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Trevitt CR, Yashwanth Kumar DR, Fowler NJ, Williamson MP. Interactions between the protein barnase and co-solutes studied by NMR. Commun Chem 2024; 7:44. [PMID: 38418894 PMCID: PMC10902301 DOI: 10.1038/s42004-024-01127-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 02/09/2024] [Indexed: 03/02/2024] Open
Abstract
Protein solubility and stability depend on the co-solutes present. There is little theoretical basis for selection of suitable co-solutes. Some guidance is provided by the Hofmeister series, an empirical ordering of anions according to their effect on solubility and stability; and by osmolytes, which are small organic molecules produced by cells to allow them to function in stressful environments. Here, NMR titrations of the protein barnase with Hofmeister anions and osmolytes are used to measure and locate binding, and thus to separate binding and bulk solvent effects. We describe a rationalisation of Hofmeister (and inverse Hofmeister) effects, which is similar to the traditional chaotrope/kosmotrope idea but based on solvent fluctuation rather than water withdrawal, and characterise how co-solutes affect protein stability and solubility, based on solvent fluctuations. This provides a coherent explanation for solute effects, and points towards a more rational basis for choice of excipients.
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Affiliation(s)
- Clare R Trevitt
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
- Certara UK Ltd, Level 2-Acero, 1 Concourse Way, Sheffield, S1 3BJ, UK
| | | | - Nicholas J Fowler
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Mike P Williamson
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK.
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2
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Hydration of Simple Model Peptides in Aqueous Osmolyte Solutions. Int J Mol Sci 2021; 22:ijms22179350. [PMID: 34502252 PMCID: PMC8431001 DOI: 10.3390/ijms22179350] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/13/2021] [Accepted: 08/24/2021] [Indexed: 12/13/2022] Open
Abstract
The biology and chemistry of proteins and peptides are inextricably linked with water as the solvent. The reason for the high stability of some proteins or uncontrolled aggregation of others may be hidden in the properties of their hydration water. In this study, we investigated the effect of stabilizing osmolyte–TMAO (trimethylamine N-oxide) and destabilizing osmolyte–urea on hydration shells of two short peptides, NAGMA (N-acetyl-glycine-methylamide) and diglycine, by means of FTIR spectroscopy and molecular dynamics simulations. We isolated the spectroscopic share of water molecules that are simultaneously under the influence of peptide and osmolyte and determined the structural and energetic properties of these water molecules. Our experimental and computational results revealed that the changes in the structure of water around peptides, caused by the presence of stabilizing or destabilizing osmolyte, are significantly different for both NAGMA and diglycine. The main factor determining the influence of osmolytes on peptides is the structural-energetic similarity of their hydration spheres. We showed that the chosen peptides can serve as models for various fragments of the protein surface: NAGMA for the protein backbone and diglycine for the protein surface with polar side chains.
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3
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Panuszko A, Stangret J, Nowosielski B, Bruździak P. Interactions between hydration spheres of two different solutes in solution: The least squares fitting with constraints as a tool to determine water properties in ternary systems. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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4
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Chialvo AA. On the Solute-Induced Structure-Making/Breaking Effect: Rigorous Links among Microscopic Behavior, Solvation Properties, and Solution Non-Ideality. J Phys Chem B 2019; 123:2930-2947. [PMID: 30794414 DOI: 10.1021/acs.jpcb.9b00364] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We studied the solute-induced perturbation of the solvent environment around a solute species from a microscopic viewpoint and propose a novel approach to the understanding of the structure-making/breaking process, regardless of the type and nature of the solute-solvent interactions. Based on the Kirkwood-Buff fluctuation formalism, we present a rigorous statistical mechanics description of the evolution of the solvent structure around the solute, analyze its response to small perturbations of the ( TP) state conditions and composition of the system, and make direct connections between a few equivalent micro- and macroscopic manifestations as probes for, and targets of, experimental measurements. We illustrate the analysis with theoretical results from integral equation calculations of model fluids and experimental evidence from available data for a variety of aqueous electrolyte and nonelectrolyte real fluid solutions. Finally, we provide a critical discussion about the inadequacy underlying a widely used de facto criterion for the classification of structure-making/breaking solutes.
