Event Title

Docking Protein Receptor TRPM8 and Ligand Methanol through AutoDock Viva and Visualization through Visual Molecular Dynamics (VMD).

Presenter Information

Jeonghyo Lee

Presentation Type

Poster Presentation

College

College of Natural Sciences

Major

Chemistry and Biochemistry

Location

Event Center A&B

Faculty Mentor

Dr. Kimberly Cousins

Start Date

5-27-2014 1:00 PM

End Date

5-27-2014 2:30 PM

Abstract

Binding affinity of menthol ligand to the Transient Receptor Potential Melastatin 8 (TRPM8) protein was examined using the computer programs AutoDock Vina and Visual Molecular Dynamics (VMD). A single run with AutoDock Vina predicts 9 possible binding modes of menthol in TRPM8. Among these 9 possible docking products, the mode with the highest affinity between menthol and TRPM8 showed interaction of menthol with residues Tyr754, Asn799, and ASP 802, which have been shown experimentally by others to be important for menthol activity. Since AutoDock Vina does not provide good visualization for bound products of menthol in TRPM8, the structure was analyzed by VMD. By using VMD, we confirmed that these Tyr754, Asn799, and ASP 802 residues are close to each other in TRPM8 receptor, and VMD provided the information to calculate the volume of the best binding pocket for menthol in TRPM8, which was 325.5 Å3. Since AutoDock Vina use a non-deterministic algorithm, it may predict different binding modes each time it is run; therefore multiple repetitions are planned to make sure the lowest energy binding mode has indeed been located. Ultimately, the analysis of conformation of eight different menthol stereoisomers in TRPM8 receptor is the goal of this research.

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May 27th, 1:00 PM May 27th, 2:30 PM

Docking Protein Receptor TRPM8 and Ligand Methanol through AutoDock Viva and Visualization through Visual Molecular Dynamics (VMD).

Event Center A&B

Binding affinity of menthol ligand to the Transient Receptor Potential Melastatin 8 (TRPM8) protein was examined using the computer programs AutoDock Vina and Visual Molecular Dynamics (VMD). A single run with AutoDock Vina predicts 9 possible binding modes of menthol in TRPM8. Among these 9 possible docking products, the mode with the highest affinity between menthol and TRPM8 showed interaction of menthol with residues Tyr754, Asn799, and ASP 802, which have been shown experimentally by others to be important for menthol activity. Since AutoDock Vina does not provide good visualization for bound products of menthol in TRPM8, the structure was analyzed by VMD. By using VMD, we confirmed that these Tyr754, Asn799, and ASP 802 residues are close to each other in TRPM8 receptor, and VMD provided the information to calculate the volume of the best binding pocket for menthol in TRPM8, which was 325.5 Å3. Since AutoDock Vina use a non-deterministic algorithm, it may predict different binding modes each time it is run; therefore multiple repetitions are planned to make sure the lowest energy binding mode has indeed been located. Ultimately, the analysis of conformation of eight different menthol stereoisomers in TRPM8 receptor is the goal of this research.