The University of Southampton

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Phone:: (023) 8059 4176
Email:: S.Khalid@soton.ac.uk

Professor Syma Khalid MChem PhD

Professor of Computational Biophysics

Related links: Personal homepage

Professor Syma Khalid is Professor of Computational Biophysics within Chemistry at the University of Southampton.

Syma graduated with a first class degree in Chemistry from the University of Warwick in 2000. She remained at Warwick to read for a PhD under the supervision of Professor P Mark Rodger. After obtaining her PhD in 2003, she moved to the University of Oxford as a postdoc in Professor Mark Sansom's lab, to study the structure-function relationship of bacterial membrane proteins. In 2007, she was appointed as RCUK fellow in Chemistry at the University of Southampton, in 2010 was appointed to full lectureship. In 2016 she was promoted to full professor She has ~15 years of experience in the development and application of molecular dynamics simulations to the study of biological molecules. Her research interests are centred around the dynamics of biomolecules in and around biological membranes. Her formal training as a chemist combined with her interest in the biological relevance of the systems she studies enables her to adopt a truly multi-disciplinary approach; collaborators include Bert van den Berg (Newcastle), Ben Luisi (Cambridge) and Peter Bond (A*STAR, Singapore). Syma's international reputation is reflected in the invitations she receives to speak at national and international meetings each year.

Syma has authored over 40 peer-reviewed papers and 4 book chapters and is on the editorial board of Scientific Reports. She serves on the management group that leads CCPBiosim. In addition, she is a local section committee member of the RSC, and also serves on the management committee of the British Biophysical Society.

Theory and Modelling in Chemical Sciences CDT

Research

Publications

Contact

Research interests

Computational Bacteriology

My 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.

Research funding

As PI

BBSRC Responsive mode grant: BB/M029573/1 (£322k)
BBSRC Industrial CASE award with Oxford Nanopore Technologies (£40k)
BBSRC Responsive mode grant: BBH0006581 (£295k)
University of Southampton Start-up funds (2 PhD studentships and £50k)
University of Southampton, Institute of Life Sciences: 3-month PDRA
University of Southampton, Institute of Life Sciences: PhD studentship
Industrially funded studentship (Oxford Nanopore technologies: £80k)
Industrially funded PDRA (Oxford Nanopore Technologies: £100k)
University of Southampton, Institute of Life Sciences: (£20k)
University of Southampton, strategic funding (£22k)

As Co-I

EU-funded Marie Curie ITN grant as Co-PI (€3.82M) PI is Alison Rodger (Warwick)
MRC-funded Project on AMR (theme 1) as Co-PI (£5m) PI is Christopher Dowson (Warwick)

Research group

Computational Systems Chemistry

Research project(s)

Khalid: Self Assembly of DNA-lipid complexes for gene therapy

Khalid: Transport mechanisms in bacteria: Autotransporters

Key Publications

Piggot, T. J., Piñeiro, Á., & Khalid, S. (2012). Molecular dynamics simulations of phosphatidylcholine membranes: a comparative force field study. Journal of Chemical Theory and Computation, 8(11), 4593-4609. DOI: 10.1021/ct3003157

Guy, A. T., Piggot, T. J., & Khalid, S. (2012). Single-stranded DNA within nanopores: conformational dynamics and implications for sequencing; a molecular dynamics simulation study. Biophysical Journal, 103(5), 1028-1036. DOI: 10.1016/j.bpj.2012.08.012

Piggot, T. J., Holdbrook, D. A., & Khalid, S. (2011). Electroporation of the E. coli and S. Aureus membranes: molecular dynamics simulations of complex bacterial membranes. The Journal of Physical Chemistry B, 115(45), 13381-13388. DOI: 10.1021/jp207013v

Chen, M., Khalid, S., Sansom, M. S. P., & Bayley, H. (2008). Outer membrane protein G: engineering a quiet pore for biosensing. Proceedings of the National Academy of Sciences of the United States of America, 105(17), 6272-6277. DOI: 10.1073/pnas.0711561105

