Literature DB >> 23797357

Protein packing defects "heat up" interfacial water.

María Belén Sierra1, Sebastián R Accordino, J Ariel Rodriguez-Fris, Marcela A Morini, Gustavo A Appignanesi, Ariel Fernández Stigliano.   

Abstract

Ligands must displace water molecules from their corresponding protein surface binding site during association. Thus, protein binding sites are expected to be surrounded by non-tightly-bound, easily removable water molecules. In turn, the existence of packing defects at protein binding sites has been also established. At such structural motifs, named dehydrons, the protein backbone is exposed to the solvent since the intramolecular interactions are incompletely wrapped by non-polar groups. Hence, dehydrons are sticky since they depend on additional intermolecular wrapping in order to properly protect the structure from water attack. Thus, a picture of protein binding is emerging wherein binding sites should be both dehydrons rich and surrounded by easily removable water. In this work we shall indeed confirm such a link between structure and dynamics by showing the existence of a firm correlation between the degree of underwrapping of the protein chain and the mobility of the corresponding hydration water molecules. In other words, we shall show that protein packing defects promote their local dehydration, thus producing a region of "hot" interfacial water which might be easily removed by a ligand upon association.

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Year:  2013        PMID: 23797357     DOI: 10.1140/epje/i2013-13062-7

Source DB:  PubMed          Journal:  Eur Phys J E Soft Matter        ISSN: 1292-8941            Impact factor:   1.890


  33 in total

1.  Relationship between structural order and the anomalies of liquid water.

Authors:  J R Errington; P G Debenedetti
Journal:  Nature       Date:  2001-01-18       Impact factor: 49.962

2.  Order, disorder, and flexibility: prediction from protein sequence.

Authors:  Lilia M Iakoucheva; A Keith Dunker
Journal:  Structure       Date:  2003-11       Impact factor: 5.006

3.  Insufficiently dehydrated hydrogen bonds as determinants of protein interactions.

Authors:  Ariel Fernández; Harold A Scheraga
Journal:  Proc Natl Acad Sci U S A       Date:  2002-12-23       Impact factor: 11.205

4.  Structural and dynamical aspects of water in contact with a hydrophobic surface.

Authors:  D C Malaspina; E P Schulz; L M Alarcón; M A Frechero; G A Appignanesi
Journal:  Eur Phys J E Soft Matter       Date:  2010-05-22       Impact factor: 1.890

5.  Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes.

Authors:  Richard A Friesner; Robert B Murphy; Matthew P Repasky; Leah L Frye; Jeremy R Greenwood; Thomas A Halgren; Paul C Sanschagrin; Daniel T Mainz
Journal:  J Med Chem       Date:  2006-10-19       Impact factor: 7.446

6.  Democratic particle motion for metabasin transitions in simple glass formers.

Authors:  G A Appignanesi; J A Rodríguez Fris; R A Montani; W Kob
Journal:  Phys Rev Lett       Date:  2006-02-08       Impact factor: 9.161

7.  Solvent-exposed backbone loosens the hydration shell of soluble folded proteins.

Authors:  Ariel Fernández; Jianping Chen; Alejandro Crespo
Journal:  J Chem Phys       Date:  2007-06-28       Impact factor: 3.488

8.  Metabasin dynamics and local structure in supercooled water.

Authors:  Jorge Ariel Rodríguez Fris; Gustavo A Appignanesi; Emilia La Nave; Francesco Sciortino
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2007-04-06

9.  Quantitative investigation of the two-state picture for water in the normal liquid and the supercooled regime.

Authors:  S R Accordino; J A Rodriguez Fris; F Sciortino; G A Appignanesi
Journal:  Eur Phys J E Soft Matter       Date:  2011-05-16       Impact factor: 1.890

10.  Wrapping effects within a proposed function-rescue strategy for the Y220C oncogenic mutation of protein p53.

Authors:  Sebastián R Accordino; J Ariel Rodríguez Fris; Gustavo A Appignanesi
Journal:  PLoS One       Date:  2013-01-24       Impact factor: 3.240

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  3 in total

1.  "Chameleonic" backbone hydrogen bonds in protein binding and as drug targets.

Authors:  C A Menéndez; S R Accordino; D C Gerbino; G A Appignanesi
Journal:  Eur Phys J E Soft Matter       Date:  2015-10-19       Impact factor: 1.890

2.  Studies on electrostatic interactions within model nano-confined aqueous environments of different chemical nature.

Authors:  Joan Manuel Montes de Oca; Cintia A Menéndez; Sebastián R Accordino; David C Malaspina; Gustavo A Appignanesi
Journal:  Eur Phys J E Soft Matter       Date:  2017-09-20       Impact factor: 1.890

3.  Hydrogen Bond Dynamic Propensity Studies for Protein Binding and Drug Design.

Authors:  Cintia A Menéndez; Sebastián R Accordino; Darío C Gerbino; Gustavo A Appignanesi
Journal:  PLoS One       Date:  2016-10-28       Impact factor: 3.240

  3 in total

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