1
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Basu I, Manna M, Mukhopadhyay C. Insights into the behavioral difference of water in the presence of GM1. FEBS Lett 2015; 589:3887-92. [DOI: 10.1016/j.febslet.2015.11.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/16/2015] [Accepted: 11/16/2015] [Indexed: 11/26/2022]
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2
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Das J, Flenner E, Kosztin I. Anomalous diffusion of water molecules in hydrated lipid bilayers. J Chem Phys 2013; 139:065102. [DOI: 10.1063/1.4817322] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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3
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Hansen FY, Peters GH, Taub H, Miskowiec A. Diffusion of water and selected atoms in DMPC lipid bilayer membranes. J Chem Phys 2013. [PMID: 23206034 DOI: 10.1063/1.4767568] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Molecular dynamics simulations have been used to determine the diffusion of water molecules as a function of their position in a fully hydrated freestanding 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) bilayer membrane at 303 K and 1 atm. The diffusion rate of water in a ∼10 Å thick layer just outside the membrane surface is reduced on average by a factor of ∼2 relative to bulk. For water molecules penetrating deeper into the membrane, there is an increasing reduction in the average diffusion rate with up to one order of magnitude decrease for those deepest in the membrane. A comparison with the diffusion rate of selected atoms in the lipid molecules shows that ∼6 water molecules per lipid molecule move on the same time scale as the lipids and may therefore be considered to be tightly bound to them. The quasielastic neutron scattering functions for water and selected atoms in the lipid molecule have been simulated and compared to observed quasielastic neutron scattering spectra from single-supported bilayer DMPC membranes.
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Affiliation(s)
- F Y Hansen
- Department of Chemistry, Technical University of Denmark, IK 207 DTU, DK-2800 Lyngby, Denmark.
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4
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Gorbachev EV, Fomina NA, Kiselev MG, Kolker AM. The influence of nanotubes with various chirality on solvent structure. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2012. [DOI: 10.1134/s0036024412080043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Qiao BF, Sega M, Holm C. Properties of water in the interfacial region of a polyelectrolyte bilayer adsorbed onto a substrate studied by computer simulations. Phys Chem Chem Phys 2012; 14:11425-32. [PMID: 22801605 DOI: 10.1039/c2cp41115f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We study the static and dynamic properties of water near a poly(styrene sulfonate)/poly(diallyldimethylammonium) (PSS/PDADMA) bilayer adsorbed onto a substrate by atomistic molecular dynamics simulations. Qualitative changes in the dynamics of water in the proximity of the adsorbed bilayer are observed - such as in the lateral diffusion, residence time and hydrogen-bonding lifetime - as compared with water in the presence of the bare substrate. Static properties of water are similarly influenced, and a high polarization of water molecules is found to be present surprisingly far from the adsorbed bilayer.
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Affiliation(s)
- Bao-Fu Qiao
- Institute for Computational Physics, Universität Stuttgart, Pfaffenwaldring 27, 70569 Stuttgart, Germany
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6
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Teixeira J. Recent experimental aspects of the structure and dynamics of liquid and supercooled water. Mol Phys 2012. [DOI: 10.1080/00268976.2011.645894] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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7
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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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8
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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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9
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Heinzelmann G, Figueiredo W, Girardi M. Orientational dynamics for an amphiphilic-solvent solution. J Chem Phys 2011; 134:064901. [PMID: 21322728 DOI: 10.1063/1.3537737] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In this work, we performed Monte Carlo simulations on a lattice model for spontaneous amphiphilic aggregation, in order to study the orientational and hydrogen-bonding dynamics of water on different regions inside the micellar solution. We employed an associating lattice gas model that mimics the aqueous solvent, which presents a rich phase diagram with first- and second-order transition lines. Even though this is a simplified model, it makes possible to investigate the orientational dynamics of water in an equilibrium solution of amphiphiles, as well as the influence of the different phases of the solvent in the interfacial and bulk water dynamics. By means of extensive simulations, we showed that, at high temperatures, the behavior of the orientational relaxation and hydrogen bonding of water molecules in the bulk, first, and second hydration shells are considerable different. We observe the appearance of a very slow component for water molecules in the first hydration shell of micelles when the system reaches a high-density phase, consistent with previous theoretical and experimental studies concerning biological water. Also, at high temperatures, we find that water molecules in the second hydration shell of micelles have an orientational decay similar to that of bulk water, but with a generally slower dynamics. Otherwise, at low temperatures, we have two components for the orientational relaxation of bulk water in the low density liquid phase, and only a single component in the high density liquid (HDL) phase, which reflect the symmetry properties of the different phases of the solvent model. In the very dense region of water molecules in the first hydration shell of micelles at low temperatures, we find two components for the orientational relaxation on both liquid phases, one of them much slower than that in the single component of bulk water in the HDL phase. This happens even though our model does not present any hindrance to the water rotational freedom caused by the presence of the amphiphiles.
