1
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Sugiyama JI, Tokunaga Y, Hishida M, Tanaka M, Takeuchi K, Satoh D, Imashimizu M. Nonthermal acceleration of protein hydration by sub-terahertz irradiation. Nat Commun 2023; 14:2825. [PMID: 37217486 DOI: 10.1038/s41467-023-38462-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 04/20/2023] [Indexed: 05/24/2023] Open
Abstract
The collective intermolecular dynamics of protein and water molecules, which overlap in the sub-terahertz (THz) frequency region, are relevant for expressing protein functions but remain largely unknown. This study used dielectric relaxation (DR) measurements to investigate how externally applied sub-THz electromagnetic fields perturb the rapid collective dynamics and influence the considerably slower chemical processes in protein-water systems. We analyzed an aqueous lysozyme solution, whose hydration is not thermally equilibrated. By detecting time-lapse differences in microwave DR, we demonstrated that sub-THz irradiation gradually decreases the dielectric permittivity of the lysozyme solution by reducing the orientational polarization of water molecules. Comprehensive analysis combining THz and nuclear magnetic resonance spectroscopies suggested that the gradual decrease in the dielectric permittivity is not induced by heating but is due to a slow shift toward the hydrophobic hydration structure in lysozyme. Our findings can be used to investigate hydration-mediated protein functions based on sub-THz irradiation.
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Affiliation(s)
- Jun-Ichi Sugiyama
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8565, Japan
| | - Yuji Tokunaga
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Mafumi Hishida
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8571, Japan
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku, Tokyo, 162-8601, Japan
| | - Masahito Tanaka
- Research Institute for Measurement and Analytical Instrumentation, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8568, Japan
| | - Koh Takeuchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Daisuke Satoh
- Research Institute for Measurement and Analytical Instrumentation, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8568, Japan
| | - Masahiko Imashimizu
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8565, Japan.
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2
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Hu K, Matsuura H, Shirakashi R. Stochastic Analysis of Molecular Dynamics Reveals the Rotation Dynamics Distribution of Water around Lysozyme. J Phys Chem B 2022; 126:4520-4530. [PMID: 35675630 DOI: 10.1021/acs.jpcb.2c00970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Water dynamics is essential to biochemical processes by mediating all such reactions, including biomolecular degeneration in solutions. To disentangle the molecular-scale distribution of water dynamics around a solute biomolecule, we investigated here the rotational dynamics of water around lysozyme by combining molecular dynamics (MD) simulations and broadband dielectric spectroscopy (BDS). A statistical analysis using the relaxation times and trajectories of every single water molecule was proposed, and the two-dimensional probability distribution of water at a distance from the lysozyme surface with a rotational relaxation time was given. For the observed lysozyme solutions of 34-284 mg/mL, we discovered that the dielectric relaxation time obtained from this distribution agrees well with the measured γ relaxation time, which suggests that rotational self-correlation of water molecules underlies the gigahertz domain of the dielectric spectra. Regardless of protein concentration, water rotational relaxation time versus the distance from the lysozyme surface revealed that the water rotation is severely retarded within 3 Å from the lysozyme surface and is nearly comparable to pure water when farther than 10 Å. The dimension of the first hydration layer was subsequently identified in terms of the relationship between the acceleration of water rotation and the distance from the protein surface.
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Affiliation(s)
- Kang Hu
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro City, Tokyo 153-8505, Japan.,Department of Mechanical Engineering, The University of Tokyo, 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Matsuura
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro City, Tokyo 153-8505, Japan.,Research Fellow of the Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Ryo Shirakashi
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro City, Tokyo 153-8505, Japan
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3
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Roy P, Sengupta N. Hydration of a small protein under carbon nanotube confinement: Adsorbed substates induce selective separation of the dynamical response. J Chem Phys 2021; 154:204702. [PMID: 34241160 DOI: 10.1063/5.0047078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The co-involvement of biological molecules and nanomaterials has increasingly come to the fore in modern-day applications. While the "bio-nano" (BN) interface presents physico-chemical characteristics that are manifestly different from those observed in isotropic bulk conditions, the underlying molecular reasons remain little understood; this is especially true of anomalies in interfacial hydration. In this paper, we leverage atomistic simulations to study differential adsorption characteristics of a small protein on the inner (concave) surface of a single-walled carbon nanotube whose diameter exceeds dimensions conducive to single-file water movement. Our findings indicate that the extent of adsorption is decided by the degree of foldedness of the protein conformational substate. Importantly, we find that partially folded substates, but not the natively folded one, induce reorganization of the protein hydration layer into an inner layer water closer to the nanotube axis and an outer layer water in the interstitial space near the nanotube walls. Further analyses reveal sharp dynamical differences between water molecules in the two layers as observed in the onset of increased heterogeneity in rotational relaxation and the enhanced deviation from Fickian behavior. The vibrational density of states reveals that the dynamical distinctions are correlated with differences in crucial bands in the power spectra. The current results set the stage for further systematic studies of various BN interfaces vis-à-vis control of hydration properties.
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Affiliation(s)
- Priti Roy
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Neelanjana Sengupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
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4
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Vasiljevic T, Toebes A, Huppertz T. Moisture sorption by dairy powders studied by low-field NMR. Int Dairy J 2021. [DOI: 10.1016/j.idairyj.2021.105062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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5
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Leitner DM, Hyeon C, Reid KM. Water-mediated biomolecular dynamics and allostery. J Chem Phys 2020; 152:240901. [DOI: 10.1063/5.0011392] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Seoul 02455, South Korea
| | - Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
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6
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Nakagawa H, Kataoka M. How can we derive hydration water dynamics with incoherent neutron scattering and molecular dynamics simulation? Biophys Physicobiol 2020; 16:213-219. [PMID: 31984174 PMCID: PMC6975894 DOI: 10.2142/biophysico.16.0_213] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 06/29/2019] [Indexed: 12/01/2022] Open
Abstract
Incoherent neutron scattering (INS) is one of the useful experimental methods for studying protein dynamics at the pico-nanosecond timescale. At this timescale, protein dynamics is highly coupled with hydration, which is observed as protein dynamical transition (PDT). INS is very sensitive to hydrogen atomic dynamics because of the large incoherent scattering cross section of hydrogen atom, and thus, the INS of a hydrated protein provides overall dynamic information about the protein, including hydration water. Separation of hydration water dynamics is essential for understanding hydration-related protein dynamics. H2O/D2O exchange is an effective method in the context of INS experiments for observing the dynamics of protein and hydration water separately. Neutron scattering is directly related to the van Hove space-time correlation function, which can be calculated quantitatively by performing molecular dynamics (MD) simulations. Diffusion and hydrogen bond dynamics of hydration water can be analyzed by performing MD simulation. MD simulation is useful for analyzing the dynamic coupling mechanism in hydration-related protein dynamics from the viewpoint of interpreting INS data because PDT is induced by hydration. In the present work, we demonstrate the methodological advantages of the H2O/D2O exchange technique in INS and the compatibility of INS and MD simulation as tools for studying protein dynamics and hydration water.