Scott, K. A., Bond, P. J., Ivetac, A., Chetwynd, A. P., Khalid, S., & Sansom, M. S. P. (2008). Coarse-grained MD simulations of membrane protein-bilayer self-assembly. Structure, 16(4), 621-630. DOI: 10.1016/j.str.2008.01.014

Articles

Boags, A., Hsu, P., Samsudin, F., Bond, P. J., & Khalid, S. (2017). Progress in molecular dynamics simulations of gram-negative bacterial cell envelopes. The Journal of Physical Chemistry Letters, 8(11), 2513-2518. DOI: 10.1021/acs.jpclett.7b00473

Graham, J. A., Essex, J., & Khalid, S. (2017). PyCGTOOL: automated generation of coarse-grained molecular dynamics models from atomistic trajectories. Journal of Chemical Information and Modeling, 57(4), 650-656. DOI: 10.1021/acs.jcim.7b00096

Jefferies, D. F., Hsu, P-C., & Khalid, S. (2017). Through the lipopolysaccharide glass: a potent antimicrobial peptide induces phase changes in membranes. Biochemistry, 56(11), 1672-1679. DOI: 10.1021/acs.biochem.6b01063

Holdbrook, D., Huber, R. G., Piggot, T., Bond, P. J., & Khalid, S. (2016). Dynamics of crowded vesicles: local and global responses to membrane composition. PLoS ONE, 11(6), 1-18. DOI: 10.1371/journal.pone.0156963

Ortiz-Suarez, M. L., Samsudin, M., Piggot, T. J., Bond, P. J., & Khalid, S. (2016). Full-length OmpA: structure, function, and membrane interactions predicted by molecular dynamics simulations. Biophysical Journal, 111(8), 1692-1702. DOI: 10.1016/j.bpj.2016.09.009

Hsu, P-C., Jefferies, D., & Khalid, S. (2016). Molecular dynamics simulations predict the pathways via which pristine fullerenes penetrate bacterial membranes. The Journal of Physical Chemistry B, 120(43), 11170-11179. DOI: 10.1021/acs.jpcb.6b06615

Witzke, S., Petersen, M., Carpenter, T. S., & Khalid, S. (2016). Molecular dynamics simulations reveal the conformational flexibility of Lipid II and its loose association with the defensin plectasin in the Staphylococcus aureus membrane. Biochemistry, 55(23), 3303-3314. DOI: 10.1021/acs.biochem.5b01315

Samsudin, M., Ortiz-Suarez, M., Piggot, T., Bond, P. J., & Khalid, S. (2016). OmpA: a flexible clamp for bacterial cell wall attachment. Structure, 24(12), 2227-2236. DOI: 10.1016/j.str.2016.10.009

van den Berg, B., Chembath, A., Jefferies, D., Basle, A., Khalid, S., & Rutherford, J. C. (2016). Structural basis for Mep2 ammonium transceptor activation by phosphorylation. Nature Communications, 7(11337), 1-11. DOI: 10.1038/ncomms11337

Carpenter, T. S., Parkin, J., & Khalid, S. (2016). The free energy of small solute permeation through the E. coli outer membrane has a distinctly asymmetric profile. The Journal of Physical Chemistry Letters, 7(17), 3346-3451. DOI: 10.1021/acs.jpclett.6b01399

Clifton, L. A., Holt, S. A., Hughes, A. V., Daulton, E. L., Arunmanee, W., Heinrich, F., ... Lakey, J. H. (2015). An accurate in vitro model of the E. coli envelope. Angewandte Chemie International Edition, 54(41), 11952-11955. DOI: 10.1002/anie.201504287

Manara, R. M. A., Wallace, E. J., & Khalid, S. (2015). DNA sequencing with MspA: molecular dynamics simulations reveal free-energy differences between sequencing and non-sequencing mutants. Scientific Reports, 5(12783), 1-7. DOI: 10.1038/srep12783

Manara, R. M. A., Guy, A. T., Wallace, E. J., & Khalid, S. (2015). Free-energy calculations reveal the subtle differences in the interactions of DNA bases with ?-hemolysin. Journal of Chemical Theory and Computation, 11(2), 810-816. DOI: 10.1021/ct501081h

