NCSI: Comparing Substrate Specificity Between Small Multidrug Resistance Transporters

Status	Completed
Mentor Name	Josh Vermaas
Mentor's XSEDE Affiliation	Research Allocation
Mentor Has Been in XSEDE Community	4-5 years
Project Title	Comparing Substrate Specificity Between Small Multidrug Resistance Transporters
Summary	This project expands upon previous work to study the substrate specificity for two related transport proteins within the small multidrug resistance transport family. Having already characterized the substrate-free states, we will be investigating how tetraphenylphosphonium and guanidinium dynamics are different within these transport proteins.
Job Description	Using VMD and NAMD together and under postdoctoral supervision, the student will develop starting models for the two proteins with small molecules bound, and characterize their dynamics after equilibrium molecular dynamics simulations. The student will spend 8-10 hours per week: -Setting up simulations -Transferring files to supercomputing centers -Performing simulations -Developing analysis scripts -Plotting results using matplotlib -Participating in group activities to learn about other molecular dynamics methods (eg. group meetings)
Computational Resources	We anticipate the first round of simulations will be tested locally, on the MSU HPCC resources the lab has bought into. Extension for these simulations will be carried out using the group’s XSEDE allocation, principally on the NCSA Delta resource where more GPUs are available.
Contribution to Community	Where I see the greatest value for this project within the larger computational biology ecosystem is to provide opportunity for diverse researchers to gain experience and training when they otherwise might be excluded. Many computationally-oriented domestic graduate students that XSEDE typically reaches are from a narrow demographic profile. This project is tailored to the research interests for a student who is underrepresented within computational science, and permits them the space to explore if this research is right for them.
Position Type	Apprentice
Training Plan	The named student and the postdoc leading the project have a good working relationship from the current semester working on the substrate-free simulations and their analysis. This furthers the research by introducing the substrates to the transport proteins. What has worked for the student to date are two 1-2 hour meetings per week (one group meeting + 1 one-on-one meeting) to discuss project progress. We also communicate via slack to alleviate any immediate questions that would otherwise impede progress.
Student Prerequisites/Conditions/Qualifications	Prior experience with VMD, NAMD, and the unix command line are essential to be able to carry out simulation preparation and analysis. Python and matplotlib familiarity are essential for analysis.
Duration	Semester
Start Date	01/03/2022
End Date	04/30/2022