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Affiliation(s)
- Hiroshi Nakagawa
- Hierarchical Structure Research Group, Materials Science Research Center, Japan Atomic Energy Agency, Naka-gun, Ibaraki 319-1195, Japan
| | - Mikio Kataoka
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.,Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society (CROSS), Naka-gun, Ibaraki, Japan
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7
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Maurer M, Oostenbrink C. Water in protein hydration and ligand recognition. J Mol Recognit 2019; 32:e2810. [PMID: 31456282 PMCID: PMC6899928 DOI: 10.1002/jmr.2810] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 12/16/2022]
Abstract
This review describes selected basics of water in biomolecular recognition. We focus on a qualitative understanding of the most important physical aspects, how these change in magnitude between bulk water and protein environment, and how the roles that water plays for proteins arise from them. These roles include mechanical support, thermal coupling, dielectric screening, mass and charge transport, and the competition with a ligand for the occupation of a binding site. The presence or absence of water has ramifications that range from the thermodynamic binding signature of a single ligand up to cellular survival. The large inhomogeneity in water density, polarity and mobility around a solute is hard to assess in experiment. This is a source of many difficulties in the solvation of protein models and computational studies that attempt to elucidate or predict ligand recognition. The influence of water in a protein binding site on the experimental enthalpic and entropic signature of ligand binding is still a point of much debate. The strong water‐water interaction in enthalpic terms is counteracted by a water molecule's high mobility in entropic terms. The complete arrest of a water molecule's mobility sets a limit on the entropic contribution of a water displacement process, while the solvent environment sets limits on ligand reactivity.
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Affiliation(s)
- Manuela Maurer
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
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8
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Sasaki K, Popov I, Feldman Y. Water in the hydrated protein powders: Dynamic and structure. J Chem Phys 2019; 150:204504. [DOI: 10.1063/1.5096881] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Kaito Sasaki
- Micro/Nano Technology Center, Tokai University, 4-1-1 Kitakaname, Hiratsuka-shi, Kanagawa, Japan
- Department of Applied Physics, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 91904, Israel
| | - Ivan Popov
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Yuri Feldman
- Department of Applied Physics, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 91904, Israel
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9
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Abstract
Much of biology happens at the protein-water interface, so all dynamical processes in this region are of fundamental importance. Local structural fluctuations in the hydration layer can be probed by 17O magnetic relaxation dispersion (MRD), which, at high frequencies, measures the integral of a biaxial rotational time correlation function (TCF)-the integral rotational correlation time. Numerous 17O MRD studies have demonstrated that this correlation time, when averaged over the first hydration shell, is longer than in bulk water by a factor 3-5. This rotational perturbation factor (RPF) has been corroborated by molecular dynamics simulations, which can also reveal the underlying molecular mechanisms. Here, we address several outstanding problems in this area by analyzing an extensive set of molecular dynamics data, including four globular proteins and three water models. The vexed issue of polarity versus topography as the primary determinant of hydration water dynamics is resolved by establishing a protein-invariant exponential dependence of the RPF on a simple confinement index. We conclude that the previously observed correlation of the RPF with surface polarity is a secondary effect of the correlation between polarity and confinement. Water rotation interpolates between a perturbed but bulk-like collective mechanism at low confinement and an exchange-mediated orientational randomization (EMOR) mechanism at high confinement. The EMOR process, which accounts for about half of the RPF, was not recognized in previous simulation studies, where only the early part of the TCF was examined. Based on the analysis of the experimentally relevant TCF over its full time course, we compare simulated and measured RPFs, finding a 30% discrepancy attributable to force field imperfections. We also compute the full 17O MRD profile, including the low-frequency dispersion produced by buried water molecules. Computing a local RPF for each hydration shell, we find that the perturbation decays exponentially with a decay "length" of 0.3 shells and that the second and higher shells account for a mere 3% of the total perturbation measured by 17O MRD. The only long-range effect is a weak water alignment in the electric field produced by an electroneutral protein (not screened by counterions), but this effect is negligibly small for 17O MRD. By contrast, we find that the 17O TCF is significantly more sensitive to the important short-range perturbations than the other two TCFs examined here.
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Affiliation(s)
- Filip Persson
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Pär Söderhjelm
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Bertil Halle
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
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10
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Abstract
Based on molecular dynamics simulations of four globular proteins in dilute aqueous solution, with three different water models, we examine several, essentially geometrical, aspects of the protein-water interface that remain controversial or incompletely understood. First, we compare different hydration shell definitions, based on spatial or topological proximity criteria. We find that the best method for constructing monolayer shells with nearly complete coverage is to use a 5 Å water-carbon cutoff and a 4 Å water-water cutoff. Using this method, we determine a mean interfacial water area of 11.1 Å2 which appears to be a universal property of the protein-water interface. We then analyze the local coordination and packing density of water molecules in the hydration shells and in subsets of the first shell. The mean polar water coordination number in the first shell remains within 1% of the bulk-water value, and it is 5% lower in the nonpolar part of the first shell. The local packing density is obtained from additively weighted Voronoi tessellation, arguably the most physically realistic method for allocating space between protein and water. We find that water in all parts of the first hydration shell, including the nonpolar part, is more densely packed than in the bulk, with a shell-averaged density excess of 6% for all four proteins. We suggest reasons why this value differs from previous experimental and computational results, emphasizing the importance of a realistic placement of the protein-water dividing surface and the distinction between spatial correlation and packing density. The protein-induced perturbation of water coordination and packing density is found to be short-ranged, with an exponential decay "length" of 0.6 shells. We also compute the protein partial volume, analyze its decomposition, and argue against the relevance of electrostriction.
