Professor Syma Khalid MChem PhD

Professor of Computational Biophysics, Head of Physical Chemistry Teaching

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

Uncovering the Secrets of Bacterial Cell Envelopes

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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. Starting her own group, she noticed the molecular models of bacterial membranes were usually missing key biochemical details (e.g. lipid type, macromolecular crowding) and has worked to address this ever since.

MChem, Warwick Univeristy, 2000

PhD, Warwick University, 2004

Theory and Modelling in Chemical Sciences CDT

Research

Responsibilities

Publications

Funding

Contact

Research interests

Syma’s research interests are centred around the dynamics of biomolecules in and around biological membranes, with a specific focus on bacterial systems. 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), Colin Kleanthous (Oxford) and Carol Robinson (Oxford).

A key current area of work for Syma is to develop molecular models and simulations methods & protocols such that they enable a ‘computational microbiology’ approach to studying bacterial cell envelopes.

Syma's international reputation is reflected in the invitations she receives to speak at national and international meetings each year. Syma has authored over 70 peer-reviewed papers and 6 book chapters. She is chair of HECBiosim. She serves on the management group that leads CCPBiosim and on the management committee of the British Biophysical Society and is on the advisory board of the Rosalind Franklin Institute for the Informatics and Artificial Intelligence Theme.

Research group

Computational Systems Chemistry

Affiliate research group

Institute for Complex Systems Simulation

Research project(s)

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

Khalid: Transport mechanisms in bacteria: Autotransporters

Head of Physical Chemistry Teaching

Chair of HECBioSim

Management Committee member of CCPBioSim

Management Committee member of British Biophysical Society

EPSRC e-Infrastructure SAT member

Rosalind Franklin Institute Advisory Board for Informatics and Artificial Intelligence Theme

ExCALIBUR steering committee

PhD Supervision

Syma has supervised 12 PhD students and 3 MPhil students to completion since 2007. She currently supervises 6 PhD students,

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Key Publications

Hsu, P-C., Samsudin, F., Shearer, J., & Khalid, S. (2017). It is complicated: curvature, diffusion and lipid sorting within the two membranes of Escherichia coli. The Journal of Physical Chemistry Letters, 8(2), 5513-5518. https://doi.org/10.1021/acs.jpclett.7b02432
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. https://doi.org/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, 1-11. [11337]. https://doi.org/10.1038/ncomms11337
Clifton, L. A., Holt, S. A., Hughes, A. V., Daulton, E. L., Arunmanee, W., Heinrich, F., Khalid, S., Jefferies, D., Charlton, T. R., Webster, J. R. P., Kinane, C. J., & Lakey, J. H. (2015). An accurate in vitro model of the E. coli envelope. Angewandte Chemie International Edition, 54(41), 11952-11955. https://doi.org/10.1002/anie.201504287

Articles

Book Chapters

Glass, W. G., Essex, J. W., Fraternali, F., Marzuoli, I., Samways, M. L., Biggin, P. C., & Khalid, S. (2021). Coarse-grained molecular dynamics simulations of membrane proteins: a practical guide. In I. Schmidt-Krey , & J. C. Gumbart (Eds.), Structure and Function of Membrane Proteins (pp. 253-273). (Methods in Molecular Biology; Vol. 2302). Humana. https://doi.org/10.1007/978-1-0716-1394-8_14
Huber, R. G., Carpenter, T. S., Dube, N., Holdbrook, D. A., Ingólfsson, H. I., Irvine, W. A., Marzinek, J. K., Samsudin, F., Allison, J. R., Khalid, S., & Bond, P. J. (2019). Multiscale Modeling and Simulation Approaches to Lipid–Protein Interactions. In J. Kleinschmidt (Ed.), Methods in Molecular Biology (pp. 1-30). (Methods in Molecular Biology; Vol. 2003). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-9512-7_1
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.

Reviews

Im, W., & Khalid, S. (2020). Molecular simulations of gram-negative bacterial membranes come of age. Annual Review of Physical Chemistry, 71, 171-188. https://doi.org/10.1146/annurev-physchem-103019-033434
Friedman, R., Khalid, S., Aponte-Santamaría, C., Arutyunova, E., Becker, M., Boyd, K. J., Christensen, M., Coimbra, J. T. S., Concilio, S., Daday, C., van Eerden, F. J., Fernandes, P. A., Gräter, F., Hakobyan, D., Heuer, A., Karathanou, K., Keller, F., Lemieux, M. J., Marrink, S. J., ... Domene, C. (2018). Understanding conformational dynamics of complex lipid mixtures relevant to biology. Journal of Membrane Biology, 251(5-6), 609-631. https://doi.org/10.1007/s00232-018-0050-y

Research Funding as lead PI

My EPSRC Established Career fellowship has achieved scores of 6, 6, 6, (maximum) from reviewers – currently awaiting interview date.
My ERC advanced grant has gone through to the second round, i.e. part B2 has been sent to reviewers. Outcome in April 2021.
BBSRC grant (joint application with Bert van den Berg) is under review at the moment.
EPRSC grant: HECBiosim EP/R029407/1, (£321k), active.
PhD studentship studentship with Oxford Nanopore Technologies, (£80k) active
Leverhulme project grant: (£125k), active.
PhD studentship: Vice Chancellor's award, Southampton & A*STAR, Singapore, (£80k), active.
PhD studentship: Institute of life sciences, Southampton & A*STAR, Singapore, (£80k)
BBSRC Responsive mode grant: BB/M029573/1, (£322k)
BBSRC Industrial CASE award with Oxford Nanopore Technologies, (£40k)
PhD studentship: Vice Chancellor's award, Southampton & A*STAR, Singapore, (£60k)
BBSRC Responsive mode grant: BBH0006581, (£295k)
PhD studentship: University of Southampton, Institute of Life Sciences, (£60k)
PhD studentship: Oxford Nanopore technologies, (£80k)
Industrially funded PDRA: Oxford Nanopore Technologies, £100k)
University of Southampton, Institute of Life Sciences: (£20k)

Research Funding as co-PI

EPSRC grant: JADE 2 EP/T022205/1, (£5.5m), as Co-PI, PI is Wesley Armour (Oxford), active.
EU-funded Marie Curie ITN grant, (€3.82m), as Co-PI, PI is Alison Rodger (Warwick)
MRC-funded Project on AMR (theme 1), (£5m), as Co-PI, PI is Christopher Dowson (Warwick)

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

Room Number: 27/2007

Professor Syma Khalid's personal home page

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