51
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Mamontov E, Chu XQ. Water–protein dynamic coupling and new opportunities for probing it at low to physiological temperatures in aqueous solutions. Phys Chem Chem Phys 2012; 14:11573-88. [DOI: 10.1039/c2cp41443k] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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52
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Abstract
This Perspective is focused on amide groups of peptides interacting with water. The 2D IR spectroscopy has already enabled structural aspects of the peptide backbone to be determined through its ability to measure the coupling between different amide-I modes. Here we describe why nonlinear IR is emerging as the method of choice to examine the fast components of the water dynamics near peptides and how isotopically edited peptide links can be used to probe the local water at a residue level in proteins. This type of research necessarily involves an intimate mix of theory and experiment. The description of the results is underpinned by relatively well established quantum-statistical theories that describe the important manifestations of peptide vibrational frequency fluctuations.
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Affiliation(s)
- Ayanjeet Ghosh
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Robin M. Hochstrasser
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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53
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Gruenbaum SM, Skinner JL. Vibrational spectroscopy of water in hydrated lipid multi-bilayers. I. Infrared spectra and ultrafast pump-probe observables. J Chem Phys 2011; 135:075101. [PMID: 21861584 PMCID: PMC3172989 DOI: 10.1063/1.3615717] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 07/02/2011] [Indexed: 11/15/2022] Open
Abstract
The vibrational spectroscopy of hydration water in dilauroylphosphatidylcholine lipid multi-bilayers is investigated using molecular dynamics simulations and a mixed quantum/classical model for the OD stretch spectroscopy of dilute HDO in H(2)O. FTIR absorption spectra, and isotropic and anisotropic pump-probe decay curves have been measured experimentally as a function of the hydration level of the lipid multi-bilayer, and our goal is to make connection with these experiments. To this end, we use third-order response functions, which allow us to include non-Gaussian frequency fluctuations, non-Condon effects, molecular rotations, and a fluctuating vibrational lifetime, all of which we believe are important for this system. We calculate the response functions using existing transition frequency and dipole maps. From the experiments it appears that there are two distinct vibrational lifetimes corresponding to HDO molecules in different molecular environments. In order to obtain these lifetimes, we consider a simple two-population model for hydration water hydrogen bonds. Assuming a different lifetime for each population, we then calculate the isotropic pump-probe decay, fitting to experiment to obtain the two lifetimes for each hydration level. With these lifetimes in hand, we then calculate FTIR spectra and pump-probe anisotropy decay as a function of hydration. This approach, therefore, permits a consistent calculation of all observables within a unified computational scheme. Our theoretical results are all in qualitative agreement with experiment. The vibrational lifetime of lipid-associated OD groups is found to be systematically shorter than that of the water-associated population, and the lifetimes of each population increase with decreasing hydration, in agreement with previous analysis. Our theoretical FTIR absorption spectra successfully reproduce the experimentally observed red-shift with decreasing lipid hydration, and we confirm a previous interpretation that this shift results from the hydrogen bonding of water to the lipid phosphate group. From the pump-probe anisotropy decay, we confirm that the reorientational motions of water molecules slow significantly as hydration decreases, with water bound in the lipid carbonyl region undergoing the slowest rotations.
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Affiliation(s)
- S M Gruenbaum
- Theoretical Chemistry Institute and Department of Chemistry, 1101 University Ave. University of Wisconsin, Madison, Wisconsin 53706, USA
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54
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Perticaroli S, Comez L, Paolantoni M, Sassi P, Morresi A, Fioretto D. Extended Frequency Range Depolarized Light Scattering Study of N-Acetyl-leucine-methylamide–Water Solutions. J Am Chem Soc 2011; 133:12063-8. [DOI: 10.1021/ja202272k] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stefania Perticaroli
- Dipartimento di Chimica, Universitá di Perugia, via Elce di Sotto, I-06123 Perugia, Italy
| | - Lucia Comez
- Dipartimento di Fisica, Universitá degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- IOM-CNR c/o Dipartimento di Fisica, Universitá di Perugia, Via Pascoli, I-06123, Perugia, Italy
| | - Marco Paolantoni
- Dipartimento di Chimica, Universitá di Perugia, via Elce di Sotto, I-06123 Perugia, Italy
| | - Paola Sassi
- Dipartimento di Chimica, Universitá di Perugia, via Elce di Sotto, I-06123 Perugia, Italy
| | - Assunta Morresi
- Dipartimento di Chimica, Universitá di Perugia, via Elce di Sotto, I-06123 Perugia, Italy
| | - Daniele Fioretto
- Dipartimento di Fisica, Universitá degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
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55
