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Kocherbitov V, Latynis J, Misiu̅nas A, Barauskas J, Niaura G. Hydration of Lysozyme Studied by Raman Spectroscopy. J Phys Chem B 2013; 117:4981-92. [DOI: 10.1021/jp4017954] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vitaly Kocherbitov
- Biomedical Science, Faculty
of Health and Society, Malmö University, SE-20506 Malmö, Sweden
| | - Jekaterina Latynis
- Institute of Biochemistry, Vilnius University, Mokslininkų 12, LT-08662
Vilnius, Lithuania
| | - Audrius Misiu̅nas
- Institute of Biochemistry, Vilnius University, Mokslininkų 12, LT-08662
Vilnius, Lithuania
- Institute
of Chemistry, Center
for Physical Sciences and Technology, Goštauto 9, LT-01108
Vilnius, Lithuania
| | - Justas Barauskas
- Biomedical Science, Faculty
of Health and Society, Malmö University, SE-20506 Malmö, Sweden
- Institute of Biochemistry, Vilnius University, Mokslininkų 12, LT-08662
Vilnius, Lithuania
| | - Gediminas Niaura
- Institute of Biochemistry, Vilnius University, Mokslininkų 12, LT-08662
Vilnius, Lithuania
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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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3
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Rickard DL, Duncan PB, Needham D. Hydration potential of lysozyme: protein dehydration using a single microparticle technique. Biophys J 2010; 98:1075-84. [PMID: 20303865 DOI: 10.1016/j.bpj.2009.11.043] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 11/18/2009] [Accepted: 11/25/2009] [Indexed: 11/25/2022] Open
Abstract
For biological molecules in aqueous solution, the hydration pressure as a function of distance from the molecular surface represents a very short-range repulsive pressure that limits atom-atom contact, opposing the attractive van der Waals pressure. Whereas the separation distance for molecules that easily arrange into ordered arrays (e.g., lipids, DNA, collagen fibers) can be determined from x-ray diffraction, many globular proteins are not as easily structured. Using a new micropipette technique, spherical, glassified protein microbeads can be made that allow determination of protein hydration as a function of the water activity (a(w)) in a surrounding medium (decanol). By adjusting a(w) of the dehydration medium, the final protein concentration of the solid microbead is controlled, and ranges from 700 to 1150 mg/mL. By controlling a(w) (and thus the osmotic pressure) around lysozyme, the repulsive pressure was determined as a function of distance between each globular, ellipsoid protein. For separation distances, d, between 2.5 and 9 A, the repulsive decay length was 1.7 A and the pressure extrapolated to d = 0 was 2.2 x 10(8) N/m(2), indicating that the hydration pressure for lysozyme is similar to other biological interfaces such as phospholipid bilayers.
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Affiliation(s)
- Deborah L Rickard
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina, USA
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Piaggio MV, Peirotti MB, Deiber JA. Analysis of the interplay among charge, hydration and shape of proteins through the modeling of their CZE mobility data. Electrophoresis 2009; 30:2328-36. [DOI: 10.1002/elps.200800743] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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6
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Fornés JA. Electrical fluctuations on the surfaces of proteins from hydrodynamic data. J Colloid Interface Sci 2008; 323:255-9. [PMID: 18502437 DOI: 10.1016/j.jcis.2008.04.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2008] [Revised: 03/27/2008] [Accepted: 04/05/2008] [Indexed: 11/27/2022]
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7
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Lau EY, Krishnan VV. Temperature dependence of protein-hydration hydrodynamics by molecular dynamics simulations. Biophys Chem 2007; 130:55-64. [PMID: 17720293 DOI: 10.1016/j.bpc.2007.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2007] [Revised: 07/14/2007] [Accepted: 07/18/2007] [Indexed: 11/19/2022]
Abstract
The dynamics of water molecules near the protein surface are different from those of bulk water and influence the structure and dynamics of the protein itself. To elucidate the temperature dependence hydration dynamics of water molecules, we present results from the molecular dynamic simulation of the water molecules surrounding two proteins (Carboxypeptidase inhibitor and Ovomucoid) at seven different temperatures (T=273 to 303 K, in increments of 5 K). Translational diffusion coefficients of the surface water and bulk water molecules were estimated from 2 ns molecular dynamics simulation trajectories. Temperature dependence of the estimated bulk water diffusion closely reflects the experimental values, while hydration water diffusion is retarded significantly due to the protein. Protein surface induced scaling of translational dynamics of the hydration waters is uniform over the temperature range studied, suggesting the importance protein-water interactions.
