties of water in the solvation shell of proteins. The solvation dynamics is found to be influenced on length-scales of several hydration layers which is significantly more than what is found for static properties. Our experiments show that the properties of this dynamical solvation shell depend on the folding state of the protein. Kinetic THz absorption studies allow us to observe the formation of the dynamical solvation shell of the native protein upon folding. The experimental results can be reproduced using MD simulations which helps to develop a molecular understanding in terms of retardation of water dynamics.
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Affiliation(s)
- Matthias Heyden
- Physikalische Chemie II, Ruhr-Universität Bochum, 44780 Bochum, Germany
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122
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123
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Agarwal M, Kushwaha HR, Chakravarty C. Local order, energy, and mobility of water molecules in the hydration shell of small peptides. J Phys Chem B 2010; 114:651-9. [PMID: 19863091 DOI: 10.1021/jp909090u] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The extent to which the presence of a biomolecular solute modifies the local energetics of water molecules, as measured by the tagged molecule potential energy (TPE), is examined using molecular dynamics simulations of the beta-hairpin of 2GB1 and the alpha-helix of deca-alanine in water. The CHARMM22 force field, in conjunction with the TIP3P solvent water model, is used for the peptides, with simulations of TIP3P and SPC/E water used as benchmarks for the behavior of bulk solvent. TIP3P water is shown to have significantly lower local tetrahedral order and higher binding energy than SPC/E at the same state point. The TIP3P and SPC/E water models show very similar dynamical correlations in the TPE fluctuations on frequency scales greater than 0.1 cm(-1). In addition, the two models show the same linear correlation between mean tetrahedral order and binding energy, suggesting that the relationship between choice of water models and simulated hydration behavior may involve a complex interplay of static and dynamic factors. The introduction of a peptide in water modifies the local TPE of water molecules as a function of distance from the biomolecular interface. There is an oscillatory variation in the TPE with distance from the peptide for water molecules lying outside a 3 A radius and extending to at least 10 A. These variations are of the order of 2-5% of the bulk TPE value and are anticorrelated with variations in local tetrahedral order in terms of locations of maxima and minima, which may be understood in terms of the relative contribution of van der Waals and Coulombic contributions to the TPE. The distance-dependent variations in local order and energetics are essentially the same for the beta-hairpin of 2GB1 as well as deca-alanine. Within a radius of 3 A, the perturbation of the solvent structure is very significant with local TPEs that are 10-15% lower than the bulk value. The chemical identity of side-chain residues and the secondary structure play an important role in determining residue-dependent variations in the TPEs. The variation in the residue-dependent tagged molecule potential energies is of the order of 3-5%, while the local residence times vary by a factor of approximately 5. The correlation of the local residence times with the local energetics within the innermost hydration layer is weak, though charged residues typically have low binding energies and large residence times.
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Affiliation(s)
- Manish Agarwal
- Department of Chemistry, Indian Institute of Technology-Delhi, New Delhi 110016, India
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124
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Sterpone F, Stirnemann G, Hynes JT, Laage D. Water Hydrogen-Bond Dynamics around Amino Acids: The Key Role of Hydrophilic Hydrogen-Bond Acceptor Groups. J Phys Chem B 2010; 114:2083-9. [DOI: 10.1021/jp9119793] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fabio Sterpone
- Department of Chemistry, Ecole Normale Supérieure, 24 rue Lhomond 75005 Paris, France, UMR ENS-CNRS-UPMC 8640, 24 rue Lhomond 75005 Paris, France, Fondation Pierre Gilles de Gennes pour la Recherche, Paris, France, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215
| | - Guillaume Stirnemann
- Department of Chemistry, Ecole Normale Supérieure, 24 rue Lhomond 75005 Paris, France, UMR ENS-CNRS-UPMC 8640, 24 rue Lhomond 75005 Paris, France, Fondation Pierre Gilles de Gennes pour la Recherche, Paris, France, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215
| | - James T. Hynes
- Department of Chemistry, Ecole Normale Supérieure, 24 rue Lhomond 75005 Paris, France, UMR ENS-CNRS-UPMC 8640, 24 rue Lhomond 75005 Paris, France, Fondation Pierre Gilles de Gennes pour la Recherche, Paris, France, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215
| | - Damien Laage
