Computational Modelling Group

Gromacs

For queries about this topic, contact Syma Khalid.

View the calendar of events relating to this topic.

Projects

Antimicrobial Peptide and E. coli Membrane Interactions

Syma Khalid (Investigator), Thomas Piggot, Nils Berglund

Antimicrobial peptides (AMPs) are known to disrupt the membranes of bacterial cells such as E. coli. I work on investigating the nature of these interactions using molecular dynamics (MD) simulations.

BioSimGrid

Jonathan Essex, Hans Fangohr (Investigators), Richard Boardman, Syma Khalid, Steven Johnston

The aim of the BioSimGrid project is to make the results of large-scale computer simulations of biomolecules more accessible to the biological community. Such simulations of the motions of proteins are a key component in understanding how the structure of a protein is related to its dynamic function.

Centre for Doctoral Training in Next Generation Computational Modelling

Hans Fangohr, Ian Hawke, Peter Horak (Investigators), Susanne Ufermann Fangohr, Ryan Pepper, Hossam Ragheb, Emanuele Zappia, Ashley Setter, David Lusher, Alvaro Perez-Diaz, Kieran Selvon, Thorsten Wittemeier, Mihails Milehins, Stephen Gow, Ioannis Begleris, Jonathon Waters, James Harrison, Joshua Greenhalgh, Rory Brown, Robert Entwistle, Paul Chambers, Jan Kamenik, Craig Rafter

The £10million Centre for Doctoral Training was launched in November 2013 and is jointly funded by EPSRC, the University of Southampton, and its partners.

The NGCM brings together world-class simulation modelling research activities from across the University of Southampton and hosts a 4-year doctoral training programme that is the first of its kind in the UK.

How far can we stretch the MARTINI?

Syma Khalid (Investigator), Ric Gillams

To date, coarse-grained lipid models have generally been parameterised to ensure the correct prediction of structural properties of membranes, such as the area per lipid and the bilayer thickness. The work described here explores the extent to which coarse-grained models are able to predict correctly bulk properties of lipids (phase behaviour) as well as the mechanical properties, such as lateral pressure profiles and stored elastic stress in bilayers. Such an evaluation is crucial for understanding the predictive capabilities of coarse-grained models.

Immunotherapy Research: Modelling MHC Class I Complex Assembly

Timothy Elliott, Jorn Werner (Investigators), Alistair Bailey

This project uses mathematical modelling and simulation to investigate mechanisms by which our cells process and present biological information that is used by our immune system to distinguish between healthy and diseased cells.

Lyotropic phase transitions of lipids studied by CG MD simulation and experimental techniques

Syma Khalid (Investigator), Josephine Corsi

A study of the phase behaviour of cationic lipid - DNA complexes such as those used for transfection by coarse grained molecular dynamics simulation. Lipid systems studied include DOPE, DOPE/DNA and DOPE/DOTAP/DNA. Structural parameters and phase behaviour observed computationally have been compared with those gained using Small Angle X-ray Scattering (SAXS) and polarising light microscopy techniques.

Membrane-Protein Interactions: The Outer Membrane of Gram-Negative Bacteria

Syma Khalid (Investigator), Pin-Chia Hsu

The aim of the project is to looking for the interaction sites, which may responsible for turning on/off activity in outer membrane protein with gram-negative bacteria membrane using molecular dynamic (MD) approach.

Multi-scale simulations of bacterial outer-membrane proteins

Syma Khalid (Investigator), Jamie Parkin

Using Iridis to run multiple simulations, I aim to simulate the outer membrane proteins of Pseudomonas aeruginosa, using X-ray crystal structures of proteins only recently resolved by Bert van den Berg, University of Massachusetts. By modelling the proteins in a realistic P. aeruginosa outer membrane, I aim to gain insight into the binding of these proteins to specific substrates and their function.

OMSys Towards a system model of a bacterial outer membrane

Syma Khalid (Investigator)

Many bacteria have an outer membrane which is the interface between the cell and its environment. The components of this membrane are well studied at an individual level, but there is a need to model and understand the outer membrane as a whole. In this project we aim to develop such a model of a bacterial outer membrane, linking computer simulations of the component molecules through to a more "systems biology" approach to modelling the outer membrane as a whole. Such an approach to modelling an OM must be multi-scale i.e. it must embrace a number of levels ranging from atomistic level modelling of e.g. the component proteins through to higher level "agent-based" modelling of the interplay of multiple components within the outer membrane as a whole. The different levels of description will be integrated to enable predictive modelling in order to explore the roles of outer membrane changes in e.g. antibiotic resistance.

Probing the oligomeric state and interaction surface of Fukutin Transmembrane Domain in lipid bilayer via Molecular Dynamics simulations

Syma Khalid, Philip Williamson (Investigators), Daniel Holdbrook, Jamie Parkin, Nils Berglund, Yuk Leung

Fukutin Transmembrane Domain (FK1TMD) is localised to the endoplasmic reticulum or Golgi Apparatus within the cell where it is believed to function as a glycosyltransferase. Its localisation within the cell is thought to be mediated by the interaction of its N-terminal transmembrane domain with the lipid bilayers surrounding these compartments, each of which possess a distinctive lipid composition. Studies have revealed that the N-terminal transmembrane domain of FK1TMD exists as dimer within dilauroylphosphatidylcholine bilayers and this interaction is driven by interactions between a characteristic TXXSS motif. Furthermore residues close to the N-terminus that have previously been shown to play a key role in the clustering of lipids are shown to play a key role in anchoring the protein in the membrane.