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Affiliation(s)
- Edmond Y Lau
- Biology and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
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Miyawaki O. Hydration state change of proteins upon unfolding in sugar solutions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:928-35. [PMID: 17581805 DOI: 10.1016/j.bbapap.2007.05.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2007] [Revised: 05/16/2007] [Accepted: 05/17/2007] [Indexed: 10/23/2022]
Abstract
Change in hydration number of proteins upon unfolding, Deltan, was obtained from the analysis of thermal unfolding behavior of proteins in various sugar solutions with water activity, a(W), varied. By applying the reciprocal form of Wyman-Tanford equation, Deltan was determined to be 133.9, 124.1, and 139.2 per protein molecule for ribonuclease A at pH=5.5, 4.2, and 2.8, respectively, 201.4 for lysozyme at pH=5.5, and 100.1 for alpha-chymotripnogen A at pH=2.0. Among the sugars tested, reducing sugars gave the lower apparent Deltan as compared with nonreducing sugars probably because of the direct interaction of reducing terminal with amino group of proteins at a high temperature. From the knowledge of Deltan, a new thermodynamic model for protein stability was proposed with explicit consideration for hydration state change of protein upon unfolding. From this model, the contribution of a(W) was proven to be always positive for stabilization of proteins and its effect is not negligible depending on Deltan and a(W).
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Affiliation(s)
- Osato Miyawaki
- Department of Food Science, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan.
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9
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Aragon S, Hahn DK. Precise boundary element computation of protein transport properties: Diffusion tensors, specific volume, and hydration. Biophys J 2006; 91:1591-603. [PMID: 16714342 PMCID: PMC1544285 DOI: 10.1529/biophysj.105.078188] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2005] [Accepted: 03/24/2006] [Indexed: 11/18/2022] Open
Abstract
A precise boundary element method for the computation of hydrodynamic properties has been applied to the study of a large suite of 41 soluble proteins ranging from 6.5 to 377 kDa in molecular mass. A hydrodynamic model consisting of a rigid protein excluded volume, obtained from crystallographic coordinates, surrounded by a uniform hydration thickness has been found to yield properties in excellent agreement with experiment. The hydration thickness was determined to be delta = 1.1 +/- 0.1 A. Using this value, standard deviations from experimental measurements are: 2% for the specific volume; 2% for the translational diffusion coefficient, and 6% for the rotational diffusion coefficient. These deviations are comparable to experimental errors in these properties. The precision of the boundary element method allows the unified description of all of these properties with a single hydration parameter, thus far not achieved with other methods. An approximate method for computing transport properties with a statistical precision of 1% or better (compared to 0.1-0.2% for the full computation) is also presented. We have also estimated the total amount of hydration water with a typical -9% deviation from experiment in the case of monomeric proteins. Both the water of hydration and the more precise translational diffusion data hint that some multimeric proteins may not have the same solution structure as that in the crystal because the deviations are systematic and larger than in the monomeric case. On the other hand, the data for monomeric proteins conclusively show that there is no difference in the protein structure going from the crystal into solution.
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Affiliation(s)
- Sergio Aragon
- Department of Chemistry & Biochemistry, San Francisco State University, San Francisco, California, USA.
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Gun'ko VM, Turov VV, Bogatyrev VM, Zarko VI, Leboda R, Goncharuk EV, Novza AA, Turov AV, Chuiko AA. Unusual properties of water at hydrophilic/hydrophobic interfaces. Adv Colloid Interface Sci 2005; 118:125-72. [PMID: 16213452 DOI: 10.1016/j.cis.2005.07.003] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2005] [Revised: 07/21/2005] [Accepted: 07/28/2005] [Indexed: 11/16/2022]
Abstract
The behaviour of water at mosaic hydrophilic/hydrophobic surfaces of different silicas and in biosystems (biomacromolecules, yeast cells, wheat seeds, bone and muscular tissues) was studied in different dispersion media over wide temperature range using 1H NMR spectroscopy with layer-by-layer freezing-out of bulk water (close to 273 K) and interfacial water (180 < T < 273 K), thermally stimulated depolarization current (TSDC) (90 < T < 270 K), infrared (IR) spectroscopy, and quantum chemical methods. Bulk water and water bound to hydrophilic/hydrophobic interfaces can be assigned to different structural types. There are (i) weakly associated interfacial water (1H NMR chemical shift delta(H) = 1.1-1.7 ppm) that can be assigned to high-density water (HDW) with collapsed structure (CS), representing individual molecules in hydrophobic pockets, small clusters and interstitial water with strongly distorted hydrogen bonds or without them, and (ii) strongly associated interfacial water (delta(H) = 4-5 ppm) with larger clusters, nano- and microdomains, and continuous interfacial layer with both HDW and low-density water (LDW). The molecular mobility of weakly associated bound water is higher (because hydrogen bonds are distorted and weakened and their number is smaller than that for strongly associated water) than that of strongly associated bound water (with strong hydrogen bonds but nevertheless weaker than that in ice Ih) that results in the difference in the temperature dependences of the 1H NMR spectra at T < 273 K. These different waters are also appear in changes in the IR and TSDC spectra.
