Publications

2024

  • Somboon K, Melling O, Lejeune M, Pinheiro GMS, Paquelin A, Bardiaux B, Nilges M, Delepelaire P, Khalid S, Izadi-Pruneyre N, (2024), Dynamic interplay between a TonB-dependent heme transporter and a TonB protein in a membrane environment, MBio. DOI: 10.1128/mbio.01781-24
  • Weerakoon D, Marzinek JK, Pedebos C, Bond PJ, Khalid S, (2024), Polymyxin B1 in the E. coli inner membrane: a complex story of protein and lipopolysaccharide mediated insertion. J Biol. Chem. DOI: 10.1016/j.jbc.2024.107754
  • Brandner AF, Prakaash D, Blanco González A, Waterhouse F, Khalid S, (2024), Faster but Not Sweeter: A Model of the Escherichia coli Re-level Lipopolysaccharide for Martini 3 and a Martini 2 version with Accelerated Kinetics, JCTC,  DOI: 10.1021/acs.jctc.4c00374
  • Smith IPS, Pedebos C, Khalid S. (2024), "Molecular Crowding Alters the Interactions of Polymyxin Lipopeptides within the Periplasm of E. coli: Insights from Molecular Dynamics", J Phys Chem B, DOI:10.1021/acs.jpcb.3c07985
  • Clark R, Newman KE, Khalid S (2024), "Titratable residues that drive RND efflux: Insights from molecular simulations", QRB Discovery, DOI: https://doi.org/10.1017/qrd.2024.6

2023

  • Dieudonné T, Kümmerer F, Laursen MJ, Stock C, Flygaard RK, Khalid S, Lenoir G, Lyons JA, Lindorff-Larsen K, Nissen P. (2023), "Activation and substrate specificity of the human P4-ATPase ATP8B1", Nature Comms, DOI:10.1038/s41467-023-42828-9
  • Silale A, Zhu Y, Witwinowski J, Smith RE, Newman KE, Bhamidimarri SP, Baslé A, Khalid S, Beloin C, Gribaldo S, van den Berg B. (2023), "Dual function of OmpM as outer membrane tether and nutrient uptake channel in diderm Firmicutes", Nature Comms, DOI: 10.1038/s41467-023-42601-y
  • Khalid S, Brandner AF, Juraschko N, Newman KE, Pedebos C, Prakaash D, Smith IPS, Waller C, Weerakoon D. (2023), "Computational microbiology of bacteria: Advancements in molecular dynamics simulations", Structure, DOI: 10.1016/j.str.2023.09.012
  • Tang H, Li H, Prakaash D, Pedebos C, Qiu X, Sauer DB, Khalid S, Duerr K, Robinson CV. (2023) "The solute carrier SPNS2 recruits (PI(4,5)P2 to synergistically regulate transport of sphingosine-1-phosphate", Mol. Cell, DOI: 10.1016/j.molcel.2023.06.033
  • Waller C, Marzinek JK, McBurnie E, Bond PJ, Williamson PTF, Khalid S (2023), "Impact on S. aureus and E. coli Membranes of Treatment with Chlorhexidine and Alcohol Solutions: Insights from Molecular Simulations and Nuclear Magnetic Resonance", J Mol Biol. DOI: 10.1016/j.jmb.2023.167953
  • Grinter R, Kropp A, Venugopal H, Senger M, Badley J, Cabotaje PR, Jia R, Duan Z, Huang P, Stripp ST, Barlow CK, Belousoff M, Shafaat HS, Cook GM, Schittenhelm RB, Vincent KA, Khalid S, Berggren G, Greening C (2023), "Structural basis for bacterial energy extraction from atmospheric hydrogen." Nature, DOI: 10.1038/s41586-023-05781-7
  • Newman KE, Khalid S, (2023) "Conformational dynamics and putative substrate extrusion pathways of the N-glycosylated outer membrane factor CmeC from Campylobacter jejuni" PLoS Comput. Biol. DOI: 10.1371/journal.pcbi.1010841
  • Newman KE, Tindall SN, Mader SL, Khalid S, Thomas GH, Van Der Woude MW, (2023)"A novel fold for acyltransferase-3 (AT3) proteins provides a framework for transmembrane acyl-group transfer", Elife, DOI: 10.7554/eLife.81547
  • Prakaash D and Khalid S (2023), "All-Atom Mesoscale Simulations Predict the Conformational Dynamics of Influenza Virus Surface Glycoproteins.", ACS Central Science (This is a commentary piece). DOI: 10.1021/acscentsci.3c00020

