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ResearcherID: B-8108-2009

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Employment (2)

University of Oxford: Oxford, Oxfordshire, GB

2021-08-01 to present | Professor of Computational Microbiology (Department of Biochemistry)
Employment
Source: Self-asserted source
Syma Khalid

University of Southampton: Southampton, Southampton, GB

2016-10-01 to 2021-07-30 | Full Professor (Chemistry)
Employment
Source: Self-asserted source
Syma Khalid

Funding (2)

MOLSImage: Combining Simulations and Imaging to Deliver Next Generation Tools for Studying Bacterial Cell Envelopes.

2021-06-30 to 2026-06-29 | Grant
Engineering and Physical Sciences Research Council (Swindon, GB)
URL: https://app.dimensions.ai/details/grant/grant.9972222
GRANT_NUMBER: EP/V030779/1
Source: Self-asserted source
Syma Khalid via DimensionsWizard

The UK High-End Computing Consortium for Biomolecular Simulation

2019-02-01 to 2023-01-31 | Grant
Engineering and Physical Sciences Research Council (Swindon, GB)
URL: https://app.dimensions.ai/details/grant/grant.7611660
GRANT_NUMBER: EP/R029407/1
Source: Self-asserted source
Syma Khalid via DimensionsWizard

Works (50 of 64)

Items per page:
Page 1 of 2

Atomistic and Coarse-Grained Simulations of Membrane Proteins: A Practical Guide.

Methods (San Diego, Calif.)
2020-02-18 | Journal article
DOI: 10.1016/j.ymeth.2020.02.007
PMID: 32084518
Source: Self-asserted source
Syma Khalid

Molecular Simulations of Gram-Negative Bacterial Membranes Come of Age.

Annual review of physical chemistry
2020-02-18 | Journal article
DOI: 10.1146/annurev-physchem-103019-033434
PMID: 32070216
Source: Self-asserted source
Syma Khalid

Simulation of subcellular structures.

Current opinion in structural biology
2020-01-29 | Journal article
DOI: 10.1016/j.sbi.2019.12.017
PMID: 32006813
Source: Self-asserted source
Syma Khalid

To infect or not to infect: molecular determinants of bacterial outer membrane vesicle internalization by host membranes.

Journal of molecular biology
2020-01-11 | Journal article
DOI: 10.1016/j.jmb.2020.01.008
PMID: 31931013
Source: Self-asserted source
Syma Khalid

A Thermodynamic Funnel Drives Bacterial Lipopolysaccharide Transfer in the TLR4 Pathway.

Structure (London, England : 1993)
2018 | Journal article
DOI: 10.1016/j.str.2018.04.007
WOSUID:

MEDLINE:29779787
Contributors: Huber, Roland G; Berglund, Nils A; Kargas, Vasileios; Marzinek, Jan K; Holdbrook, Daniel A; Khalid, Syma; Piggot, Thomas J; Schmidtchen, Artur; Bond, Peter J
Source: Self-asserted source
Syma Khalid via ResearcherID

Brauns Lipoprotein Facilitates OmpA Interaction with the Escherichia coli Cell Wall

Biophysical Journal
2018 | Journal article
WOSUID:

WOS:000430450000140
Contributors: Samsudin, Firdaus; Boags, Alister; Piggot, Thomas J.; Khalid, Syma
Source: Self-asserted source
Syma Khalid via ResearcherID

Communication between the leaflets of asymmetric membranes revealed from coarse-grain molecular dynamics simulations

Scientific Reports
2018 | Journal article
DOI: 10.1038/s41598-018-20227-1
WOSUID:

WOS:000423430400017
Contributors: Shearer, Jonathan; Khalid, Syma
Source: Self-asserted source
Syma Khalid via ResearcherID

Directional Porin Binding of Intrinsically Disordered Protein Sequences Promotes Colicin Epitope Display in the Bacterial Periplasm

Biochemistry
2018 | Journal article
DOI: 10.1021/acs.biochem.8b00621
WOSUID:

WOS:000440103500015
Contributors: Housden, Nicholas G.; Rassam, Patrice; Lee, Sejeong; Samsudin, Firdaus; Kaminska, Renata; Sharp, Connor; Goult, Jonathan D.; Francis, Marie-Louise; Khalid, Syma; Bayley, Hagan et al.
Source: Self-asserted source
Syma Khalid via ResearcherID

Electric-Field-Driven Translocation of ssDNA through Hydrophobic Nanopores.

