(Q30010103)

21 May 2017

title

Interfacial water molecules in SH3 interactions: Getting the full picture on polyproline recognition by protein-protein interaction domains (English)

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protein-protein interaction

21 May 2017

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2

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Ana Zafra-Ruano

series ordinal

1

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language of work or name

English

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publication date

11 May 2012

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21 May 2017

number of pages

12

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based on heuristic

inferred from page(s)

published in

FEBS Letters

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21 May 2017

volume

586

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21 May 2017

issue

17

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21 May 2017

page(s)

2619-2630

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Interaction domains: from simple binding events to complex cellular behavior

21 May 2017

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A thermodynamic and kinetic analysis of the folding pathway of an SH3 domain entropically stabilised by a redesigned hydrophobic core

21 January 2018

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The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved.

21 January 2018

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Obligatory steps in protein folding and the conformational diversity of the transition state

21 January 2018

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Experiment and theory highlight role of native state topology in SH3 folding

21 January 2018

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Conformational analysis of peptides corresponding to beta-hairpins and a beta-sheet that represent the entire sequence of the alpha-spectrin SH3 domain.

21 January 2018

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The native state conformational ensemble of the SH3 domain from alpha-spectrin

21 January 2018

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Solution structure, dynamics, and thermodynamics of the native state ensemble of the Sem-5 C-terminal SH3 domain

21 January 2018

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Cooperative propagation of local stability changes from low-stability and high-stability regions in a SH3 domain

21 January 2018

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Characterizing the role of ensemble modulation in mutation-induced changes in binding affinity

21 January 2018

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Exploiting the basis of proline recognition by SH3 and WW domains: design of N-substituted inhibitors

21 January 2018

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Specific interactions outside the proline-rich core of two classes of Src homology 3 ligands

21 January 2018

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Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening

21 January 2018

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Versatile retargeting of SH3 domain binding by modification of non-conserved loop residues

21 January 2018

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RT loop flexibility enhances the specificity of Src family SH3 domains for HIV-1 Nef

21 January 2018

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The SH3 domain of Eps8 exists as a novel intertwined dimer

21 January 2018

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A novel peptide-SH3 interaction.

21 January 2018

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Specific oncogenic activity of the Src-family tyrosine kinase c-Yes in colon carcinoma cells

21 January 2018

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Specificity in signaling by c-Yes

21 January 2018

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Two binding orientations for peptides to the Src SH3 domain: development of a general model for SH3-ligand interactions

21 January 2018

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Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains

21 January 2018

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The tryptophan switch: changing ligand-binding specificity from type I to type II in SH3 domains

21 January 2018

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21 January 2018

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21 January 2018

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21 January 2018

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Mona/Gads SH3C binding to hematopoietic progenitor kinase 1 (HPK1) combines an atypical SH3 binding motif, R/KXXK, with a classical PXXP motif embedded in a polyproline type II (PPII) helix

21 January 2018

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Atypical polyproline recognition by the CMS N-terminal Src homology 3 domain

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

A noncanonical SH3 domain binding motif links BK channels to the actin cytoskeleton via the SH3 adapter cortactin

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Structural basis for specific binding of the Gads SH3 domain to an RxxK motif-containing SLP-76 peptide: a novel mode of peptide recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Efficient T-cell receptor signaling requires a high-affinity interaction between the Gads C-SH3 domain and the SLP-76 RxxK motif

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

SH2 and SH3 domains as targets for anti-proliferative agents

21 January 2018

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SH2 and SH3 domains: potential targets for anti-cancer drug design

21 January 2018

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Inhibitors of Ras signal transduction as antitumor agents

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Nef surfaces: where to interfere with function

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Acquisition of Fyn-selective SH3 domain ligands via a combinatorial library strategy

21 January 2018

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Synthetic inhibitors of proline-rich ligand-mediated protein-protein interaction: potent analogs of UCS15A.

21 January 2018

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A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

A miniprotein scaffold used to assemble the polyproline II binding epitope recognized by SH3 domains.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Rational design of specific high-affinity peptide ligands for the Abl-SH3 domain

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Molecular modeling of the interaction of polyproline-based peptides with the Abl-SH3 domain: rational modification of the interaction

21 January 2018

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21 January 2018

Drugging the undruggable

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Design of peptoid analogue dimers and measure of their affinity for Grb2 SH3 domains.

21 January 2018

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Synthesis of 5-, 6- and 7-substituted-2-aminoquinolines as SH3 domain ligands

21 January 2018

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Identification and specificity studies of small-molecule ligands for SH3 protein domains

21 January 2018

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Improving SH3 domain ligand selectivity using a non-natural scaffold

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Ligand recognition by SH3 and WW domains: the role of N-alkylation in PPII helices

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

A thermodynamic approach to the affinity optimization of drug candidates

21 January 2018

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Do enthalpy and entropy distinguish first in class from best in class?

