Two graduate students will present their research at the next Beckman Graduate Student Seminar: Behzad Mehrafrooz, Center for Biophysics and Quantitative Biology; and Michael Pence, chemistry.

The event takes place Wednesday, Feb. 7 at noon in 5602 Beckman Institute. Register to attend and receive lunch.

Single-molecule protein sequencing using a digestion- free nanopore approach

Behzad Mehrafrooz

Reading the amino acid sequence of individual proteins with high precision and throughput holds promise to deliver the most detailed portrait of a biological cell. In the absence of natural mechanisms to copy, read, or transcribe protein sequences, abiological approaches to protein sequencing have taken a lead. One such approach is nanopore sequencing, where the amino acid sequence of a protein is read as the protein chain is moved through a nanopore reader. In contrast to DNA strand which carries a uniform negative charge regardless of its nucleotide sequence, capturing and keeping an unevenly charged peptide taut through the nanopore's constriction is a major challenge in nanopore sequencing of proteins. In collaboration with the Wanunu lab (Northeastern U.), we have shown that a unidirectional transport of full-length proteins can be accomplished using a guanidinium chloride solution (Nat. Biotech. doi:10.1038/s41587-022-01598-3). Our MD simulations suggest that this unexpected result originates from a giant electro-osmotic force (EOF) produced by the binding of the guanidinium ions to the inner surface of the nanopore. Furthermore, we evaluated the generality of this guanidinium-induced EOF effect by simulating other biological nanopores, including alpha- hemolysin, MspA, aerolysin, and CsgG. In all four systems, we observed guanidinium ions bind to the inner surface of the nanopore and render a positively charged surface. The positive surface charge produces a powerful electro-osmotic effect regardless of the local charge of the nanopore surface, offering a realistic pathway to nanopore protein sequencing.

Behzad Mehrafrooz is a fifth-year Ph.D. student in the Center for Biophysics and Quantitative Biology working under the supervision of Professor Aleksei Aksimentiev. His research is mainly focused on nanopore-based protein sequencing using solid-state and biological nanopores. Behzad received his B.S. degree in mechanical engineering from K.N. Toosi University of Technology in 2014, and his master's in 2017 from Sharif University of Technology, Tehran, Iran. Outside his academic commitments, he enjoys playing violin, hiking and traveling.

Waste to wealth: Automated optimization of electrochemical biomass valorization

Michael PenceEvery year, tens of gigatons of biomass are produced. This waste presents an exciting opportunity, as biomass processing generates a variety of byproducts that can be transformed into value-added platform chemicals. One way to do this is through electrochemistry, which is an environmentally friendly method of valorization. To develop catalysts that are generally active towards the various species in biomass byproducts, a broad range of substrate molecules and reaction conditions must be screened and optimized, which requires exploring a substantially large chemical space. To make such extensive characterization possible, I will be using closed-loop experimentation for fully automated optimization of electrochemical valorization of biomass byproducts.

In this talk I discuss the development of the automated electrochemical platform, the Electrolab, and its use in characterizing electrocatalysis of the oxidization of alcohol and aldehyde functional groups, present in biomass byproducts such as glycerol, furfurals, and polyols to generate value-added products. I will show how the Electrolab enables the study of large combinations of substrate and catalysts across a range of solution conditions, leading autonomous identification of top-performing systems.

Michael Pence is a fourth-year graduate student in the Department of Chemistry working under Professor Joaquín Rodríguez-López. He uses automated solution handling robots and microfabricated devices to characterize electrochemical systems for energy storage and catalysis. He received his B.S. in chemistry from Indiana University, where he was first introduced to electrochemistry in the lab of Professor Dennis Peters.