Two graduate students will present their research at the next Beckman Institute Graduate Student Seminar: Archit Vasan, Center for Biophysics and Quantitative Biology; and Michael Pence, chemistry.
The hybrid seminar will take place at noon on Wednesday, Nov. 2 in 1005 Beckman and on Zoom. Lunch will be provided to in-person attendees.
Register in advance to attend.
Investigating molecular mechanisms of antibiotic permeation through outer membrane porins
Archit Vasan is pursuing his Ph.D. in the Center for Biophysics and Quantitative Biology under the guidance of Professor Emad Tajkhorshid. In his doctoral work, he uses atomic-resolution simulations to study mechanisms of antibiotic permeation into Gram-negative bacteria. His current work incorporates free energy calculations, Markov state models, and molecular dynamics simulations.
Despite the increasing capability of supercomputers and new algorithms, sufficient conformational sampling of slow molecular processes still remains daunting in molecular dynamics methods. One such problem arises in studying antibiotic permeation mechanisms through the outer membrane, or OM, porins of multi-drug resistant Gram-negative pathogens, because the narrow constriction region of these porins hinders translation and rotation of antibiotics. To exhaustively sample antibiotic conformations, we developed a grid-based workflow to create a comprehensive dataset of discrete antibiotic poses. Then, we used this dataset to determine the most likely permeation pathway using our novel Monte Carlo and graph theory-based algorithm. The pathway is then used to calculate permeation free energies using existing enhanced sampling methods. We applied this approach to rationalize our experimental findings that the addition of a primary amine can generate broad-spectrum antibiotics. We found a lower energetic barrier against the permeation of aminated compounds through OM porins, substantiating their greater OM permeability. Further analysis revealed that the amine facilitates permeation by enabling antibiotics to align their dipoles to the luminal electric field of porins and form favorable electrostatic interactions with specific, highly conserved charged residues. The importance of these interactions in permeation was further validated with experimental mutagenesis and whole cell accumulation assays. Overall, we offer a new computational approach for calculating free-energy and obtaining mechanistic insight to processes where relevant molecular conformations cannot be efficiently captured.
Developing a tiny toolbox for automated electrochemical characterization
Michael Pence is a graduate student in the Department of Chemistry working under Professor Joaquín Rodríguez-López. He uses microfabricated devices to measure electrochemical dynamics, both at the electrode surface and in solution. He received his B.S. in chemistry from Indiana University, where he was first introduced to electrochemistry in the lab of Professor Dennis Peters.
In recent years, chemistry has seen a dramatic shift towards high-throughput, autonomous experimentation. This paradigm shows great promise for developing new molecules and materials for applications in energy storage and conversion, but electrochemical characterization presents a major bottleneck in developing a fully automated system. Conventional electrochemical characterization techniques struggle in a variety of experimental conditions and can often produce data that is difficult to analyze. New methodologies and techniques must be developed that address these issues.
To create automation-friendly techniques, we need to think small. Microscale electrodes can overcome challenges that traditional techniques would typically encounter and open the door for new and exciting measurements. I use microfabrication to create low-cost electrochemical devices that can fit in the palm of your hand but still have the same analytical capability as state-of-the-art electrochemical instrumentation. These microfabricated devices enable automated characterization of energy-storage molecules at high concentrations in non-aqueous electrolyte systems and can be coupled with solution-handling robots to facilitate high-throughput electrochemical experimentation.
Learn more about Beckman's Graduate Student Seminar Series.
Read Q&As with student researchers on Beckman's Student Researcher Spotlight page.