21 January 2018

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Compensating enthalpic and entropic changes hinder binding affinity optimization

21 January 2018

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ITC in the post-genomic era...? Priceless

21 January 2018

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Thermodynamics-based drug design: strategies for inhibiting protein-protein interactions

21 January 2018

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21 January 2018

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Adding calorimetric data to decision making in lead discovery: a hot tip

21 January 2018

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Finding a better path to drug selectivity

21 January 2018

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Calorimetry and thermodynamics in drug design

21 January 2018

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Measurements of binding thermodynamics in drug discovery

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Overcoming drug resistance in HIV-1 chemotherapy: the binding thermodynamics of Amprenavir and TMC-126 to wild-type and drug-resistant mutants of the HIV-1 protease

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Thermodynamics of binding to SH3 domains: the energetic impact of polyproline II (PII) helix formation

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Thermodynamic dissection of the binding energetics of proline-rich peptides to the Abl-SH3 domain: implications for rational ligand design

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Structural and thermodynamic characterization of the interaction of the SH3 domain from Fyn with the proline-rich binding site on the p85 subunit of PI3-kinase

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

The role of backbone motions in ligand binding to the c-Src SH3 domain

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Orientation of peptide fragments from Sos proteins bound to the N-terminal SH3 domain of Grb2 determined by NMR spectroscopy

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Recognition of lysine-rich peptide ligands by murine cortactin SH3 domain: CD, ITC, and NMR studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Dynamic Nef and Nef dynamics: how structure could explain the complex activities of this small HIV protein

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

SAP couples Fyn to SLAM immune receptors

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Structural basis of PxxDY motif recognition in SH3 binding

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

SH3 domains of Grb2 adaptor bind to PXpsiPXR motifs within the Sos1 nucleotide exchange factor in a discriminate manner

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Ligand-induced changes in dynamics in the RT loop of the C-terminal SH3 domain of Sem-5 indicate cooperative conformational coupling

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Ligand-induced strain in hydrogen bonds of the c-Src SH3 domain detected by NMR.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Mutational analysis of the regulatory function of the c-Abl Src homology 3 domain

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Mechanisms of autoinhibition and STI-571/imatinib resistance revealed by mutagenesis of BCR-ABL.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Characterization of the interaction of natural proline-rich peptides with five different SH3 domains.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Crystal structure of the abl-SH3 domain complexed with a designed high-affinity peptide ligand: implications for SH3-ligand interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Structural parameterization of the binding enthalpy of small ligands

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Thermodynamic dissection of the binding energetics of KNI-272, a potent HIV-1 protease inhibitor

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Role of Interfacial Water Molecules in Proline-rich Ligand Recognition by the Src Homology 3 Domain of Abl

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Interfacial water molecules in SH3 interactions: a revised paradigm for polyproline recognition.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Docking of hydrophobic ligands with interaction-based matching algorithms.

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Molecular docking with ligand attached water molecules.

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Ligand-protein cross-docking with water molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Solvated docking: introducing water into the modelling of biomolecular complexes.

21 January 2018

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Modeling water molecules in protein-ligand docking using GOLD.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

De novo ligand design with explicit water molecules: an application to bacterial neuraminidase.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

The effect of a tightly bound water molecule on scaffold diversity in the computer-aided de novo ligand design of CDK2 inhibitors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Including tightly-bound water molecules in de novo drug design. Exemplification through the in silico generation of poly(ADP-ribose)polymerase ligands.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

The role of water molecules in computational drug design

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Win some, lose some: enthalpy-entropy compensation in weak intermolecular interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

The Entropic Cost of Bound Water in Crystals and Biomolecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

The role of water in sequence-independent ligand binding by an oligopeptide transporter protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Thermodynamics of buried water clusters at a protein-ligand binding interface

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Thermodynamic consequences of disrupting a water-mediated hydrogen bond network in a protein:pheromone complex

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Structure-based design of potent inhibitors of scytalone dehydratase: displacement of a water molecule from the active site

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Crystallographic and calorimetric analysis of peptide binding to OppA protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Enthalpy of hydrogen bond formation in a protein-ligand binding reaction

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Involvement of water in carbohydrate-protein binding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

Predicting conserved water-mediated and polar ligand interactions in proteins using a K-nearest-neighbors genetic algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

WaterScore: a novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes

21 January 2018

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https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

HINT: a new method of empirical hydrophobic field calculation for CoMFA.

21 January 2018

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A computational tool to optimize ligand selectivity between two similar biomacromolecular targets

21 January 2018

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A computational procedure for determining energetically favorable binding sites on biologically important macromolecules

21 January 2018

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The statistical-thermodynamic basis for computation of binding affinities: a critical review

21 January 2018

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Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method.

21 January 2018

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Inhibitors to the Src SH2 domain: a lesson in structure--thermodynamic correlation in drug design.

21 January 2018

1 reference

https://api.crossref.org/works/10.1016%2FJ.FEBSLET.2012.04.057

The structural basis of sequence-independent peptide binding by OppA protein

21 January 2018

1 reference

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Hydration dynamics of the collagen triple helix by NMR.

21 January 2018

1 reference

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The application of thermodynamic methods in drug design

21 January 2018

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10.1016/J.FEBSLET.2012.04.057

21 January 2018

Identifiers

DOI

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21 May 2017

1 reference