PRESENTATION BY
Dr Jing Huang
Computer-Aided Drug Design Centre – University of Maryland and
Laboratory of Computational Biology – National Heart, Lung and Blood Institute
USA

PRESENTATION TITLE
Simulations of Intrinsically Disordered Proteins with Advanced Protein Force Fields

ABSTRACT
The abundance and functional significance of intrinsically disordered peptides and proteins (IDPs) in eukaryotes has become widely recognised. Instead of folding into a single, well-defined three-dimensional structure, an IDP fluctuates between an ensemble of conformational states, allowing it to undertake different interactions with different consequences as required to function in protein-protein interaction networks. Molecular simulation appears to be the method of choice to generate the conformational ensembles of IDPs, however, the empirical force fields (FFs) used in simulations were mostly developed targeting folded proteins and might need improvement concerning their accuracy in simulating IDPs. The recent development of the additive CHARMM36m protein FF that yields more accurate conformational sampling for IDPs will be presented and its strength and weakness discussed. After overviewing recent theoretical developments and parametrization efforts, the presenter will show how the Drude protein FF is capable of capturing folding cooperativity of a model peptide and of generating conformational sampling of an IDP that is consistent with NMR and SAXS measurements.

ABOUT THE PRESENTER
Jing Huang received a BSc in 2005 and a MSc in 2007 from the Department of Physics at Tsinghua University and a PhD in Chemistry from the University of Basel under the supervision of Markus Meuwly in 2011. With an enthusiasm for force field development and a fellowship from Swiss National Science Foundation on “Improving force field with NMR and pKa data”, he moved to the US in 2012 to work with Alex MacKerell at the Computer-Aided Drug Design Centre at the University of Maryland School of Pharmacy. Since 2015 he also holds a joint appointment at the Laboratory of Computational Biology at the National Heart, Lung and Blood Institute, National Institutes of Health. This fall he will start his own lab in the newly established Westlake Institute for Advanced Study in Hangzhou, China.

DATE:           Thursday, 10 August 2017
TIME:            11h00
VENUE:        MSG-025 MSSI Building Extension

Tea/coffee will be available at 10h45
For further information, please contact:  pierre.cazade@ul.ie