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Sen L, Fares MA, Liang B, Gao L, Wang B, Wang T, Su YJ. Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns. Biol Direct 2011; 6:29. [PMID: 21639885 PMCID: PMC3129321 DOI: 10.1186/1745-6150-6-29] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 06/03/2011] [Indexed: 11/10/2022] Open
Abstract
Background The chloroplast-localized ribulose-1, 5-biphosphate carboxylase/oxygenase (Rubisco), the primary enzyme responsible for autotrophy, is instrumental in the continual adaptation of plants to variations in the concentrations of CO2. The large subunit (LSU) of Rubisco is encoded by the chloroplast rbcL gene. Although adaptive processes have been previously identified at this gene, characterizing the relationships between the mutational dynamics at the protein level may yield clues on the biological meaning of such adaptive processes. The role of such coevolutionary dynamics in the continual fine-tuning of RbcL remains obscure. Results We used the timescale and phylogenetic analyses to investigate and search for processes of adaptive evolution in rbcL gene in three gymnosperm families, namely Podocarpaceae, Taxaceae and Cephalotaxaceae. To understand the relationships between regions identified as having evolved under adaptive evolution, we performed coevolutionary analyses using the software CAPS. Importantly, adaptive processes were identified at amino acid sites located on the contact regions among the Rubisco subunits and on the interface between Rubisco and its activase. Adaptive amino acid replacements at these regions may have optimized the holoenzyme activity. This hypothesis was pinpointed by evidence originated from our analysis of coevolution that supported the correlated evolution between Rubisco and its activase. Interestingly, the correlated adaptive processes between both these proteins have paralleled the geological variation history of the concentration of atmospheric CO2. Conclusions The gene rbcL has experienced bursts of adaptations in response to the changing concentration of CO2 in the atmosphere. These adaptations have emerged as a result of a continuous dynamic of mutations, many of which may have involved innovation of functional Rubisco features. Analysis of the protein structure and the functional implications of such mutations put forward the conclusion that this evolutionary scenario has been possible through a complex interplay between adaptive mutations, often structurally destabilizing, and compensatory mutations. Our results unearth patterns of evolution that have likely optimized the Rubisco activity and uncover mutational dynamics useful in the molecular engineering of enzymatic activities. Reviewers This article was reviewed by Prof. Christian Blouin (nominated by Dr W Ford Doolittle), Dr Endre Barta (nominated by Dr Sandor Pongor), and Dr Nicolas Galtier.
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Affiliation(s)
- Lin Sen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
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56
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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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57
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Qvist J, Schober H, Halle B. Structural dynamics of supercooled water from quasielastic neutron scattering and molecular simulations. J Chem Phys 2011; 134:144508. [DOI: 10.1063/1.3578472] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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58
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Sinha SK, Bandyopadhyay S. Differential flexibility of the secondary structures of lysozyme and the structure and ordering of surrounding water molecules. J Chem Phys 2011; 134:115101. [DOI: 10.1063/1.3560442] [Citation(s) in RCA: 26] [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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59
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Russo D, Teixeira J, Kneller L, Copley JRD, Ollivier J, Perticaroli S, Pellegrini E, Gonzalez MA. Vibrational Density of States of Hydration Water at Biomolecular Sites: Hydrophobicity Promotes Low Density Amorphous Ice Behavior. J Am Chem Soc 2011; 133:4882-8. [DOI: 10.1021/ja109610f] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniela Russo
- CNR-IOM c/o Institut Laue Langevin, 6 rue J. Horowitz BP156, F-38042 Grenoble, France
| | - José Teixeira
- Laboratoire Léon Brillouin (CEA/CNRS), CEA Saclay, 91191 Gif-sur Yvette Cedex, France
| | - Larry Kneller
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6102, United States
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - John R. D. Copley
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6102, United States
| | - Jacques Ollivier
- Institut Laue Langevin, 6 rue J. Horowitz BP156, F-38042 Grenoble, France
| | - Stefania Perticaroli
- Dipartimento di Chimica, Università degli Studi di Perugia, Sezione di Chimica Fisica, via Elce di sotto 8, I-06123 Perugia, Italia
| | - Eric Pellegrini
- Institut Laue Langevin, 6 rue J. Horowitz BP156, F-38042 Grenoble, France
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60
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Mazur K, Heisler IA, Meech SR. THz Spectra and Dynamics of Aqueous Solutions Studied by the Ultrafast Optical Kerr Effect. J Phys Chem B 2011; 115:2563-73. [DOI: 10.1021/jp111764p] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Kamila Mazur
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Ismael A. Heisler
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Stephen R. Meech
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
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61