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Affiliation(s)
- Filip Persson
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Pär Söderhjelm
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Bertil Halle
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
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11
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Choi JH, Lee H, Choi HR, Cho M. Graph Theory and Ion and Molecular Aggregation in Aqueous Solutions. Annu Rev Phys Chem 2018; 69:125-149. [DOI: 10.1146/annurev-physchem-050317-020915] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jun-Ho Choi
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
- Current affiliation: Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Hochan Lee
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Hyung Ran Choi
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
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12
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Kurzweil-Segev Y, Popov I, Eisenberg I, Yochelis S, Keren N, Paltiel Y, Feldman Y. Confined water dynamics in a hydrated photosynthetic pigment-protein complex. Phys Chem Chem Phys 2017; 19:28063-28070. [PMID: 28994836 DOI: 10.1039/c7cp05417c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Water is of fundamental importance for life. It plays a critical role in all biological systems. In phycocyanin, a pigment-protein complex, the hydration level influences its absorption spectrum. However, there is currently a gap in the understanding of how protein interfaces affect water's structure and properties. This work presents combined dielectric and calorimetric measurements of hydrated phycocyanin with different levels of hydration in a broad temperature interval. Based on the dielectric and calorimetric tests, it was shown that two types of water exist in the phycocyanin hydration shell. One is confined water localized inside the phycocyanin ring and the second is the water that is embedded in the protein structure and participates in the protein solvation. The water confined in the phycocyanin ring melts at the temperature 195 ± 3 K and plays a role in the solvation at higher temperatures. Moreover, the dynamics of all types of water was found to be effected by the presence of the ionic buffer.
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Affiliation(s)
- Yael Kurzweil-Segev
- Applied Physics Department and the Center for Nano-Science and Nano-Technology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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13
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Choi JH, Cho M. Ion aggregation in high salt solutions. VI. Spectral graph analysis of chaotropic ion aggregates. J Chem Phys 2016; 145:174501. [DOI: 10.1063/1.4966246] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jun-Ho Choi
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Korea University, Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Korea University, Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
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14
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Choi JH, Cho M. Ion aggregation in high salt solutions. V. Graph entropy analyses of ion aggregate structure and water hydrogen bonding network. J Chem Phys 2016; 144:204126. [DOI: 10.1063/1.4952648] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Jun-Ho Choi
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Korea University, Seoul 02841, South Korea and Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Korea University, Seoul 02841, South Korea and Department of Chemistry, Korea University, Seoul 02841, South Korea
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15
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Khodadadi S, Sokolov AP. Atomistic details of protein dynamics and the role of hydration water. Biochim Biophys Acta Gen Subj 2016; 1861:3546-3552. [PMID: 27155577 DOI: 10.1016/j.bbagen.2016.04.028] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 04/26/2016] [Accepted: 04/27/2016] [Indexed: 11/19/2022]
Abstract
BACKGROUND The importance of protein dynamics for their biological activity is now well recognized. Different experimental and computational techniques have been employed to study protein dynamics, hierarchy of different processes and the coupling between protein and hydration water dynamics. Yet, understanding the atomistic details of protein dynamics and the role of hydration water remains rather limited. SCOOP OF REVIEW Based on overview of neutron scattering, molecular dynamic simulations, NMR and dielectric spectroscopy results we present a general picture of protein dynamics covering time scales from faster than ps to microseconds and the influence of hydration water on different relaxation processes. MAJOR CONCLUSIONS Internal protein dynamics spread over a wide time range from faster than picosecond to longer than microseconds. We suggest that the structural relaxation in hydrated proteins appears on the microsecond time scale, while faster processes present mostly motion of side groups and some domains. Hydration water plays a crucial role in protein dynamics on all time scales. It controls the coupled protein-hydration water relaxation on 10-100ps time scale. This process defines the friction for slower protein dynamics. Analysis suggests that changes in amount of hydration water affect not only general friction, but also influence significantly the protein's energy landscape. GENERAL SIGNIFICANCE The proposed atomistic picture of protein dynamics provides deeper understanding of various relaxation processes and their hierarchy, similarity and differences between various biological macromolecules, including proteins, DNA and RNA. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo".
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Affiliation(s)
- Sheila Khodadadi
- Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands; Delft Project management B.V., Delft University of Technology, Delft, The Netherlands
| | - Alexei P Sokolov
- Joint Institute for Neutron Sciences, University of Tennessee, Knoxville, TN, USA.
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16
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Agranovich D, Renhart I, Ben Ishai P, Katz G, Bezman D, Feldman Y. A microwave sensor for the characterization of bovine milk. Food Control 2016. [DOI: 10.1016/j.foodcont.2015.11.032] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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17
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Kurzweil-Segev Y, Greenbaum (Gutina) A, Popov I, Golodnitsky D, Feldman Y. The role of the confined water in the dynamic crossover of hydrated lysozyme powders. Phys Chem Chem Phys 2016; 18:10992-9. [DOI: 10.1039/c6cp01084a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work presents combined dielectric and calorimetric measurements of hydrated lysozyme powders with different levels of hydration in a broad temperature interval.
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Affiliation(s)
- Y. Kurzweil-Segev
- The Hebrew University of Jerusalem
- Department of Applied Physics
- Jerusalem 91904
- Israel
| | - A. Greenbaum (Gutina)
- The Hebrew University of Jerusalem
- Department of Applied Physics
- Jerusalem 91904
- Israel
| | - I. Popov
- The Hebrew University of Jerusalem
- Department of Applied Physics
- Jerusalem 91904
- Israel
- Institute of Physics
| | - D. Golodnitsky
- School of Chemistry
- Applied Materials Research Center
- Tel Aviv University
- Tel Aviv
- Israel
| | - Yu. Feldman
- The Hebrew University of Jerusalem
- Department of Applied Physics
- Jerusalem 91904
- Israel
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18
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Rani P, Biswas P. Diffusion of Hydration Water around Intrinsically Disordered Proteins. J Phys Chem B 2015; 119:13262-70. [PMID: 26418258 DOI: 10.1021/acs.jpcb.5b07248] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydration water dynamics around globular proteins have attracted considerable attention in the past decades. This work investigates the hydration water dynamics around partially/fully intrinsically disordered proteins and compares it to that of the globular proteins via molecular dynamics simulations. The translational diffusion of the hydration water is examined by evaluating the mean-square displacement and the velocity autocorrelation function, while the rotational diffusion is probed through the dipole-dipole time correlation function. The results reveal that the translational and rotational motions of water molecules at the surface of intrinsically disordered proteins/regions are less restricted as compared to those around globular proteins/ordered regions, which is reflected in their higher diffusion coefficient and lower orientational relaxation time. The restricted mobility of hydration water in the vicinity of the protein leads to a sublinear diffusion in a heterogeneous interface. A positive correlation between the mean number of hydrogen bonds and the diffusion coefficient of hydration water implies higher mobility of water molecules at the surface of disordered proteins, which is due to their higher number of hydrogen bonds. Enhanced hydration water mobility around disordered proteins/regions is also related to their higher hydration capacity, low hydrophobicity, and increased internal protein motions. Thus, we generalize that the intrinsically disordered proteins/regions are associated with higher hydration water mobility as compared to globular protein/ordered regions, which may help to elucidate their varied functional specificity.
