Molecular dynamics study of water rotational relaxation in saccharide solution for the development of bioprotective agent

[1]  R. Shirakashi,et al.  Dynamic Electric Field Alignment Determines the Water Rotational Motion around Protein. , 2023, The journal of physical chemistry. B.

[2]  P. Gallo,et al.  Protein hydration water: focus on low density and high density local structures upon cooling , 2022, Journal of Molecular Liquids.

[3]  R. Shirakashi,et al.  Stochastic Analysis of Molecular Dynamics Reveals the Rotation Dynamics Distribution of Water around Lysozyme. , 2022, The journal of physical chemistry. B.

[4]  R. Shirakashi,et al.  Prediction of water relaxation time using near infrared spectroscopy , 2022, Journal of Food Process Engineering.

[5]  D. Murakami,et al.  Effect of Osmolytes on Water Mobility Correlates with Their Stabilizing Effect on Proteins. , 2022, The journal of physical chemistry. B.

[6]  F. Sciortino,et al.  Advances in the study of supercooled water , 2021, The European Physical Journal E.

[7]  M. Morón.  Protein hydration shell formation: Dynamics of water in biological systems exhibiting nanoscopic cavities , 2021 .

[8]  R. Shirakashi,et al.  Effect of Relaxation Times in Preservative Solution on Protein Deterioration Rate. , 2020, The journal of physical chemistry. B.

[9]  N. Shimizu,et al.  Short-Distance Intermolecular Correlations of Mono- and Disaccharides in Condensed Solutions: Bulky Character of Trehalose , 2020, ACS omega.

[10]  D. Harries,et al.  Properties of Aqueous Trehalose Mixtures: Glass Transition and Hydrogen Bonding , 2020, Journal of chemical theory and computation.

[11]  M. Toner,et al.  Exploring Dynamics and Structure of Biomolecules, Cryoprotectants, and Water Using Molecular Dynamics Simulations: Implications for Biostabilization and Biopreservation. , 2019, Annual review of biomedical engineering.

[12]  O. Steinhauser,et al.  Computational spectroscopy of trehalose, sucrose, maltose, and glucose: A comprehensive study of TDSS, NQR, NOE, and DRS. , 2019, The Journal of chemical physics.

[13]  B. Bagchi,et al.  Mechanism of Solvent Control of Protein Dynamics. , 2019, Physical review letters.

[14]  N. Zhang,et al.  Computational investigation of the conformation transitions of DNA in modified water models , 2018, Journal of Molecular Liquids.

[15]  David M. Smith,et al.  Water in an electric field does not dance alone: The relation between equilibrium structure, time dependent viscosity and molecular motions , 2018, Journal of Molecular Liquids.

[16]  B. Halle,et al.  How proteins modify water dynamics. , 2018, The Journal of chemical physics.

[17]  P. Bolhuis,et al.  Water structure and dynamics in the hydration layer of a type III anti-freeze protein. , 2018, Physical chemistry chemical physics : PCCP.

[18]  R Pisano,et al.  Water entrapment and structure ordering as protection mechanisms for protein structural preservation. , 2018, The Journal of chemical physics.

[19]  Weizhong Li,et al.  Protective mechanisms of α,α-trehalose revealed by molecular dynamics simulations , 2018 .

[20]  O. Steinhauser,et al.  Towards a complete characterization of the δ-dispersion in dielectric spectroscopy of protein-water systems. , 2017, Physical chemistry chemical physics : PCCP.

[21]  B. Bagchi,et al.  Distinguishing dynamical features of water inside protein hydration layer: Distribution reveals what is hidden behind the average. , 2017, The Journal of chemical physics.

[22]  W. Thiel,et al.  Distinct Protein Hydration Water Species Defined by Spatially Resolved Spectra of Intermolecular Vibrations , 2017, The journal of physical chemistry. B.

[23]  K. Shiraga,et al.  Characterization of the hydrogen-bond network of water around sucrose and trehalose: Microwave and terahertz spectroscopic study. , 2017, The Journal of chemical physics.

[24]  B. L. de Groot,et al.  CHARMM36m: an improved force field for folded and intrinsically disordered proteins , 2016, Nature Methods.

[25]  R. Biswas,et al.  How Heterogeneous Are Trehalose/Glycerol Cryoprotectant Mixtures? A Combined Time-Resolved Fluorescence and Computer Simulation Investigation. , 2016, The journal of physical chemistry. B.

[26]  Majed Chergui,et al.  Retardation of Bulk Water Dynamics by Disaccharide Osmolytes. , 2016, The journal of physical chemistry. B.

[27]  S. Corezzi,et al.  Molecular properties of aqueous solutions: a focus on the collective dynamics of hydration water. , 2016, Soft matter.

[28]  P G Bolhuis,et al.  Dynamics of Hydration Water around Native and Misfolded α-Lactalbumin. , 2016, The journal of physical chemistry. B.

[29]  A. Roy,et al.  A Comparative Study of the Influence of Sugars Sucrose, Trehalose, and Maltose on the Hydration and Diffusion of DMPC Lipid Bilayer at Complete Hydration: Investigation of Structural and Spectroscopic Aspect of Lipid-Sugar Interaction. , 2016, Langmuir : the ACS journal of surfaces and colloids.

[30]  Alexander D. MacKerell,et al.  CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field , 2015, Journal of chemical theory and computation.

[31]  G. Cottone,et al.  Proteins in saccharides matrices and the trehalose peculiarity: Biochemical and biophysical properties , 2015 .

