Literature DB >> 22998120

Why the solvation water around proteins is more dense than bulk water.

Anna Kuffel1, Jan Zielkiewicz.   

Abstract

The main aim of this work is to propose a rational explanation of the commonly observed phenomenon of increasing water density within solvation shell of proteins. We have observed that the geometry of the water-water hydrogen bond network within solvation layer differs from the one in bulk water, and it is the result of interactions of water molecules with protein surface. Altered geometry of the network reflects changes in the structure of solvation water. Our explanation of the observed changes is based on model proposed by Tanaka (Tanaka, H. J. Chem. Phys. 2000, 112, 799). According to this model, in liquid water exist some special structures formed by water molecules thanks to their unique ability to create the branched network of hydrogen bonds. These structures have two characteristic features: a low potential energy of internal interactions and a large specific volume. We provide some evidence for the supposition that deformation of the geometry of the water-water hydrogen bond network is responsible for destabilization of these structures and therefore for increased local density of water. Our model is constructed on the basis of the analysis of solvation water of some specific protein, the motor head of kinesin. Subsequently, we used it for description of solvation of purely hydrophobic surface. It has been found that in this case an unoccupied space between the hydrophobic surface and neighboring solvation layer exists. It has been found that thickness of this region depends on local geometry of the water-protein interface, and it is a result of maintaining a balance between water-surface interactions and water-water interactions. In our opinion, existence of this space region is one of the main factors that differentiates the hydrophobic hydration from hydration of the native form of kinesin. Its existence also explains why the density is greater for solvation water around the native form of the protein than in the vicinity of the hydrophobic surface.

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Year:  2012        PMID: 22998120     DOI: 10.1021/jp305172t

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


  9 in total

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2.  Free energetics of carbon nanotube association in aqueous inorganic NaI salt solutions: Temperature effects using all-atom molecular dynamics simulations.

Authors:  Shu-Ching Ou; Di Cui; Matthew Wezowicz; Michela Taufer; Sandeep Patel
Journal:  J Comput Chem       Date:  2015-04-13       Impact factor: 3.376

3.  Analytical 2-Dimensional Model of Nonpolar and Ionic Solvation in Water.

Authors:  Ajeet Kumar Yadav; Pradipta Bandyopadhyay; Tomaz Urbic; Ken A Dill
Journal:  J Phys Chem B       Date:  2021-02-04       Impact factor: 2.991

4.  A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). II. Temperature transferability and structural properties at low temperature.

Authors:  Jaehyeok Jin; Alexander J Pak; Yining Han; Gregory A Voth
Journal:  J Chem Phys       Date:  2021-01-28       Impact factor: 3.488

5.  Characterization of the Local Structure in Liquid Water by Various Order Parameters.

Authors:  Elise Duboué-Dijon; Damien Laage
Journal:  J Phys Chem B       Date:  2015-06-19       Impact factor: 2.991

6.  Ice formation and solvent nanoconfinement in protein crystals.

Authors:  David W Moreau; Hakan Atakisi; Robert E Thorne
Journal:  IUCrJ       Date:  2019-03-13       Impact factor: 4.769

7.  Influence of Water Polarization Caused by Phonon Resonance on Catalytic Activity of Enolase.

Authors:  Jadwiga Pietkiewicz; Regina Danielewicz; Czesław Wandzel; Jarosław Beznosiuk; Andrzej Szuba; Małgorzata Samsel-Czekała; Andrzej Gamian
Journal:  ACS Omega       Date:  2021-02-01

8.  Crustwater: Modeling Hydrophobic Solvation.

Authors:  Ajeet Kumar Yadav; Pradipta Bandyopadhyay; Evangelos A Coutsias; Ken A Dill
Journal:  J Phys Chem B       Date:  2022-08-04       Impact factor: 3.466

9.  Wildtype and A30P mutant alpha-synuclein form different fibril structures.

Authors:  Søren Bang Nielsen; Francesca Macchi; Samuele Raccosta; Annette Eva Langkilde; Lise Giehm; Anders Kyrsting; Anna Sigrid Pii Svane; Mauro Manno; Gunna Christiansen; Niels Christian Nielsen; Lene Oddershede; Bente Vestergaard; Daniel Erik Otzen
Journal:  PLoS One       Date:  2013-07-04       Impact factor: 3.240

  9 in total

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