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Affiliation(s)
- Pooja Rani
- Department of Chemistry, University of Delhi , Delhi 110007, India
| | - Parbati Biswas
- Department of Chemistry, University of Delhi , Delhi 110007, India
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19
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Draganski AR, Corradini MG, Ludescher RD. Revisiting time-resolved protein phosphorescence. APPLIED SPECTROSCOPY 2015; 69:1074-1081. [PMID: 26253845 DOI: 10.1366/14-07799] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Analysis of time-resolved phosphorescence data from proteins presents certain problems. Care must be taken in establishing that the analysis is not confounded in the early part of the decay by other emitting species. These species may include tyrosine, impurities found in the solvent, or impurities bound to the protein. In this paper, analysis of the phosphorescence of simple mixtures of tryptophan, tyrosine, and tryptophan + tyrosine in glycerol-water solvent has demonstrated the necessity of accounting for tyrosine emission in the analysis of protein phosphorescence. The tyrosine emission is especially strong at cold temperatures and becomes negligible above approximately 185 K in this solvent. Two fitting procedures have been developed to describe the bimodal emission that results from a single-tryptophan protein that contains a significant number of tyrosine residues. The methods utilize either a maximum entropy method-derived lifetime distribution or the stretched exponential function. In both cases some prior information regarding the expected decay characteristics of the tryptophan residue is applied to guide the separation of the tryptophan component from the tyrosine component. This prior information is obtained by comparing the tail of the protein decay to decays of free-tryptophan in solvent at a variety of temperatures until a match is found having close overlap on a log-intensity decay plot.
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Affiliation(s)
- Andrew R Draganski
- Rutgers University, Department of Food Science, 65 Dudley Road, New Brunswick, NJ 08901 USA
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20
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Khodadadi S, Sokolov AP. Protein dynamics: from rattling in a cage to structural relaxation. SOFT MATTER 2015; 11:4984-4998. [PMID: 26027652 DOI: 10.1039/c5sm00636h] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present an overview of protein dynamics based mostly on results of neutron scattering, dielectric relaxation spectroscopy and molecular dynamics simulations. We identify several major classes of protein motions on the time scale from faster than picoseconds to several microseconds, and discuss the coupling of these processes to solvent dynamics. Our analysis suggests that the microsecond backbone relaxation process might be the main structural relaxation of the protein that defines its glass transition temperature, while faster processes present some localized secondary relaxations. Based on the overview, we formulate a general picture of protein dynamics and discuss the challenges in this field.
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Affiliation(s)
- S Khodadadi
- Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
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21
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Floros S, Liakopoulou-Kyriakides M, Karatasos K, Papadopoulos GE. Detailed study of the dielectric function of a lysozyme solution studied with molecular dynamics simulations. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015; 44:599-611. [DOI: 10.1007/s00249-015-1052-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Revised: 05/28/2015] [Accepted: 06/02/2015] [Indexed: 11/30/2022]
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22
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Vajda T, Perczel A. Role of water in protein folding, oligomerization, amyloidosis and miniprotein. J Pept Sci 2014; 20:747-59. [PMID: 25098401 DOI: 10.1002/psc.2671] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 06/03/2014] [Accepted: 06/06/2014] [Indexed: 01/02/2023]
Abstract
The essential involvement of water in most fundamental extra-cellular and intracellular processes of proteins is critically reviewed and evaluated in this article. The role of water in protein behavior displays structural ambivalence; it can protect the disordered peptide-chain by hydration or helps the globular chain-folding, but promotes also the protein aggregation, as well (see: diseases). A variety of amyloid diseases begins as benign protein monomers but develops then into toxic amyloid aggregates of fibrils. Our incomplete knowledge of this process emphasizes the essential need to reveal the principles of governing this oligomerization. To understand the biophysical basis of the simpler in vitro amyloid formation may help to decipher also the in vivo way. Nevertheless, to ignore the central role of the water's effect among these events means to receive an uncompleted picture of the true phenomenon. Therefore this review represents a stopgap role, because the most published studies--with a few exceptions--have been neglected the crucial importance of water in the protein research. The following questions are discussed from the water's viewpoint: (i) interactions between water and proteins, (ii) protein hydration/dehydration, (iii) folding of proteins and miniproteins, (iv) peptide/protein oligomerization, and (v) amyloidosis.
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Affiliation(s)
- Tamás Vajda
- MTA-ELTE Protein Modelling Research Group, Eötvös Loránd University and Laboratory of Structural Chemistry & Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, 1117, Hungary
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23
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Gruenbaum SM, Skinner JL. Vibrational spectroscopy of water in hydrated lipid multi-bilayers. III. Water clustering and vibrational energy transfer. J Chem Phys 2014; 139:175103. [PMID: 24206336 DOI: 10.1063/1.4827018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Water clustering and connectivity around lipid bilayers strongly influences the properties of membranes and is important for functions such as proton and ion transport. Vibrational anisotropic pump-probe spectroscopy is a powerful tool for understanding such clustering, as the measured anisotropy depends upon the time-scale and degree of intra- and intermolecular vibrational energy transfer. In this article, we use molecular dynamics simulations and theoretical vibrational spectroscopy to help interpret recent experimental measurements of the anisotropy of water in lipid multi-bilayers as a function of both lipid hydration level and isotopic substitution. Our calculations are in satisfactory agreement with the experiments of Piatkowski, Heij, and Bakker, and from our simulations we can directly probe water clustering and connectivity. We find that at low hydration levels, many water molecules are in fact isolated, although up to 70% of hydration water forms small water clusters or chains. At intermediate hydration levels, water forms a wide range of cluster sizes, while at higher hydration levels, the majority of water molecules are part of a large, percolating water cluster. Therefore, the size, number, and nature of water clusters are strongly dependent on lipid hydration level, and the measured anisotropy reflects this through its dependence on intermolecular energy transfer.
