Literature DB >> 26486885

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

C A Menéndez1, S R Accordino1, D C Gerbino1, G A Appignanesi2.   

Abstract

We carry out a time-averaged contact matrix study to reveal the existence of protein backbone hydrogen bonds (BHBs) whose net persistence in time differs markedly form their corresponding PDB-reported state. We term such interactions as "chameleonic" BHBs, CBHBs, precisely to account for their tendency to change the structural prescription of the PDB for the opposite bonding propensity in solution. We also find a significant enrichment of protein binding sites in CBHBs, relate them to local water exposure and analyze their behavior as ligand/drug targets. Thus, the dynamic analysis of hydrogen bond propensity might lay the foundations for new tools of interest in protein binding-site prediction and in lead optimization for drug design.

Entities:  

Keywords:  Soft Matter: Interfacial Phenomena and Nanostructured Surfaces

Mesh:

Substances:

Year:  2015        PMID: 26486885     DOI: 10.1140/epje/i2015-15107-3

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


  16 in total

1.  Adherence of packing defects in soluble proteins.

Authors:  Ariel Fernández; L Ridgway Scott
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2.  Wrapping mimicking in drug-like small molecules disruptive of protein-protein interfaces.

Authors:  Sebastián R Accordino; Marcela A Morini; María Belén Sierra; J Ariel Rodríguez Fris; Gustavo A Appignanesi; Ariel Fernández
Journal:  Proteins       Date:  2012-04-16

Review 3.  Hydrophobicity of proteins and interfaces: insights from density fluctuations.

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Journal:  Annu Rev Chem Biomol Eng       Date:  2011       Impact factor: 11.059

4.  Studies leading to potent, dual inhibitors of Bcl-2 and Bcl-xL.

Authors:  Milan Bruncko; Thorsten K Oost; Barbara A Belli; Hong Ding; Mary K Joseph; Aaron Kunzer; Darlene Martineau; William J McClellan; Michael Mitten; Shi-Chung Ng; Paul M Nimmer; Tilman Oltersdorf; Cheol-Min Park; Andrew M Petros; Alexander R Shoemaker; Xiaohong Song; Xilu Wang; Michael D Wendt; Haichao Zhang; Stephen W Fesik; Saul H Rosenberg; Steven W Elmore
Journal:  J Med Chem       Date:  2007-01-26       Impact factor: 7.446

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.  Protein packing defects "heat up" interfacial water.

Authors:  María Belén Sierra; Sebastián R Accordino; J Ariel Rodriguez-Fris; Marcela A Morini; Gustavo A Appignanesi; Ariel Fernández Stigliano
Journal:  Eur Phys J E Soft Matter       Date:  2013-06-25       Impact factor: 1.890

7.  A dry ligand-binding cavity in a solvated protein.

Authors:  Johan Qvist; Monika Davidovic; Donald Hamelberg; Bertil Halle
Journal:  Proc Natl Acad Sci U S A       Date:  2008-04-21       Impact factor: 11.205

8.  A unifying motif of intermolecular cooperativity in protein associations.

Authors:  S R Accordino; J A Rodriguez Fris; G A Appignanesi; A Fernández
Journal:  Eur Phys J E Soft Matter       Date:  2012-07-16       Impact factor: 1.890

9.  In vivo activation of the p53 pathway by small-molecule antagonists of MDM2.

Authors:  Lyubomir T Vassilev; Binh T Vu; Bradford Graves; Daisy Carvajal; Frank Podlaski; Zoran Filipovic; Norman Kong; Ursula Kammlott; Christine Lukacs; Christian Klein; Nader Fotouhi; Emily A Liu
Journal:  Science       Date:  2004-01-02       Impact factor: 47.728

10.  Integrating fragment assembly and biophysical methods in the chemical advancement of small-molecule antagonists of IL-2: an approach for inhibiting protein-protein interactions.

Authors:  Brian C Raimundo; Johan D Oslob; Andrew C Braisted; Jennifer Hyde; Robert S McDowell; Mike Randal; Nathan D Waal; Jennifer Wilkinson; Chul H Yu; Michelle R Arkin
Journal:  J Med Chem       Date:  2004-06-03       Impact factor: 7.446

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  3 in total

1.  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

2.  Theoretical models to predict the inhibitory effect of ligands of sphingosine kinase 1 using QTAIM calculations and hydrogen bond dynamic propensity analysis.

Authors:  Marcela Vettorazzi; Cintia Menéndez; Lucas Gutiérrez; Sebastián Andujar; Gustavo Appignanesi; Ricardo D Enriz
Journal:  J Comput Aided Mol Des       Date:  2018-07-03       Impact factor: 3.686

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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