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Das DK, Mondal T, Mandal U, Bhattacharyya K. Probing deuterium isotope effect on structure and solvation dynamics of human serum albumin. Chemphyschem 2011; 12:814-22. [PMID: 21341353 DOI: 10.1002/cphc.201000912] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 01/18/2011] [Indexed: 12/20/2022]
Abstract
The deuterium isotopic effect on the structure and solvation dynamics of the protein, human serum albumin (HSA), has been studied by using circular dichroism (CD), femtosecond up-conversion, FRET, and single-molecule spectroscopy. The CD spectra suggest that D(2)O affects the structure of HSA, leading to a 20% decrease in the helical structure. The FRET study indicates that the distance of C153 from the lone tryptophan residue of HSA is quite similar (≈21 Å) in H(2)O and D(2)O, and hence, the location of the probe in the protein remains the same in the two solvents. The single-molecule study suggests that coumarin 153 (C153) binds almost exclusively (>96%) to one site of HSA. Solvation dynamics of C153 in HSA is found to be markedly retarded in D(2)O compared with H(2)O. In H(2)O, the solvation of C153 bound to HSA is found to be biexponential with one component of 7 ps (30%) and a long component of 350 ps (70%). In D(2)O, we detected a short component of 4 ps (41%) and a long component of 950 ps (59%). Thus, the ultraslow component of the solvation dynamics of C153 bound to HSA in D(2)O (950 ps) is 2.5-fold slower than that in H(2)O (350 ps). The marked deuterium isotope effect has been ascribed to water molecules confined in the protein environment and to a lesser extent to the structural modification of protein by D(2)O.
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Affiliation(s)
- Dibyendu Kumar Das
- Physical Chemistry Department, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
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62
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Kwon OH, Yoo TH, Othon CM, Van Deventer JA, Tirrell DA, Zewail AH. Hydration dynamics at fluorinated protein surfaces. Proc Natl Acad Sci U S A 2010; 107:17101-6. [PMID: 20855583 PMCID: PMC2951393 DOI: 10.1073/pnas.1011569107] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Water-protein interactions dictate many processes crucial to protein function including folding, dynamics, interactions with other biomolecules, and enzymatic catalysis. Here we examine the effect of surface fluorination on water-protein interactions. Modification of designed coiled-coil proteins by incorporation of 5,5,5-trifluoroleucine or (4S)-2-amino-4-methylhexanoic acid enables systematic examination of the effects of side-chain volume and fluorination on solvation dynamics. Using ultrafast fluorescence spectroscopy, we find that fluorinated side chains exert electrostatic drag on neighboring water molecules, slowing water motion at the protein surface.
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Affiliation(s)
- Oh-Hoon Kwon
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and
- Physical Biology Center for Ultrafast Science and Technology, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125
| | - Tae Hyeon Yoo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and
| | - Christina M. Othon
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and
- Physical Biology Center for Ultrafast Science and Technology, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125
| | - James A. Van Deventer
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and
| | - David A. Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and
| | - Ahmed H. Zewail
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; and
- Physical Biology Center for Ultrafast Science and Technology, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125
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63
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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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64
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Mazur K, Heisler IA, Meech SR. Ultrafast Dynamics and Hydrogen-Bond Structure in Aqueous Solutions of Model Peptides. J Phys Chem B 2010; 114:10684-91. [DOI: 10.1021/jp106423a] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Kamila Mazur
- School of Chemistry, University of East Anglia Norwich NR4 7TJ, United Kingdom
| | - Ismael A. Heisler
- School of Chemistry, University of East Anglia Norwich NR4 7TJ, United Kingdom
| | - Stephen R. Meech
- School of Chemistry, University of East Anglia Norwich NR4 7TJ, United Kingdom
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65
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Russo D, Copley JR, Ollivier J, Teixeira J. On the behaviour of water hydrogen bonds at biomolecular sites: Dependences on temperature and on network dimensionality. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2009.12.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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66
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Stadler AM. Dynamics in Biological Systems as seen by QENS. Z PHYS CHEM 2010. [DOI: 10.1524/zpch.2010.6099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
Quasielastic incoherent neutron scattering is a well suited and established experimental method to study protein and water dynamics in the picosecond to nanosecond time- and Ångstrom length-scale. Using deuterium labelling either protein or water motions can be selected and brought into focus. Protein and cell water dynamics were separately studied in red blood cells. A consistent picture of cytoplasmic water and protein dynamics in whole cells is emerging from recent experimental results.