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Affiliation(s)
- S M Gruenbaum
- Theoretical Chemistry Institute and Department of Chemistry, 1101 University Ave., University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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24
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Banerji A, Navare C. Fractal nature of protein surface roughness: a note on quantification of change of surface roughness in active sites, before and after binding. J Mol Recognit 2013; 26:201-14. [PMID: 23526774 DOI: 10.1002/jmr.2264] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 01/07/2013] [Accepted: 01/11/2013] [Indexed: 11/09/2022]
Abstract
Year 2010 marked the 25th year since we came to know that roughness of a protein surface has fractal symmetry. Ever since the publication of Lewis and Rees' paper, hundreds of works from a spectrum of perspectives have established that fractal dimension (FD) can be considered as a reliable marker that describes roughness of protein surface objectively. In this article, we introduce readers to the fundamentals of fractals and present categorical biophysical and geometrical reasons as to why FD-based constructs can describe protein surface roughness more accurately. We then review the commonality (and the lack of it) between numerous approaches that have attempted to investigate protein surface with fractal measures, before exploring the patterns in the results that they have produced. Apart from presenting the genealogy of approaches and results, we present an analysis that quantifies the difference in surface roughness in stretches of protein surface containing the active site, before and after binding to ligands, to underline the utility of FD-based measures further. It has been found that surface stretches containing the active site, in general, undergo a significant increment in its roughness after binding. After presenting the entire repertoire of FD-based surface roughness studies, we talk about two yet-unexplored problems where application of FD-based techniques can help in deciphering underlying patterns of surface interactions. Finally, we list the limitations of FD-based constructs and put down several precautions that one must take while working with them.
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Affiliation(s)
- Anirban Banerji
- Bioinformatics Centre, University of Pune, Pune, Maharashtra, India.
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25
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Sokolowska D, Dziob D, Gorska U, Kieltyka B, Moscicki JK. Electric conductivity percolation in naturally dehydrating, lightly wetted, hydrophilic fumed silica powder. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:062404. [PMID: 23848694 DOI: 10.1103/physreve.87.062404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 11/23/2012] [Indexed: 06/02/2023]
Abstract
In studying the dehydration of surface-moistened fumed silica Aerosil powders, we found a conductivity percolation transition at low hydration levels. Both the percolation exponent and the threshold are typical for correlated site-bond transitions in complex two-dimensional (2D) systems. The exponent values, 0.94-1.10, are indicative of severe heterogeneity in the conducting medium. The surface moisture at the percolation threshold takes on a universal value of 0.65 mg([H2O])/m(2)([silica]), independent of the silica grain size, and equivalent to twice the first hydration monolayer. This level is just sufficient to sustain a quasi-2D, hydrogen-bonded water network spanning the silica surface.
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Affiliation(s)
- Dagmara Sokolowska
- Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Krakow, Poland
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26
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Analysis of Bulk and Hydration Water During Thermal Lysozyme Denaturation Using Raman Scattering. FOOD BIOPHYS 2013. [DOI: 10.1007/s11483-013-9294-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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27
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Yu D, Hennig M, Mole RA, Li JC, Wheeler C, Strässle T, Kearley GJ. Proline induced disruption of the structure and dynamics of water. Phys Chem Chem Phys 2013; 15:20555-64. [DOI: 10.1039/c3cp51874d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Lerbret A, Affouard F, Hédoux A, Krenzlin S, Siepmann J, Bellissent-Funel MC, Descamps M. How strongly does trehalose interact with lysozyme in the solid state? Insights from molecular dynamics simulation and inelastic neutron scattering. J Phys Chem B 2012; 116:11103-16. [PMID: 22894179 DOI: 10.1021/jp3058096] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Therapeutic proteins are usually conserved in glassy matrixes composed of stabilizing excipients and a small amount of water, which both control their long-term stability, and thus their potential use in medical treatments. To shed some light on the protein-matrix interactions in such systems, we performed molecular dynamics (MD) simulations on matrixes of (i) the model globular protein lysozyme (L), (ii) the well-known bioprotectant trehalose (T), and (iii) the 1:1 (in weight) lysozyme/trehalose mixture (LT), at hydration levels h of 0.0, 0.075, and 0.15 (in g of water/g of protein or sugar). We also supplemented these simulations with complementary inelastic neutron scattering (INS) experiments on the L, T, and LT lyophilized (freeze-dried) samples. The densities and free volume distributions indicate that trehalose improves the molecular packing of the LT glass with respect to the L one. Accordingly, the low-frequency vibrational densities of states (VDOS) and the mean square displacements (MSDs) of lysozyme reveal that it is less flexible-and thus less likely to unfold-in the presence of trehalose. Furthermore, at low contents (h = 0.075), water systematically stiffens the vibrational motions of lysozyme and trehalose, whereas it increases their MSDs on the nanosecond (ns) time scale. This stems from the hydrogen bonds (HBs) that lysozyme and trehalose form with water, which, interestingly, are stronger than the ones they form with each other but which, nonetheless, relax faster on the ns time scale, given the larger mobility of water. Moreover, lysozyme interacts preferentially with water in the hydrated LT mixtures, and trehalose appears to slow down significantly the relaxation of lysozyme-water HBs. Overall, our results suggest that the stabilizing efficiency of trehalose arises from its ability to (i) increase the number of HBs formed by proteins in the dry state and (ii) make the HBs formed by water with proteins stable on long (>ns) time scales.
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Affiliation(s)
- Adrien Lerbret
- Unité Matériaux Et Transformations, UMR CNRS 8207, Université Lille Nord de France, USTL, 59655 Villeneuve d'Ascq, France.
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29
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Belton PS. NMR studies of hydration in low water content biopolymer systems. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2011; 49 Suppl 1:S127-S132. [PMID: 22290703 DOI: 10.1002/mrc.2848] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The problem of characterising the behaviour of water and biopolymers by NMR in low water content biopolymer systems is discussed. A low water content system is defined, and the problems of characterising the relaxation behaviour of the water are analysed. In the case of protons, the types of protons contributing to the signal and the exchange mechanism between them cannot be systematised in terms of existing models that have been developed for high water content systems. It is suggested that any successful model must take account of at least three separate pools of water including water vapour. Experimental results indicate that although the motion of the biopolymer is radically affected by water, the reverse is not necessarily true. It is concluded that the use of nuclei such as (13)C and (15)N may be very effectively used to characterise biopolymer motion, but the use of both (1)H and (2)H for characterising water is still problematic. Despite the formidable experimental and theoretical difficulties, (17)O NMR may be the only way to finally to untangle the problem.
