Behavior of H-FABP-fatty acid complex in a protein crystal simulation

Crystallographic data comes from a space-time average over all the unit cells within the crystal, so dynamic phenomena do not contribute significantly to the diffraction data. Many efforts have been made to reconstitute the movement of the macromolecules and explore the microstates that the confined...

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Detalles Bibliográficos
Autores principales: Espinosa Silva, Yanis Ricardo, Álvarez, Hugo Ariel, Howard, Eduardo Ignacio, Carlevaro, Carlos Manuel
Formato: Articulo Preprint
Lenguaje:Inglés
Publicado: 2018
Materias:
Biología
H-FABP-fatty acid
Protein crystal simulation
Principal component analysis
Acceso en línea:http://sedici.unlp.edu.ar/handle/10915/102636
https://ri.conicet.gov.ar/11336/93833
https://arxiv.org/abs/1806.06102
Aporte de:
SEDICI (UNLP) de Universidad Nacional de La Plata
id I19-R120-10915-102636
record_format dspace
institution Universidad Nacional de La Plata
institution_str I-19
repository_str R-120
collection SEDICI (UNLP)
language Inglés
topic Biología
H-FABP-fatty acid
Protein crystal simulation
Principal component analysis
spellingShingle Biología
H-FABP-fatty acid
Protein crystal simulation
Principal component analysis
Espinosa Silva, Yanis Ricardo
Álvarez, Hugo Ariel
Howard, Eduardo Ignacio
Carlevaro, Carlos Manuel
Behavior of H-FABP-fatty acid complex in a protein crystal simulation
topic_facet Biología
H-FABP-fatty acid
Protein crystal simulation
Principal component analysis
description Crystallographic data comes from a space-time average over all the unit cells within the crystal, so dynamic phenomena do not contribute significantly to the diffraction data. Many efforts have been made to reconstitute the movement of the macromolecules and explore the microstates that the confined proteins can adopt in the crystalline network. In this paper, we explored different strategies to simulate a heart fatty acid binding proteins (H-FABP) crystal starting from high resolution coordinates obtained at room temperature, describing in detail the procedure to study protein crystals (in particular H-FABP) by means of Molecular Dynamics simulations, and exploring the role of ethanol as a co-solute that can modify the stability of the protein and facilitate the interchange of fatty acids. Also, we introduced crystallographic restraints in our crystal models, according to experimental isotropic B-factors and analyzed the H-FABP crystal motions using Principal Component Analysis, isotropic and anisotropic B-factors. Our results suggest that restrained MD simulations based in experimental B?factors produce lower simulated B-factors than simulations without restraints,leading to more accurate predictions of the temperature factors. However, the systems without positional restraints represent a higher microscopic heterogeneity in the crystal.
format Articulo
Preprint
author Espinosa Silva, Yanis Ricardo
Álvarez, Hugo Ariel
Howard, Eduardo Ignacio
Carlevaro, Carlos Manuel
author_facet Espinosa Silva, Yanis Ricardo
Álvarez, Hugo Ariel
Howard, Eduardo Ignacio
Carlevaro, Carlos Manuel
author_sort Espinosa Silva, Yanis Ricardo
title Behavior of H-FABP-fatty acid complex in a protein crystal simulation
title_short Behavior of H-FABP-fatty acid complex in a protein crystal simulation
title_full Behavior of H-FABP-fatty acid complex in a protein crystal simulation
title_fullStr Behavior of H-FABP-fatty acid complex in a protein crystal simulation
title_full_unstemmed Behavior of H-FABP-fatty acid complex in a protein crystal simulation
title_sort behavior of h-fabp-fatty acid complex in a protein crystal simulation
publishDate 2018
url http://sedici.unlp.edu.ar/handle/10915/102636
https://ri.conicet.gov.ar/11336/93833
https://arxiv.org/abs/1806.06102
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