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5
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Geethu PM, Ranganathan VT, Satapathy DK. Inferences on hydrogen bond networks in water from isopermitive frequency investigations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:315103. [PMID: 29944119 DOI: 10.1088/1361-648x/aacf2c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Intermolecular hydrogen bonds play a crucial role in determining the unique characteristics of liquid water. We present low-frequency (1 Hz-40 MHz) dielectric spectroscopic investigations on water in the presence and absence of added solutes at different temperatures from 10 °C to 60 °C. The intersection points of temperature dependent permittivity contours at the vicinity of isopermitive frequency (IPF) in water are recorded and its properties are presumed to be related to the extent of hydrogen bond networks in water. IPF is defined as the frequency at which the relative permittivity of water is almost independent of temperature. The set of intersection points of temperature dependent permittivity contours at the vicinity of IPF are characterized by the mean [Formula: see text] and root-mean-square deviation/standard deviation [Formula: see text] associated with IPF. The tunability of M IPF by the addition of NaCl and MgCl2 salt emphasizes the strong correlation between the concentration of ions in water and the M IPF. The [Formula: see text] is surmised to be related to the orientational correlations of water dipoles as well as to the intermolecular hydrogen bond networks in water. Further, alterations in [Formula: see text] is observed with the addition of kosmotropic and chaotropic solutes into water and are thought to arise due to the restructuring of hydrogen bond networks in water in presence of added solutes. Notably, the solute induced reconfiguration of hydrogen bond networks in water or often-discussed structure making/breaking effects of the added solutes in water can be inferred, albeit qualitatively, by examining the M IPF and [Formula: see text]. Further, the Gaussian deconvoluted OH-stretching modes present in the Raman spectra of water and aqueous solutions of IPA and DMF strongly endorses the structural rearrangements occurring in water in presence of kosmotropes and chaotropes and are in line with the results derived from the root-mean-square deviation in IPF.
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Affiliation(s)
- P M Geethu
- Soft Materials Laboratory, Department of Physics, Indian Institute of Technology Madras, 600036, India
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6
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Gaynanova GA, Valeeva FG, Kushnazarova RA, Bekmukhametova AM, Zakharov SV, Mirgorodskaya AB, Zakharova LY. Effect of Hydrotropic Compounds on the Self-Organization
and Solubilization Properties of Cationic Surfactants. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2018. [DOI: 10.1134/s0036024418070129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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Alavi Z, Zocchi G. Dissipation at the angstrom scale: Probing the surface and interior of an enzyme. Phys Rev E 2018; 97:052402. [PMID: 29906977 DOI: 10.1103/physreve.97.052402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Indexed: 06/08/2023]
Abstract
Pursuing a materials science approach to understanding the deformability of enzymes, we introduce measurements of the phase of the mechanical response function within the nanorheology paradigm. Driven conformational motion of the enzyme is dissipative as characterized by the phase measurements. The dissipation originates both from the surface hydration layer and the interior of the molecule, probed by examining the effect of point mutations on the mechanics. We also document changes in the mechanics of the enzyme examined, guanylate kinase, upon binding its four substrates. GMP binding stiffens the molecule, ATP and ADP binding softens it, while there is no clear mechanical signature of GDP binding. A hyperactive two-Gly mutant is found to possibly trade specificity for speed. Global deformations of enzymes are shown to be dependent on both hydration layer and polypeptide chain dynamics.