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67
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Malardier-Jugroot C, Bowron DT, Soper AK, Johnson ME, Head-Gordon T. Structure and water dynamics of aqueous peptide solutions in the presence of co-solvents. Phys Chem Chem Phys 2010; 12:382-92. [DOI: 10.1039/b915346b] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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68
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Zhang L, Yang Y, Kao YT, Wang L, Zhong D. Protein hydration dynamics and molecular mechanism of coupled water-protein fluctuations. J Am Chem Soc 2009; 131:10677-91. [PMID: 19586028 DOI: 10.1021/ja902918p] [Citation(s) in RCA: 155] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Protein surface hydration is fundamental to its structural stability and flexibility, and water-protein fluctuations are essential to biological function. Here, we report a systematic global mapping of water motions in the hydration layer around a model protein of apomyoglobin in both native and molten globule states. With site-directed mutagenesis, we use intrinsic tryptophan as a local optical probe to scan the protein surface one at a time with single-site specificity. With femtosecond resolution, we examined 16 mutants in two states and observed two types of water-network relaxation with distinct energy and time distributions. The first water motion results from the local collective hydrogen-bond network relaxation and occurs in a few picoseconds. The initial hindered motions, observed in bulk water in femtoseconds, are highly suppressed and drastically slow down due to structured water-network collectivity in the layer. The second water-network relaxation unambiguously results from the lateral cooperative rearrangements in the inner hydration shell and occurs in tens to hundreds of picoseconds. Significantly, this longtime dynamics is the coupled interfacial water-protein motions and is the direct measurement of such cooperative fluctuations. These local protein motions, although highly constrained, are necessary to assist the longtime water-network relaxation. A series of correlations of hydrating water dynamics and coupled fluctuations with local protein's chemical and structural properties were observed. These results are significant and reveal various water behaviors in the hydration layer with wide heterogeneity. We defined a solvation speed and an angular speed to quantify the water-network rigidity and local protein flexibility, respectively. We also observed that the dynamic hydration layer extends to more than 10 A. Finally, from native to molten globule states, the hydration water networks loosen up, and the protein locally becomes more flexible with larger global plasticity and partial unfolding.
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Affiliation(s)
- Luyuan Zhang
- Department of Physics, Program of Biophysics, The Ohio State University, Columbus, Ohio 43210, USA
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69
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70
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Johnson ME, Malardier-Jugroot C, Head-Gordon T. Effects of co-solvents on peptide hydration water structure and dynamics. Phys Chem Chem Phys 2009; 12:393-405. [PMID: 20023817 DOI: 10.1039/b915888j] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We evaluate the molecular response of hydration water as a function of temperature and proximity to the surface of the peptide N-acetyl-leucine-methylamide (NALMA) when in the presence of the kosmotrope co-solvent glycerol or the chaotrope co-solvent dimethyl sulfoxide (DMSO), using molecular dynamics simulation with a polarizable force field. These detailed microscopic studies complement established thermodynamic analysis on the role of co-solvents in shifting the equilibrium for proteins away from or towards the native folded state. We find that the structure of the water at the peptide interfaces reflects an increase in hydration number in the glycerol solution and a decrease in hydration numbers in the DMSO solution. While the water dynamics around NALMA in the presence of both co-solvents is slower than that observed with the water solvent alone, in the DMSO mixture we no longer measure a separation in water motion time scales at low temperatures as is seen in the pure water solvent, but rather one single relaxation time. In the glycerol, however, we do observe a separation of time scales at low temperatures, supporting the hypothesis that hydration water near a hydrophobic solute evolves on a separate time scale than the extensive hydrogen-bonding network of more bulk-like water. Our simulation studies highlight the differences in the two co-solvent solutions due to the relative frequency of water contacts with the hydrophobic vs. hydrophilic peptide surface, and direct water interactions with the co-solvents.
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Affiliation(s)
- Margaret E Johnson
- UCSF/UCB Joint Graduate Group in Bioengineering, Berkeley, CA 94720, USA.
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71
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Pieniazek PA, Lin YS, Chowdhary J, Ladanyi BM, Skinner JL. Vibrational Spectroscopy and Dynamics of Water Confined inside Reverse Micelles. J Phys Chem B 2009; 113:15017-28. [DOI: 10.1021/jp906784t] [Citation(s) in RCA: 126] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Piotr A. Pieniazek
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Yu-Shan Lin
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Janamejaya Chowdhary
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Branka M. Ladanyi
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - J. L. Skinner
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
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72
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Johnson ME, Malardier-Jugroot C, Murarka RK, Head-Gordon T. Hydration water dynamics near biological interfaces. J Phys Chem B 2009; 113:4082-92. [PMID: 19425247 DOI: 10.1021/jp806183v] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We performed classical molecular dynamics simulations using both fixed-charge and polarizable water and protein force fields to contrast the hydration dynamics near hydrophilic and amphiphilic peptides as a function of temperature. The high peptide concentrations we use serve as a model for the surface of folded proteins where hydration layers around each residue overlap significantly. Through simulation we determine that there are notable differences in the water dynamics analyzed from the outer and inner hydration layer regions of the amphiphilic peptide solution that explains the experimentally observed presence of two translational relaxations, while the hydrophilic peptide solution shows only a single non-Arrhenius translational process with no distinction between hydration layers. Given that water dynamics for the amphiphilic peptide system reproduces all known rotational and translational hydration dynamical anomalies exhibited by hydration water near protein surfaces, our analysis provides strong evidence that dynamical signatures near biological interfaces arises because of frustration in the hydration dynamics induced by chemical heterogeneity, as opposed to just topological roughness, of the protein surface.