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Affiliation(s)
- G Heinzelmann
- School of Physics, University of Sydney, New South Wales 2006, Australia.
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10
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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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11
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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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12
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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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13
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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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14
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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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15
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Russo D, Teixeira J, Ollivier J. The impact of hydration water on the dynamics of side chains of hydrophobic peptides: from dry powder to highly concentrated solutions. J Chem Phys 2009; 130:235101. [PMID: 19548762 DOI: 10.1063/1.3154383] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Elastic and quasielastic neutron scattering experiments are used to investigate the dynamics of side chains in proteins, using hydrophobic peptides, from dry and hydrated powders up to solutions, as models. The changes of the internal dynamics of a prototypical hydrophobic amino acid, N-acetyl-leucine-methylamide, and alanine amino acids are investigated as a function of water/peptide molecular ratio. While previous results have shown that, in concentrated solution, when the hydrophobic side chains are hydrated by a single hydration water layer, the only allowed motions are confined and can be attributed to librational/rotational movements associated with the methyl groups. In the present work we observe a dynamical evolution from dry to highly hydrated powder. We also observe rotational and diffusive motions and a dynamical transition at approximately 250 K for long side chain peptides while for peptides with short side chains, there is no dynamical transition but only rotational motions. With a local measurement of the influence of hydration water dynamics on the amino acid side chains dynamics, we provide unique experimental evidence that the structural and dynamical properties of interfacial water strongly influence the side chain dynamics and the activation of diffusive motions. We also emphasize that the side chain length has a role on the onset of dynamical transition.
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Affiliation(s)
- Daniela Russo
- Institut Laue Langevin, CNR-INFM and CRS/Soft, 6 rue J. Horowitz BP156, F-38042 Grenoble, France.
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16
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Osaka N, Shibayama M, Kikuchi T, Yamamuro O. Quasi-Elastic Neutron Scattering Study on Water and Polymer Dynamics in Thermo/Pressure Sensitive Polymer Solutions. J Phys Chem B 2009; 113:12870-6. [DOI: 10.1021/jp902960b] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Noboru Osaka
- Neutron Science Laboratory, Institute for Solid State Physics, University of Tokyo, 106-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Mitsuhiro Shibayama
- Neutron Science Laboratory, Institute for Solid State Physics, University of Tokyo, 106-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Tatsuya Kikuchi
- Neutron Science Laboratory, Institute for Solid State Physics, University of Tokyo, 106-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Osamu Yamamuro
- Neutron Science Laboratory, Institute for Solid State Physics, University of Tokyo, 106-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
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17
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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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18
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Zhang Z, Berkowitz ML. Orientational Dynamics of Water in Phospholipid Bilayers with Different Hydration Levels. J Phys Chem B 2009; 113:7676-80. [DOI: 10.1021/jp900873d] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhancheng Zhang
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Max L Berkowitz
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
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19
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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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20
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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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21
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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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22
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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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23
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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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24
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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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25
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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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26
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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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27
