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SUMMARY:Biomolecular interactions in crowded cellular environments - Dr Yu
 ji Sugita\, Theoretical Molecular Science Laboratory\, RIKEN Cluster for P
 ioneering Research
DTSTART:20190912T131500Z
DTEND:20190912T141500Z
UID:TALK129775@talks.cam.ac.uk
CONTACT:Chloe Barker
DESCRIPTION:Proteins\, nucleic acids\, and other biomacromolecules work as
  molecular machinery in a living cell. The effect of cellular environments
  on protein structure and function have been examined experimentally or th
 eoretically. Since the inside of a cell is highly crowded with a large num
 ber of biomacromolecules\, macromolecular crowding effect has been conside
 red as one of the most important cellular effects on proteins. However\, c
 onventional methodologies and software hindered us from performing reliabl
 e molecular simulations in the environments. The GENESIS (GENeralized-Ense
 mble SImulation System) software has been developed to overcome the diffic
 ulty by introducing advanced techniques in parallelization and optimizatio
 n of the code [1\,2]. Using GENESIS\, we succeeded in atomistic simulation
 s of the bacterial cytoplasm [3] and an entire gene locus (GATA4) [4]\, wh
 ich include more than 100 million and 1 billion atoms in their simulation 
 systems\, respectively. We also have extended the simulation time limitati
 on by developing various enhanced conformational sampling methods [5] as w
 ell as allowing a large time step using a new definition of temperature in
  MD simulation [6]. Atomistic MD simulations of the bacterial cytoplasm ha
 ve revealed the importance of weak non-specific interactions between prote
 ins and between proteins and metabolites. This might be important for in-s
 ilico drug discovery in near future.\n\nReferences\n[1] Jung et al. WIRE
 ’s Rev. Comp. Mol. Sci. 2015\, 5\, 310-323. [2] Kobayashi et al. JCC 201
 7\, 38\, 2193-2206. [3] Yu et al. eLife 2016\, 5\, 1-22. [4] Jung et al. J
 CC 2019\, 40\, 1919-1930. [5] For a review\; Sugita et al. Biomolecular Si
 mulations\, 155-177\, Springer\, 2019. [6] Jung et al. JCTC 2019\, 15\, 84
 -94.\n
LOCATION:Pfizer Lecture Theatre\,  Department of Chemistry
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