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Affiliation(s)
- Zahra Alavi
- Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, California 90095, USA
- Department of Physics and Astronomy, Loyola Marymount University Los Angeles, Los Angeles, California 90095, USA
| | - Giovanni Zocchi
- Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, California 90095, USA
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8
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Casanova-Morales N, Alavi Z, Wilson CAM, Zocchi G. Identifying Chaotropic and Kosmotropic Agents by Nanorheology. J Phys Chem B 2018. [DOI: 10.1021/acs.jpcb.7b12782] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nathalie Casanova-Morales
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380494, Chile
| | - Zahra Alavi
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380494, Chile
- Department of Physics, Loyola Marymount University, Los Angeles 90045, United States
| | - Christian A. M. Wilson
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380494, Chile
| | - Giovanni Zocchi
- Department of Physics and Astronomy, University of California—Los Angeles, Los Angeles, California 90095, United States
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9
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Draganski AR, Friedman JM, Ludescher RD. Solvent-Slaved Dynamic Processes Observed by Tryptophan Phosphorescence of Human Serum Albumin. Biophys J 2017; 112:881-891. [PMID: 28297647 DOI: 10.1016/j.bpj.2016.12.048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 12/16/2016] [Accepted: 12/23/2016] [Indexed: 10/20/2022] Open
Abstract
Despite extensive experimental and computational efforts to understand the nature of the hierarchy of protein fluctuations and the modulating role of the protein hydration shell, a detailed microscopic description of the dynamics of the protein-solvent system has yet to be achieved. By using single tryptophan protein phosphorescence, we follow site-specific internal protein dynamics over a broad temperature range and demonstrate three independent dynamic processes. Process I is seen at temperatures below the bulk solvent Tg, has low activation energy, and is likely due to fast vibrations that may be enabled by water mobility on the protein surface. Process II is observed above 170 K, with activation energy typical of β relaxations in a glass; it has the same temperature dependence as fluctuations of hydration shell waters. Process III is observed at T > 200 K; it has super-Arrhenius temperature dependence and closely follows the primary relaxation of the bulk. The fluorescence of pyranine bound to the protein reports on the mobility of water in the hydration shell; it reveals a shift in emission spectra with increasing temperature, indicative of a changing H-bond network at the surface of the protein. These results support a model of solvent-slaved protein dynamics.
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Affiliation(s)
- Andrew R Draganski
- Department of Food Science, Rutgers University, New Brunswick, New Jersey
| | - Joel M Friedman
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York.
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10
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Schrader AM, Cheng CY, Israelachvili JN, Han S. Communication: Contrasting effects of glycerol and DMSO on lipid membrane surface hydration dynamics and forces. J Chem Phys 2017; 145:041101. [PMID: 27475340 DOI: 10.1063/1.4959904] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Glycerol and dimethyl sulfoxide (DMSO) are commonly used cryoprotectants in cellular systems, but due to the challenges of measuring the properties of surface-bound solvent, fundamental questions remain regarding the concentration, interactions, and conformation of these solutes at lipid membrane surfaces. We measured the surface water diffusivity at gel-phase dipalmitoylphosphatidylcholine (DPPC) bilayer surfaces in aqueous solutions containing ≤7.5 mol. % of DMSO or glycerol using Overhauser dynamic nuclear polarization. We found that glycerol similarly affects the diffusivity of water near the bilayer surface and that in the bulk solution (within 20%), while DMSO substantially increases the diffusivity of surface water relative to bulk water. We compare these measurements of water dynamics with those of equilibrium forces between DPPC bilayers in the same solvent mixtures. DMSO greatly decreases the range and magnitude of the repulsive forces between the bilayers, whereas glycerol increases it. We propose that the differences in hydrogen bonding capability of the two solutes leads DMSO to dehydrate the lipid head groups, while glycerol affects surface hydration only as much as it affects the bulk water properties. The results suggest that the mechanism of the two most common cryoprotectants must be fundamentally different: in the case of DMSO by decoupling the solvent from the lipid surface, and in the case of glycerol by altering the hydrogen bond structure and intermolecular cohesion of the global solvent, as manifested by increased solvent viscosity.
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Affiliation(s)
- Alex M Schrader
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - Chi-Yuan Cheng
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
| | - Jacob N Israelachvili
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - Songi Han
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
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11
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Naughton BS, Reich NO. Mechanisms of Protein Translocation on DNA Are Differentially Responsive to Water Activity. Biochemistry 2016; 55:6957-6960. [PMID: 27992993 DOI: 10.1021/acs.biochem.6b00872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Water plays important but poorly understood roles in the functions of most biomolecules. We are interested in understanding how proteins use diverse search mechanisms to locate specific sites on DNA; here we present a study of the role of closely associated waters in diverse translocation mechanisms. The bacterial DNA adenine methyltransferase, Dam, moves across large segments of DNA using an intersegmental hopping mechanism, relying in part on movement through bulk water. In contrast, other proteins, such as the bacterial restriction endonuclease EcoRI, rely on a sliding mechanism, requiring the protein to stay closely associated with DNA. Here we probed how these two mechanistically distinct proteins respond to well-characterized osmolytes, dimethyl sulfoxide (DMSO), and glycerol. The ability of Dam to move over large segments of DNA is not impacted by either osmolyte, consistent with its minimal reliance on a sliding mechanism. In contrast, EcoRI endonuclease translocation is significantly enhanced by DMSO and inhibited by glycerol, providing further corroboration that these proteins rely on distinct translocation mechanisms. The well-established similar effects of these osmolytes on bulk water, and their differential effects on macromolecule-associated waters, support our results and provide further evidence of the importance of water in interactions between macromolecules and their ligands.