ACS nano
2018 | Journal article
DOI: 10.1021/acsnano.8b03365
WOSUID:

MEDLINE:29985578
Contributors: Haynes, Taylor; Smith, Iain P S; Wallace, E Jayne; Trick, Jemma L; Sansom, Mark S P; Khalid, Syma
Source: Self-asserted source
Syma Khalid via ResearcherID

The Cell Envelope of Gram-Negative Bacteria: The More we Know; The More we Don't Know!

Biophysical Journal
2018 | Journal article
WOSUID:

WOS:000429315800043
Contributors: Khalid, Syma
Source: Self-asserted source
Syma Khalid via ResearcherID

The role of the jaw subdomain of peptidoglycan glycosyltransferases for lipid II polymerization.

Cell surface (Amsterdam)
2018 | Journal article
DOI: 10.1016/j.tcsw.2018.06.002
WOSUID:

MEDLINE:30046666
Contributors: Punekar, Avinash S; Samsudin, Firdaus; Lloyd, Adrian J; Dowson, Christopher G; Scott, David J; Khalid, Syma; Roper, David I
Source: Self-asserted source
Syma Khalid via ResearcherID

PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories

Journal of Chemical Information and Modeling
2017 | Journal article
DOI: 10.1021/acs.jcim.7b00096
WOSUID:

WOS:000400204900005
Contributors: Graham, James A.; Essex, Jonathan W.; Khalid, Syma
Source: Self-asserted source
Syma Khalid via ResearcherID

Through the Lipopolysaccharide Glass: A Potent Antimicrobial Peptide Induces Phase Changes in Membranes

Biochemistry
2017 | Journal article
DOI: 10.1021/acs.biochem.6b01063
WOSUID:

WOS:000397478500010
Contributors: Jefferies, Damien; Hsu, Pin-Chia; Khalid, Syma
Source: Self-asserted source
Syma Khalid via ResearcherID

Dynamics of Crowded Vesicles: Local and Global Responses to Membrane Composition

Plos One
2016 | Journal article
DOI: 10.1371/journal.pone.0156963
WOSUID:

WOS:000378029800023
Contributors: Holdbrook, Daniel A.; Huber, Roland G.; Piggot, Thomas J.; Bond, Peter J.; Khalid, Syma
Source: Self-asserted source
Syma Khalid via ResearcherID

Encapsulated membrane proteins: A simplified system for molecular simulation

Biochimica Et Biophysica Acta-Biomembranes
2016 | Journal article
DOI: 10.1016/j.bbamem.2016.02.039
WOSUID:

WOS:000382340100024
Contributors: Lee, Sarah C.; Khalid, Syma; Pollock, Naomi L.; Knowles, Tim J.; Edler, Karen; Rothnie, Alice J.; Thomas, Owen R. T.; Dafforn, Timothy R.
Source: Self-asserted source
Syma Khalid via ResearcherID

Full-Length OmpA: Structure, Function, and Membrane Interactions Predicted by Molecular Dynamics Simulations

Biophysical Journal
2016 | Journal article
DOI: 10.1016/j.bpj.2016.09.009
WOSUID:

WOS:000386315900014
Contributors: Ortiz-Suarez, Maite L.; Samsudin, Firdaus; Piggot, Thomas J.; Bond, Peter J.; Khalid, Syma
Source: Self-asserted source
Syma Khalid via ResearcherID

