MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories

Handle URI:
http://hdl.handle.net/10754/334604
Title:
MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories
Authors:
Abdel-Azeim, Safwat ( 0000-0001-8611-1251 ) ; Chermak, Edrisse ( 0000-0002-2716-5724 ) ; Vangone, Anna; Oliva, Romina; Cavallo, Luigi ( 0000-0002-1398-338X )
Abstract:
Background: Molecular Dynamics ( MD) simulations of protein complexes suffer from the lack of specific tools in the analysis step. Analyses of MD trajectories of protein complexes indeed generally rely on classical measures, such as the RMSD, RMSF and gyration radius, conceived and developed for single macromolecules. As a matter of fact, instead, researchers engaged in simulating the dynamics of a protein complex are mainly interested in characterizing the conservation/variation of its biological interface. Results: On these bases, herein we propose a novel approach to the analysis of MD trajectories or other conformational ensembles of protein complexes, MDcons, which uses the conservation of inter-residue contacts at the interface as a measure of the similarity between different snapshots. A "consensus contact map" is also provided, where the conservation of the different contacts is drawn in a grey scale. Finally, the interface area of the complex is monitored during the simulations. To show its utility, we used this novel approach to study two protein-protein complexes with interfaces of comparable size and both dominated by hydrophilic interactions, but having binding affinities at the extremes of the experimental range. MDcons is demonstrated to be extremely useful to analyse the MD trajectories of the investigated complexes, adding important insight into the dynamic behavior of their biological interface. Conclusions: MDcons specifically allows the user to highlight and characterize the dynamics of the interface in protein complexes and can thus be used as a complementary tool for the analysis of MD simulations of both experimental and predicted structures of protein complexes.
KAUST Department:
KAUST Catalysis Center (KCC)
Citation:
Abdel-Azeim S, Chermak E, Vangone A, Oliva R, Cavallo L (2014) MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories. BMC Bioinformatics 15: S1. doi:10.1186/1471-2105-15-S5-S1.
Publisher:
BioMed Central
Journal:
BMC Bioinformatics
Issue Date:
6-May-2014
DOI:
10.1186/1471-2105-15-S5-S1
PubMed ID:
25077693
PubMed Central ID:
PMC4095001
Type:
Article
ISSN:
1471-2105
Appears in Collections:
Articles; KAUST Catalysis Center (KCC)

Full metadata record

DC FieldValue Language
dc.contributor.authorAbdel-Azeim, Safwaten
dc.contributor.authorChermak, Edrisseen
dc.contributor.authorVangone, Annaen
dc.contributor.authorOliva, Rominaen
dc.contributor.authorCavallo, Luigien
dc.date.accessioned2014-11-11T14:31:41Z-
dc.date.available2014-11-11T14:31:41Z-
dc.date.issued2014-05-06en
dc.identifier.citationAbdel-Azeim S, Chermak E, Vangone A, Oliva R, Cavallo L (2014) MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories. BMC Bioinformatics 15: S1. doi:10.1186/1471-2105-15-S5-S1.en
dc.identifier.issn1471-2105en
dc.identifier.pmid25077693en
dc.identifier.doi10.1186/1471-2105-15-S5-S1en
dc.identifier.urihttp://hdl.handle.net/10754/334604en
dc.description.abstractBackground: Molecular Dynamics ( MD) simulations of protein complexes suffer from the lack of specific tools in the analysis step. Analyses of MD trajectories of protein complexes indeed generally rely on classical measures, such as the RMSD, RMSF and gyration radius, conceived and developed for single macromolecules. As a matter of fact, instead, researchers engaged in simulating the dynamics of a protein complex are mainly interested in characterizing the conservation/variation of its biological interface. Results: On these bases, herein we propose a novel approach to the analysis of MD trajectories or other conformational ensembles of protein complexes, MDcons, which uses the conservation of inter-residue contacts at the interface as a measure of the similarity between different snapshots. A "consensus contact map" is also provided, where the conservation of the different contacts is drawn in a grey scale. Finally, the interface area of the complex is monitored during the simulations. To show its utility, we used this novel approach to study two protein-protein complexes with interfaces of comparable size and both dominated by hydrophilic interactions, but having binding affinities at the extremes of the experimental range. MDcons is demonstrated to be extremely useful to analyse the MD trajectories of the investigated complexes, adding important insight into the dynamic behavior of their biological interface. Conclusions: MDcons specifically allows the user to highlight and characterize the dynamics of the interface in protein complexes and can thus be used as a complementary tool for the analysis of MD simulations of both experimental and predicted structures of protein complexes.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.rights.urihttp://creativecommons.org/licenses/by/2.0/en
dc.titleMDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectoriesen
dc.typeArticleen
dc.contributor.departmentKAUST Catalysis Center (KCC)en
dc.identifier.journalBMC Bioinformaticsen
dc.identifier.pmcidPMC4095001en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionDepartment of Chemistry and Biology, University of Salerno, Via Ponte don Melillo 84084, Fisciano (SA), Italyen
dc.contributor.institutionDepartment of Sciences and Technologies, University "Parthenope" of Naples, Centro Direzionale Isola C4 80143, Naples, Italyen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorAbdel-Azeim, Safwaten
kaust.authorChermak, Edrisseen
kaust.authorCavallo, Luigien

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