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Ebbinghaus S, Kim SJ, Heyden M, Yu X, Gruebele M, Leitner DM, Havenith M. Protein Sequence- and pH-Dependent Hydration Probed by Terahertz Spectroscopy. J Am Chem Soc 2008; 130:2374-5. [DOI: 10.1021/ja0746520] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Simon Ebbinghaus
- Department of Physical Chemistry II, Ruhr-Universität Bochum 44780 Bochum, Germany, Department of Physics and Department of Chemistry and Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801, and Department of Chemistry, University of Nevada, Reno, Nevada 89557
| | - Seung Joong Kim
- Department of Physical Chemistry II, Ruhr-Universität Bochum 44780 Bochum, Germany, Department of Physics and Department of Chemistry and Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801, and Department of Chemistry, University of Nevada, Reno, Nevada 89557
| | - Matthias Heyden
- Department of Physical Chemistry II, Ruhr-Universität Bochum 44780 Bochum, Germany, Department of Physics and Department of Chemistry and Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801, and Department of Chemistry, University of Nevada, Reno, Nevada 89557
| | - Xin Yu
- Department of Physical Chemistry II, Ruhr-Universität Bochum 44780 Bochum, Germany, Department of Physics and Department of Chemistry and Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801, and Department of Chemistry, University of Nevada, Reno, Nevada 89557
| | - Martin Gruebele
- Department of Physical Chemistry II, Ruhr-Universität Bochum 44780 Bochum, Germany, Department of Physics and Department of Chemistry and Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801, and Department of Chemistry, University of Nevada, Reno, Nevada 89557
| | - David M. Leitner
- Department of Physical Chemistry II, Ruhr-Universität Bochum 44780 Bochum, Germany, Department of Physics and Department of Chemistry and Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801, and Department of Chemistry, University of Nevada, Reno, Nevada 89557
| | - Martina Havenith
- Department of Physical Chemistry II, Ruhr-Universität Bochum 44780 Bochum, Germany, Department of Physics and Department of Chemistry and Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801, and Department of Chemistry, University of Nevada, Reno, Nevada 89557
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28
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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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29
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Affiliation(s)
- Philip Ball
- Nature, 4-6 Crinan Street, London N1 9XW, U.K
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30
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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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31
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Oleinikova A, Smolin N, Brovchenko I. Influence of water clustering on the dynamics of hydration water at the surface of a lysozyme. Biophys J 2007; 93:2986-3000. [PMID: 17631539 PMCID: PMC2025659 DOI: 10.1529/biophysj.107.108753] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2007] [Accepted: 06/20/2007] [Indexed: 11/18/2022] Open
Abstract
Dynamics of hydration water at the surface of a lysozyme molecule is studied by computer simulations at various hydration levels in relation with water clustering and percolation transition. Increase of the translational mobility of water molecules at the surface of a rigid lysozyme molecule upon hydration is governed by the water-water interactions. Lysozyme dynamics strongly affect translational motions of water and this dynamic coupling is maximal at hydration levels, corresponding to the formation of a spanning water network. Anomalous diffusion of hydration water does not depend on hydration level up to monolayer coverage and reflects spatial disorder. Rotational dynamics of water molecules show stretched exponential decay at low hydrations. With increasing hydration, we observe appearance of weakly bound water molecules with bulklike rotational dynamics, whose fraction achieves 20-25% at the percolation threshold.
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Affiliation(s)
- Alla Oleinikova
- Physical Chemistry Department, Dortmund University, Dortmund, Germany
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32
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Chakraborty S, Bandyopadhyay S. Correlation between the Dynamics of Hydrogen Bonds and the Local Density Reorganization in the Protein Hydration Layer. J Phys Chem B 2007; 111:7626-30. [PMID: 17559262 DOI: 10.1021/jp072350e] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
An atomistic molecular dynamics simulation of the protein villin headpiece subdomain or HP-36 has been carried out with explicit water to explore the microscopic inhomogeneity of local density reorganization of the hydration layers of the three alpha-helical segments of the protein. The density reorganization of the hydration layer of helix-3 is found to occur faster than that for the hydration layers of the other two helices. It is noticed that such inhomogeneous density reorganization at the surface of different secondary structures exhibits excellent correlation with the microscopic dynamics of hydrogen bonds between the protein residues and the hydration water. Further, it is observed that the reorientation of water molecules involved in the formation and breaking of protein-water or water-water hydrogen bonds plays an important role in determining the dynamics of local density of the hydration layer. The faster density reorganization of the hydration layer of helix-3 is also consistent with the functionality of HP-36, as helix-3 contains several active site residues.
