Comparison of Linear vs. Cyclic RGD Pentapeptide Interactions with Integrin α<sub>v</sub>β<sub>3</sub> by Molecular Dynamics Simulations
Na Li | Simei Qiu | Ying Fang | Jianhua Wu | Quhuan Li
Integrin α<sub>v</sub>β<sub>3</sub> interacting with the short Arg-Gly-Asp (RGD) motif plays a critical role in the progression of several types of tumors. However, the effects of the RGD structure (cyclic or linear) with integrin α<sub>v</sub>β<sub>3</sub> at the atomic level remain poorly understood. Here, we performed association and dissociation dynamic simulations for integrin α<sub>v</sub>β<sub>3</sub> in complex with a linear or cyclic pentapeptide by steered molecular dynamics simulations. Compared with cyclic RGD, the linear RGD peptide triggers instability of the configurational changes, mainly resting with the RGD domain due to its flexibility. The main interaction energy between Mg<sup>2+</sup> and cyclic RGD is much stronger than that of the linear RGD system by the well shield to lessen attacks by free water molecules. The force-dependent dissociation results show that it is easier for linear RGD peptides to leave the active site and much quicker than the cyclic RGD ligand, whereas it is harder to enter the appropriate active binding site in linear RGD. The Ser<sup>123</sup>-Asp<sup>RGD</sup> bond may play a critical role in the allosteric pathway. Our findings provide insights into the dynamics of α<sub>v</sub>β<sub>3</sub> interactions with linear and cyclic RGD ligands and contribute to the application of RGD-based strategies in preclinical therapy.
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