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Affiliation(s)
- Brigitte S Naughton
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106, United States
| | - Norbert O Reich
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106, United States
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12
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Polysaccharide structures and interactions in a lithium chloride/urea/water solvent. Carbohydr Polym 2016; 149:231-41. [DOI: 10.1016/j.carbpol.2016.04.102] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 04/18/2016] [Accepted: 04/23/2016] [Indexed: 11/22/2022]
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13
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Russo D, Rea G, Lambreva MD, Haertlein M, Moulin M, De Francesco A, Campi G. Water Collective Dynamics in Whole Photosynthetic Green Algae as Affected by Protein Single Mutation. J Phys Chem Lett 2016; 7:2429-2433. [PMID: 27300078 DOI: 10.1021/acs.jpclett.6b00949] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In the context of the importance of water molecules for protein function/dynamics relationship, the role of water collective dynamics in Chlamydomonas green algae carrying both native and mutated photosynthetic proteins has been investigated by neutron Brillouin scattering spectroscopy. Results show that single point genetic mutation may notably affect collective density fluctuations in hydrating water providing important insight on the transmission of information possibly correlated to biological functionality. In particular, we highlight that the damping factor of the excitations is larger in the native compared to the mutant algae as a signature of a different plasticity and structure of the hydrogen bond network.
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Affiliation(s)
- Daniela Russo
- CNR Istituto Officina dei Materiali c/o Institut Laue Langevin , 38042 Grenoble, France
- Institut Lumière Matière, Université de Lyon 1 , 69100 Lyon, France
| | - Giuseppina Rea
- CNR Istituto di Crystallografia 00015 Monterotondo Scalo, 70126 Roma, Italy
| | - Maya D Lambreva
- CNR Istituto di Crystallografia 00015 Monterotondo Scalo, 70126 Roma, Italy
| | - Michael Haertlein
- ILL Deuteration Laboratory, Partnership for Structural Biology, 38042 Grenoble, France
- Life Sciences Group, Institut Laue-Langevin , 38000 Grenoble, France
| | - Martine Moulin
- ILL Deuteration Laboratory, Partnership for Structural Biology, 38042 Grenoble, France
- Life Sciences Group, Institut Laue-Langevin , 38000 Grenoble, France
| | - Alessio De Francesco
- CNR Istituto Officina dei Materiali c/o Institut Laue Langevin , 38042 Grenoble, France
| | - Gaetano Campi
- CNR Istituto di Crystallografia 00015 Monterotondo Scalo, 70126 Roma, Italy
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14
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Mamontov E, O'Neill H. Microscopic relaxations in a protein sustained down to 160K in a non-glass forming organic solvent. Biochim Biophys Acta Gen Subj 2016; 1861:3513-3519. [PMID: 27154287 DOI: 10.1016/j.bbagen.2016.04.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 04/24/2016] [Accepted: 04/25/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND We have studied microscopic dynamics of a protein in carbon disulfide, a non-glass forming solvent, down to its freezing temperature of ca. 160K. METHODS We have utilized quasielastic neutron scattering. RESULTS A comparison of lysozyme hydrated with water and dissolved in carbon disulfide reveals a stark difference in the temperature dependence of the protein's microscopic relaxation dynamics induced by the solvent. In the case of hydration water, the common protein glass-forming solvent, the protein relaxation slows down in response to a large increase in the water viscosity on cooling down, exhibiting a well-known protein dynamical transition. The dynamical transition disappears in non-glass forming carbon disulfide, whose viscosity remains a weak function of temperature all the way down to freezing at just below 160K. The microscopic relaxation dynamics of lysozyme dissolved in carbon disulfide is sustained down to the freezing temperature of its solvent at a rate similar to that measured at ambient temperature. CONCLUSIONS Our results demonstrate that protein dynamical transition is not merely solvent-assisted, but rather solvent-induced, or, more precisely, is a reflection of the temperature dependence of the solvent's glass-forming dynamics. GENERAL SIGNIFICANCE We hypothesize that, if the long debated idea regarding the direct link between the microscopic relaxations and the biological activity in proteins is correct, then not only the microscopic relaxations, but also the activity, could be sustained in proteins all the way down to the freezing temperature of a non-glass forming solvent with a weak temperature dependence of its viscosity. 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)
- E Mamontov
- Chemical and Engineering Materials Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States.
