title: Structure-fluctuation-function relationships of seven pro-angiogenic isoforms of VEGFA, important mediators of tumorigenesis.
abstract: Vascular endothelial growth factor A (VEGFA) has different biological activities and plays a central role in tumor proliferation, angiogenesis and metastasis. Different VEGFA isoforms are generated by alternative splice site selection of exons 6, 7 and 8. In this paper, we analyzed the physical and chemical properties of the VEGFA exon 6 sequence, and modeled the three-dimensional structures of the regions corresponding to exons 6, 7 and 8 of six different pro-angiogenic isoforms of VEGFA in comparison to the experimental structure of VEGFA_165 by a combined approach of fold recognition and comparative modeling strategies and molecular dynamics simulations. Our results showed that i) exon 6 is a very flexible polycation with high disordered propensity, features well conserved in all mammals, ii) the structures of all the isoforms are stabilized by H-bond sub-networks organized around HUB residues and, iii) the charge content of exon 6 modulates the intrinsic structural preference of its flexible backbone, which can be described as an ensemble of conformations. Moreover, complexes between NRP-1 and VEGFA isoforms were modeled by molecular docking to study what isoforms are able to bind NRP-1. The analysis of complexes evidenced that VEGFA_121, VEGFA_145, VEGFA_183, VEGFA_189 and VEGFA_206, containing exons 7 and 8a, are able to interact with NRP-1 because they have the key regions of exons 7b and/or 8a. An overview of the isoforms shows how the fluctuations are the main guidance of their biological function. MD simulations also provide insights into factors that stabilize the binding regions of isoforms.
authors.affiliation: Istituto Nazionale Tumori "Fondazione Pascale"-IRCCS, Naples, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Bergantino
authors.affiliation: Doctorate in Computational Biology, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Naples, Italy.
authors.forename: Stefano
authors.initials: S
authors.lastname: Guariniello
authors.affiliation: Doctorate in Computational Biology, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Naples, Italy.
authors.forename: Raffaele
authors.initials: R
authors.lastname: Raucci
authors.affiliation: Doctorate in Computational Biology, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Naples, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Colonna
authors.affiliation: Istituto Nazionale Tumori "Fondazione Pascale"-IRCCS, Naples, Italy.
authors.forename: Antonella
authors.initials: A
authors.lastname: De Luca
authors.affiliation: Istituto Nazionale Tumori "Fondazione Pascale"-IRCCS, Naples, Italy.
authors.forename: Nicola
authors.initials: N
authors.lastname: Normanno
authors.affiliation: Istituto Nazionale Tumori "Fondazione Pascale"-IRCCS, Naples, Italy. Electronic address: s.costantini@istitutotumori.na.it.
authors.forename: Susan
authors.initials: S
authors.lastname: Costantini
mesh_terms: D000595:Amino Acid Sequence; D043925:Angiogenesis Inducing Agents / Q000737:chemistry; D063646:Carcinogenesis / Q000235:genetics / Q000378:metabolism; D006801:Humans; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D039942:Neuropilin-1 / Q000737:chemistry / Q000378:metabolism; D054730:Protein Interaction Domains and Motifs; D020033:Protein Isoforms / Q000737:chemistry / Q000502:physiology; D020836:Protein Structure, Quaternary; D016415:Sequence Alignment; D013329:Structure-Activity Relationship; D042461:Vascular Endothelial Growth Factor A / Q000737:chemistry* / Q000502:physiology*
chemical_list: D043925:Angiogenesis Inducing Agents; D020033:Protein Isoforms; C467484:VEGFA protein, human; D042461:Vascular Endothelial Growth Factor A; D039942:Neuropilin-1
keywords: Angiogenesis; Cancer; Conformational ensemble; Molecular dynamics; Network analysis; VEGFA isoform