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Affiliation(s)
- Margaret E Johnson
- Department of Bioengineering, University of California, Berkeley, 94720, USA
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Qvist J, Persson E, Mattea C, Halle B. Time scales of water dynamics at biological interfaces: peptides, proteins and cells. Faraday Discuss 2009; 141:131-44; discussion 175-207. [PMID: 19227355 DOI: 10.1039/b806194g] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Water 2H and 17O spin relaxation is used to study water dynamics in the hydration layers of two small peptides, two globular proteins and in living cells of two microorganisms. The dynamical heterogeneity of hydration water is characterized by performing relaxation measurements over a wide temperature range, extending deeply into the supercooled regime, or by covering a wide frequency range. Protein hydration layers can be described by a power-law distribution of rotational correlation times with an exponent close to 2. This distribution comprises a small fraction of protein-specific hydration sites, where water rotation is strongly retarded, and a dominant fraction of generic hydration sites, where water rotation is as fast as in the hydration shells of small peptides. The generic dynamic perturbation factor is less than 2 at room temperature and exhibits a maximum near 260 K. The dynamic perturbation is induced by H-bond constraints that interfere with the cooperative mechanism that facilitates rotation in bulk water. Because these constraints are temperature-independent, hydration water does not follow the super-Arrhenius temperature dependence of bulk water. Water in living cells behaves as expected from studies of simpler model systems, the only difference being a larger fraction of secluded (strongly perturbed) hydration sites associated with the supramolecular organization in the cell. Intracellular water that is not in direct contact with biopolymers has essentially the same dynamics as bulk water. There is no significant difference in cell water dynamics between mesophilic and halophilic organisms, despite the high K+ and Na+ concentrations in the latter.
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Affiliation(s)
- Johan Qvist
- Center for Molecular Protein Science, Department of Biophysical Chemistry, Lund University, SE-22100 Lund, Sweden
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74
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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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75
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Laage D. Reinterpretation of the Liquid Water Quasi-Elastic Neutron Scattering Spectra Based on a Nondiffusive Jump Reorientation Mechanism. J Phys Chem B 2009; 113:2684-7. [DOI: 10.1021/jp900307n] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Damien Laage
- Ecole Normale Supérieure, Département de Chimie, 24 rue Lhomond, F-75005 Paris, France, CNRS, UMR 8640 PASTEUR, 24 rue Lhomond, F-75005 Paris, France
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76
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Stadler AM, Embs JP, Digel I, Artmann GM, Unruh T, Büldt G, Zaccai G. Cytoplasmic water and hydration layer dynamics in human red blood cells. J Am Chem Soc 2009; 130:16852-3. [PMID: 19053467 DOI: 10.1021/ja807691j] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dynamics of water in human red blood cells was measured with quasielastic incoherent neutron scattering in the temperature range between 290 and 320 K. Neutron spectrometers with time resolutions of 40, 13, and 7 ps were combined to cover time scales of bulk water dynamics to reduced mobility interfacial water motions. A major fraction of approximately 90% of cell water is characterized by a translational diffusion coefficient similar to bulk water. A minor fraction of approximately 10% of cellular water exhibits reduced dynamics. This slow water fraction was attributed to dynamically bound water on the surface of hemoglobin which accounts for approximately half of the hydration layer.
