- Título: Revealing Physics from Life’s Key Protein Machines in Metabolic and Genetic Control
- Palestrante: Jin Yu (Beijing Computational Science Research Center)
- Resumo: Bio-molecular machines are made of nano- to micrometer scale protein complexes as mechano- chemical vehicles with energy self-sufficiency. My researches have been focused on physical mechanisms of these naturally evolved machines, for example, on how they maintain sufficiently high energy efficiency and accuracy despite of environmental noises and fluctuations. Advancements in single molecule technologies and high-resolution structural characterizations in recent years have made individual molecule interrogations possible . On the other hand, physicists also started pondering about the internal complexities and operations of these microscopic machines above the proof of principles . By utilizing a spectrum of molecular modeling and simulation techniques, high-performance computing, along with statistical mechanics and stochastic methods, we aim at providing physical insights of life’s fundamental machines as well as exploring artificial design strategies for bio-medical advancements . Here I will briefly introduce two types of molecular machines we have recently studied: A highly efficient metabolic machine that achieves sequential ATP hydrolyses around its protein ring to further enable a rotor in the center , and a smallest transcription machine that moves along DNA to synthesize RNA so that to transcribe the genetic information from DNA to RNA [5,6].
 C Bustamante, W Cheng and YX Mejia. Revisiting the Central Dogma One Molecule at a Time. Cell 2011 (144) 480
 D Chowdhury. Stochastic mechano-chemical kinetics of molecular motors: a multidisciplinary enterprise from a physicist’s perspective. Physics Reports 2013 (529) 1
 J Yu. Coordination and control inside simple biomolecular machines. In Protein Conformation Dynamics, Advances in Experimental Medicine and Biology, by Springer 2014 (805) 353
 L Dai, H Flechsig, and J Yu. Deciphering intrinsic inter-subunit couplings that lead to sequential hydrolysis of F1-ATPase ring. Biophysical Journal 2017 (113) 1440
 J Yu. Computational investigations on polymerase actions in gene transcription and replication: Combining physical modeling and atomistic simulations. Chinese Physics B 2016 (25) 018706
 L-T Da, C E, Y Shuai, S Wu, X-D Su, and J Yu. T7 RNA polymerase translocation is facilitated by helix opening on the fingers domain that may also prevent backtracking. Nucleic Acids Research 2017 (45) 7909 equal contribution
- Sobre a palestrante:
BS and MS, Physics, Tsinghua University, 1998 and 2001
PhD, Physics, University of Illinois at Urbana- Champaign (UIUC), 2007
Dr Jin Yu obtained her degrees in physics. During her graduate study, she worked with Prof Klaus Schulten (UIUC) in theoretical and computational biophysics, in collaboration with Prof Taekjip Ha’s lab in single molecule physics. As a postdoctoral fellow, she worked with Prof George Oster (UC Berkeley) in mathematical and physical modeling as well as with Prof Carlos Bustamante’s lab in studying bimolecular machinery. Dr Yu led her independent research on computational biophysics in CSRC since 2012 (Google Citation).
Research interests: To study how protein and DNA/RNA machinery work in coordination and control, as well as how they achieve biological functions with sufficiently high efficiency and fidelity among noises and fluctuations. Particular interest is on genetic and epigenetic regulation, and on how essential bimolecular entities evolve and impact on evolution (view lab research page). Positions open to graduate students and postdoctoral researchers!