| | - H O'Neill
- Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
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15
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Smeeton LC, Farrell JD, Oakley MT, Wales DJ, Johnston RL. Structures and Energy Landscapes of Hydrated Sulfate Clusters. J Chem Theory Comput 2015; 11:2377-84. [DOI: 10.1021/acs.jctc.5b00151] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lewis C. Smeeton
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - James D. Farrell
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Mark T. Oakley
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - David J. Wales
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Roy L. Johnston
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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16
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Aluminum-induced entropy in biological systems: implications for neurological disease. J Toxicol 2014; 2014:491316. [PMID: 25349607 PMCID: PMC4202242 DOI: 10.1155/2014/491316] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 07/28/2014] [Indexed: 12/14/2022] Open
Abstract
Over the last 200 years, mining, smelting, and refining of aluminum (Al) in various forms have increasingly exposed living species to this naturally abundant metal. Because of its prevalence in the earth's crust, prior to its recent uses it was regarded as inert and therefore harmless. However, Al is invariably toxic to living systems and has no known beneficial role in any biological systems. Humans are increasingly exposed to Al from food, water, medicinals, vaccines, and cosmetics, as well as from industrial occupational exposure. Al disrupts biological self-ordering, energy transduction, and signaling systems, thus increasing biosemiotic entropy. Beginning with the biophysics of water, disruption progresses through the macromolecules that are crucial to living processes (DNAs, RNAs, proteoglycans, and proteins). It injures cells, circuits, and subsystems and can cause catastrophic failures ending in death. Al forms toxic complexes with other elements, such as fluorine, and interacts negatively with mercury, lead, and glyphosate. Al negatively impacts the central nervous system in all species that have been studied, including humans. Because of the global impacts of Al on water dynamics and biosemiotic systems, CNS disorders in humans are sensitive indicators of the Al toxicants to which we are being exposed.
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17
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Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A. Accurate SAXS profile computation and its assessment by contrast variation experiments. Biophys J 2014; 105:962-74. [PMID: 23972848 DOI: 10.1016/j.bpj.2013.07.020] [Citation(s) in RCA: 422] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 07/03/2013] [Accepted: 07/11/2013] [Indexed: 12/29/2022] Open
Abstract
A major challenge in structural biology is to characterize structures of proteins and their assemblies in solution. At low resolution, such a characterization may be achieved by small angle x-ray scattering (SAXS). Because SAXS analyses often require comparing profiles calculated from many atomic models against those determined by experiment, rapid and accurate profile computation from molecular structures is needed. We developed fast open-source x-ray scattering (FoXS) for profile computation. To match the experimental profile within the experimental noise, FoXS explicitly computes all interatomic distances and implicitly models the first hydration layer of the molecule. For assessing the accuracy of the modeled hydration layer, we performed contrast variation experiments for glucose isomerase and lysozyme, and found that FoXS can accurately represent density changes of this layer. The hydration layer model was also compared with a SAXS profile calculated for the explicit water molecules in the high-resolution structures of glucose isomerase and lysozyme. We tested FoXS on eleven protein, one DNA, and two RNA structures, revealing superior accuracy and speed versus CRYSOL, AquaSAXS, the Zernike polynomials-based method, and Fast-SAXS-pro. In addition, we demonstrated a significant correlation of the SAXS score with the accuracy of a structural model. Moreover, FoXS utility for analyzing heterogeneous samples was demonstrated for intrinsically flexible XLF-XRCC4 filaments and Ligase III-DNA complex. FoXS is extensively used as a standalone web server as a component of integrative structure determination by programs IMP, Chimera, and BILBOMD, as well as in other applications that require rapidly and accurately calculated SAXS profiles.
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Affiliation(s)
- Dina Schneidman-Duhovny
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.
