Understand Functional Conformational Changes of Large Biomolecules - PowerPoint PPT Presentation

Understand Functional Conformational Changes of Large Biomolecules with Computer Tools Siqin CAO On behalf of Xuhui Huang's group 2503, July 10, Summer Camp 2019

Central Dogma of Molecular Biology

RNA polymerase and transcription cycle Cell 127 , 941, (2006); Cell 149 , 1431, (2012)

Backtracking observed from computer simulations Da, Pardo, Xu, Zhang, Gao,Wang, Huang, Nature Communications 7 , 11244, (2016)

Backtracking observed from computer simulations Da, Pardo, Xu, Zhang, Gao,Wang, Huang, Nature Communications 7 , 11244, (2016)

Computer simulations for biomolecules Levitt, M., Nature Structural Biology 8 , 392-393 (2001); Bioinfomatics 5 , 2015

Kinetic Model C 1 ( x 1 , x 2 , . . . x N , t ) C 2 ( x 1 , x 2 , . . . x N , t ) C ( x 1 , x 2 , . . . x N , t ) C 3 ( x 1 , x 2 , . . . x N , t ) = e ̂ ℒ t C ( x 1 , x 2 , . . . x N ,0) C 4 ( x 1 , x 2 , . . . x N , t ) C 5 ( x 1 , x 2 , . . . x N , t ) Chodera. Noé. Pande, Hummer, Shuttle, Levy....

Markov State Model Kinetic Lumping Clustering (splitting) Conformations Microstate Model Macrostate Model

Clustering and state decomposition K-Centers APLoD (Adaptive Partitioning by Local Density- Peaks) APM (Automatic State Partitioning for Multibody Systems) Fu Kit Sheong etc, JCTC 11 , 17 (2015); Liu Song etc, JCC 38 , 152 (2017)

Paths and dominant paths TPT (Transition path theory) Path lumping TAPS (Traveling-salesman Based Automated Path Searching Method) F. Noé etc, PNAS 106 , 19011 (2009); L. Meng, etc. JCP 147 , 044112 (2017); L. Zhu etc. JCP 150 , 124105 (2019)

Self-assembly Block Copolymer Amphiphilic molecule PYR PYN Phys. Chem. Chem. Phys. 18 , 23494-23499, (2016); J. Phys. Chem. Lett. 8 , 1798–1803, (2017)

Acknowledgement