- Department of Chemistry, Ecole Normale Supérieure, 24 rue Lhomond 75005 Paris, France, UMR ENS-CNRS-UPMC 8640, 24 rue Lhomond 75005 Paris, France, Fondation Pierre Gilles de Gennes pour la Recherche, Paris, France, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215
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125
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LeBard DN, Matyushov DV. Protein–water electrostatics and principles of bioenergetics. Phys Chem Chem Phys 2010; 12:15335-48. [DOI: 10.1039/c0cp01004a] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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126
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Pérez-Hernández N, Luong TQ, Pérez C, Martín JD, Havenith M. Pore size dependent dynamics of confined water probed by FIR spectroscopy. Phys Chem Chem Phys 2010; 12:6928-32. [DOI: 10.1039/c000985g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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127
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Schmidt DA, Birer Ö, Funkner S, Born BP, Gnanasekaran R, Schwaab GW, Leitner DM, Havenith M. Rattling in the Cage: Ions as Probes of Sub-picosecond Water Network Dynamics. J Am Chem Soc 2009; 131:18512-7. [DOI: 10.1021/ja9083545] [Citation(s) in RCA: 126] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Diedrich A. Schmidt
- Department of Physical Chemistry II, Ruhr-University Bochum, 44780 Bochum, Germany, and Department of Chemistry, University of Nevada, Reno, Nevada 89557
| | - Özgür Birer
- Department of Physical Chemistry II, Ruhr-University Bochum, 44780 Bochum, Germany, and Department of Chemistry, University of Nevada, Reno, Nevada 89557
| | - Stefan Funkner
- Department of Physical Chemistry II, Ruhr-University Bochum, 44780 Bochum, Germany, and Department of Chemistry, University of Nevada, Reno, Nevada 89557
| | - Benjamin P. Born
- Department of Physical Chemistry II, Ruhr-University Bochum, 44780 Bochum, Germany, and Department of Chemistry, University of Nevada, Reno, Nevada 89557
| | - Ramachandran Gnanasekaran
- Department of Physical Chemistry II, Ruhr-University Bochum, 44780 Bochum, Germany, and Department of Chemistry, University of Nevada, Reno, Nevada 89557
| | - Gerhard W. Schwaab
- Department of Physical Chemistry II, Ruhr-University Bochum, 44780 Bochum, Germany, and Department of Chemistry, University of Nevada, Reno, Nevada 89557
| | - David M. Leitner
- Department of Physical Chemistry II, Ruhr-University Bochum, 44780 Bochum, Germany, and Department of Chemistry, University of Nevada, Reno, Nevada 89557
| | - Martina Havenith
- Department of Physical Chemistry II, Ruhr-University Bochum, 44780 Bochum, Germany, and Department of Chemistry, University of Nevada, Reno, Nevada 89557
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128
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Segura JJ, Verdaguer A, Cobián M, Hernández ER, Fraxedas J. Amphiphillic Organic Crystals. J Am Chem Soc 2009; 131:17853-9. [DOI: 10.1021/ja905961h] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- J. J. Segura
- Centre d’Investigació en Nanociència i Nanotecnologia, CIN2 (CSIC-ICN), Edifici CM7, Esfera UAB, Campus de Bellaterra, E-08193 Barcelona, Spain, and Institut de Ciència de Materials de Barcelona ICMAB (CSIC), Campus de Bellaterra, E-08193 Barcelona, Spain
| | - A. Verdaguer
- Centre d’Investigació en Nanociència i Nanotecnologia, CIN2 (CSIC-ICN), Edifici CM7, Esfera UAB, Campus de Bellaterra, E-08193 Barcelona, Spain, and Institut de Ciència de Materials de Barcelona ICMAB (CSIC), Campus de Bellaterra, E-08193 Barcelona, Spain
| | - M. Cobián
- Centre d’Investigació en Nanociència i Nanotecnologia, CIN2 (CSIC-ICN), Edifici CM7, Esfera UAB, Campus de Bellaterra, E-08193 Barcelona, Spain, and Institut de Ciència de Materials de Barcelona ICMAB (CSIC), Campus de Bellaterra, E-08193 Barcelona, Spain
| | - E. R. Hernández
- Centre d’Investigació en Nanociència i Nanotecnologia, CIN2 (CSIC-ICN), Edifici CM7, Esfera UAB, Campus de Bellaterra, E-08193 Barcelona, Spain, and Institut de Ciència de Materials de Barcelona ICMAB (CSIC), Campus de Bellaterra, E-08193 Barcelona, Spain
| | - J. Fraxedas
- Centre d’Investigació en Nanociència i Nanotecnologia, CIN2 (CSIC-ICN), Edifici CM7, Esfera UAB, Campus de Bellaterra, E-08193 Barcelona, Spain, and Institut de Ciència de Materials de Barcelona ICMAB (CSIC), Campus de Bellaterra, E-08193 Barcelona, Spain
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129
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Muthuselvi L, Dhathathreyan A. Understanding dynamics of myoglobin in heterogeneous aqueous environments using coupled water fractions. Adv Colloid Interface Sci 2009; 150:55-62. [PMID: 19442960 DOI: 10.1016/j.cis.2009.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Revised: 04/08/2009] [Accepted: 04/08/2009] [Indexed: 11/19/2022]
Abstract
