title: Computational study of pH-dependent oligomerization and ligand binding in Alt a 1, a highly allergenic protein with a unique fold.
abstract: Alt a 1 is a highly allergenic protein from Alternaria fungi responsible for several respiratory diseases. Its crystal structure revealed a unique β-barrel fold that defines a new family exclusive to fungi and forms a symmetrical dimer in a butterfly-like shape as well as tetramers. Its biological function is as yet unknown but its localization in cell wall of Alternaria spores and its interactions in the onset of allergy reactions point to a function to transport ligands. However, at odds with binding features in β-barrel proteins, monomeric Alt a 1 seems unable to harbor ligands because the barrel is too narrow. Tetrameric Alt a 1 is able to bind the flavonoid quercetin, yet the stability of the aggregate and the own ligand binding are pH-dependent. At pH 6.5, which Alt a 1 would meet when secreted by spores in bronchial epithelium, tetramer-quercetin complex is stable. At pH 5.5, which Alt a 1 would meet in apoplast when infecting plants, the complex breaks down. By means of a combined computational study that includes docking calculations, empirical pKa estimates, Poisson-Boltzmann electrostatic potentials, and Molecular Dynamics simulations, we identified a putative binding site at the dimeric interface between subunits in tetramer. We propose an explanation on the pH-dependence of both oligomerization states and protein-ligand affinity of Alt a 1 in terms of electrostatic variations associated to distinct protonation states at different pHs. The uniqueness of this singular protein can thus be tracked in the combination of all these features.
authors.affiliation: Department of Biotechnology and Centre for Plant Genomics and Biotechnology (CBGP), Technical University of Madrid, Pozuelo de Alarcon, 28223, Madrid, Spain.
authors.forename: María
authors.initials: M
authors.lastname: Garrido-Arandia
authors.affiliation: Department of Biotechnology and Centre for Plant Genomics and Biotechnology (CBGP), Technical University of Madrid, Pozuelo de Alarcon, 28223, Madrid, Spain.
authors.forename: Jorge
authors.initials: J
authors.lastname: Bretones
authors.affiliation: Department of Biotechnology and Centre for Plant Genomics and Biotechnology (CBGP), Technical University of Madrid, Pozuelo de Alarcon, 28223, Madrid, Spain.|Immunology Section, Department of Experimental Medical Sciences, Lund University, BMC D14, 22184, Lund, Sweden.
authors.forename: Cristina
authors.initials: C
authors.lastname: Gómez-Casado
authors.affiliation: Department of Biotechnology and Centre for Plant Genomics and Biotechnology (CBGP), Technical University of Madrid, Pozuelo de Alarcon, 28223, Madrid, Spain.
authors.forename: Nuria
authors.initials: N
authors.lastname: Cubells
authors.affiliation: Department of Biotechnology and Centre for Plant Genomics and Biotechnology (CBGP), Technical University of Madrid, Pozuelo de Alarcon, 28223, Madrid, Spain.
authors.forename: Araceli
authors.initials: A
authors.lastname: Díaz-Perales
authors.affiliation: Department of Natural Systems and Resources and Centre for Plant Genomics and Biotechnology (CBGP), Technical University of Madrid, 28040, Madrid, Spain. luis.fpacios@upm.es.
authors.forename: Luis F
authors.initials: LF
authors.lastname: Pacios
mesh_terms: D000485:Allergens / Q000737:chemistry / Q000378:metabolism*; D000528:Alternaria / Q000737:chemistry; D001665:Binding Sites; D006863:Hydrogen-Ion Concentration; D008024:Ligands; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D017510:Protein Folding; D055672:Static Electricity
chemical_list: D000485:Allergens; D008024:Ligands
keywords: Allergenic proteins; Electrostatic potentials; Ligand–protein docking; Molecular dynamics; Oligomerization; Protein–ligand binding