University of Southampton, Systems & Synthetic Biology Modelling Group
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Welcome to Dr Syma Khalid's research group


We are based in the Chemical Biology sub-section of the School of Chemistry, University of Southampton. Our research involves the application of computational techniques to the study of large biological molecules and systems including bacterial outer membrane proteins and nucleic acids. A key area of research involves capturing the biological complexity of bacterial membranes in our simulations, with a particular focus on the outer membranes of Gram-negative bacteria. In this context are developing computational models and tools to link biomolecular simulations and systems biology. We are also interested in applying the knowledge gained from studying biological systems to aid the design of synthetic systems for applications in bionanotechnology.

We have strong links with experimental groups in biophysics, biochemistry, chemical biology and structural biology.

To find out more, please follow the links above or visit our blog




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Latest news:

We thank Oxford Nanopore Technologies for continued support of our work

Our blog is launched!

Our coarse-grained DNA model is available for download from the MARTINI website

Congratulations to Andrew Guy for being awarded a Gold Award at the 2010 Faculty of Engineering, Science and Mathematics Postgraduate Research Showcase event

Congratulations to Dr Tom Piggot for being awarded a US Partnership Award from CCPB

Congratulations to Lucy Garner on being awarded a Platinum Exscitec Award and a British Science Association Gold Award for her summer project in the SSBM group

University of Southampton invests £3 million in UK's most powerful university-owned supercomputer.
Click on link for further details

Latest Publications:

Marius P, Leung YM, Piggot T.J, , Khalid S and Williamson P.T.(2011), "Probing the oligomeric state and interaction surfaces of Fukutin-I in dilauroylphosphateidylcholine bilayers" in press

Piggot T.J, Holdbrook D.A and Khalid S (2011), "Electroporation of the E. coli and S. Aureus Membranes: Molecular Dynamics Simulations of Complex Bacterial Membranes.". J Phys Chem B (abstract)

Bond P.J, Guy A.T , Heron A, Bayley H and Khalid S (2011), "Molecular dynamics simulations of DNA within a nanopore: arginine-phosphate tethering and a binding/sliding mechanism for translocation". Biochemistry (abstract)

Piñeiro A, Bond P.J, and Khalid S (2011), "Exploring the conformational dynamics and membrane interactions of PorB from C. glutamicum: a multi-scale molecular dynamics simulation study". BBA Biomembranes (abstract)

Vohra S, Hall BA, Holdbrook HA , Khalid S, Biggin P.C, (2010), "Bookshelf: a simple curation system for the storage of biomolecular simulation data". Database - in press.

Kurze A, Michie K.A, Dixon S.E, Mishra A, Itoh T, Khalid S, Strmecki L, Shirahige K, Haering C H, Löwe J and Nasmyth K, (2010), "A positively charged channel within the Smc1/Smc3 hinge required for sister chromatid cohesion". Embo J (abstract)

Holdbrook HA , Leung YM, Piggot TJ, Marius P, Williamson PT and Khalid S, (2010), "Stability and Membrane Orientation of the Fukutin Transmembrane Domain: A Combined Multiscale Molecular Dynamics and Circular Dichroism Study". Biochemistry . (abstract)

Bond PJ & Khalid S, (2010), "Antimicrobial and Cell-Penetrating Peptides: Structure, Assembly and Mechanisms of Membrane Lysis via Atomistic and Coarse-Grained Molecular Dynamics Simulations". Protein Pept.Letters . (abstract)

Corsi J, Hawtin RW, Ces O, Attard GS, Khalid S, (2010), "DNA Lipoplexes: Formation of the Inverse Hexagonal Phase Observed by Coarse-Grained Molecular Dynamics Simulation". Langmuir . (abstract)

Mishra A, Hu B, Kurze A, Beckouët F, Farcas AM, Dixon SE, Katou Y, Khalid S, Shirahige K and Nasmyth K.(2010), "Both Interaction Surfaces within Cohesin's Hinge Domain Are Essential for Its Stable Chromosomal Association". Current Biology . (abstract)

Ainalem ML, Campbell RA, Khalid S, Gillams RJ , Rennie AR, Nylander T.(2010), "On the Ability of PAMAM Dendrimers and Dendrimer/DNA Aggregates To Penetrate POPC Model Biomembranes". J Phys Chem B. (abstract)




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Last updated 18/02/11