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Affiliation(s)
- Peter S Belton
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, UK.
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de los Santos F, Franzese G. Understanding diffusion and density anomaly in a coarse-grained model for water confined between hydrophobic walls. J Phys Chem B 2011; 115:14311-20. [PMID: 22129131 DOI: 10.1021/jp206197t] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We study, by Monte Carlo simulations, a coarse-grained model of a water monolayer between hydrophobic walls at partial hydration, with a wall-to-wall distance of about 0.5 nm. We analyze how the diffusion constant parallel to the walls, D(∥), changes and correlates to the phase diagram of the system. We find a locus of D(∥) maxima and a locus of D(∥) minima along isotherms, with lines of constant D(∥) resembling the melting line of bulk water. The two loci of D(∥) extrema envelope the line of temperatures of density maxima at constant P. We show how these loci are related to the anomalous volume behavior due to the hydrogen bonds. At much lower T, confined water becomes subdiffusive, and we discuss how this behavior is a consequence of the increased correlations among water molecules when the hydrogen bond network develops. Within the subdiffusive region, although translations are largely hampered, we observe that the hydrogen bond network can equilibrate, and its rearrangement is responsible for the appearance of density minima along isobars. We clarify that the minima are not necessarily related to the saturation of the hydrogen bond network.
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Affiliation(s)
- Francisco de los Santos
- Departamento de Electromagnetismo y Física de la Materia, Universidad de Granada, Fuentenueva s/n, 18071 Granada, Spain
| | - Giancarlo Franzese
- Departamento de Física Fundamental, Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Spain
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31
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Cametti C, Marchetti S, Gambi C, Onori G. Dielectric Relaxation Spectroscopy of Lysozyme Aqueous Solutions: Analysis of the δ-Dispersion and the Contribution of the Hydration Water. J Phys Chem B 2011; 115:7144-53. [DOI: 10.1021/jp2019389] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- C. Cametti
- Department of Physics and INFM CRS-SOFT, “La Sapienza” University of Rome, Piazzale A. Moro 5, I-00185, Rome, Italy
| | - S. Marchetti
- Department of Physics, University of Florence and CNISM, Via G. Sansone 1, 50019 Sesto Fiorentino, Florence, Italy
| | - C.M.C. Gambi
- Department of Physics, University of Florence and CNISM, Via G. Sansone 1, 50019 Sesto Fiorentino, Florence, Italy
| | - G. Onori
- Department of Physics and INFM CRS-SOFT, University of Perugia, Via G. Pascoli, Perugia, Italy
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32
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Khodadadi S, Curtis JE, Sokolov AP. Nanosecond Relaxation Dynamics of Hydrated Proteins: Water versus Protein Contributions. J Phys Chem B 2011; 115:6222-6. [DOI: 10.1021/jp1122213] [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)
- S. Khodadadi
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - J. E. Curtis
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - A. P. Sokolov
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States, and Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
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33
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Belton P. Spectroscopic Approaches to the Understanding of Water in Foods. FOOD REVIEWS INTERNATIONAL 2011. [DOI: 10.1080/87559129.2010.535234] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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34
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Angulo-Sherman A, Mercado-Uribe H. Dielectric spectroscopy of water at low frequencies: The existence of an isopermitive point. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.01.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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35
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Gnanasekaran R, Xu Y, Leitner DM. Dynamics of water clusters confined in proteins: a molecular dynamics simulation study of interfacial waters in a dimeric hemoglobin. J Phys Chem B 2010; 114:16989-96. [PMID: 21126033 DOI: 10.1021/jp109173t] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Water confined in proteins exhibits dynamics distinct from the dynamics of water in the bulk or near the surface of a biomolecule. We examine the water dynamics at the interface of the two globules of the homodimeric hemoglobin from Scapharca inaequivalvis (HbI) by molecular dynamics (MD) simulations, with focus on water-protein hydrogen bond lifetimes and rotational anisotropy of the interfacial waters. We find that relaxation of the waters at the interface of both deoxy- and oxy-HbI, which contain a cluster of 17 and 11 interfacial waters, respectively, is well described by stretched exponentials with exponents from 0.1 to 0.6 and relaxation times of tens to thousands of picoseconds. The interfacial water molecules of oxy-HbI exhibit slower rotational relaxation and hydrogen bond rearrangement than those of deoxy-HbI, consistent with an allosteric transition from unliganded to liganded conformers involving the expulsion of several water molecules from the interface. Though the interfacial waters are translationally and rotationally static on the picosecond time scale, they contribute to fast communication between the globules via vibrations. We find that the interfacial waters enhance vibrational energy transport across the interface by ≈10%.
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36
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Ye S, Markelz A. Hydration Effects on Energy Relaxation of Ferric Cytochrome C Films after Soret-Band Photoexcitation. J Phys Chem B 2010; 114:15151-7. [DOI: 10.1021/jp104217j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Shuji Ye
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China 230026, and Department of Physics, University at Buffalo, SUNY, 239 Fronczak Hall, Buffalo, New York 14260-1500, United States
| | - Andrea Markelz
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China 230026, and Department of Physics, University at Buffalo, SUNY, 239 Fronczak Hall, Buffalo, New York 14260-1500, United States
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37
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Nanosecond motions in proteins impose bounds on the timescale distributions of local dynamics. Biophys J 2009; 97:2080-8. [PMID: 19804740 DOI: 10.1016/j.bpj.2009.07.036] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2009] [Revised: 06/16/2009] [Accepted: 07/23/2009] [Indexed: 11/21/2022] Open
Abstract
We elucidate the physics of protein dynamical transition via 10-100-ns molecular dynamics simulations at temperatures spanning 160-300 K. By tracking the energy fluctuations, we show that the protein dynamical transition is marked by a crossover from nonstationary to stationary processes that underlie the dynamics of protein motions. A two-timescale function captures the nonexponential character of backbone structural relaxations. One timescale is attributed to the collective segmental motions and the other to local relaxations. The former is well defined by a single-exponential, nanosecond decay, operative at all temperatures. The latter is described by a set of processes that display a distribution of timescales. Although their average remains on the picosecond timescale, the distribution is markedly contracted at the onset of the transition. It is shown that the collective motions impose bounds on timescales spanned by local dynamical processes. The nonstationary character below the transition implicates the presence of a collection of substates whose interactions are restricted. At these temperatures, a wide distribution of local-motion timescales, extending beyond that of nanoseconds, is observed. At physiological temperatures, local motions are confined to timescales faster than nanoseconds. This relatively narrow window makes possible the appearance of multiple channels for the backbone dynamics to operate.