THE NORM MATE TRANSPORTER FROM N. GONORRHEAE: INSIGHTS INTO DRUG & ION BINDING FROM ATOMISTIC MOLECULAR DYNAMICS SIMULATIONS

Syma Khalid (Investigator), Daniel Holdbrook, Thomas Piggot, Yuk Leung

The multidrug and toxic compound extrusion (MATE) transporters extrude a wide variety of substrates out of both mammalian and bacterial cells via the electrochemical gradient of protons and cations across the membrane. Multiple atomistic simulation are performed on a MATE transporter, NorM from Neisseria gonorrheae (NorM_NG) and NorM from Vibrio cholera (NorM_VC). These simulations have allowed us to identify the nature of the drug-protein/ion-protein interactions, and secondly determine how these interactions contribute to the conformational rearrangements of the protein.

Using Molecular Dynamics to Understand the Antibacterial Mechanisms of Daptomycin & Chlorhexidine to Target the Bacterial Membrane

This project aims to use molecular dynamics techniques to understand how antimicrobial peptides, daptomycin and chlorhexidine, disrupt both gram positive and negative cell membranes on an atomic level.

Using Molecular Dynamics to Understand the Antibacterial Mechanisms of Daptomycin & Chlorhexidine to Target the Bacterial Membrane

This project aims to use molecular dynamics techniques to understand how antimicrobial peptides, daptomycin and chlorhexidine, disrupt both gram positive and negative cell membranes on an atomic level.

Using Molecular Dynamics to Understand the Antibacterial Mechanisms of Daptomycin & Chlorhexidine to Target the Bacterial Membrane

Syma Khalid (Investigator), Eilish McBurnie

This project aims to use molecular dynamics techniques to understand how antimicrobial peptides, daptomycin and chlorhexidine, disrupt both gram positive and negative cell membranes on an atomic level.

People

Timothy Elliott
Professor, Medicine (FM)
Jonathan Essex
Professor, Chemistry (FNES)
Hans Fangohr
Professor, Engineering Sciences (FEE)
Nicolas Green
Reader, Electronics and Computer Science (FPAS)
Peter Horak
Reader, Optoelectronics Research Centre
Jorn Werner
Reader, Biological Sciences (FNES)
Ian Hawke
Lecturer, Mathematics (FSHS)
Syma Khalid
Principal Research Fellow, Chemistry (FNES)
Richard Boardman
Senior Research Fellow, Engineering Sciences (FEE)
Philip Williamson
Senior Research Fellow, Biological Sciences (FNES)
Alistair Bailey
Research Fellow, Medicine (FM)
Steven Johnston
Research Fellow, Engineering Sciences (FEE)
Ioannis Begleris
Postgraduate Research Student, Engineering Sciences (FEE)
Rory Brown
Postgraduate Research Student, Civil Engineering & the Environment (FEE)
Paul Chambers
Postgraduate Research Student, Engineering Sciences (FEE)
Robert Entwistle
Postgraduate Research Student, Engineering Sciences (FEE)
Ric Gillams
Postgraduate Research Student, Chemistry (FNES)
Stephen Gow
Postgraduate Research Student, Engineering Sciences (FEE)
Joshua Greenhalgh
Postgraduate Research Student, Engineering Sciences (FEE)
James Harrison
Postgraduate Research Student, Engineering Sciences (FEE)
Jan Kamenik
Postgraduate Research Student, Engineering Sciences (FEE)
Yuk Leung
Postgraduate Research Student, Chemistry (FNES)
David Lusher
Postgraduate Research Student, Engineering Sciences (FEE)
Jamie Parkin
Postgraduate Research Student, Chemistry (FNES)
Alvaro Perez-Diaz
Postgraduate Research Student, Engineering Sciences (FEE)
Can Pervane
Postgraduate Research Student, Electronics and Computer Science (FPAS)
Craig Rafter
Postgraduate Research Student, Engineering Sciences (FEE)
Hossam Ragheb
Postgraduate Research Student, Engineering Sciences (FEE)
Álvaro Ruiz-Serrano
Postgraduate Research Student, Chemistry (FNES)
Kieran Selvon
Postgraduate Research Student, Engineering Sciences (FEE)
Ashley Setter
Postgraduate Research Student, Engineering Sciences (FEE)
Jonathon Waters
Postgraduate Research Student, Engineering Sciences (FEE)
Thorsten Wittemeier
Postgraduate Research Student, Engineering Sciences (FEE)
Emanuele Zappia
Postgraduate Research Student, Engineering Sciences (FEE)
Petrina Butler
Administrative Staff, Research and Innovation Services
Susanne Ufermann Fangohr
Administrative Staff, Civil Engineering & the Environment (FEE)
Josephine Corsi
Alumnus, University of Southampton
Mihails Milehins
Alumnus, University of Southampton
Nils Berglund
None, None
Daniel Holdbrook
None, None
Pin-Chia Hsu
None, None
Eilish McBurnie
None, None
Thomas Piggot
None, None