Gray, A., Harlen, O. G., Harris, S. A., Khalid, S., Leung, Y. M., Lonsdale, R., ... Richardson, R. A. (2015). In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation. Acta Crystallographica Section D Biological Crystallography, 71(1), 162-172. DOI: 10.1107/S1399004714026777

Ashworth Briggs, E. L., Gomes, R. G. B., Elhussein, M., Collier, W., Stuart Findlow, I., Khalid, S., ... Williamson, P. T. F. (2015). Interaction between the NS4B amphipathic helix, AH2, and charged lipid headgroups alters membrane morphology and AH2 oligomeric state — Implications for the Hepatitis C virus life cycle. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1848(8), 1671-1677. DOI: 10.1016/j.bbamem.2015.04.015

Berglund, N., Piggot, T. J., Jefferies, D., Sessions, R. B., Bond, P. J., & Khalid, S. (2015). Interaction of the antimicrobial peptide polymyxin b1 with both membranes of E. coli: a molecular dynamics study. PLoS Computational Biology, 11(4), 1-17. DOI: 10.1371/journal.pcbi.1004180

Cournia, Z., Allen, T. W., Andricioaei, I., Antonny, B., Baum, D., Brannigan, G., ... Bondar, A-N. (2015). Membrane protein structure, function, and dynamics: a perspective from experiments and theory. The Journal of Membrane Biology, 248(4), 611-640. DOI: 10.1007/s00232-015-9802-0

Viollier, P. H., Strahl, H., Turlan, C., Khalid, S., Bond, P. J., Kebalo, J-M., ... Carpousis, A. J. (2015). Membrane recognition and dynamics of the RNA Degradosome. PLoS Genetics, 11(2), e1004961-[23pp]. DOI: 10.1371/journal.pgen.1004961

Parkin, J., Chavent, M., & Khalid, S. (2015). Molecular simulations of gram-negative bacterial membranes: a vignette of some recent successes. Biophysical Journal, 109(3), 461-468. DOI: 10.1016/j.bpj.2015.06.050

Khalid, S., Berglund, N., Holdbrook, D., Leung, Y., & Parkin, J. (2015). The membranes of Gram-negative bacteria: progress in molecular modelling and simulation. Biochemical Society Transactions, 43(2), 162-167. DOI: 10.1042/BST20140262

Manara, R., Tomasio, S., & Khalid, S. (2015). The nucleotide capture region of alpha hemolysin: insights into nanopore design for DNA sequencing from molecular dynamics simulations. Nanomaterials, 5(1), 144-153. DOI: 10.3390/nano5010144

Parkin, J., & Khalid, S. (2014). Atomistic molecular-dynamics simulations enable prediction of the Arginine Permeation Pathway through OccD1/OprD from pseudomonas aeruginosa. Biophysical Journal, 107(8), 1853-1861. DOI: 10.1016/j.bpj.2014.08.035

Leung, Y. M., Holdbrook, D. A., Piggot, T. J., & Khalid, S. (2014). The NorM MATE transporter from N. gonorrhoeae: insights into drug and ion Binding from atomistic molecular dynamics simulations. Biophysical Journal, 107(2), 460-468. DOI: 10.1016/j.bpj.2014.06.005

Piggot, T. J., Holdbrook, D. A., & Khalid, S. (2013). Conformational dynamics and membrane interactions of the E. coli outer membrane protein FecA: A molecular dynamics simulation study. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1828(2), 284-293. DOI: 10.1016/j.bbamem.2012.08.021

Holdbrook, D. A., Piggot, T. J., Sansom, M. S. P., & Khalid, S. (2013). Stability and membrane interactions of an autotransport protein: MD simulations of the Hia translocator domain in a complex membrane environment. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1828(2), 715-723. DOI: 10.1016/j.bbamem.2012.09.002

Eren, E., Parkin, J., Adelanwa, A., Cheneke, B., Movileanu, L., Khalid, S., & van den Berg, B. (2013). Toward understanding the outer membrane uptake of small molecules by Pseudomonas aeruginosa. The Journal of Biological Chemistry, 288(17), 12042-12053. DOI: 10.1074/jbc.M113.463570

