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Comparative in silico study of the differences in the structure and ligand interaction properties of three alpha-expansin proteins from Fragaria chiloensis fruit

dc.contributor.authorValenzuela-Riffo F.
dc.contributor.authorGaete-Eastman C.
dc.contributor.authorStappung Y.
dc.contributor.authorLizana R.
dc.contributor.authorHerrera R.
dc.contributor.authorMoya-León M.A.
dc.contributor.authorMorales-Quintana L.
dc.date.accessioned2020-09-02T22:29:54Z
dc.date.available2020-09-02T22:29:54Z
dc.date.issued2019
dc.identifier10.1080/07391102.2018.1517610
dc.identifier.citation37, 12, 3245-3258
dc.identifier.issn07391102
dc.identifier.urihttps://hdl.handle.net/20.500.12728/6506
dc.descriptionExpansins are cell wall proteins associated with several processes, including changes in the cell wall during ripening of fruit, which matches softening of the fruit. We have previously reported an increase in expression of specific expansins transcripts during softening of Fragaria chiloensis fruit. Here, we characterized three α-expansins. Their full-length sequences were obtained, and through qRT-PCR (real-time PCR) analyses, their transcript accumulation during softening of F. chiloensis fruit was confirmed. Interestingly, differential but overlapping expression patterns were observed. With the aim of elucidating their roles, 3D protein models were built using comparative modeling methodology. The models obtained were similar and displayed cellulose binding module(CBM) with a β-sandwich structure, and a catalytic domain comparable to the catalytic core of protein of the family 45 glycosyl hydrolase. An open groove located at the central part of each expansin was described; however, the shape and size are different. Their protein–ligand interactions were evaluated, showing favorable binding affinity energies with xyloglucan, homogalacturonan, and cellulose, cellulose being the best ligand. However, small differences were observed between the protein–ligand conformations. Molecular mechanics-generalized Born-surface area (MM-GBSA) analyses indicate the major contribution of van der Waals forces and non-polar interactions. The data provide a dynamic view of interaction between expansins and cellulose as putative cell wall ligands at the molecular scale. Communicated by Ramaswamy H. Sarma. © 2018, © 2018 Informa UK Limited, trading as Taylor & Francis Group.
dc.language.isoen
dc.publisherTaylor and Francis Ltd.
dc.subjectfruit ripening
dc.subjectmolecular dynamics simulations
dc.subjectmolecular modeling
dc.subjectplant cell wall
dc.subjectRT-qPCR
dc.subjectalpha expansin
dc.subjectcellulose
dc.subjectglucan
dc.subjectglycosidase
dc.subjecthomogalacturonan
dc.subjectplant protein
dc.subjectpolymer
dc.subjectpolysaccharide
dc.subjectunclassified drug
dc.subjectxyloglucan
dc.subjectligand
dc.subjectpectin
dc.subjectplant protein
dc.subjectpolygalacturonic acid
dc.subjectxylan
dc.subjectArticle
dc.subjectbinding affinity
dc.subjectcatalysis
dc.subjectcell wall
dc.subjectcomparative study
dc.subjectcomputer model
dc.subjectcontrolled study
dc.subjectenergy
dc.subjectFragaria
dc.subjectFragaria chiloensis
dc.subjectgenetic analysis
dc.subjectnonhuman
dc.subjectpriority journal
dc.subjectprotein analysis
dc.subjectprotein expression
dc.subjectprotein interaction
dc.subjectprotein protein interaction
dc.subjectprotein structure
dc.subjectquantitative analysis
dc.subjectreverse transcription polymerase chain reaction
dc.subjectsurface area
dc.subjectchemistry
dc.subjectfruit
dc.subjectgene expression regulation
dc.subjectmolecular dynamics
dc.subjectphysiology
dc.subjectprotein conformation
dc.subjectCell Wall
dc.subjectCellulose
dc.subjectFragaria
dc.subjectFruit
dc.subjectGene Expression Regulation, Plant
dc.subjectGlucans
dc.subjectLigands
dc.subjectMolecular Dynamics Simulation
dc.subjectPectins
dc.subjectPlant Proteins
dc.subjectProtein Conformation
dc.subjectXylans
dc.titleComparative in silico study of the differences in the structure and ligand interaction properties of three alpha-expansin proteins from Fragaria chiloensis fruit
dc.typeArticle


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