Molecular Dynamics Simulations Predict the Pathways via Which Pristine Fullerenes Penetrate Bacterial Membranes

Journal of Physical Chemistry B
2016 | Journal article
DOI: 10.1021/acs.jpcb.6b06615
WOSUID:

WOS:000387198500010
Contributors: Hsu, Pin-Chia; Jefferies, Damien; Khalid, Syma
Source: Self-asserted source
Syma Khalid via ResearcherID

Molecular Dynamics Simulations Reveal the Conformational Flexibility of Lipid II and Its Loose Association with the Defensin Plectasin in the Staphylococcus aureus Membrane

Biochemistry
2016 | Journal article
DOI: 10.1021/acs.biochem.5b01315
WOSUID:

WOS:000378016500014
Contributors: Witzke, Sarah; Petersen, Michael; Carpenter, Timothy S.; Khalid, Syma
Source: Self-asserted source
Syma Khalid via ResearcherID

OmpA: A Flexible Clamp for Bacterial Cell Wall Attachment

Structure
2016 | Journal article
DOI: 10.1016/j.str.2016.10.009
WOSUID:

WOS:000393211300022
Contributors: Samsudin, Firdaus; Ortiz-Suarez, Maite L.; Piggot, Thomas J.; Bond, Peter J.; Khalid, Syma
Source: Self-asserted source
Syma Khalid via ResearcherID

Structural basis for Mep2 ammonium transceptor activation by phosphorylation

Nature Communications
2016 | Journal article
DOI: 10.1038/ncomms11337
WOSUID:

WOS:000374293500001
Contributors: van den Berg, Bert; Chembath, Anupama; Jefferies, Damien; Basle, Arnaud; Khalid, Syma; Rutherford, Julian C.
Source: Self-asserted source
Syma Khalid via ResearcherID

The Free Energy of Small Solute Permeation through the Escherichia coli Outer Membrane Has a Distinctly Asymmetric Profile

Journal of Physical Chemistry Letters
2016 | Journal article
DOI: 10.1021/acs.jpclett.6b01399
WOSUID:

WOS:000382603300026
Contributors: Carpenter, Timothy S.; Parkin, Jamie; Khalid, Syma
Source: Self-asserted source
Syma Khalid via ResearcherID

An Accurate In Vitro Model of the E. coli Envelope

Angewandte Chemie-International Edition
2015 | Journal article
DOI: 10.1002/anie.201504287
WOSUID:

WOS:000363396000008
Contributors: Clifton, Luke A.; Holt, Stephen A.; Hughes, Arwel V.; Daulton, Emma L.; Arunmanee, Wanatchaporn; Heinrich, Frank; Khalid, Syma; Jefferies, Damien; Charlton, Timothy R.; Webster, John R. P. et al.
Source: Self-asserted source
Syma Khalid via ResearcherID

DNA sequencing with MspA: Molecular Dynamics simulations reveal free-energy differences between sequencing and non-sequencing mutants

Scientific Reports
2015 | Journal article
DOI: 10.1038/srep12783
WOSUID:

WOS:000359195100001
Contributors: Manara, Richard M. A.; Wallace, E. Jayne; Khalid, Syma
Source: Self-asserted source
Syma Khalid via ResearcherID

Free-Energy Calculations Reveal the Subtle Differences in the Interactions of DNA Bases with alpha-Hemolysin

Journal of Chemical Theory and Computation
2015 | Journal article
DOI: 10.1021/ct501081h
WOSUID:

WOS:000349934400040
Contributors: Manara, Richard M. A.; Guy, Andrew T.; Wallace, E. Jayne; Khalid, Syma
Source: Self-asserted source
Syma Khalid via ResearcherID

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
2015 | Journal article
DOI: 10.1016/j.bbamem.2015.04.015
WOSUID:

MEDLINE:25944559
Contributors: Ashworth Briggs, Esther L; Gomes, Rafael G B; Elhussein, Malaz; Collier, William; Stuart Findlow, I; Khalid, Syma; McCormick, Chris J; Williamson, Philip T F
Source: Self-asserted source
Syma Khalid via ResearcherID

Interaction of the Antimicrobial Peptide Polymyxin B1 with Both Membranes of E. coli: A Molecular Dynamics Study

Plos Computational Biology
2015 | Journal article
DOI: 10.1371/journal.pcbi.1004180
WOSUID:

WOS:000354517600032
Contributors: Berglund, Nils A.; Piggot, Thomas J.; Jefferies, Damien; Sessions, Richard B.; Bond, Peter J.; Khalid, Syma
Source: Self-asserted source
Syma Khalid via ResearcherID

Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory

Journal of Membrane Biology
2015 | Journal article
DOI: 10.1007/s00232-015-9802-0
WOSUID:

WOS:000358417900001
Contributors: Cournia, Zoe; Allen, Toby W.; Andricioaei, Ioan; Antonny, Bruno; Baum, Daniel; Brannigan, Grace; Buchete, Nicolae-Viorel; Deckman, Jason T.; Delemotte, Lucie; del Val, Coral et al.
Source: Self-asserted source
Syma Khalid via ResearcherID

Molecular Simulations of Gram-Negative Bacterial Membranes: A Vignette of Some Recent Successes

Biophysical Journal
2015 | Journal article
DOI: 10.1016/j.bpj.2015.06.050
WOSUID:

WOS:000359180400003
Contributors: Parkin, Jamie; Chavent, Matthieu; Khalid, Syma
Source: Self-asserted source
Syma Khalid via ResearcherID

The membranes of Gram-negative bacteria: progress in molecular modelling and simulation

Biochemical Society Transactions
2015 | Journal article
DOI: 10.1042/BST20140262
WOSUID:

WOS:000352293500006
Contributors: Khalid, Syma; Berglund, Nils A.; Holdbrook, Daniel A.; Leung, Yuk M.; Parkin, Jamie
Source: Self-asserted source
Syma Khalid via ResearcherID

Atomistic Molecular-Dynamics Simulations Enable Prediction of the Arginine Permeation Pathway through OccD1/OprD from Pseudomonas aeruginosa

Biophysical Journal
2014 | Journal article
DOI: 10.1016/j.bpj.2014.08.035
WOSUID:

WOS:000343682700011
Contributors: Parkin, Jamie; Khalid, Syma
Source: Self-asserted source
Syma Khalid via ResearcherID

The NorM MATE Transporter from N-gonorrhoeae: Insights into Drug and Ion Binding from Atomistic Molecular Dynamics Simulations

Biophysical Journal
2014 | Journal article
DOI: 10.1016/j.bpj.2014.06.005
WOSUID:

WOS:000339148500021
Contributors: Leung, Yuk Ming; Holdbrook, Daniel A.; Piggot, Thomas J.; Khalid, Syma
Source: Self-asserted source
Syma Khalid via ResearcherID

Conformational dynamics and membrane interactions of the E. coli outer membrane protein FecA: A molecular dynamics simulation study

Biochimica Et Biophysica Acta-Biomembranes
2013 | Journal article
DOI: 10.1016/j.bbamem.2012.08.021
WOSUID:

WOS:000315004600013
Contributors: Piggot, Thomas J.; Holdbrook, Daniel A.; Khalid, Syma
Source: Self-asserted source
Syma Khalid via ResearcherID

Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study

Journal of Chemical Theory and Computation
2012 | Journal article
DOI: 10.1021/ct3003157
WOSUID:

WOS:000311191900060
Contributors: Piggot, Thomas J.; Pineiro, Angel; Khalid, Syma
Source: Self-asserted source
Syma Khalid via ResearcherID

Probing the oligomeric state and interaction surfaces of Fukutin-I in dilauroylphosphatidylcholine bilayers