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Krushelnitsky A, Zinkevich T, Mukhametshina N, Tarasova N, Gogolev Y, Gnezdilov O, Fedotov V, Belton P, Reichert D. 13C and 15N NMR study of the hydration response of T4 lysozyme and alphaB-crystallin internal dynamics. J Phys Chem B 2009; 113:10022-34. [PMID: 19603846 DOI: 10.1021/jp900337x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The response to hydration of the internal protein dynamics was studied by the means of solid state NMR relaxation and magic angle spinning exchange techniques. Two proteins, lysozyme from bacteriophage T4 and human alphaB-crystallin were used as exemplars. The relaxation rates R1 and R1rho of 13C and 15N nuclei were measured as a function of a hydration level of the proteins in the range 0-0.6 g of water/g of protein. Both proteins were totally 15N-enriched with natural 13C abundance. The relaxation rates were measured for different spectral bands (peaks) that enabled the characterization of the dynamics separately for the backbone, side chains, and CH3 and NH3+ groups. The data obtained allowed a comparative analysis of the hydration response of the protein dynamics in different frequency ranges and different sites in the protein for two different proteins and two magnetic nuclei. The most important result is a demonstration of a qualitatively different response to hydration of the internal dynamics in different frequency ranges. The amplitude of the fast (nanosecond time scale) motion gradually increases with increasing hydration, whereas that of the slow (microsecond time scale) motion increases only until the hydration level 0.2-0.3 g of water/g of protein and then shows almost no hydration dependence. The reason for such a difference is discussed in terms of the different physical natures of these two dynamic processes. Backbone and side chain nuclei show the same features of the response of dynamics with hydration despite the fact that the backbone motional amplitudes are much smaller than those of side chains. Although T4 lysozyme and alphaB-crystallin possess rather different structural and biochemical properties, both proteins show qualitatively very similar hydration responses. In addition to the internal motions, exchange NMR data enabled the identification of one more type of motion in the millisecond to second time scale that appears only at high hydration levels. This motion was attributed to the restricted librations of the protein as a whole.
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Affiliation(s)
- A Krushelnitsky
- Kazan Institute of Biochemistry and Biophysics, Kazan, Russia.
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Profiling of dynamics in protein-lipid-water systems: a time-resolved fluorescence study of a model membrane protein with the label BADAN at specific membrane depths. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 39:647-56. [PMID: 19760185 PMCID: PMC2841254 DOI: 10.1007/s00249-009-0538-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 08/19/2009] [Accepted: 08/26/2009] [Indexed: 12/03/2022]
Abstract
Profiles of lipid-water bilayer dynamics were determined from picosecond time-resolved fluorescence spectra of membrane-embedded BADAN-labeled M13 coat protein. For this purpose, the protein was labeled at seven key positions. This places the label at well-defined locations from the water phase to the center of the hydrophobic acyl chain region of a phospholipid model membrane, providing us with a nanoscale ruler to map membranes. Analysis of the time-resolved fluorescence spectroscopic data provides the characteristic time constant for the twisting motion of the BADAN label, which is sensitive to the local flexibility of the protein–lipid environment. In addition, we obtain information about the mobility of water molecules at the membrane–water interface. The results provide an unprecedented nanoscale profiling of the dynamics and distribution of water in membrane systems. This information gives clear evidence that the actual barrier of membranes for ions and aqueous solvents is located at the region of carbonyl groups of the acyl chains.
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40
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Aksan A, Hubel A, Bischof JC. Frontiers in biotransport: water transport and hydration. J Biomech Eng 2009; 131:074004. [PMID: 19640136 DOI: 10.1115/1.3173281] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Biotransport, by its nature, is concerned with the motions of molecules in biological systems while water remains as the most important and the most commonly studied molecule across all disciplines. In this review, we focus on biopreservation and thermal therapies from the perspective of water, exploring how its molecular motions, properties, kinetic, and thermodynamic transitions govern biotransport phenomena and enable preservation or controlled destruction of biological systems.
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Affiliation(s)
- Alptekin Aksan
- Center for Biotransport, Institute for Engineering in Medicine, University of Minnesota, Minneapolis, MN 55455, USA
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41
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Abstract
Biotransport, by its nature, is concerned with the motions of molecules in biological systems while water remains as the most important and the most commonly studied molecule across all disciplines. In this review, we focus on biopreservation and thermal therapies from the perspective of water, exploring how its molecular motions, properties, kinetic, and thermodynamic transitions govern biotransport phenomena and enable preservation or controlled destruction of biological systems.
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Affiliation(s)
- Alptekin Aksan
- Center for Biotransport, Institute for Engineering in Medicine, University of Minnesota, Minneapolis, MN 55455; Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455
| | - Allison Hubel
- Center for Biotransport, Institute for Engineering in Medicine, University of Minnesota, Minneapolis, MN 55455; Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455
| | - John C. Bischof
- Center for Biotransport, Institute for Engineering in Medicine, University of Minnesota, Minneapolis, MN 55455; Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455
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42
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Jansson H, Kargl F, Fernandez-Alonso F, Swenson J. Dynamics of a protein and its surrounding environment: A quasielastic neutron scattering study of myoglobin in water and glycerol mixtures. J Chem Phys 2009; 130:205101. [DOI: 10.1063/1.3138765] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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43
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Romero-Vargas Castrillón S, Giovambattista N, Aksay IA, Debenedetti PG. Evolution from Surface-Influenced to Bulk-Like Dynamics in Nanoscopically Confined Water. J Phys Chem B 2009; 113:7973-6. [DOI: 10.1021/jp9025392] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Santiago Romero-Vargas Castrillón
- Department of Chemical Engineering, Princeton University, Princeton New Jersey 08544-5263, and Physics Department, Brooklyn College of the City University of New York, Brooklyn, New York 11210
| | - Nicolás Giovambattista
- Department of Chemical Engineering, Princeton University, Princeton New Jersey 08544-5263, and Physics Department, Brooklyn College of the City University of New York, Brooklyn, New York 11210
| | - Ilhan A. Aksay
- Department of Chemical Engineering, Princeton University, Princeton New Jersey 08544-5263, and Physics Department, Brooklyn College of the City University of New York, Brooklyn, New York 11210
| | - Pablo G. Debenedetti
- Department of Chemical Engineering, Princeton University, Princeton New Jersey 08544-5263, and Physics Department, Brooklyn College of the City University of New York, Brooklyn, New York 11210
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44
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Mamontov E, Vlcek L, Wesolowski DJ, Cummings PT, Rosenqvist J, Wang W, Cole DR, Anovitz LM, Gasparovic G. Suppression of the dynamic transition in surface water at low hydration levels: a study of water on rutile. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 79:051504. [PMID: 19518459 DOI: 10.1103/physreve.79.051504] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Revised: 03/06/2009] [Indexed: 05/15/2023]
Abstract
Our quasielastic neutron-scattering experiments and molecular-dynamics simulations probing surface water on rutile (TiO2) have demonstrated that a sufficiently high hydration level is a prerequisite for the temperature-dependent crossover in the nanosecond dynamics of hydration water. Below the monolayer coverage of mobile surface water, a weak temperature dependence of the relaxation times with no apparent crossover is observed. We associate the dynamic crossover with interlayer jumps of the mobile water molecules, which become possible only at a sufficiently high hydration level.
