Month: December 2024

Join the CQB & DMI for a special seminar with Dr. Yongshae Shin. Dr. Shin is an Associate Professor in the Department of Mechanical Engineering at Seoul National University, and an Adjunct Professor in the Interdisciplinary Program in Bioengineering and Department of Biological Sciences. The focus of Prof. Shin’s group research is to understand and engineer self-organization processes in living systems. Of particular interest are biomolecular condensation, especially its biophysical mechanisms and physiological functions. For this, he combines multiple approaches including single-molecule resolution quantitative imaging, reconstitution of biomolecular condensates both in test tube and in cellulo, and optogenetic manipulation of biological phase separation. He received his BS in Mechanical and Aerospace Engineering from Seoul National University, and MS/PhD degrees in Mechanical Engineering from Massachusetts Institute of Technology. He then went on to Princeton University as a Postdoctoral Research Associate in the Department of Chemical and Biological Engineering. He was selected as the World Economic Forum Young Scientist in 2019.

 

Abstract: Biomolecular condensates represent a condensed state of living matter, widely observed in various cellular processes. Condensates are composed of a set of distinct molecular components, organizing diverse biochemical reactions. How condensate function emerges from the collective interactions of its components remains elusive. In this talk, I will discuss our ongoing efforts to study the biophysical basis of condensate-driven cellular functions. I will first introduce density as a key parameter that can impact condensate function. Using refractive-index imaging, we uncovered that intracellular condensates exhibit a broad range of density, where RNA plays a key regulatory role in lowering condensate density. I will then switch to the second topic probing the effect of RNA condensation on translation activity. Using optogenetic cellular reconstitution, we found that condensation itself provides suppressive microenvironments for mRNA translation, and solidifying condensates further inhibits translation activities. Our works highlight an intimate link between the physical properties of condensates and associated biochemical functions.

Join the CQB for our last seminar series of the Fall 2024 semester on Friday, December 6, 2024 from 3-4:00 pm in Wilkinson 021.  We will be hearing from our guest speaker, Dr. Jim Pfaendtner.

Jim Pfaendtner is the Louis Martin-Vega Dean of Engineering at NC State University. Previously, Pfaendtner served as chair of the Department of Chemical Engineering at the University of Washington. His research focuses on using computer simulations to understand molecular behavior for applications in biotechnology and advanced materials. Pfaendtner earned his B.S. in chemical engineering from Georgia Tech and his Ph.D. from Northwestern University.

Abstract:

Peptoids, or n-substitued glycines, are complex and diverse oligomeric structures which have been explored for a number of biomimetic applications including drug delivery, surfactants, and catalysts. In contrast to their peptide counterparts, on peptoids the sidechain is bonded to the backbone nitrogen resulting in a flexible omega backbone dihedral that is able to isomerize into both stable cis- and trans- backbone conformations. This unique feature of peptoids allows for these structures to potentially span a significantly larger configurational space of chemical and structural functionality through the careful tuning of their side chains. This vast chemical and structural space has created significant challenges for rational design of new structures and functions as the underlying molecular scale driving forces that give rise to sequence/structure/function relationships have proven difficult to uncover.

This talk will highlight recent developments from our group in the use of statistical mechanical tools to accelerate molecular simulations of rare events like peptoid folding, aggregation and adsorption on inorganic surfaces. The first part of the talk focuses on studies of peptoid folding. Peptoids can freely explore a 12-dimensional helical configurational space with stabilization dictated largely by interactions between sidechains. I will discuss the thermodynamic basis of helix stabilization by chiral sidechains as well as fundamental aspects of the simulation science and the role of solvent in folding. Implications for rational design of higher order (tertiary structures) will be discussed. The remainder of the talk focuses on the use of peptoids in biomineralization. We discuss the rational design of peptoid mimics of the well-known R5/silaffin system, compare their nanoscale properties with peptides, and highlight experimental findings showing the efficacy of peptoids in biomineralization applications as well as similarities and differences between the peptoid and peptide systems. If available time remains, I will briefly discuss our group’s use of machine learning models to assist in high throughput screening towards inverse design of new sequences that precisely tune surface adsorption energies for biomolecules.