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18
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Dimitrijev Dwyer M, Brech M, Yu L, Middelberg AP. Intensified expression and purification of a recombinant biosurfactant protein. Chem Eng Sci 2014. [DOI: 10.1016/j.ces.2013.10.024] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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19
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Lebendiker M, Danieli T. Production of prone-to-aggregate proteins. FEBS Lett 2013; 588:236-46. [DOI: 10.1016/j.febslet.2013.10.044] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 10/30/2013] [Accepted: 10/31/2013] [Indexed: 12/16/2022]
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20
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Russo D, Gonzalez MA, Pellegrini E, Combet J, Ollivier J, Teixeira J. Evidence of Dynamical Constraints Imposed by Water Organization around a Bio–Hydrophobic Interface. J Phys Chem B 2013; 117:2829-36. [DOI: 10.1021/jp3094885] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniela Russo
- CNR-IOM c/o Institut Laue Langevin, 6 rue J.
Horowitz BP156, F-38042 Grenoble, France
| | | | - Eric Pellegrini
- Institut Laue Langevin, 6 rue J. Horowitz BP156, F-38042 Grenoble, France
| | - J. Combet
- Institut Laue Langevin, 6 rue J. Horowitz BP156, F-38042 Grenoble, France
| | - J. Ollivier
- Institut Laue Langevin, 6 rue J. Horowitz BP156, F-38042 Grenoble, France
| | - José Teixeira
- Laboratoire Léon Brillouin (CEA/CNRS), CEA Saclay, 91191 Gif-sur-Yvette Cedex France
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21
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Deary ME, Mousa SM, Martin Davies D. Effect of kosmotrope and chaotrope anions on rate and equilibria processes for the α-cyclodextrin catalysed reaction of 3-chloroperbenzoic acid with iodide. J INCL PHENOM MACRO 2013. [DOI: 10.1007/s10847-012-0279-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Haberler M, Schröder C, Steinhauser O. Hydrated Ionic Liquids with and without Solute: The Influence of Water Content and Protein Solutes. J Chem Theory Comput 2012; 8:3911-28. [PMID: 26593031 DOI: 10.1021/ct300191s] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In this computational study, the network of 1-ethyl-3-methylimidazolium trifluoromethanesulfonate/water mixtures is analyzed in the presence (and absence) of the protein ubiquitin and a zinc finger motif. Thereby, common radial distribution functions are decomposed into contributions from different Voronoi shells, and the mutual orientation of cations, anions, and water in the bulk phase as a function of the water mole fraction is discussed. Single particle translation and the reorientation of the dipolar axis seem to follow hydrodynamic relations. Using the body-fixed frame as an alternative reference system, translation and rotation can be decomposed into contributions along and about the axes of a well-defined orthogonal trihedron, thus elucidating the principal motions of the cations and anions as a function of the water mole fraction. The structural dipolar orientation may be correlated with single particle dynamics and can be characterized by the static collective Kirkwood order parameter.
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Affiliation(s)
- Michael Haberler
- University of Vienna, Department of Computational Biological Chemistry, Austria
| | - Christian Schröder
- University of Vienna, Department of Computational Biological Chemistry, Austria
| | - Othmar Steinhauser
- University of Vienna, Department of Computational Biological Chemistry, Austria
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23
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Chu XQ, Mamontov E, O'Neill H, Zhang Q. Apparent Decoupling of the Dynamics of a Protein from the Dynamics of its Aqueous Solvent. J Phys Chem Lett 2012; 3:380-385. [PMID: 26285855 DOI: 10.1021/jz201435q] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Studies of the low-temperature dynamics of proteins in aqueous solutions are limited by the crystallization of water. In this work, we use a solution of LiCl in D2O as a solvent for a protein to prevent crystallization and study the dynamics of both the protein and its aqueous solvent by quasielastic neutron scattering (QENS) in the temperature range of 210 to 290 K. Our results reveal that, while the dynamics of the aqueous solvent undergoes a crossover at about 220 K, the dynamics of the protein itself shows no transition at this temperature. The prevailing view is that the β-fluctuations of the protein are governed by the α-fluctuations of the solvent; therefore, observation of the apparent decoupling between the dynamics of the protein and its solvent below the crossover temperature is remarkable.