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77
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Kondo M, Heisler IA, Conyard J, Rivett JPH, Meech SR. Reactive Dynamics in Confined Liquids: Interfacial Charge Effects on Ultrafast Torsional Dynamics in Water Nanodroplets. J Phys Chem B 2009; 113:1632-9. [DOI: 10.1021/jp808991g] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Minako Kondo
- School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Ismael A. Heisler
- School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Jamie Conyard
- School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Jasmine P. H. Rivett
- School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Stephen R. Meech
- School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, U.K
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78
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Mondal SK, Sahu K, Bhattacharyya K. Study of Biological Assemblies by Ultrafast Fluorescence Spectroscopy. REVIEWS IN FLUORESCENCE 2009. [DOI: 10.1007/978-0-387-88722-7_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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79
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Hydration profiles of amyloidogenic molecular structures. J Biol Phys 2008; 34:577-90. [PMID: 19669515 DOI: 10.1007/s10867-008-9122-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Accepted: 10/20/2008] [Indexed: 10/21/2022] Open
Abstract
Hydration shells of normal proteins display regions of highly structured water as well as patches of less structured bulk-like water. Recent studies suggest that isomers with larger surface densities of patches of bulk-like water have an increased propensity to aggregate. These aggregates are toxic to the cellular environment. Hence, the early detection of these toxic deposits is of paramount medical importance. We show that various morphological states of association of such isomers can be differentiated from the normal protein background based on the characteristic partition between bulk, caged, and surface hydration water and the magnetic resonance (MR) signals of this water. We derive simple mathematical equations relating the compartmentalization of water to the local hydration fraction and the packing density of the newly formed molecular assemblies. Then, we employ these equations to predict the MR response of water constrained by protein aggregation. Our results indicate that single units and compact aggregates that contain no water between constituents induce a shift of the MR signal from normal protein background to values in the hyperintensity domain (bright spots), corresponding to bulk water. In contrast, large plaques that cage significant amounts of water between constituents are likely to generate MR responses in the hypointensity domain (dark spots), typical for strongly correlated water. The implication of these results is that amyloids can display both dark and bright spots when compared to the normal gray background tissue on MR images. In addition, our findings predict that the bright spots are more likely to correspond to amyloids in their early stage of development. The results help explain the MR contrast patterns of amyloids and suggest a new approach for identifying unusual protein aggregation related to disease.
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80
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Sasisanker P, Weingärtner H. Hydration Dynamics of Water near an Amphiphilic Model Peptide at Low Hydration Levels: A Dielectric Relaxation Study. Chemphyschem 2008; 9:2802-8. [DOI: 10.1002/cphc.200800508] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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81
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82
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Dynamics of water in LiCl and CaCl2 aqueous solutions confined in silica matrices: A backscattering neutron spectroscopy study. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2008.05.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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83
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Russo D, Ollivier J, Teixeira J. Water hydrogen bond analysis on hydrophilic and hydrophobic biomolecule sites. Phys Chem Chem Phys 2008; 10:4968-74. [PMID: 18688541 DOI: 10.1039/b807551b] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Elastic and quasielastic neutron scattering experiments have been used to investigate the hydrogen bonding network dynamics of hydration water on hydrophilic and hydrophobic sites. To this end the evolution of hydration water dynamics of a prototypical hydrophobic amino acid with polar backbone, N-acetyl-leucine-methylamide (NALMA), and hydrophilic amino acid, N-acetyl-glycine-methylamide (NAGMA), has been investigated as a function of the molecular ratio water : peptide. The results suggest that the dynamical contribution of the intrinsic and low hydration molecules of water is characteristic of pure librational/rotational movement. The water molecule remains attached to the hydrophilic site with only the possibility of hindered rotations that eventually break the bond with the peptide and reform it immediately after. A gradual evolution from librational motions to hindered rotations is observed as a function of temperature. When the hydration increases, we observe (together with the hindered rotations of hydrogen bonds) a slow diffusion of water molecules on the surface of the peptides.
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Affiliation(s)
- Daniela Russo
- CNR-INFM & CRS/Soft, c/o Institut Laue Langevin, 6 rue J. Horowitz, Grenoble, France
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84
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Sinha SK, Chakraborty S, Bandyopadhyay S. Thickness of the hydration layer of a protein from molecular dynamics simulation. J Phys Chem B 2008; 112:8203-9. [PMID: 18547099 DOI: 10.1021/jp8000724] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Water molecules around a protein exhibit slow dynamics with respect to that of pure bulk water. One important issue in protein hydration is the thickness of the hydration layer (i.e., the distance from the protein surface up to which the water dynamics is influenced by the protein). Estimation of thickness is crucial to understand better the properties of "biological water" and the role that it plays in guiding the protein's function. We have performed an atomistic molecular dynamics simulation of an aqueous solution of the protein villin headpiece subdomain or HP-36 to estimate the thickness of its hydration water. In particular, several dynamical properties of water around different segments (three alpha-helices) of the protein have been calculated by varying the thickness of the hydration layers. It is found that in general the influence of the helices on water properties extends beyond the first hydration layer. However, the heterogeneous nature of water among the first hydration layers of the three helices diminishes as the thickness is increased. It indicates that, for a small protein such as HP-36, the thickness of "biological water" is uniform for different segments of the protein.