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Affiliation(s)
- Sudip Chakraborty
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur-721302, India
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33
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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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34
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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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35
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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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36
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Malardier-Jugroot C, Head-Gordon T. Separable cooperative and localized translational motions of water confined by a chemically heterogeneous environment. Phys Chem Chem Phys 2007; 9:1962-71. [PMID: 17431524 DOI: 10.1039/b616997j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report quasi-elastic neutron scattering experiments at two resolutions that probe timescales of picoseconds to nanoseconds for the hydration dynamics of water, confined in a concentrated solution of N-acetyl-leucine-methylamide (NALMA) peptides in water over a temperature range of 248 K to 288 K. The two QENS resolutions used allow for a clean separation of two observable translational components, and ultimately two very different relaxation processes, that become evident when analyzed under a combination of the jump diffusion model and the relaxation cage model. The first translational motion is a localized beta-relaxation process of the bound surface water, and exhibits an Arrhenius temperature dependence and a large activation energy of approximately 8 kcal mol(-1). The second non-Arrhenius translational component is a dynamical signature of the alpha-relaxation of more fluid water, exhibiting a glass transition temperature of approximately 116 K when fit to the Volger Fulcher Tamman functional form. These peptide solutions provide a novel experimental system for examining confinement in order to understand the dynamical transition in bulk supercooled water by removing the unwanted interface of the confining material on water dynamics.
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37
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Fedorov MV, Goodman JM, Schumm S. Solvent effects and hydration of a tripeptide in sodium halide aqueous solutions: an in silico study. Phys Chem Chem Phys 2007; 9:5423-35. [DOI: 10.1039/b706564g] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Pal S, Maiti PK, Bagchi B. Exploring DNA groove water dynamics through hydrogen bond lifetime and orientational relaxation. J Chem Phys 2006; 125:234903. [PMID: 17190573 DOI: 10.1063/1.2403872] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Dynamics of water molecules in the grooves of DNA are of great interest both for practical (functionality of DNA) and fundamental (as examples of confined systems) interest. Here the authors employ atomistic molecular dynamics simulations to understand varying water dynamics at the minor and the major grooves of a 38 base-pair long DNA duplex in water. In order to understand and quantify the diversity in the nature of hydrogen bond due to many hydrogen bond donors and acceptors present in the four bases, they have undertaken study of hydrogen bond lifetime (HBLT) correlation functions of all the specific hydrogen bonds between the base atoms and water molecules. They find that the HBLT correlation functions are in general multiexponential, with the average lifetime depending significantly on the specificity and may thus be biologically relevant. The average hydrogen bond lifetime is longer in the minor groove than that in the major groove by almost a factor of 2. Analysis further shows that water hydrogen bonds with phosphate oxygen have substantially shorter lifetimes than those with the groove atoms. They also compute two different orientational time correlation functions (OTCFs) of the water molecules present at the major and the minor grooves and attempt to correlate OTCF with HBLT correlation function. The OTCFs in the minor groove exhibit three time scales, with the time constant of the slowest component one to two orders of magnitude longer than what is observed for bulk water. A slow component is also present for the major groove water but with shorter time constant. Interestingly, correlation between reformations allowed HBLT correlation function [C(HB)(t)] and the OTCF markedly deviates from each other in the grooves, indicating enhanced rigidity of water molecules in the grooves.
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Affiliation(s)
- Subrata Pal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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39
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Bandyopadhyay S, Chakraborty S, Bagchi B. Exploration of the Secondary Structure Specific Differential Solvation Dynamics between the Native and Molten Globule States of the Protein HP-36. J Phys Chem B 2006; 110:20629-34. [PMID: 17034252 DOI: 10.1021/jp0633547] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent experiments have shown that the time dependence of fluorescence Stokes shift of a chromophore is substantially different when the chromophore is located in a molten globule (MG) state and in the native state of the same protein. To understand the origin of this difference, particularly the role of water in the differential solvation of the protein in the native and the MG states, we have carried out fully atomistic molecular dynamics simulations with explicit water of a partially unfolded MG state of the protein HP-36 and compared the results with the solvation dynamics of the protein in the folded native state. It is observed that the polar solvation dynamics of the three helical segments of the protein is influenced in a nonuniform heterogeneous manner in the MG state. While the equilibrium solvation time correlation function for helix-3 has been found to relax faster in the MG state as compared to that in the native state, the decay of the corresponding function for the other two helices slows down in the MG state. A careful analysis shows that the origin of such heterogeneous relative solvation behavior lies in the differential location of the polar probe residues and their exposure to bulk solvent. We find a significant negative cross-correlation between the contribution (to the solvation energy of a tagged amino acid residue) of water and the other groups of the protein, indicating a competing role in solvation. The sensitivity of solvation dynamics to the secondary structure and the immediate environment can be used to discriminate the partially unfolded and folded states. These results therefore should be useful in explaining recent solvation dynamics experiments on native and MG states of proteins.