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Affiliation(s)
- Xiang-Qiang Chu
- †Neutron Scattering Science Division and ‡Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Eugene Mamontov
- †Neutron Scattering Science Division and ‡Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Hugh O'Neill
- †Neutron Scattering Science Division and ‡Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Qiu Zhang
- †Neutron Scattering Science Division and ‡Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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24
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Identifying solubility-promoting buffers for intrinsically disordered proteins prior to purification. Methods Mol Biol 2012; 896:415-27. [PMID: 22821541 DOI: 10.1007/978-1-4614-3704-8_28] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Intrinsically disordered proteins are anticipated to be more prone to aggregation than folded, stable proteins. Chemical additives included in the buffer can help maintain proteins in a soluble, monomeric state. However, the array of chemicals that impact protein solubility is staggering, precluding iterative testing of chemical conditions during purification. Herein, we describe a filter-based aggregation assay to rapidly identify chemical additives that maintain solubility for a protein of interest. A hierarchical approach to buffer selection is provided, in which the type of chemical which best improves solubility is first determined, followed by identifying the optimal chemical and its most effective concentration. Finally, combinations of chemical additives can be assessed if necessary. Although this assay can be applied to purified protein, partially purified protein, or aggregated protein, this protocol specifically details the use of this assay for crude cell lysate. This approach allows identification of solubility-promoting buffers prior to the initial protein purification.
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25
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Mamontov E, Chu XQ. Water–protein dynamic coupling and new opportunities for probing it at low to physiological temperatures in aqueous solutions. Phys Chem Chem Phys 2012; 14:11573-88. [DOI: 10.1039/c2cp41443k] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Russo D, Pellegrini E, Gonzalez MA, Perticaroli S, Teixeira J. In situ molecular dynamics analysis of the water hydrogen bond at biomolecular sites: Hydrophobicity enhances dynamics heterogeneity. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.10.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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27
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Russo D, Teixeira J, Kneller L, Copley JRD, Ollivier J, Perticaroli S, Pellegrini E, Gonzalez MA. Vibrational Density of States of Hydration Water at Biomolecular Sites: Hydrophobicity Promotes Low Density Amorphous Ice Behavior. J Am Chem Soc 2011; 133:4882-8. [DOI: 10.1021/ja109610f] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniela Russo
- CNR-IOM c/o Institut Laue Langevin, 6 rue J. Horowitz BP156, F-38042 Grenoble, France
| | - José Teixeira
- Laboratoire Léon Brillouin (CEA/CNRS), CEA Saclay, 91191 Gif-sur Yvette Cedex, France
| | - Larry Kneller
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6102, United States
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - John R. D. Copley
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6102, United States
| | - Jacques Ollivier
- Institut Laue Langevin, 6 rue J. Horowitz BP156, F-38042 Grenoble, France
| | - Stefania Perticaroli
- Dipartimento di Chimica, Università degli Studi di Perugia, Sezione di Chimica Fisica, via Elce di sotto 8, I-06123 Perugia, Italia
| | - Eric Pellegrini
- Institut Laue Langevin, 6 rue J. Horowitz BP156, F-38042 Grenoble, France
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28
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Achyuta AKH, Stephens KD, Pryce Lewis HG, Murthy SK. Mitigation of reactive human cell adhesion on poly(dimethylsiloxane) by immobilized trypsin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:4160-7. [PMID: 20214394 PMCID: PMC2924170 DOI: 10.1021/la903441u] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Occlusion or blockage of silicone shunts utilized in the treatment of hydrocephalus is a major challenge that is currently addressed by multiple shunt replacements. Shunt occlusion is caused by the adhesion and proliferation of reactive cells, such as glial and vascular cells, into the lumen of the catheter and on valve components. This in vitro study describes how the adhesive behavior of four human cell types on poly(dimethylsiloxane) (PDMS) surfaces can be suppressed by functionalization with trypsin, a proteolytic enzyme. The covalently conjugated trypsin retained its proteolytic activity and acted in a dose-dependent manner. Trypsin-modified PDMS surfaces supported significantly lower adhesion of normal human astrocytes, human microglia, human dermal fibroblasts, and human umbilical vein endothelial cells compared to unmodified PDMS surfaces (p < 0.0001). Immunofluorescence imaging of cellular fibronectin and quantitative adsorption experiments with serum components indicated that the PDMS surfaces immobilized with trypsin inhibited surface remodeling by all cell types and resisted protein adsorption. The impact of this work lies in the recognition that the well-known proteolytic characteristics of trypsin can be harnessed by covalent surface immobilization to suppress cell adhesion and protein adsorption.
