Literature DB >> 21761828

Mapping the hydration dynamics of ubiquitin.

Nathaniel V Nucci1, Maxim S Pometun, A Joshua Wand.   

Abstract

The nature of water's interaction with biomolecules such as proteins has been difficult to examine in detail at atomic resolution. Solution NMR spectroscopy is potentially a powerful method for characterizing both the structural and temporal aspects of protein hydration but has been plagued by artifacts. Encapsulation of the protein of interest within the aqueous core of a reverse micelle particle results in a general slowing of water dynamics, significant reduction in hydrogen exchange chemistry and elimination of contributions from bulk water thereby enabling the use of nuclear Overhauser effects to quantify interactions between the protein surface and hydration water. Here we extend this approach to allow use of dipolar interactions between hydration water and hydrogens bonded to protein carbon atoms. By manipulating the molecular reorientation time of the reverse micelle particle through use of low viscosity liquid propane, the T(1ρ) relaxation time constants of (1)H bonded to (13)C were sufficiently lengthened to allow high quality rotating frame nuclear Overhauser effects to be obtained. These data supplement previous results obtained from dipolar interactions between the protein and hydrogens bonded to nitrogen and in aggregate cover the majority of the molecular surface of the protein. A wide range of hydration dynamics is observed. Clustering of hydration dynamics on the molecular surface is also seen. Regions of long-lived hydration water correspond with regions of the protein that participate in molecular recognition of binding partners suggesting that the contribution of the solvent entropy to the entropy of binding has been maximized through evolution.

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Year:  2011        PMID: 21761828      PMCID: PMC3155818          DOI: 10.1021/ja202033k

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  39 in total

1.  Hydrophobicity: two faces of water.

Authors:  David Chandler
Journal:  Nature       Date:  2002-05-30       Impact factor: 49.962

2.  A model binding site for testing scoring functions in molecular docking.

Authors:  Binqing Q Wei; Walter A Baase; Larry H Weaver; Brian W Matthews; Brian K Shoichet
Journal:  J Mol Biol       Date:  2002-09-13       Impact factor: 5.469

Review 3.  Dynamics of water in biological recognition.

Authors:  Samir Kumar Pal; Ahmed H Zewail
Journal:  Chem Rev       Date:  2004-04       Impact factor: 60.622

4.  Interfacial free energy and the hydrophobic effect.

Authors:  C Tanford
Journal:  Proc Natl Acad Sci U S A       Date:  1979-09       Impact factor: 11.205

5.  Cold denaturation of encapsulated ubiquitin.

Authors:  Maxim S Pometun; Ronald W Peterson; Charles R Babu; A Joshua Wand
Journal:  J Am Chem Soc       Date:  2006-08-23       Impact factor: 15.419

Review 6.  The ubiquitin system.

Authors:  A Hershko; A Ciechanover
Journal:  Annu Rev Biochem       Date:  1998       Impact factor: 23.643

7.  Site-specific hydration dynamics in the nonpolar core of a molten globule by dynamic nuclear polarization of water.

Authors:  Brandon D Armstrong; Jennifer Choi; Carlos López; Darryl A Wesener; Wayne Hubbell; Silvia Cavagnero; Songi Han
Journal:  J Am Chem Soc       Date:  2011-03-28       Impact factor: 15.419

8.  Reverse micelle encapsulation of membrane-anchored proteins for solution NMR studies.

Authors:  Kathleen G Valentine; Ronald W Peterson; Jamil S Saad; Michael F Summers; Xianzhong Xu; James B Ames; A Joshua Wand
Journal:  Structure       Date:  2010-01-13       Impact factor: 5.006

9.  Reverse micelles in integral membrane protein structural biology by solution NMR spectroscopy.

Authors:  Joseph M Kielec; Kathleen G Valentine; Charles R Babu; A Joshua Wand
Journal:  Structure       Date:  2009-03-11       Impact factor: 5.006

10.  Dynamics of protein and peptide hydration.

Authors:  Kristofer Modig; Edvards Liepinsh; Gottfried Otting; Bertil Halle
Journal:  J Am Chem Soc       Date:  2004-01-14       Impact factor: 15.419

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  35 in total

1.  Protein structural and surface water rearrangement constitute major events in the earliest aggregation stages of tau.

Authors:  Anna Pavlova; Chi-Yuan Cheng; Maia Kinnebrew; John Lew; Frederick W Dahlquist; Songi Han
Journal:  Proc Natl Acad Sci U S A       Date:  2015-12-28       Impact factor: 11.205

2.  Site-specific hydration dynamics of globular proteins and the role of constrained water in solvent exchange with amphiphilic cosolvents.

Authors:  John T King; Evan J Arthur; Charles L Brooks; Kevin J Kubarych
Journal:  J Phys Chem B       Date:  2012-05-07       Impact factor: 2.991

3.  Defining the Apoptotic Trigger: THE INTERACTION OF CYTOCHROME c AND CARDIOLIPIN.

Authors:  Evan S O'Brien; Nathaniel V Nucci; Brian Fuglestad; Cecilia Tommos; A Joshua Wand
Journal:  J Biol Chem       Date:  2015-10-20       Impact factor: 5.157

4.  Role of cavities and hydration in the pressure unfolding of T4 lysozyme.

Authors:  Nathaniel V Nucci; Brian Fuglestad; Evangelia A Athanasoula; A Joshua Wand
Journal:  Proc Natl Acad Sci U S A       Date:  2014-09-08       Impact factor: 11.205

5.  Dominant Alcohol-Protein Interaction via Hydration-Enabled Enthalpy-Driven Binding Mechanism.

Authors:  Yuan Chong; Alfred Kleinhammes; Pei Tang; Yan Xu; Yue Wu
Journal:  J Phys Chem B       Date:  2015-04-17       Impact factor: 2.991

6.  Cholesterol enhances surface water diffusion of phospholipid bilayers.

Authors:  Chi-Yuan Cheng; Luuk L C Olijve; Ravinath Kausik; Songi Han
Journal:  J Chem Phys       Date:  2014-12-14       Impact factor: 3.488

7.  Water-Protein Interactions Coupled with Protein Conformational Transition.

Authors:  Soichiro Kitazawa; Yu Aoshima; Takuro Wakamoto; Ryo Kitahara
Journal:  Biophys J       Date:  2018-08-08       Impact factor: 4.033

Review 8.  The dark energy of proteins comes to light: conformational entropy and its role in protein function revealed by NMR relaxation.

Authors:  A Joshua Wand
Journal:  Curr Opin Struct Biol       Date:  2012-12-13       Impact factor: 6.809

Review 9.  High-resolution NMR spectroscopy of encapsulated proteins dissolved in low-viscosity fluids.

Authors:  Nathaniel V Nucci; Kathleen G Valentine; A Joshua Wand
Journal:  J Magn Reson       Date:  2014-04       Impact factor: 2.229

10.  Anomalously Rapid Hydration Water Diffusion Dynamics Near DNA Surfaces.

Authors:  John M Franck; Yuan Ding; Katherine Stone; Peter Z Qin; Songi Han
Journal:  J Am Chem Soc       Date:  2015-09-10       Impact factor: 15.419

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