Literature DB >> 16852340

Properties of spanning water networks at protein surfaces.

Nikolai Smolin1, Alla Oleinikova, Ivan Brovchenko, Alfons Geiger, Roland Winter.   

Abstract

The formation of a spanning two-dimensional hydrogen-bonded water network at the surface of proteins via a percolation transition enables their biological function. We show in detail how the spanning (percolating) water network appears at the surfaces of model hydrophilic spheres and at the surface of a single protein (lysozyme) molecule. We have found essential correlations of the linear extension, radius of gyration, and position of the center of mass of the largest water cluster with its size. The specific two-peak structure of the probability distribution of the largest cluster size allowed us to study various properties separately for spanning and nonspanning largest clusters. The radius of gyration of the spanning cluster always exceeds the radii of the spheres or the effective radius of the protein. Any spanning cluster envelops essentially more than half of the surface area. The temporal decay of the spanning networks shows a stretched exponential character. Their average lifetime at the percolation threshold is about the lifetime of a water-water hydrogen bond.

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Year:  2005        PMID: 16852340     DOI: 10.1021/jp050153e

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


  8 in total

1.  Crystal structures, dynamics and functional implications of molybdenum-cofactor biosynthesis protein MogA from two thermophilic organisms.

Authors:  Shankar Prasad Kanaujia; Jeyaraman Jeyakanthan; Akeo Shinkai; Seiki Kuramitsu; Shigeyuki Yokoyama; Kanagaraj Sekar
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2010-12-21

2.  Influence of water clustering on the dynamics of hydration water at the surface of a lysozyme.

Authors:  Alla Oleinikova; Nikolai Smolin; Ivan Brovchenko
Journal:  Biophys J       Date:  2007-07-13       Impact factor: 4.033

3.  Quantitative fluorescence correlation spectroscopy reveals a 1000-fold increase in lifetime of protein functionality.

Authors:  Dianwen Zhang; Hannes Lans; Wim Vermeulen; Aufried Lenferink; Cees Otto
Journal:  Biophys J       Date:  2008-06-27       Impact factor: 4.033

Review 4.  Protein-ligand (un)binding kinetics as a new paradigm for drug discovery at the crossroad between experiments and modelling.

Authors:  M Bernetti; A Cavalli; L Mollica
Journal:  Medchemcomm       Date:  2017-01-30       Impact factor: 3.597

5.  Water-mediated ionic interactions in protein structures.

Authors:  R Sabarinathan; K Aishwarya; R Sarani; M Kirti Vaishnavi; K Sekar
Journal:  J Biosci       Date:  2011-06       Impact factor: 1.826

6.  Crowding induced collective hydration of biological macromolecules over extended distances.

Authors:  John T King; Evan J Arthur; Charles L Brooks; Kevin J Kubarych
Journal:  J Am Chem Soc       Date:  2013-12-16       Impact factor: 15.419

7.  Lone pair ... pi interactions between water oxygens and aromatic residues: quantum chemical studies based on high-resolution protein structures and model compounds.

Authors:  Alok Jain; Venkatnarayan Ramanathan; Ramasubbu Sankararamakrishnan
Journal:  Protein Sci       Date:  2009-03       Impact factor: 6.725

8.  Modeling structure and flexibility of Candida antarctica lipase B in organic solvents.

Authors:  Peter Trodler; Jürgen Pleiss
Journal:  BMC Struct Biol       Date:  2008-02-06
  8 in total

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