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Affiliation(s)
- V M Gun'ko
- Institute of Surface Chemistry, 17 General Naumov Street, 03164 Kiev, Ukraine.
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Bánó M, Marek J. How thick is the layer of thermal volume surrounding the protein? Biophys Chem 2005; 120:44-54. [PMID: 16242836 DOI: 10.1016/j.bpc.2005.09.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2005] [Revised: 09/23/2005] [Accepted: 09/25/2005] [Indexed: 10/25/2022]
Abstract
Investigation on the volume properties of protein hydration layers is reported. Presented results are based on combination of Monte Carlo modeling and available experimental data. Six globular proteins with known data are chosen for analysis. Analyzing the model and the experimental results we found that water molecules bound to proteins by hydrogen bond are preferentially located at the places with local depressions on the protein surface. Consequently, the hydration level is not strictly proportional to the area of charged and polar surfaces, but also depends on the shape of the molecular surface. The thickness of the thermal volume layer as calculated in the framework of the scaled particle theory is 0.6-0.65 A for chosen proteins. The obtained value is significantly lower than that presented for proteins in earlier papers (where proportionality between the hydration level and the area of charged and polar surfaces was assumed), but is close to the value published for small solute molecules. Discussion including the influence of protein size and the thermal motion of the surface is presented.
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Affiliation(s)
- Mikulás Bánó
- Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 04353 Kosice, Slovak Republic.
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Rai N, Nöllmann M, Spotorno B, Tassara G, Byron O, Rocco M. SOMO (SOlution MOdeler) differences between X-Ray- and NMR-derived bead models suggest a role for side chain flexibility in protein hydrodynamics. Structure 2005; 13:723-34. [PMID: 15893663 DOI: 10.1016/j.str.2005.02.012] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2004] [Revised: 02/02/2005] [Accepted: 02/03/2005] [Indexed: 11/27/2022]
Abstract
Reduced numbers of frictional/scattering centers are essential for tractable hydrodynamic and small-angle scattering data modeling. We present a method for generating medium-resolution models from the atomic coordinates of proteins, basically by using two nonoverlapping spheres of differing radii per residue. The computed rigid-body hydrodynamic parameters of BPTI, RNase A, and lysozyme models were compared with a large database of critically assessed experimental values. Overall, very good results were obtained, but significant discrepancies between X-ray- and NMR-derived models were found. Interestingly, they could be accounted for by properly considering the extent to which highly mobile surface side chains differently affect translational/rotational properties. Models of larger structures, such as fibrinogen fragment D and citrate synthase, also produced consistent results. Foremost among this method's potential applications is the overall conformation and dynamics of modular/multidomain proteins and of supramolecular complexes. The possibility of merging data from high- and low-resolution structures greatly expands its scope.
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Affiliation(s)
- Nithin Rai
- Division of Infection & Immunity, Institute of Biomedical & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
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Friedman R, Nachliel E, Gutman M. Molecular dynamics of a protein surface: ion-residues interactions. Biophys J 2005; 89:768-81. [PMID: 15894639 PMCID: PMC1366628 DOI: 10.1529/biophysj.105.058917] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2005] [Accepted: 04/28/2005] [Indexed: 11/18/2022] Open
Abstract
Time-resolved measurements indicated that protons could propagate on the surface of a protein or a membrane by a special mechanism that enhanced the shuttle of the proton toward a specific site. It was proposed that a suitable location of residues on the surface contributes to the proton shuttling function. In this study, this notion was further investigated by the use of molecular dynamics simulations, where Na(+) and Cl(-) are the ions under study, thus avoiding the necessity for quantum mechanical calculations. Molecular dynamics simulations were carried out using as a model a few Na(+) and Cl(-) ions enclosed in a fully hydrated simulation box with a small globular protein (the S6 of the bacterial ribosome). Three independent 10-ns-long simulations indicated that the ions and the protein's surface were in equilibrium, with rapid passage of the ions between the protein's surface and the bulk. However, it was noted that close to some domains the ions extended their duration near the surface, thus suggesting that the local electrostatic potential hindered their diffusion to the bulk. During the time frame in which the ions were detained next to the surface, they could rapidly shuttle between various attractor sites located under the electrostatic umbrella. Statistical analysis of the molecular dynamics and electrostatic potential/entropy consideration indicated that the detainment state is an energetic compromise between attractive forces and entropy of dilution. The similarity between the motion of free ions next to a protein and the proton transfer on the protein's surface are discussed.