[32]  Naoshi Kondo,et al.  Broadband dielectric spectroscopy of glucose aqueous solution: Analysis of the hydration state and the hydrogen bond network. , 2015, The Journal of chemical physics.

[33]  H. Bakker,et al.  A femtosecond mid-infrared study of the dynamics of water in aqueous sugar solutions. , 2015, Physical chemistry chemical physics : PCCP.

[34]  S. Corezzi,et al.  Solvent Sharing Models for Non-Interacting Solute Molecules: The Case of Glucose and Trehalose Water Solutions , 2013, Food Biophysics.

[35]  P Sassi,et al.  Hydration and aggregation in mono- and disaccharide aqueous solutions by gigahertz-to-terahertz light scattering and molecular dynamics simulations. , 2012, The journal of physical chemistry. B.

[36]  B. Halle,et al.  Hydration and mobility of trehalose in aqueous solution. , 2012, The journal of physical chemistry. B.

[37]  R. Fulton.  The effect of the spatial nonlocality of the Kirkwood g-factor on the determination of the long wavelength dielectric functions in dipolar fluids. , 2012, The Journal of chemical physics.

[38]  Fabio Sterpone,et al.  Magnitude and molecular origin of water slowdown next to a protein. , 2012, Journal of the American Chemical Society.

[39]  P. Gallo,et al.  Understanding the Mechanisms of Bioprotection: A Comparative Study of Aqueous Solutions of Trehalose and Maltose upon Supercooling , 2011 .

[40]  Fabio Sterpone,et al.  Reorientation and allied dynamics in water and aqueous solutions. , 2011, Annual review of physical chemistry.

[41]  Alexander D. MacKerell,et al.  Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. , 2010, The journal of physical chemistry. B.

[42]  D. Fioretto,et al.  Rotational dynamics of trehalose in aqueous solutions studied by depolarized light scattering. , 2010, The Journal of chemical physics.

[43]  Jeffery B. Klauda,et al.  CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. , 2009, Biophysical journal.

[44]  Taehoon Kim,et al.  CHARMM‐GUI: A web‐based graphical user interface for CHARMM , 2008, J. Comput. Chem..

[45]  Gudrun Niehues,et al.  Long-range influence of carbohydrates on the solvation dynamics of water--answers from terahertz absorption measurements and molecular modeling simulations. , 2008, Journal of the American Chemical Society.

[46]  Luyuan Zhang,et al.  Mapping hydration dynamics around a protein surface , 2007, Proceedings of the National Academy of Sciences.

[47]  F. Scarponi,et al.  Separate dynamics of solute and solvent in water–glucose solutions by depolarized light scattering , 2007 .

[48]  M. Parrinello,et al.  Canonical sampling through velocity rescaling. , 2007, The Journal of chemical physics.

[49]  H. Frauenfelder,et al.  Protein folding is slaved to solvent motions , 2006, Proceedings of the National Academy of Sciences.

[50]  Seunho Jung,et al.  Molecular dynamics simulations of trehalose as a 'dynamic reducer' for solvent water molecules in the hydration shell. , 2006, Carbohydrate research.

[51]  James T. Hynes,et al.  A Molecular Jump Mechanism of Water Reorientation , 2006, Science.

[52]  Hans Frauenfelder,et al.  Bulk-solvent and hydration-shell fluctuations, similar to α- and β-fluctuations in glasses, control protein motions and functions , 2004 .

[53]  S. N. Timasheff,et al.  Protein hydration, thermodynamic binding, and preferential hydration. , 2002, Biochemistry.

[54]  S. Engelsen,et al.  The diluted aqueous solvation of carbohydrates as inferred from molecular dynamics simulations and NMR spectroscopy. , 2001, Biophysical chemistry.

[55]  H. Lüdemann,et al.  c,T-dependence of the viscosity and the self-diffusion coefficients in some aqueous carbohydrate solutions. , 2000, Carbohydrate research.

[56]  Berk Hess,et al.  LINCS: A linear constraint solver for molecular simulations , 1997, J. Comput. Chem..

[57]  P. Karplus,et al.  Molecular Dynamics Studies of the Hydration of α,α-Trehalose , 1997 .

[58]  S. N. Timasheff,et al.  The thermodynamic mechanism of protein stabilization by trehalose. , 1997, Biophysical chemistry.

[59]  J. Glosli,et al.  Comments on P3M, FMM, and the Ewald method for large periodic Coulombic systems , 1995, cond-mat/9511134.

[60]  P. Belton,et al.  IR and Raman spectroscopic studies of the interaction of trehalose with hen egg white lysozyme , 1994, Biopolymers.

[61]  H. Lüdemann,et al.  c , T-Dependence of the Self Diffusion in Concentrated Aqueous Sucrose Solutions , 1994 .

[62]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[63]  T. Straatsma,et al.  THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS , 1987 .

[64]  Evans,et al.  Molecular dynamics of water in a strong electric field: Electric-field-induced translational anisotropy. , 1987, Physical review. A, General physics.

[65]  M. Parrinello,et al.  Crystal structure and pair potentials: A molecular-dynamics study , 1980 .

[66]  C. Angell,et al.  Contrasting dynamics of fragile and non-fragile polyalcohols through the glass, and dynamical, transitions: A comparison of neutron scattering and dielectric relaxation data for sorbitol and glycerol. , 2017, Biochimica et biophysica acta. General subjects.

[67]  S. Corezzi,et al.  Hydration and aggregation of lysozyme by extended frequency range depolarized light scattering , 2015 .

[68]  David E. Golan,et al.  Protein therapeutics: a summary and pharmacological classification , 2008, Nature Reviews Drug Discovery.