Revealing Physics and Design Principle of Life’s Key Protein Machines in Metabolic and Genetic Control

Jin Yu
Computational Science Research Center, Beijing
Thursday, February 21, 2019
10:00 am
NS2 1201
Bio-molecular machines are made of nano- to micrometer scale protein complexes as mechano- chemical vehicles with energetic self-sufficiency. My researches have focused on revealing physical mechanisms of these naturally evolved machines, for example, on how they achieve high cooperativity, energy efficiency, and accuracy of performance despite of environmental noises and fluctuations. Advancements on single-molecule dynamics and high-resolution structure characterizations have made individual molecular interrogations possible. Consequently, physicists are able to probe internal complexities and operational essentials of these microscopic machines beyond proof of principle. By utilizing a spectrum of molecular modeling and simulation techniques, high performance computing, as well as statistical mechanics and stochastic methods, we aim at bringing physical insights of life’s key protein machines together with exploring nature’s design principles to assist bio-medical advancements. In this talk I will focus on two types of protein machines we studied in recent years: A highly efficient metabolic machine that achieves sequential ATP hydrolyses on a ring-shaped multi-subunit architecture, which draws our attention to inter-subunit couplings or nearest-neighbor interactions that allow for long-range regulation; A smallest transcription machine that moves along DNA to synthesize RNA via mechano-chemical coupling and information fidelity control, which drives our further exploration on how protein machines and factors search and recognize on the genome.
Jun Allard