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Affiliation(s)
- Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur-721302, India.
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40
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Hassanali AA, Li T, Zhong D, Singer SJ. A Molecular Dynamics Study of Lys-Trp-Lys: Structure and Dynamics in Solution Following Photoexcitation. J Phys Chem B 2006; 110:10497-508. [PMID: 16722759 DOI: 10.1021/jp0601926] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report studies of the structure and dynamics of a tripeptide Lys-Trp-Lys (KWK) in aqueous solution following photoexcitation by molecular dynamics simulations. For ground-state KWK, we observe three stable conformations with free energy differences of less than 5.2 kJ/mol. Each conformer is stabilized by a pi-cation interaction between one of three protonated amino groups and the indole moiety. For the excited state of tryptophan in KWK, the simulated molecular dynamics of the three isomers are similar, all in good agreement with recent femtosecond experiments (J. Phys. Chem. B 2005, 109, 16901). Specifically, we observe: (1) the fluorescence anisotropy is dominated by a single-exponential component and decays in approximately 130 ps, (2) the total dynamic Stokes shift reaches approximately 2700 cm(-1), and (3) the excited state relaxation dynamics occurs on several time scales ranging from femtoseconds to tens of picoseconds. The relaxation dynamics involve rapid initial response of neighboring water, followed by local motions of flexible peptide chains. These processes drive global restructuring of the tripeptide on a rather flat energy surface, inducing slower dynamics evident in both the water and protein contributions to the stabilization energy of the photoexcited chromophore. The water and protein dynamics are strongly correlated. On a still longer time scale, we observe isomerization of two excited state conformers to the other most stable one, an analogue for evolution of trajectories along the funnel on the rugged free energy landscape to the final "native" state. Our studies suggest new experiments to detect this unique dynamics.
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Affiliation(s)
- Ali A Hassanali
- Biophysics Program, Ohio State University, Columbus, Ohio 43210, USA
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41
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Bhide SY, Berkowitz ML. Structure and dynamics of water at the interface with phospholipid bilayers. J Chem Phys 2005; 123:224702. [PMID: 16375490 DOI: 10.1063/1.2132277] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have performed two molecular-dynamics simulations to study the structural and dynamical properties of water at the interface with phospholipid bilayers. In one of the simulations the bilayer contained neutral phospholipid molecules, dioleoylphosphatidylcholine (DOPC); in the second simulation the bilayer contained charged lipid molecules, dioleoylphosphatidylserine (DOPS). From the density profile of water we observe that water next to the DOPS bilayer is more perturbed as compared to water near the DOPC bilayer. Using an energetic criterion for the determination of hydrogen bonding we find that water molecules create strong hydrogen bonds with the headgroups of the phospholipid molecules. Due to the presence of these bonds and also due to the confinement of water, the translational and orientational dynamics of water at the interface are slowed down. The degree of slowing down of the dynamics depends upon the location of water molecules near a lipid headgroup.
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Affiliation(s)
- Shreyas Y Bhide
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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42
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Bandyopadhyay S, Chakraborty S, Bagchi B. Secondary Structure Sensitivity of Hydrogen Bond Lifetime Dynamics in the Protein Hydration Layer. J Am Chem Soc 2005; 127:16660-7. [PMID: 16305255 DOI: 10.1021/ja054462u] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The heterogeneous nature of a protein surface plays an essential role in its biological activity and molecular recognition, and this role is mediated at least partly through the surrounding water molecules. We have performed atomistic molecular dynamics simulations of an aqueous solution of HP-36 to investigate the correlation between the dynamics of the hydration layer water molecules and the lifetimes of protein-water hydrogen bonds. The nonexponential hydrogen bond lifetime correlation functions have been analyzed by using the formalism of Luzar and Chandler, which allowed identification of the quasi-bound states in the surface and quantification of the dynamic equilibrium between quasi-bound and free water molecules in terms of time-dependent rate of interconversion. It is noticed that, irrespective of the structural heterogeneity of different segments of the protein, namely the three alpha-helices, the positively charged amino acid residues form longer-lived hydrogen bonds with water. The overall relaxation behavior of protein-water hydrogen bonds is found to differ significantly among the three helices of the protein. Study of water number density fluctuation reveals that the hydration layer of helix-3 is much less rigid, which can be correlated with faster structural relaxation of the hydrogen bonds between its residues and water. This also agrees excellently with faster translational and rotational motions of water near helix-3, and hence the lower rigidity of its hydration layer. The lower rigidity of the helix-3 hydration layer also correlates well with the biological activity of the protein, as several of the active-site residues of HP-36 are located in helix-3.
