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Computational study of FaEXPA1, a strawberry alpha expansin protein, through molecular modeling and molecular dynamics simulation studies

dc.contributor.authorValenzuela-Riffo F.
dc.contributor.authorRamos P.
dc.contributor.authorMorales-Quintana L.
dc.date.accessioned2020-09-02T22:29:54Z
dc.date.available2020-09-02T22:29:54Z
dc.date.issued2018
dc.identifier10.1016/j.compbiolchem.2018.05.018
dc.identifier.citation76, , 79-86
dc.identifier.issn14769271
dc.identifier.urihttps://hdl.handle.net/20.500.12728/6510
dc.descriptionChanges in the cellulose-hemicellulose fraction take place during ripening of strawberry fruit and are associated with the activity of a set of proteins and hydrolytic enzymes. Expansins are proteins located in the cell wall with no catalytic activity. In this context, FaEXPA1 was previously reported to have a high accumulation rate during fruit ripening in three different strawberry cultivars. In order to understand at the molecular level the expansin mechanism mode, a 3D model of FaEXPA1 protein was built by comparative modeling. FaEXPA1 protein model displayed two domains, a cellulose-binding domain with a β-sandwich structure, and a second domain that included a HFD motif with a similar structure to the catalytic core of endoglucanase V from Humicola insolens. Additionally, in the center of the structure, an open groove was formed. Finally, using a cellulose polymer as a ligand, the protein-ligand interaction was evaluated by molecular dynamic (MD) simulation. Two MD simulations showed that FaEXPA1 can interact with cellulose via the flat aromatic surface of its binding domain D2, composed mainly of residues Trp99 and Trp225. In addition, FaEXPA1 formed a high number of hydrogen bonds with the glycan chain and the Asn81, Phe114 and Asn211 residues. © 2018 Elsevier Ltd
dc.language.isoen
dc.publisherElsevier Ltd
dc.subjectCellulose
dc.subjectExpansin protein
dc.subjectMolecular dynamic simulation
dc.subjectPlant cell wall
dc.subjectStrawberry
dc.subjectCatalyst activity
dc.subjectCellulose
dc.subjectComputational chemistry
dc.subjectFruits
dc.subjectHydrogen bonds
dc.subjectLigands
dc.subjectPlants (botany)
dc.subjectProteins
dc.subjectWalls (structural partitions)
dc.subjectComparative modeling
dc.subjectComputational studies
dc.subjectHemicellulose fraction
dc.subjectMolecular dynamics simulations
dc.subjectPlant cell wall
dc.subjectProtein-ligand interactions
dc.subjectStrawberry
dc.subjectStrawberry cultivars
dc.subjectMolecular dynamics
dc.subjectBinding
dc.subjectCellulose
dc.subjectFruits
dc.subjectHydrogen Bonds
dc.subjectLigands
dc.subjectProteins
dc.subjectResidues
dc.subjectRipening
dc.subjectcellulose
dc.subjectligand
dc.subjectplant protein
dc.subjectprotein binding
dc.subjectamino acid sequence
dc.subjectbinding site
dc.subjectchemistry
dc.subjectFragaria
dc.subjectgenetics
dc.subjecthydrogen bond
dc.subjectmetabolism
dc.subjectmolecular dynamics
dc.subjectmutation
dc.subjectAmino Acid Sequence
dc.subjectBinding Sites
dc.subjectCellulose
dc.subjectFragaria
dc.subjectHydrogen Bonding
dc.subjectLigands
dc.subjectMolecular Dynamics Simulation
dc.subjectMutation
dc.subjectPlant Proteins
dc.subjectProtein Binding
dc.titleComputational study of FaEXPA1, a strawberry alpha expansin protein, through molecular modeling and molecular dynamics simulation studies
dc.typeArticle


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