European Biophysics Journal With Biophysics Letters
2012 | Journal article
DOI: 10.1007/s00249-011-0773-5
WOSUID:

WOS:000299751600007
Contributors: Marius, P.; Leung, Yuk Ming; Piggot, T. J.; Khalid, S.; Williamson, P. T. F.
Source: Self-asserted source
Syma Khalid via ResearcherID

Single-Stranded DNA within Nanopores: Conformational Dynamics and Implications for Sequencing; a Molecular Dynamics Simulation Study

Biophysical Journal
2012 | Journal article
DOI: 10.1016/j.bpj.2012.08.012
WOSUID:

WOS:000308510200020
Contributors: Guy, Andrew T.; Piggot, Thomas J.; Khalid, Syma
Source: Self-asserted source
Syma Khalid via ResearcherID

A positively charged channel within the Smc1/Smc3 hinge required for sister chromatid cohesion

Embo Journal
2011 | Journal article
DOI: 10.1038/emboj.2010.315
WOSUID:

WOS:000287179100013
Contributors: Kurze, A; Michie, KA; Dixon, SE; Mishra, A; Itoh, T; Khalid, S; Strmecki, L; Shirahige, K; Haering, CH; Lowe, J et al.
Source: Self-asserted source
Syma Khalid via ResearcherID

Electroporation of the E. coli and S. Aureus Membranes: Molecular Dynamics Simulations of Complex Bacterial Membranes

Journal of Physical Chemistry B
2011 | Journal article
DOI: 10.1021/jp207013v
WOSUID:

WOS:000296686000031
Contributors: Piggot, Thomas J.; Holdbrook, Daniel A.; Khalid, Syma
Source: Self-asserted source
Syma Khalid via ResearcherID

Exploring the conformational dynamics and membrane interactions of PorB from C. glutamicum: A multi-scale molecular dynamics simulation study

Biochimica Et Biophysica Acta-Biomembranes
2011 | Journal article
DOI: 10.1016/j.bbamem.2011.02.015
WOSUID:

WOS:000290705700037
Contributors: Pineiro, Angel; Bond, Peter J.; Khalid, Syma
Source: Self-asserted source
Syma Khalid via ResearcherID

Molecular Dynamics Simulations of DNA within a Nanopore: Arginine-Phosphate Tethering and a Binding/Sliding Mechanism for Translocation

Biochemistry
2011 | Journal article
DOI: 10.1021/bi101404n
WOSUID:

WOS:000290056000019
Contributors: Bond, PJ; Guy, AT; Heron, AJ; Bayley, H; Khalid, S
Source: Self-asserted source
Syma Khalid via ResearcherID

Antimicrobial and Cell-Penetrating Peptides: Structure, Assembly and Mechanisms of Membrane Lysis via Atomistic and Coarse-Grained Molecular Dynamic Simulations

Protein and Peptide Letters
2010 | Journal article
WOSUID:

WOS:000284651900002
Contributors: Bond, PJ; Khalid, S
Source: Self-asserted source
Syma Khalid via ResearcherID

Bookshelf: a simple curation system for the storage of biomolecular simulation data

Database-the Journal of Biological Databases and Curation
2010 | Journal article
DOI: 10.1093/database/baq033
WOSUID:

WOS:000208191400033
Contributors: Vohra, Shabana; Hall, Benjamin A.; Holdbrook, Daniel A.; Khalid, Syma; Biggin, Philip C.
Source: Self-asserted source
Syma Khalid via ResearcherID

Both Interaction Surfaces within Cohesin's Hinge Domain Are Essential for Its Stable Chromosomal Association

CURRENT BIOLOGY
2010 | Journal article
DOI: 10.1016/j.cub.2009.12.059
WOSUID:

WOS:000275149200027
Contributors: MISHRA, A; HU, B; KURZE, A; BECKOUET, F; FARCAS, AM; DIXON, SE; KATOU, Y; KHALID, S; SHIRAHIGE, K; NASMYTH, K
Source: Self-asserted source
Syma Khalid via ResearcherID