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Affiliation(s)
- Eugene Mamontov
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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45
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Abstract
In recent years, significant progress has been made towards uncovering the physical mechanisms of low-hydration polymorphism in double-helical DNA. The effect appears to be mechanistically similar in different biological systems, and it is due to the ability of water to form spanning H-bonded networks around biomacromolecules via a quasi-two-dimensional percolation transition. In the case of DNA, disintegration of the spanning H-bonded network leads to electrostatic condensation of DNA strands because, below the percolation threshold, water loses its high dielectric permittivity, whereas the concentration of neutralizing counterions becomes high. In this Concept article arguments propose that this simple electrostatic mechanism represents the universal origin of low-hydration polymorphism in DNA.
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Affiliation(s)
- Alexey K Mazur
- CNRS UPR9080, Institut de Biologie Physico-Chimique, 13, rue Pierre et Marie Curie, Paris, France.
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46
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Brovchenko I, Oleinikova A. Which Properties of a Spanning Network of Hydration Water Enable Biological Functions? Chemphyschem 2008; 9:2695-702. [DOI: 10.1002/cphc.200800662] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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47
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Khodadadi S, Pawlus S, Sokolov AP. Influence of Hydration on Protein Dynamics: Combining Dielectric and Neutron Scattering Spectroscopy Data. J Phys Chem B 2008; 112:14273-80. [PMID: 18942780 DOI: 10.1021/jp8059807] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- S. Khodadadi
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, and Institute of Physics, Silesian University, ul. Uniwersytecka 4, 40-007 Katowice, Poland
| | - S. Pawlus
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, and Institute of Physics, Silesian University, ul. Uniwersytecka 4, 40-007 Katowice, Poland
| | - A. P. Sokolov
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, and Institute of Physics, Silesian University, ul. Uniwersytecka 4, 40-007 Katowice, Poland
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48
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Mallamace F, Corsaro C, Broccio M, Branca C, González-Segredo N, Spooren J, Chen SH, Stanley HE. NMR evidence of a sharp change in a measure of local order in deeply supercooled confined water. Proc Natl Acad Sci U S A 2008; 105:12725-9. [PMID: 18753633 PMCID: PMC2526099 DOI: 10.1073/pnas.0805032105] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Indexed: 11/18/2022] Open
Abstract
Using NMR, we measure the proton chemical shift delta, of supercooled nanoconfined water in the temperature range 195 K < T < 350 K. Because delta is directly connected to the magnetic shielding tensor, we discuss the data in terms of the local hydrogen bond geometry and order. We argue that the derivative -( partial differential ln delta/ partial differentialT)(P) should behave roughly as the constant pressure specific heat C(P)(T), and we confirm this argument by detailed comparisons with literature values of C(P)(T) in the range 290-370 K. We find that -( partial differential ln delta/ partial differentialT)(P) displays a pronounced maximum upon crossing the locus of maximum correlation length at approximately 240 K, consistent with the liquid-liquid critical point hypothesis for water, which predicts that C(P)(T) displays a maximum on crossing the Widom line.
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Affiliation(s)
- F. Mallamace
- *Dipartimento di Fisica e Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, Universitá di Messina, Villaggio Sant'Agata CP 55, 98166 Messina, Italy
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139; and
| | - C. Corsaro
- *Dipartimento di Fisica e Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, Universitá di Messina, Villaggio Sant'Agata CP 55, 98166 Messina, Italy
| | - M. Broccio
- *Dipartimento di Fisica e Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, Universitá di Messina, Villaggio Sant'Agata CP 55, 98166 Messina, Italy
| | - C. Branca
- *Dipartimento di Fisica e Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, Universitá di Messina, Villaggio Sant'Agata CP 55, 98166 Messina, Italy
| | - N. González-Segredo
- *Dipartimento di Fisica e Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, Universitá di Messina, Villaggio Sant'Agata CP 55, 98166 Messina, Italy
| | - J. Spooren
- *Dipartimento di Fisica e Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia, Universitá di Messina, Villaggio Sant'Agata CP 55, 98166 Messina, Italy
| | - S.-H. Chen
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139; and
| | - H. E. Stanley
- Centre for Polymer Studies and Department of Physics, Boston University, Boston, MA 02215
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49
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Brovchenko I, Krukau A, Oleinikova A, Mazur AK. Ion dynamics and water percolation effects in DNA polymorphism. J Am Chem Soc 2007; 130:121-31. [PMID: 18052374 DOI: 10.1021/ja0732882] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The dynamics of ions and water at the surface of DNA are studied by computer simulations in a wide range of hydrations involving the zone of low-hydration polymorphism in DNA. The long-range mobility of ions exhibits a stepwise increase at three distinct hydration levels. The first of them is close to the midpoint of the water percolation transition as well as the midpoint of the transition between A- and B-DNA forms. It coincides with the onset of the dissociation of ion pairs on the DNA surface probably caused by the increase in the water dielectric permittivity due to the appearance of the spanning hydrogen-bonding network. The other two steps are attributed to the formation of percolating water layers on the surface of DNA accompanied by the progressive escape of ions from the DNA surface. The results agree with earlier experimental data and further corroborate the suggested universal mechanism of the low hydration polymorphism in DNA including intraduplex electrostatic condensation close to the water percolation threshold.
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Affiliation(s)
- Ivan Brovchenko
- Physical Chemistry, Technical University of Dortmund, Otto-Hahn-Str. 6, Dortmund, D-44227, Germany
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