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CDLC

2019

Seminar Series (2019) | Center for Chemical Dynamics in Living Cells



Exploring the Behavior of Proteins and Surfactants on Biological Interfaces Using Molecular Dynamics Simulations


Hyonseok Hwang

Professor, Department of Chemistry, Kangwon National University

Abstract

The Interaction of peptides and small molecules with biological interfaces such as cell membranes plays a crucial role in preserving the integrity of living organisms and regulating the permeation of substantial materials required for the cell metabolism. In this regard, it is of consequence to assess the interaction of biomolecules with biological interfaces at the atomistic level. In the first part of my talk cyclic peptide nanotubes (CPNs), a synthetic ion channel embedded in cell membranes, are introduced and the energetics and dynamics of the transport of ions and glucose through CPNs are addressed using potential of mean force (PMF) profiles and position-dependent diffusion coefficient calculations of the permeants via molecular dynamics (MD) simulations. The second part focuses on the micelle formation of a kind of surfactants and interactions of the surfactant micelles with ceramide lipid bilayers and composite real skin model membranes. Based on the findings from MD simulations, the effects of surfactants used in cosmetics and detergents on the human skin are briefly addressed.

May 17, 2019, 5-7 pm

Room # B119, Building # 310



Microbial Synthetic Biology for Rational and Evolutionary Engineering


Gyoo Yeol Jung

Professor, Department of Chemical Engineering/I-Bio Program, POSTECH

Abstract

Pathway optimization of microbial metabolism is essential for the production of commercially valuable chemicals such as biofuels, platform chemicals and biologically active compounds. To achieve the successful design or redesign of microbial metabolism, robustness of naturally occurring biological systems has to be relieved so that cells can be easily redesigned. Although extremely huge efforts have been made to find genetic target to improve metabolic function of the microorganisms, there still exists the additional room for the non-rational approach. Currently, typical approach for metabolic engineering uses both rational approach as well as non-rational methods such as combinatorial and evolutionary methods. One of the most critical problems of metabolic engineering is especially robustness of the biological systems. Bacterial cells are generally evolved at the various levels from DNA to protein for maintaining their robustness against the changing circumstances. Therefore, general strategy to modify cellular physiology depending the robustness or flexibility of the biological systems should be required. In this study, we developed the general tools to modify the biological robustness at the various levels including translation and protein levels. For translation level control, a model to predict the translation efficiency based on the mRNA’s secondary structure and consequently expression level can be precisely controllable for any genes of interest. Additionally, intracellular metabolite sensor named “riboselector” to regulate metabolic distribution will be presented. The potentials of the platform technology developed in this study for the application to the production of biofuels and commodity chemicals.

April 5, 2019, 5-7 pm

Room # B119, Building # 310



Selection of Heterogeneity in Stochastic Gene Expression of Diploid Cells


Cheol-Min Ghim

Professor, School of Life Science & Department of Physics, UNIST

Abstract

Stochastic gene expression has been extensively studied in natural and synthetic gene expression systems. However, the majority of those contributions, if not all, were concentrated on the haploid systems, where a single allele is inherited by asexual reproduction. Largely left unexplored is the question of how much the allelic imbalance in chromatin accessibility or divergence in transcription factor binding sites would impact the organismal fitness and thus shaped the sequence evolution. Here, we explicitly consider diploid systems with homo- and heterozygous combination of alleles in the regulatory sequences rather than the primary coding sequence and characterize the genetic noise profiles associated with the zygosity. In particular, we show that the heterozygosity may arise as an outcome of evolutionary selection, when the regulatory proteins are subject to stochastic fluctuations, acting as a source of extrinsic noise. Based on this buffering mechanism in heterozygote, we discuss the relevance of our results to the recent reports on the balancing selection enriched in the cis-regulatory sequences of immune cells and epithelial cells.

March 8, 2019, 5-7 pm

Room # B119, Building # 310



Distant Communications in Biology


Jong-Bong Lee

Professor, Department of Physics and School of Interdisciplinary Bioscience & Bioengineering, POSTECH, Pohang, Korea

Abstract

Single-molecule imaging is capable of visualizing the mechanics of biomolecules or their complex in real-time with nanometer accuracy and detecting intermediate and rare populations of molecules as well, which help us decipher the biophysical events. These advantages have facilitated our understanding of a variety of biological problems. Using novel single-molecule techniques, we successfully visualized stochastic orchestration of proteins involved in the reactions that are based on thermal fluctuation-driven motions. We also revealed the formation mechanism of intercellular nanotube that is a novel actin filament-driven bridge connecting cells, which is recognized as a new pathway for the distant transport of cytoplasmic components, virus, and pathogenic substances between cells. In this colloquium, I will present the mechanistic studies of molecule-to-molecule communications during DNA mismatch repair and the intercellular nanotube for cell-to-cell communications.

January 10, 2019, 5-7 pm

Room # B119, Building # 310

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