DNA Lipoplexes: Formation of the Inverse Hexagonal Phase Observed by Coarse-Grained Molecular Dynamics Simulation

Langmuir
2010 | Journal article
DOI: 10.1021/la101448m
WOSUID:

WOS:000279756700074
Contributors: CORSI, J; HAWTIN, RW; CES, O; ATTARD, GS; KHALID, S
Source: Self-asserted source
Syma Khalid via ResearcherID

On the Ability of PAMAM Dendrimers and Dendrimer/DNA Aggregates To Penetrate POPC Model Biomembranes

Journal of Physical Chemistry B
2010 | Journal article
DOI: 10.1021/jp9119809
WOSUID:

WOS:000278004300012
Contributors: AINALEM, ML; CAMPBELL, RA; KHALID, S; GILLAMS, RJ; RENNIE, AR; NYLANDER, T
Source: Self-asserted source
Syma Khalid via ResearcherID

Stability and Membrane Orientation of the Fukutin Transmembrane Domain: A Combined Multiscale Molecular Dynamics and Circular Dichroism Study

Biochemistry
2010 | Journal article
DOI: 10.1021/bi101743w
WOSUID:

WOS:000285429200006
Contributors: Holdbrook, DA; Leung, YM; Piggot, TJ; Marius, P; Williamson, PTF; Khalid, S
Source: Self-asserted source
Syma Khalid via ResearcherID

Coarse-grained MD simulations of membrane protein-bilayer self-assembly

STRUCTURE
2008 | Journal article
DOI: 10.1016/j.str.2008.01.014
WOSUID:

WOS:000254932300013
Contributors: SCOTT, KA; BOND, PJ; IVETAC, A; et al.
Source: Self-asserted source
Syma Khalid via ResearcherID

Conformational dynamics of the mitochondrial ADP/ATP carrier: a simulation study

MOLECULAR MEMBRANE BIOLOGY
2008 | Journal article
DOI: 10.1080/09687680802459271
WOSUID:

WOS:000261191600005
Contributors: JOHNSTON, JM; KHALID, S; SANSOM, MSP
Source: Self-asserted source
Syma Khalid via ResearcherID

DNA and lipid bilayers: self-assembly and insertion

JOURNAL OF THE ROYAL SOCIETY INTERFACE
2008 | Journal article
DOI: 10.1098/rsif.2008.0239.focus
WOSUID:

WOS:000261642600009
Contributors: KHALID, S; BOND, PJ; HOLYOAKE, J; et al.
Source: Self-asserted source
Syma Khalid via ResearcherID

OmpA: Gating and dynamics via molecular dynamics simulations

BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
2008 | Journal article
DOI: 10.1016/j.bbamem.2007.05.024
WOSUID:

WOS:000259877200013
Contributors: KHALID, S; BOND, PJ; CARPENTER, T; et al.
Source: Self-asserted source
Syma Khalid via ResearcherID

Outer membrane protein G: Engineering a quiet pore for biosensing

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2008 | Journal article
DOI: 10.1073/pnas.0711561105
WOSUID:

WOS:000255534100013
Contributors: CHEN, M; KHALID, S; SANSOM, MSP; et al.
Source: Self-asserted source
Syma Khalid via ResearcherID
Items per page:
Page 1 of 2

Peer review (31 reviews for 12 publications/grants)

Review activity for Accounts of chemical research. (2)
Review activity for ACS central science. (1)
Review activity for ACS infectious diseases. (1)
Review activity for ACS nano. (2)
Review activity for ACS sensors. (1)
Review activity for Biochemistry. (1)
Review activity for Chemical reviews. (2)
Review activity for Journal of chemical information and modeling. (6)
Review activity for Journal of chemical theory and computation : (5)
Review activity for Langmuir : (2)
Review activity for The journal of physical chemistry letters. (2)
Review activity for The journal of physical chemistry. (6)
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