Computational elucidation on activation and deactivation dynamics of VEGFR-2 transmembrane domain and a subsequent design of Anti-VEGF aptamer heterodimer

Abstract

and then, through a rigorous extraction process based on ensemble docking and binding free energy calculations, the structures of V7t1:del5-1 bound to $VEGF_{165}$ were predicted. Also, we applied this computational protocol for modeling a new aptamer heterodimer, RNV66:del5-1.

Molecular dynamics (MD) simulation has been widely used to study the dynamics of important biomolecular processes such as conformational changes, ligand binding, and protein folding. In this paper, we explored how angiogenesis can be controlled from two perspectives, even for the purpose of diagnosing and treating various diseases related to angiogenesis, using various computational methods including MD simulation. Vascular endothelial growth factor 165 ($VEGF_{165}$) plays a crucial role in angiogenesis as a prominent isoform by binding to VEGF receptors and facilitating signal transduction into the cell. Therefore, elucidating the activation and deactivation mechanisms of VEGF receptors is of great importance. Additionally, by developing effective inhibitors targeting VEGF, it may be possible to regulate angiogenesis effectively. The VEGFR-2 is a member of receptor tyrosine kinases (RTKs) and is a dimeric membrane protein that functions as a primary regulator of angiogenesis. As is usual with RTKs, spatial alignment of its transmembrane domain (TMD) is essential toward VEGFR-2 activation. Experimentally, the helix rotations within TMD around their own helical axes are known to participate importantly toward the activation process in VEGFR-2, but the detailed dynamics of the interconversion between the active and inactive TMD forms have not been clearly elucidated at the molecular level. Here, we attempt to elucidate the process by using coarse grained (CG) molecular dynamics (MD) simulations. As a result, we have demonstrated that the pivoting motion of TMD helices is essential for TMD activation and deactivation to occur. DNA aptamers have emerged as potent therapeutic molecules, exhibiting high specificity and affinity for target proteins such as VEGF. Recent studies have demonstrated that a DNA aptamer heterodimer, comprising the aptamers “V7t1” and “del5-1” (V7t1:del5-1), exhibits a greater affinity towards $VEGF_{165}$ compared to its monomeric components. However, due to the high flexibility of the linker involved in both aptamer heterodimer and $VEGF_{165}$, the experimentally resolved structure of aptamer heterodimer bound to $VEGF_{165}$ is unknown. To overcome these limitations, we obtained an ensemble of structures for both VEGF and V7t1:del5-1 considering both small- and large-scale motions