This work presents an analysis of near environment of myoglobin (Mb) in different aqueous solutions (in the presence of NaCl, sucrose, trehalose, urea, and glycerol) using the coupled water fractions measured using a quartz crystal microbalance (QCM). The secondary structural features of the protein from circular dichroic (CD) spectroscopy and the coupled water fractions give important clues to the overall dynamics of the protein. Using time resolved fluorescence, these leads have been applied to understand the observed lifetime relaxations of Mb. Though the time scales of observation of coupled water and the lifetimes are very different, our study suggests that the trends in coupled water fraction seem to be good indicators for regulation of the relaxation dynamics of the protein. The relaxations generally show a triphasic distribution of time scales. The initial relaxation in the picoseconds time scale represents the local motions of coupled water followed by a slightly slower decay in hundreds of picoseconds attributable to coupled water-'quasi free' water interactions. The third nanosecond lifetime is due to changes in transitions in isomers of hydrated protein. The dynamics of coupled water in Mb with NaCl is the fastest (around 21 ps) and is slowest in glycerol (250 ps). The results strongly indicate that it is the resident times of water molecules that play a dominant role in the overall stability of protein in a particular hydrated isomer and not just always the number of such water molecules in the hydrated protein.
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Affiliation(s)
- L Muthuselvi
- Chemical Lab., CLRI (CSIR), Adyar, Chennai 600 020, India
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130
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Schmidt DA, Scipioni R, Boero M. Water Solvation Properties: An Experimental and Theoretical Investigation of Salt Solutions at Finite Dilution. J Phys Chem A 2009; 113:7725-9. [DOI: 10.1021/jp9016932] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Diedrich A. Schmidt
- International Center for Young Scientists, National Institute for Materials Science, Tsukuba, 305-0044, Japan, Department of Physical Chemistry II, Ruhr-University Bochum, 44780 Bochum, Germany, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS-UDS, 23 rue du Loess, BP 43, F-67034 Strasbourg, France, and CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Roberto Scipioni
- International Center for Young Scientists, National Institute for Materials Science, Tsukuba, 305-0044, Japan, Department of Physical Chemistry II, Ruhr-University Bochum, 44780 Bochum, Germany, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS-UDS, 23 rue du Loess, BP 43, F-67034 Strasbourg, France, and CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Mauro Boero
- International Center for Young Scientists, National Institute for Materials Science, Tsukuba, 305-0044, Japan, Department of Physical Chemistry II, Ruhr-University Bochum, 44780 Bochum, Germany, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS-UDS, 23 rue du Loess, BP 43, F-67034 Strasbourg, France, and CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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131
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Daub CD, Leung K, Luzar A. Structure of Aqueous Solutions of Monosodium Glutamate. J Phys Chem B 2009; 113:7687-700. [DOI: 10.1021/jp810379m] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher D. Daub
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, and Sandia National Laboratories, MS 1415, Albuquerque, New Mexico 87185
| | - Kevin Leung
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, and Sandia National Laboratories, MS 1415, Albuquerque, New Mexico 87185
| | - Alenka Luzar
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, and Sandia National Laboratories, MS 1415, Albuquerque, New Mexico 87185
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132
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Feibelman PJ. Water--From Interfaces to the Bulk. Concluding remarks. Faraday Discuss 2009; 141:467-75. [PMID: 19227370 DOI: 10.1039/b817311g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Peter J Feibelman
- Sandia National Laboratories Albuquerque, Albuquerque, NM 87185-1415, USA.
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133
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Born B, Weingärtner H, Bründermann E, Havenith M. Solvation Dynamics of Model Peptides Probed by Terahertz Spectroscopy. Observation of the Onset of Collective Network Motions. J Am Chem Soc 2009; 131:3752-5. [DOI: 10.1021/ja808997y] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Benjamin Born
- Lehrstuhl für Physikalische Chemie 2, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Hermann Weingärtner
- Lehrstuhl für Physikalische Chemie 2, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Erik Bründermann
- Lehrstuhl für Physikalische Chemie 2, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Martina Havenith
- Lehrstuhl für Physikalische Chemie 2, Ruhr-Universität Bochum, 44780 Bochum, Germany
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134
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Kim S, Born B, Havenith M, Gruebele M. Echtzeitnachweis von Änderungen im Protein-Wassernetzwerk während der Proteinfaltung mit Terahertz-Absorptionsspektroskopie. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200802281] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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