Piggot, T. J., Piñeiro, Á., & Khalid, S. (2012). Molecular dynamics simulations of phosphatidylcholine membranes: a comparative force field study. Journal of Chemical Theory and Computation, 8(11), 4593-4609. DOI: 10.1021/ct3003157

Guy, A. T., Piggot, T. J., & Khalid, S. (2012). Single-stranded DNA within nanopores: conformational dynamics and implications for sequencing; a molecular dynamics simulation study. Biophysical Journal, 103(5), 1028-1036. DOI: 10.1016/j.bpj.2012.08.012

Kurze, A., Michie, K. A., Dixon, S. E., Mishra, A., Itoh, T., Khalid, S., ... Nasmyth, K. (2011). A positively charged channel within the Smc1/Smc3 hinge required for sister chromatid cohesion. The EMBO Journal, 30(2), 364-378. DOI: 10.1038/emboj.2010.315

Piggot, T. J., Holdbrook, D. A., & Khalid, S. (2011). Electroporation of the E. coli and S. Aureus membranes: molecular dynamics simulations of complex bacterial membranes. The Journal of Physical Chemistry B, 115(45), 13381-13388. DOI: 10.1021/jp207013v

Piñeiro, Á., Bond, P. J., & Khalid, S. (2011). Exploring the conformational dynamics and membrane interactions of PorB from C. glutamicum: a multi-scale molecular dynamics simulation study. Biochimica et Biophysica Acta (BBA) - Biomembranes. DOI: 10.1016/j.bbamem.2011.02.015

Marius, P., Leung, Y. M., Piggot, T., Khalid, S., & Williamson, P. T. F. (2011). Probing the oligomeric state and interaction surfaces of Fukutin-I in dilauroylphosphatidylcholine bilayers. European Biophysics Journal. DOI: 10.1007/s00249-011-0773-5

Vohra, S., Hall, B. A., Holdbrook, D. A., Khalid, S., & Biggin, P. C. (2010). Bookshelf: a simple curation system for the storage of biomolecular simulation data. Database, 2010, baq033. DOI: 10.1093/database/baq033

Mishra, A., Hu, B., Kurze, A., Beckouët, F., Farcas, A-M., Dixon, S. E., ... Nasmyth, K. (2010). Both interaction surfaces within cohesin's hinge domain are essential for its stable chromosomal association. Current Biology, 20(4), 279-289. DOI: 10.1016/j.cub.2009.12.059

Corsi, J., Hawtin, R. W., Ces, O., Attard, G. S., & Khalid, S. (2010). DNA lipoplexes: Formation of the inverse hexagonal phase observed by coarse-grained molecular dynamics simulation. Langmuir, 26(14), 12119-12125. DOI: 10.1021/la101448m

Holdbrook, D. A., Leung, Y. M., Piggot, T., Marius, P., Williamson, P. T. F., & Khalid, S. (2010). Stability and membrane orientation of the fukutin transmembrane domain: a combined multiscale molecular dynamics and circular dichroism study. Biochemistry, 49(51), 10796-10802. DOI: 10.1021/bi101743w

Scott, K. A., Bond, P. J., Ivetac, A., Chetwynd, A. P., Khalid, S., & Sansom, M. S. P. (2008). Coarse-grained MD simulations of membrane protein-bilayer self-assembly. Structure, 16(4), 621-630. DOI: 10.1016/j.str.2008.01.014

Johnston, J. M., Khalid, S., & Sansom, M. S. P. (2008). Conformational dynamics of the mitochondrial ADP/ATP carrier: a simulation study. Molecular Membrane Biology, 25(6-7), 506-517. DOI: 10.1080/09687680802459271

Khalid, S., Bond, P. J., Holyoake, J., Hawtin, R. W., & Sansom, M. S. P. (2008). DNA and lipid bilayers: self-assembly and insertion. Journal of the Royal Society, Interface, 5(S3), 241-250. DOI: 10.1098/rsif.2008.0239.focus

Khalid, S., Bond, P. J., Carpenter, T., & Sansom, M. S. P. (2008). OmpA: Gating and dynamics via molecular dynamics simulations. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1778(9), 1871-1880. DOI: 10.1016/j.bbamem.2007.05.024