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Affiliation(s)
- Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur-721302, India.
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43
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Mamontov E. High-resolution neutron-scattering study of slow dynamics of surface water molecules in zirconium oxide. J Chem Phys 2005; 123:24706. [PMID: 16050765 DOI: 10.1063/1.1949171] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have performed a quasielastic neutron-scattering experiment on backscattering spectrometer with sub-mueV resolution to investigate the slow dynamics of surface water in zirconium oxide using the sample studied previously with a time-of-flight neutron spectrometer [E. Mamontov, J. Chem. Phys. 121, 9087 (2004)]. The backscattering measurements in the temperature range of 240-300 K have revealed a translational dynamics slower by another order of magnitude compared to the translational dynamics of the outer hydration layer observed in the time-of-flight experiment. The relaxation function of this slow motion is described by a stretched exponential with the stretch factors between 0.8 and 0.9, indicating a distribution of the relaxation times. The temperature dependence of the average residence time is non-Arrhenius, suggesting that the translational motion studied in this work is more complex than surface jump diffusion previously observed for the molecules of the outer hydration layer. The observed slow dynamics is ascribed to the molecules of the inner hydration layer that form more hydrogen bonds compared to the molecules of the outer hydration layer. Despite being slower by two orders of magnitude, the translational motion of the molecules of the inner hydration layer may have more in common with bulk water compared to the outer hydration layer, the dynamics of which is slower than that of bulk water by just one order of magnitude.
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Affiliation(s)
- E Mamontov
- National Institute of Standards and Technology (NIST) Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8562, USA.
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44
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Russo D, Murarka RK, Copley JRD, Head-Gordon T. Molecular view of water dynamics near model peptides. J Phys Chem B 2005; 109:12966-75. [PMID: 16852609 PMCID: PMC2684815 DOI: 10.1021/jp051137k] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Incoherent quasi-elastic neutron scattering (QENS) has been used to measure the dynamics of water molecules in solutions of a model protein backbone, N-acetyl-glycine-methylamide (NAGMA), as a function of concentration, for comparison with results for water dynamics in aqueous solutions of the N-acetyl-leucine-methylamide (NALMA) hydrophobic peptide at comparable concentrations. From the analysis of the elastic incoherent structure factor, we find significant fractions of elastic intensity at high and low concentrations for both solutes, which corresponds to a greater population of protons with rotational time scales outside the experimental resolution (>13 ps). The higher-concentration solutions show a component of the elastic fraction that we propose is due to water motions that are strongly coupled to the solute motions, while for low-concentration solutions an additional component is activated due to dynamic coupling between inner and outer hydration layers. An important difference between the solute types at the highest concentration studied is found from stretched exponential fits to their experimental intermediate scattering functions, showing more pronounced anomalous diffusion signatures for NALMA, including a smaller stretched exponent beta and a longer structural relaxation time tau than those found for NAGMA. The more normal water diffusion exhibited near the hydrophilic NAGMA provides experimental support for an explanation of the origin of the anomalous diffusion behavior of NALMA as arising from frustrated interactions between water molecules when a chemical interface is formed upon addition of a hydrophobic side chain, inducing spatial heterogeneity in the hydration dynamics in the two types of regions of the NALMA peptide. We place our QENS measurements on model biological solutes in the context of other spectroscopic techniques and provide both confirming as well as complementary dynamic information that attempts to give a unifying molecular view of hydration dynamics signatures near peptides and proteins.
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Affiliation(s)
- Daniela Russo
- Authors to whom correspondence should be addressed. E-mail: ;
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