On the structure, interactions, and dynamics of bound VEGF.
The vascular endothelial growth factor (VEGF) is believed to be the most important protein in the regulation of the angiogenic cascade. Thus, exploring the structure and dynamical properties of this growth factor and the influence of receptor and inhibitor binding to these properties may reveal new insights on VEGF's biological process and inhibition opportunities. Here we describe an analysis of molecular dynamics simulations of VEGF bound to the Flt-1 receptor, VEGF bound to the v107 peptide inhibitor, and also VEGF bound to a mutant v107. We analyze the effects of binding to VEGF regarding three aspects: structure, interactions, and dynamics. We found that the structure of VEGF is not significantly perturbed upon binding. We analyze the individual contribution of the VEGF residues to the total interaction energy of binding to Flt-1 and v107. We also compare dynamical variables such as thermal fluctuations and correlations with those of the unbound form. We found that receptor binding is able to promote stronger perturbations on the VEGF dynamical behavior than VEGF inhibitor binding. VEGF motions in the receptor bound complex are shown to be less correlated than motions of unbound VEGF. The work addresses the changes on conformational flexibility of the isolated VEGF upon binding, as well as changes in structure and side-chain rearrangements.
Horta
Bruno Araújo Cautiero
BA
Physical Organic Chemistry Group, Departamento de Química Orgânica, Instituto de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, CT, Bloco A, Laboratory 609, Rio de Janeiro, RJ 21941-909, Brazil. bruno@iq.ufrj.br
Cirino
José Jair Vianna
JJ
de Alencastro
Ricardo Bicca
RB
D001665:Binding Sites; D003198:Computer Simulation; D006860:Hydrogen Bonding; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology; D025341:Principal Component Analysis; D011485:Protein Binding; D011487:Protein Conformation; D013997:Time Factors; D042461:Vascular Endothelial Growth Factor A / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000378:metabolism; D040281:Vascular Endothelial Growth Factor Receptor-1 / Q000737:chemistry* / Q000378:metabolism
D010455:Peptides; D042461:Vascular Endothelial Growth Factor A; D040281:Vascular Endothelial Growth Factor Receptor-1