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SUMMARY:High Throughput Approaches to Biological Signalling Processes -  D
 r. Benjamin Hall Structural Bioinformatics & Computational Biochemistry Un
 it / Oxford Centre for Integrative Systems Biology\, University of Oxford
DTSTART:20091211T133000Z
DTEND:20091211T143000Z
UID:TALK21789@talks.cam.ac.uk
CONTACT:16771
DESCRIPTION:Transmembrane helices play a multiple vital roles in cell func
 tion\, including intercell signalling\nprocesses\, channel gating and acti
 ve transport. As such\, there exists a considerable amount of\ndata on the
  biological function and structural properties of naturally occurring heli
 ces and their\nmutants. Simulation studies can provide insight into the dy
 namics and behaviour of\nbiomolecular systems in a variety of environments
 \, but however such analyses are\ncomputationally expensive and typically 
 difficult to automate. Coarse grain simulations are\nbecoming an increasin
 gly popular tool for understanding the properties of biological systems\,\
 novercoming canonical limits of atomistic simulations such as timescale or
  system size. Both\nsuch techniques involve several manual steps\, includi
 ng system build\, simulation set up and\nanalysis. Here we present Sidekic
 k\, a piece of software which automates these processes to\nallow for the 
 set up of massive numbers of coarse grain simulations on the basis of a sm
 all set\nof input sequences\, or a single sequence and a scanning mutation
 . We validate the methodology \nby comparison with data from high throughp
 ut experiments relating the insertion of peptides into \nthe membrane by t
 he translocon. We then use the technique to predict the biophysical change
 s \ninduced by a variety of mutations of bacterial methyl accepting chemor
 eceptor protein \ntransmembrane helices described in the literature. By ob
 serving the change in positions and \norientations of the helix with diffe
 rent mutations\, we propose that a swinging piston model \ndominates the s
 ignalling event\, though there may be a lesser role for rotation of the he
 lix.\n\nHis website: http://sbcb.bioch.ox.ac.uk/hall.php
LOCATION:Lecture Theatre\, Department of Biochemistry\,  (Sanger Building)
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