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Affiliation(s)
- Sudipta Kumar Sinha
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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85
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Laage D, Hynes JT. On the Residence Time for Water in a Solute Hydration Shell: Application to Aqueous Halide Solutions. J Phys Chem B 2008; 112:7697-701. [DOI: 10.1021/jp802033r] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Damien Laage
- Ecole Normale Supérieure, Département de Chimie, 24 rue Lhomond, F-75005 Paris, France, CNRS, UMR 8640 PASTEUR, F-75005 Paris, France, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309
| | - James T. Hynes
- Ecole Normale Supérieure, Département de Chimie, 24 rue Lhomond, F-75005 Paris, France, CNRS, UMR 8640 PASTEUR, F-75005 Paris, France, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309
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86
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Chakraborty S, Bandyopadhyay S. Dynamics of water in the hydration layer of a partially unfolded structure of the protein HP-36. J Phys Chem B 2008; 112:6500-7. [PMID: 18433159 DOI: 10.1021/jp710904c] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Atomistic molecular dynamics simulations of the folded native structure and a partially unfolded molten globule structure of the protein villin headpiece subdomain or HP-36 have been carried out with explicit solvent to explore the effects of unfolding on the dynamical behavior of water present in the hydration layers of different segments (three alpha-helices) of the protein. The calculations revealed that the unfolding of helix-2 influences the translational and rotational motions of water present in the hydration layers of the three helices in a heterogeneous manner. It is observed that a correlation exists between the unfolding of helix-2 and the microscopic kinetics of protein-water hydrogen bonds formed by its residues. This in turn has an influence on the rigidity of the hydration layers of the helices in the unfolded structure versus that in the folded native structure. These results should provide a microscopic explanation to recent solvation dynamics experiments on folded native and unfolded structures of proteins.
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Affiliation(s)
- Sudip Chakraborty
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur, India
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87
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The impact of kosmotropes and chaotropes on bulk and hydration shell water dynamics in a model peptide solution. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2007.08.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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88
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Smolin N, Winter R. Effect of Temperature, Pressure, and Cosolvents on Structural and Dynamic Properties of the Hydration Shell of SNase: A Molecular Dynamics Computer Simulation Study. J Phys Chem B 2008; 112:997-1006. [DOI: 10.1021/jp076440v] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nikolai Smolin
- Physical Chemistry and Biophysical Chemistry, Department of Chemistry, University of Dortmund, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Roland Winter
- Physical Chemistry and Biophysical Chemistry, Department of Chemistry, University of Dortmund, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
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89
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Malardier-Jugroot C, Johnson ME, Murarka RK, Head-Gordon T. Aqueous peptides as experimental models for hydration water dynamics near protein surfaces. Phys Chem Chem Phys 2008; 10:4903-8. [DOI: 10.1039/b806995f] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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90
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Murarka RK, Head-Gordon T. Dielectric Relaxation of Aqueous Solutions of Hydrophilic versus Amphiphilic Peptides. J Phys Chem B 2008; 112:179-86. [DOI: 10.1021/jp073440m] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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91
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92
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Affiliation(s)
- Philip Ball
- Nature, 4-6 Crinan Street, London N1 9XW, U.K
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93
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Chakraborty S, Sinha SK, Bandyopadhyay S. Low-Frequency Vibrational Spectrum of Water in the Hydration Layer of a Protein: A Molecular Dynamics Simulation Study. J Phys Chem B 2007; 111:13626-31. [DOI: 10.1021/jp0746401] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Sudip Chakraborty
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
| | - Sudipta Kumar Sinha
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
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94
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Ghosh S, Mandal U, Adhikari A, Dey S, Bhattacharyya K. Study of organized and biological systems using an ultrafast laser. INT REV PHYS CHEM 2007. [DOI: 10.1080/01442350701416888] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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95
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Sahu K, Mondal SK, Ghosh S, Bhattacharyya K. Ultrafast Dynamics in Biological Systems and in Nano-Confined Environments. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007. [DOI: 10.1246/bcsj.80.1033] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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96
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Pizzitutti F, Marchi M, Sterpone F, Rossky PJ. How protein surfaces induce anomalous dynamics of hydration water. J Phys Chem B 2007; 111:7584-90. [PMID: 17564431 DOI: 10.1021/jp0717185] [Citation(s) in RCA: 194] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Water around biomolecules slows down with respect to pure water, and both rotation and translation exhibit anomalous time dependence in the hydration shell. The origin of such behavior remains elusive. We use molecular dynamics simulations of water dynamics around several designed protein models to establish the connection between the appearance of the anomalous dynamics and water-protein interactions. For the first time we quantify the separate effect of protein topological and energetic disorder on the hydration water dynamics. When a static protein structure is simulated, we show that both types of disorder contribute to slow down water diffusion, and that allowing for protein motion, increasing the spatial dimensionality of the interface, reduces the anomalous character of hydration water. The rotation of water is, instead, altered by the energetic disorder only; indeed, when electrostatic interactions between the protein and water are switched off, water reorients even faster than in the bulk. The dynamics of water is also related to the collective structure--à voir the hydrogen bond (H-bond) network--formed by the solvent enclosing the protein surface. We show that, as expected for a full hydrated protein, when the protein surface offers pinning sites (charged or polar sites), the superficial water-water H-bond network percolates throughout the whole surface, hindering the water diffusion, whereas it does not when the protein surface lacks electrostatic interactions with water and the water diffusion is enhanced.
