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dc.contributor.author
Grosso, Marcos Alberto
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dc.contributor.author
Kalstein, Adrian
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dc.contributor.author
Parisi, Gustavo Daniel
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dc.contributor.author
Roitberg, Adrián
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dc.contributor.author
Fernández Alberti, Sebastián
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dc.date.available
2020-03-01T19:53:23Z
dc.date.issued
2015-06
dc.identifier.citation
Grosso, Marcos Alberto; Kalstein, Adrian; Parisi, Gustavo Daniel; Roitberg, Adrián; Fernández Alberti, Sebastián; On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein; American Institute of Physics; Journal of Chemical Physics; 142; 24; 6-2015; 1-13
dc.identifier.issn
0021-9606
dc.identifier.uri
http://hdl.handle.net/11336/98598
dc.description.abstract
The native state of a protein consists of an equilibrium of conformational states on an energy landscape rather than existing as a single static state. The co-existence of conformers with different ligand-affinities in a dynamical equilibrium is the basis for the conformational selection model for ligand binding. In this context, the development of theoretical methods that allow us to analyze not only the structural changes but also changes in the fluctuation patterns between conformers will contribute to elucidate the differential properties acquired upon ligand binding. Molecular dynamics simulations can provide the required information to explore these features. Its use in combination with subsequent essential dynamics analysis allows separating large concerted conformational rearrangements from irrelevant fluctuations. We present a novel procedure to define the size and composition of essential dynamics subspaces associated with ligand-bound and ligand-free conformations. These definitions allow us to compare essential dynamics subspaces between different conformers. Our procedure attempts to emphasize the main similarities and differences between the different essential dynamics in an unbiased way. Essential dynamics subspaces associated to conformational transitions can also be analyzed. As a test case, we study the glutaminase interacting protein (GIP), composed of a single PDZ domain. Both GIP ligand-free state and glutaminase L peptide-bound states are analyzed. Our findings concerning the relative changes in the flexibility pattern upon binding are in good agreement with experimental Nuclear Magnetic Resonance data.
dc.format
application/pdf
dc.language.iso
eng
dc.publisher
American Institute of Physics
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dc.rights
info:eu-repo/semantics/openAccess
dc.rights.uri
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.subject
Conformational dynamics
dc.subject
Subspaces
dc.subject
Eigen values
dc.subject
Molecular conformation
dc.subject
Nuclear magnetic resonance
dc.subject.classification
Otras Ciencias Químicas
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dc.subject.classification
Ciencias Químicas
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dc.subject.classification
CIENCIAS NATURALES Y EXACTAS
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dc.title
On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein
dc.type
info:eu-repo/semantics/article
dc.type
info:ar-repo/semantics/artículo
dc.type
info:eu-repo/semantics/publishedVersion
dc.date.updated
2020-02-26T15:02:15Z
dc.journal.volume
142
dc.journal.number
24
dc.journal.pagination
1-13
dc.journal.pais
Estados Unidos
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dc.journal.ciudad
New York
dc.description.fil
Fil: Grosso, Marcos Alberto. Universidad Nacional de Quilmes; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
dc.description.fil
Fil: Kalstein, Adrian. Universidad Nacional de Quilmes; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
dc.description.fil
Fil: Parisi, Gustavo Daniel. Universidad Nacional de Quilmes; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
dc.description.fil
Fil: Roitberg, Adrián. University of Florida; Estados Unidos
dc.description.fil
Fil: Fernández Alberti, Sebastián. Universidad Nacional de Quilmes; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
dc.journal.title
Journal of Chemical Physics
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dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/url/http://scitation.aip.org/content/aip/journal/jcp/142/24/10.1063/1.4922925
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/doi/http://dx.doi.org/10.1063/1.4922925
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