Literature DB >> 23841646

Structure and dynamics of urea/water mixtures investigated by vibrational spectroscopy and molecular dynamics simulation.

J K Carr1, L E Buchanan, J R Schmidt, M T Zanni, J L Skinner.   

Abstract

Urea/n class="Chemical">water is an archetypical "biological" mixture and is especially well-known for its relevance to protein thermodynamics as urea acts as a protein denaturant at high concentration. This behavior has given rise to an extended debate concerning urea's influence on water structure. On the basis of a variety of methods and of definitions of the water structure, urea has been variously described as a structure-breaker, a structure-maker, or as remarkably neutral toward water. Because of its sensitivity to microscopic structure and dynamics, vibrational spectroscopy can help resolve these debates. We report experimental and theoretical spectroscopic results for the OD stretch of HOD/H2O/urea mixtures (linear IR, 2DIR, and pump-probe anisotropy decay) and for the CO stretch of urea-D4/D2O mixtures (linear IR only). Theoretical results are obtained using existing approaches for water and a modification of a frequency map developed for acetamide. All absorption spectra are remarkably insensitive to urea concentration, consistent with the idea that urea only very weakly perturbs the water structure. Both this work and experiments by Rezus and Bakker, however, show that water's rotational dynamics are slowed down by urea. Analysis of the simulations casts doubt on the suggestion that urea immobilizes particular doubly hydrogen bonded water molecules.

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Year:  2013        PMID: 23841646      PMCID: PMC3808478          DOI: 10.1021/jp4037217

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  67 in total

1.  Coherent microscopic picture for urea-induced denaturation of proteins.

Authors:  Zaixing Yang; Peng Xiu; Biyun Shi; Lan Hua; Ruhong Zhou
Journal:  J Phys Chem B       Date:  2012-07-24       Impact factor: 2.991

2.  The hydrogen bond network structure within the hydration shell around simple osmolytes: urea, tetramethylurea, and trimethylamine-N-oxide, investigated using both a fixed charge and a polarizable water model.

Authors:  Anna Kuffel; Jan Zielkiewicz
Journal:  J Chem Phys       Date:  2010-07-21       Impact factor: 3.488

3.  The effect of urea on the structure of water: a molecular dynamics simulation.

Authors:  A Idrissi; M Gerard; P Damay; M Kiselev; Y Puhovsky; E Cinar; P Lagant; G Vergoten
Journal:  J Phys Chem B       Date:  2010-04-08       Impact factor: 2.991

4.  Characterization of spectral diffusion from two-dimensional line shapes.

Authors:  Sean T Roberts; Joseph J Loparo; Andrei Tokmakoff
Journal:  J Chem Phys       Date:  2006-08-28       Impact factor: 3.488

5.  Self-association of urea in aqueous solutions: a Voronoi polyhedron analysis study.

Authors:  Abdenacer Idrissi; Pierre Damay; Kitamura Yukichi; Pal Jedlovszky
Journal:  J Chem Phys       Date:  2008-10-28       Impact factor: 3.488

6.  Hydration free energy difference of acetone, acetamide, and urea.

Authors:  Pál Jedlovszky; Abdenacer Idrissi
Journal:  J Chem Phys       Date:  2008-10-28       Impact factor: 3.488

Review 7.  Role of solvation effects in protein denaturation: from thermodynamics to single molecules and back.

Authors:  Jeremy L England; Gilad Haran
Journal:  Annu Rev Phys Chem       Date:  2011       Impact factor: 12.703

8.  Hydrogen bonding and Raman, IR, and 2D-IR spectroscopy of dilute HOD in liquid D2O.

Authors:  B Auer; R Kumar; J R Schmidt; J L Skinner
Journal:  Proc Natl Acad Sci U S A       Date:  2007-06-18       Impact factor: 11.205

9.  Water in the half shell: structure of water, focusing on angular structure and solvation.

Authors:  Kim A Sharp; Jane M Vanderkooi
Journal:  Acc Chem Res       Date:  2010-02-16       Impact factor: 22.384

10.  Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: lessons for protein denaturation mechanism.

Authors:  Edward P O'Brien; Ruxandra I Dima; Bernard Brooks; D Thirumalai
Journal:  J Am Chem Soc       Date:  2007-05-16       Impact factor: 15.419

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  9 in total

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Authors:  Koushik Kasavajhala; Swetha Bikkina; Indrajit Patil; Alexander D MacKerell; U Deva Priyakumar
Journal:  J Phys Chem B       Date:  2015-02-23       Impact factor: 2.991

Review 2.  Proteins in binary solvents.

Authors:  Francesco Spinozzi; Paolo Mariani; Maria Grazia Ortore
Journal:  Biophys Rev       Date:  2016-03-18

3.  Mechanism of Protein Denaturation: Partial Unfolding of the P22 Coat Protein I-Domain by Urea Binding.

Authors:  Rebecca L Newcomer; LaTasha C R Fraser; Carolyn M Teschke; Andrei T Alexandrescu
Journal:  Biophys J       Date:  2015-12-15       Impact factor: 4.033

4.  Effects of the Hydration State on the Mid-Infrared Spectra of Urea and Creatinine in Relation to Urine Analyses.

Authors:  Katherine V Oliver; Amandine Maréchal; Peter R Rich
Journal:  Appl Spectrosc       Date:  2016-05-11       Impact factor: 2.388

5.  Water-Induced Restructuring of the Surface of a Deep Eutectic Solvent.

Authors:  Rahul Gera; Carolyn J Moll; Aditi Bhattacherjee; Huib J Bakker
Journal:  J Phys Chem Lett       Date:  2022-01-12       Impact factor: 6.475

6.  Photophysical Properties of BADAN Revealed in the Study of GGBP Structural Transitions.

Authors:  Alexander V Fonin; Sergey A Silonov; Iuliia A Antifeeva; Olga V Stepanenko; Olesya V Stepanenko; Anna S Fefilova; Olga I Povarova; Anastasia A Gavrilova; Irina M Kuznetsova; Konstantin K Turoverov
Journal:  Int J Mol Sci       Date:  2021-10-15       Impact factor: 5.923

7.  Mechanism of Osmolyte Stabilization-Destabilization of Proteins: Experimental Evidence.

Authors:  Marcin Stasiulewicz; Aneta Panuszko; Piotr Bruździak; Janusz Stangret
Journal:  J Phys Chem B       Date:  2022-04-20       Impact factor: 3.466

8.  Remdesivir Strongly Binds to RNA-Dependent RNA Polymerase, Membrane Protein, and Main Protease of SARS-CoV-2: Indication From Molecular Modeling and Simulations.

Authors:  Faez Iqbal Khan; Tongzhou Kang; Haider Ali; Dakun Lai
Journal:  Front Pharmacol       Date:  2021-07-07       Impact factor: 5.988

9.  Time-dependent X-ray diffraction studies on urea/hen egg white lysozyme complexes reveal structural changes that indicate onset of denaturation.

Authors:  Tushar Raskar; Sagar Khavnekar; Madhusoodan Hosur
Journal:  Sci Rep       Date:  2016-08-30       Impact factor: 4.379

  9 in total

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