Chen, M., Khalid, S., Sansom, M. S. P., & Bayley, H. (2008). Outer membrane protein G: engineering a quiet pore for biosensing. Proceedings of the National Academy of Sciences of the United States of America, 105(17), 6272-6277. DOI: 10.1073/pnas.0711561105

Carpenter, T., Bond, P. J., Khalid, S., Sansom, M. S. P., & Voth, G. A. (Ed.) (2008). Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel. Biophysical Journal, 95(8), 3790-3801. DOI: 10.1529/biophysj.108.131078

Khalid, S., & Sansom, M. S. P. (2007). A comparative molecular dynamics simulation study of the TonB-Dependent transporters: FpvA, FhuA, FecA, FepA and BtuB. Biophysical Journal, (2007 Abstracts), p.554A.

Carpenter, T., Khalid, S., & Sansom, M. S. P. (2007). A multidomain outer membrane protein from Pasteurella multocida: Modelling and simulation studies of PmOmpA. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1768(11), 2831-2840. DOI: 10.1016/j.bbamem.2007.07.025

Bond, P. J., Holyoake, J., Ivetac, A., Khalid, S., & Sansom, M. S. P. (2007). Coarse-grained molecular dynamics simulations of membrane proteins and peptides. Journal of Structural Biology, 157(3), 593-605. DOI: 10.1016/j.jsb.2006.10.004

Peberdy, J. C., Malina, J., Khalid, S., Hannon, M. J., & Rodger, A. (2007). Influence of surface shape on DNA binding of bimetallo helicates. Journal of Inorganic Biochemistry, 101(11-12), 1937-1945. DOI: 10.1016/j.jinorgbio.2007.07.005

Haider, S., Khalid, S., Tucker, S. J., Ashcroft, F. M., & Sansom, M. S. P. (2007). Molecular dynamics simulations of inwardly rectifying (Kir) potassium channels: A comparative study. Biochemistry, 46(12), 3643-3652.

Khalid, S., Hannon, M. J., Rodger, A., & Rodger, P. M. (2007). Shape effects on the activity of synthetic major-groove binding ligands. Journal of Molecular Graphics and Modelling, 25(6), 794-800. DOI: 10.1016/j.jmgm.2006.07.004

Khalid, S., Bond, P. J., Deol, S. S., & Sansom, M. S. P. (2006). Modeling and simulations of a bacterial outer membrane protein: OprF from Pseudomonas aeruginosa. Proteins: Structure, Function, and Bioinformatics, 63(1), 6-15. DOI: 10.1002/prot.20845

Khalid, S., & Samsom, M. S. P. (2006). Molecular dynamics simulations of a bacterial autotransporter: NalP from Neisseria meningitidis. Molecular Membrane Biology, 23(6), 499-508. DOI: 10.1080/09687860600849531

Khalid, S., Hannon, M. J., Rodger, A., & Rodger, P. M. (2006). Simulations of DNA coiling around a synthetic supramolecular cylinder that binds the DNA major groove. Chemistry - A European Journal, 12(13), 3493-3506. DOI: 10.1002/chem.200501168

Khalid, S., Rodger, P. M., & Rodger, A. (2005). Theoretical aspects of the enantiomeric resolution of dimetallo helicates with different surface topologies on cellulose columns. Journal of Liquid Chromatography & Related Technologies, 28(19), 2995-3003. DOI: 10.1080/10826070500294966

Khalid, S., & Rodger, P. M. (2004). Molecular dynamics simulations of DNA and its complexes. Progress in Reaction Kinetics and Mechanism, 29(3), 167-186. DOI: 10.3184/007967404777726232

Book Chapter

Sansom, M., Bond, P. J., Khalid, S., & Balali-Mood, K. (2006). Molecular simulations of membrane proteins: Protein/membrane interactions. In Abstracts of Papers. American Chemical Society.

Professor Syma Khalid
Chemistry University of Southampton Highfield Southampton SO17 1BJ

Room Number:27/3037

Telephone:(023) 8059 4176
Email:S.Khalid@soton.ac.uk

Professor Syma Khalid's personal home page

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