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Affiliation(s)
- Anil Kumar H. Achyuta
- Department of Chemical Engineering, Northeastern University, 360 Huntington Ave., 342 SN, Boston, Massachusetts 02115, USA
| | - Kyle D. Stephens
- Department of Chemical Engineering, Northeastern University, 360 Huntington Ave., 342 SN, Boston, Massachusetts 02115, USA
| | | | - Shashi K. Murthy
- Department of Chemical Engineering, Northeastern University, 360 Huntington Ave., 342 SN, Boston, Massachusetts 02115, USA
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29
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Zayed JM, Nouvel N, Rauwald U, Scherman OA. Chemical complexity—supramolecular self-assembly of synthetic and biological building blocks in water. Chem Soc Rev 2010; 39:2806-16. [DOI: 10.1039/b922348g] [Citation(s) in RCA: 145] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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30
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Russo D, Teixeira J, Ollivier J. The impact of hydration water on the dynamics of side chains of hydrophobic peptides: from dry powder to highly concentrated solutions. J Chem Phys 2009; 130:235101. [PMID: 19548762 DOI: 10.1063/1.3154383] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Elastic and quasielastic neutron scattering experiments are used to investigate the dynamics of side chains in proteins, using hydrophobic peptides, from dry and hydrated powders up to solutions, as models. The changes of the internal dynamics of a prototypical hydrophobic amino acid, N-acetyl-leucine-methylamide, and alanine amino acids are investigated as a function of water/peptide molecular ratio. While previous results have shown that, in concentrated solution, when the hydrophobic side chains are hydrated by a single hydration water layer, the only allowed motions are confined and can be attributed to librational/rotational movements associated with the methyl groups. In the present work we observe a dynamical evolution from dry to highly hydrated powder. We also observe rotational and diffusive motions and a dynamical transition at approximately 250 K for long side chain peptides while for peptides with short side chains, there is no dynamical transition but only rotational motions. With a local measurement of the influence of hydration water dynamics on the amino acid side chains dynamics, we provide unique experimental evidence that the structural and dynamical properties of interfacial water strongly influence the side chain dynamics and the activation of diffusive motions. We also emphasize that the side chain length has a role on the onset of dynamical transition.
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Affiliation(s)
- Daniela Russo
- Institut Laue Langevin, CNR-INFM and CRS/Soft, 6 rue J. Horowitz BP156, F-38042 Grenoble, France.
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31
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Effect of acetylsalicylic acid on the current–voltage characteristics of planar lipid membranes. Biophys Chem 2009; 142:27-33. [DOI: 10.1016/j.bpc.2009.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Revised: 02/27/2009] [Accepted: 03/01/2009] [Indexed: 10/21/2022]
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32
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Max B, Torrado AM, Moldes AB, Converti A, Domínguez JM. Ferulic acid and p-coumaric acid solubilization by alkaline hydrolysis of the solid residue obtained after acid prehydrolysis of vine shoot prunings: Effect of the hydroxide and pH. Biochem Eng J 2009. [DOI: 10.1016/j.bej.2008.09.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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33
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Russo D, Ollivier J, Teixeira J. Water hydrogen bond analysis on hydrophilic and hydrophobic biomolecule sites. Phys Chem Chem Phys 2008; 10:4968-74. [PMID: 18688541 DOI: 10.1039/b807551b] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Elastic and quasielastic neutron scattering experiments have been used to investigate the hydrogen bonding network dynamics of hydration water on hydrophilic and hydrophobic sites. To this end the evolution of hydration water dynamics of a prototypical hydrophobic amino acid with polar backbone, N-acetyl-leucine-methylamide (NALMA), and hydrophilic amino acid, N-acetyl-glycine-methylamide (NAGMA), has been investigated as a function of the molecular ratio water : peptide. The results suggest that the dynamical contribution of the intrinsic and low hydration molecules of water is characteristic of pure librational/rotational movement. The water molecule remains attached to the hydrophilic site with only the possibility of hindered rotations that eventually break the bond with the peptide and reform it immediately after. A gradual evolution from librational motions to hindered rotations is observed as a function of temperature. When the hydration increases, we observe (together with the hindered rotations of hydrogen bonds) a slow diffusion of water molecules on the surface of the peptides.
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Affiliation(s)
- Daniela Russo
- CNR-INFM & CRS/Soft, c/o Institut Laue Langevin, 6 rue J. Horowitz, Grenoble, France
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