Application of Funnel Metadynamics to the Platelet Integrin αIIbβ3 in Complex with an RGD Peptide
Abstract
:1. Introduction
2. Results
2.1. Structural Comparison between Cryo-EM and Reference Crystal Structures of Integrin αIIbβ3
2.2. Structural Dynamics of Integrin β-I Domain: Insights from Funnel Metadynamics Simulations
2.3. Assessing Sampling Efficiency: Evaluation of Funnel Metadynamics Simulations
2.4. Evaluation of RGD Interactions with the Binding Site of αIIbβ3 Integrin
3. Discussion
4. Methods
4.1. Structure Setup for Equilibrium, Steered MD, and Funnel Metadynamics
4.2. Steered Molecular Dynamics Simulations
4.3. Funnel Metadynamics Simulations
4.4. Equilibrium Molecular Dynamics Simulations without Divalent Cations and RGD
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Integrin Residues Interacting with RGD | Frames (%) | References |
---|---|---|
αIIb chain | ||
Glu-157 | 0 | [34] |
Asp-159 | 69% | [29,30,34] |
Phe-160 | 99% | [15,17,22,29] |
Ser-161 | 71% | [29] |
Trp-162 | 6% | [29] |
Asp-163 * | 31% | [17,22,29] |
Arg-165 | 0.51% | [27] |
Tyr-166 | 6% | [27] |
Tyr-189 | 99% | [16,17,23,24,27,37] |
Tyr-190 | 100% | [15,16,17,29,33,37] |
Phe-191 | 1.4% | [27] |
Leu-192 | 43% | [15,16] |
Asp-224 | 53% | [15,16,17,22,25,30,33,34,37] |
Ser-225 | 31% | [17,23,25] |
Ser-226 | 8% | [27,37] |
Glu-229 | 0 | [34,37] |
Phe-230 (Tyr-230) | 0 (0.001%) | [37] |
Phe-231 | 71% | [15,16,17,22,29] |
Asp-232 * | 6% | [15,16,17,22,23,25,32,33,34,37] |
Tyr-234 | 0 | [37] |
Trp-260 | 0 | [37] |
Ser-161 | 0 | [37] |
Arg-281 | 0 | [34] |
β3 chain | ||
Asp-119 | 100% | Binds Mg2+ |
Leu-120 | 46% | false positive |
Ser-121 | 99% | [22,23,29,35] |
Tyr-122 | 44% | [16,17,22,31,35,36] |
Ser-123 | 31% | [16,17,22,23,29,35,36] |
Lys-125 | 0 | [30,36] |
Lys-126 | 0 | [36] |
Asp-127 | 0 | [29,32,34] |
Val-157 | 8.4% | false positive |
Tyr-164 | 0 | [46] |
Tyr-166 * | 14% | [17,33] |
Glu-171 | 0 | [32] |
Ser-211 | 0 | [32] |
Ser-213 | 66% | [22,47] |
Arg-214 | 98% | [16,17,29,30,31,36,37] |
Asn-215 | 76% | [15,16,17,22,29,30,31,35,36] |
Arg-216 | 58% | [17,22,23,25,36] |
Asp-217 | 51% | [35,37] |
Ala-218 * | 97% | [15,16,17,22,25,29,33,37] |
Glu-220 | 100% | [15,33] |
Gly-222 | 0 | [32] |
Thr-250 | 41% | false positive |
Asp-251 * | 56% | [29,33] |
Ala-252 | 72% | [29] |
Glu-312 | 0 | [32,34] |
Asn-313 | 0 | [29,32] |
Mg2+ ion (MIDAS) | 100% | [16,17,22,23,30,31,34,36] |
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Coffman, R.E.; Bidone, T.C. Application of Funnel Metadynamics to the Platelet Integrin αIIbβ3 in Complex with an RGD Peptide. Int. J. Mol. Sci. 2024, 25, 6580. https://doi.org/10.3390/ijms25126580
Coffman RE, Bidone TC. Application of Funnel Metadynamics to the Platelet Integrin αIIbβ3 in Complex with an RGD Peptide. International Journal of Molecular Sciences. 2024; 25(12):6580. https://doi.org/10.3390/ijms25126580
Chicago/Turabian StyleCoffman, Robert E., and Tamara C. Bidone. 2024. "Application of Funnel Metadynamics to the Platelet Integrin αIIbβ3 in Complex with an RGD Peptide" International Journal of Molecular Sciences 25, no. 12: 6580. https://doi.org/10.3390/ijms25126580