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Affiliation(s)
- Francesco Pizzitutti
- Commissariat a l'Energie Atomique, DSV-DBJC-SBFM, Centre d'Etudes, Saclay, 91191 Gif-sur-Yvette Cedex, France
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97
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Murarka RK, Head-Gordon T. Single particle and collective hydration dynamics for hydrophobic and hydrophilic peptides. J Chem Phys 2007; 126:215101. [PMID: 17567218 DOI: 10.1063/1.2737050] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We have conducted extensive molecular dynamics simulations to study the single particle and collective dynamics of water in solutions of N-acetyl-glycine-methylamide, a model hydrophilic protein backbone, and N-acetyl-leucine-methylamide, a model (amphiphilic) hydrophobic peptide, as a function of peptide concentration. Various analytical models commonly used in the analysis of incoherent quasielastic neutron scattering (QENS), are tested against the translational and rotational intermediate scattering function, the mean square displacement of the water molecule center of mass, and fits to the second-order rotational correlation function of water evaluated directly from the simulation data. We find that while the agreement between the model-free analysis and analytical QENS models is quantitatively poor, the qualitative feature of dynamical heterogeneity due to caging is captured well by all approaches. The center of mass collective and single particle intermediate scattering functions of water calculated for these peptide solutions show that the crossover from collective to single particle-dominated motions occurs at a higher value of Q for high concentration solutions relative to low concentration because of the greater restriction in movement of water molecules due to confinement. Finally, we have shown that at the same level of confinement of the two peptides, the aqueous amphiphilic amino acid solution shows the strongest deviation between single particle and collective dynamics relative to the hydrophilic amino acid, indicating that chemical heterogeneity induces even greater spatial heterogeneity in the water dynamics.
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Affiliation(s)
- Rajesh K Murarka
- Department of Bioengineering, University of California, Berkeley, California 94720, USA
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98
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Russo D, Hura GL, Copley JRD. Effects of hydration water on protein methyl group dynamics in solution. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2007; 75:040902. [PMID: 17500858 DOI: 10.1103/physreve.75.040902] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2007] [Indexed: 05/15/2023]
Abstract
Elastic and quasielastic neutron scattering experiments have been used to investigate the dynamics of methyl groups in a protein-model hydrophobic peptide in solution. The results suggest that, when the hydrophobic side chains are hydrated by a single hydration water layer, the only allowed motions are confined and attributed to librational and rotational movement associated with the methyl groups. They provide unique experimental evidence that the structural and dynamical properties of the interfacial water strongly influence the side-chain dynamics and the activation of diffusive motion.
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Affiliation(s)
- Daniela Russo
- CNR-INFM & CRS/SOFT, c/o Institut Laue Langevin, 6 rue J. Horowitz, BP156, F-38042 Grenoble, France
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99
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Liang T, Walsh TR. Simulation of the hydration structure of glycyl-alanine. MOLECULAR SIMULATION 2007. [DOI: 10.1080/08927020601155378] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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100
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Garberoglio G, Sega M, Vallauri R. Inhomogeneity effects on the structure and dynamics of water at the surface of a membrane: A computer simulation study. J Chem Phys 2007; 126:125103. [PMID: 17411165 DOI: 10.1063/1.2715880] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The authors report the structural and dynamical properties of water interacting with the surface of a lipid bilayer. Three regions have been identified, which show different dynamical regimes of water: a region of strong water-solute interaction, a transition region, and the bulk water region. The dynamics of the strong-interacting water is dominated by caging effects, as shown by the analysis of the self-intermediate scattering function, and by the disrupture of water's hydrogen bond network, while the smooth transition to bulk water is traced back to the roughness of the bilayer surface.
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Affiliation(s)
- G Garberoglio
- Dipartimento di Fisica, Università di Trento, Via Sommarive 14, Povo, TN, Italy
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