Visualization and comparison of molecular dynamics simulations of leukotriene C4, leukotriene D4, and leukotriene E4 |
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| Affiliation: | 1. Division of Cardiovascular Disease, University of Alabama at Birmingham, Birmingham, AL (Dr Bittner);2. Division of Cardiology, University of Colorado School of Medicine, Aurora, CO (Dr Schwartz);3. Mount Sinai Heart, Icahn School of Medicine at Mount Sinai Health System, New York, NY, USA (Dr Bhatt);4. National Heart Centre, Singapore (Dr Chua);5. Clinical Trials Unit, Department of Pharmacology, Faculty of Medicine, University of Kelaniya, Sri Lanka (Dr De Silva);6. Estudios Cardiológicos Latino América, Instituto Cardiovascular de Rosario, Rosario, Argentina (Dr Diaz);7. Canadian VIGOUR Centre, University of Alberta, Edmonton, Alberta, Canada (Dr Goodman);8. St. Michael''s Hospital, University of Toronto, Toronto, Ontario, Canada (Dr Goodman);9. Stanford Center for Clinical Research, Department of Medicine, Stanford University, Stanford, CA (Dr Harrington);10. Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands (Dr Jukema);11. Netherlands Heart Institute, Utrecht, the Netherlands (Dr Jukema);12. Regeneron Pharmaceuticals, Inc, Tarrytown, NY, USA (Dr McGinniss, Pordy);13. Sanofi, Montreal, Canada (Dr Garon);14. Sanofi Research and Development, Paris, France (Dr Scemama);15. Green Lane Cardiovascular Research Unit, Te Whatu Ora – Health New Zealand, Te Toka Tumai, and University of Auckland, Auckland, New Zealand (Dr White);p. Université Paris-Cité, Institut Universitaire de France, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat, FACT (French Alliance for Cardiovascular Trials), and INSERM U1148, Paris, France (Dr Steg);q. CPC Clinical Research and Division of Cardiology, University of Colorado School of Medicine, Aurora, CO (Dr Szarek);r. State University of New York, Downstate Health Sciences University, Brooklyn, NY (Dr Szarek) |
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| Abstract: | Molecular dynamics simulations of leukotriene C4 (LTC4), leukotriene D4 (LTD4), and leukotriene E4 (LTE4) were carried out, and the data were visualized in an animated video format. Three-dimensional ghost images show the positions of the heavy atoms of all three molecules throughout the simulations. The ghost images can be superimposed to give a single three-dimensional image in which the shapes of the most populated conformers of each molecule are apparent and can be compared. Leukotriene D4 was found to occupy mostly T-shaped conformations, while LTC4 occupied mostly cup-shaped conformations, and LTE4 occupied a wide range of conformations spanning the LTD4 and LTC4 types. Digital filtering and graphing of the internal geometries of the molecules as a function of time revealed differences in dynamic behavior. The results are discussed in light of current knowledge about leukotriene receptors. |
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