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Affiliation(s)
- Ran Friedman
- Laser Laboratory for Fast Reactions in Biology, Department of Biochemistry, The George S. Wise Faculty for Life Sciences, Tel Aviv University, Israel
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Alexeeva TA, Lebovka NI, Gun'ko VM, Strashko VV, Mikhalovsky SV. Characteristics of interfacial water affected by proteins adsorbed on activated carbon. J Colloid Interface Sci 2004; 278:333-41. [PMID: 15450452 DOI: 10.1016/j.jcis.2004.06.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2003] [Accepted: 06/03/2004] [Indexed: 11/25/2022]
Abstract
The influence of proteins (bovine serum albumin, BSA, and mouse gamma-globulin, IgG) physically adsorbed or covalently attached via coupling with N-cyclohexyl-N'-(2-morpholinoethyl) carbodiimide methyl-p-toluenesulfonate, CMC, to the surface of activated carbon SCN (spherical carbon with nitrogen) on the mobility of interfacial water molecules was studied by means of 1H NMR spectroscopy with freezing-out of bulk water at 180 < T < 273 K. Relaxation processes in the interfacial non-freezing water were investigated measuring transverse time t2 of proton relaxation dependence on the presence of proteins and CMC. The distribution function of activation free energy of relaxation (with a maximum at 20-22 kJ/mol) was calculated for the protein-water-carbon systems using a regularization procedure and the relationships between t2 and the amounts of the interfacial water unfrozen at T < 250 K assuming the Arrhenius-type dependence for t2(-1) on temperature. The state of unfrozen water in pores of SCN shows that the low temperature relaxation processes occur in narrow pores with half-width X < 1.5 nm.
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Affiliation(s)
- T A Alexeeva
- Institute of Physics, Prospect Nauki 46, 02022 Kiev, Ukraine
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Kabir SR, Yokoyama K, Mihashi K, Kodama T, Suzuki M. Hyper-mobile water is induced around actin filaments. Biophys J 2004; 85:3154-61. [PMID: 14581215 PMCID: PMC1303591 DOI: 10.1016/s0006-3495(03)74733-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
When introduced into water, some molecules and ions (solutes) enforce the hydrogen-bonded network of neighboring water molecules that are thus restrained from thermal motions and are less mobile than those in the bulk phase (structure-making or positive hydration effect), and other solutes cause the opposite effect (structure-breaking or negative hydration effect). Using a method of microwave dielectric spectroscopy recently developed to measure the rotational mobility (dielectric relaxation frequency) of water hydrating proteins and the volume of hydration shells, the hydration of actin filament (F-actin) has been studied. The results indicate that F-actin exhibits both the structure-making and structure-breaking effects. Thus, apart from the water molecules with lowered rotational mobility that make up a typical hydration shell, there are other water molecules around the F-actin which have a much higher mobility than that of bulk water. No such dual hydration has been observed for myoglobin studied as the representative example of globular proteins which all showed qualitatively similar dielectric spectra. The volume fraction of the mobilized (hyper-mobile) water is roughly equal to that of the restrained water, which is two-thirds of the molecular volume of G-actin in size. The dielectric spectra of aqueous solutions of urea and potassium-halide salts have also been studied. The results suggest that urea and I(-) induce the hyper-mobile states of water, which is consistent with their well-known structure-breaking effect. The molecular surface of actin is rich in negative charges, which along with its filamentous structure provides a structural basis for the induction of a hyper-mobile state of water. A possible implication of the findings of the present study is discussed in relation to the chemomechanical energy transduction through interaction with myosin in the presence of ATP.
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Affiliation(s)
- Syed Rashel Kabir
- Department of Materials Science and Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
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Bánó M, Marek J, Stupák M. Hydrodynamic parameters of hydrated macromolecules: Monte Carlo calculation. Phys Chem Chem Phys 2004. [DOI: 10.1039/b315620f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
The background and purpose of the British Biophysical Society Discussion meeting, The Hydration Problem in Solution Biophysics, held at the University of Glasgow, 12 September 2000, is described, particularly in relation to previous meetings in this field. Whereas a study of the nature and dynamic properties of water associated with a molecule is an important topic by itself, the collection of papers based on this meeting focus mainly on its affect in interpreting biophysical data in terms of macromolecular shape in a solution environment, particularly under dilute and very dilute systems. The techniques considered are largely hydrodynamically or thermodynamically based and supplemented by molecular modeling strategies; but in the context of how these could be used in conjunction with techniques like X-ray crystallography, NMR and neutron scattering.
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Affiliation(s)
- S E Harding
- NCMH Physical Biochemistry Laboratory, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK.
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