2022

  • Böhning J, Ghrayeb M, Pedebos C, Abbas DK, Khalid S, Chai L, Bharat TAM (2022), "Donor-strand exchange drives assembly of the TasA scaffold in Bacillus subtilis biofilms", Nature Comms, DOI: 10.1038/s41467-022-34700-z
  • Webby MN, Oluwole AO, Pedebos C, Inns PG, Olerinyova A, Prakaash D, Housden NG, Benn G, Sun D, Hoogenboom BW, Kukura P, Mohammed S, Robinson CV, Khalid S, Kleanthous C (2022) "Lipids mediate supramolecular outer membrane protein assembly in bacteria", Science Advances, DOI: 10.1126/sciadv.adc9566
  • van den Berg B, Silale A, Basle A, Bradner A F, Mader S, Khalid, S, (2022), "Structural basis for host recognition and superinfection exclusion by bacteriophage T5", Proc. Natl. Acad. Sci. USA, https://doi.org/10.1073/pnas.2211672119
  • Dommer A, et al, (2022) "#CovidisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV2 in a respiratory aerosol", The International Journal of High Performance Computing Applications, https://doi.org/10.1177/10943420221128233
  • Zuzic L, Samsudin F, Shivgan AT, Raghuvamsi PV, Marzinek JK, Boags A, Pedebos C, Tulsian NK, Warwicker J, MacAry P, Crispin M, Khalid S, Anand GS, Bond PJ. (2022) "Uncovering cryptic pockets in the SARS-CoV-2 glycoprotein", Structure, 10.1016/j.str.2022.05.006
  • Khalid S, Schroeder C, Bond PJ, Duncan AL. (2022) “What have molecular simulations contributed to understanding of Gram-negative bacterial cell envelopes?”  Microbiology, 168(3). https://doi.org/10.1099/mic.0.001165
  • Pedebos C, Khalid S. (2022) “Simulations of the spike: molecular dynamics and SARS-CoV-2.” Nat Rev Microbiol, 20, 192. https://doi.org/10.1038/s41579-022-00699-9
  • Miles CM, Hsu P, Dixon A, Khalid S, Sosso GC. (2022) “Lipid bilayers as potential ice nucleating agents.” Phys. Chem. Chem. Phys. https://doi.org/10.1039/D1CP05465 

2021

  • Rattu P, Glencross F, Mader SL, Skylaris CK, Matthews SJ, Rouse SR, Khalid S. (2021) “Atomistic level characterisation of ssDNA translocation through the E. coli proteins CsgG and CsgF for nanopore sequencing.” Comput. Struct. Biotechnol. J., 19, 6417-6430. https://doi.org/10.1016/j.csbj.2021.11.014
  • Weerakoon D, Petrov K, Pedebos C, Khalid S. (2021) “Polymyxin B1 within the E. coli cell envelope: insights from molecular dynamics simulations”. Biophys Rev, 13, 1061–1070. https://doi.org/10.1007/s12551-021-00869-8
  • van den Berg B, Pedebos C, Bolla JR, Robinson CV, Baslé A, Khalid S. (2021) “Structural basis for silicic acid uptake by higher plants”. J. Mol. Biol., 433(21), 167226. https://doi.org/10.1016/j.jmb.2021.167226
  • Mann D, Fan J, Somboon K, Farrell DP, Muenks A, Tzokov SB, DiMaio F, Khalid S, Miller SI, Bergeron JRC. (2021) “Structure and lipid dynamics in the maintenance of lipid asymmetry inner membrane complex of A. baumannii”. Commun Biol., 4, 817. https://doi.org/10.1038/s42003-021-02318-4
  • York A, Lloyd AJ, del Genio CI, Shearer J, Hinxman KJ, Fritz K, Fulop V, Khalid S, Dowson C, Roper D. (2021) “Structure-based modelling and dynamics of MurM, a Streptococcus pneumoniae penicillin resistance determinant that functions at the cytoplasmic membrane interface”. Structure, 29(7), 731-742.e6. https://doi.org/10.1016/j.str.2021.03.001
  • Pedebos C, Smith IPS, Boags A, Khalid S. (2021). “The Hitchhiker’s Guide to the Periplasm: Unexpected Molecular Interactions of Polymyxin B1 in E. coli”. Structure, 29(5), 444-456.e2. https://doi.org/10.1016/j.str.2021.01.009
  • Gao Y, Lee J, Smith IPS, Lee H, Kim S, Qi Y, Klauda JB, Widmalm G, Khalid S, Im W. (2021) “CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides”. J Chem Inf Model, 61, 2, 831–839. https://doi.org/10.1021/acs.jcim.0c01360
  • Rattu P, Belzunces B, Haynes T, Skylaris CK, Khalid S. (2021) “Translocation of flexible and tensioned ssDNA through in silico designed hydrophobic nanopores with two constrictions”. Nanoscale, 13, 1673-1679. https://doi.org/10.1039/d0nr04890a
  • Lizio MG, Campana M, De Poli M, Jefferies DF, Cullen W, Andrushchenko V, Chmel NP, Bouř P, Khalid S, Clayden J, Blanch E, Rodger A, Webb SJ. (2021) “Insight into mechanism of action and peptide-membrane interactions of Aib-rich peptides: multi-technique experimental and theoretical analysis”. ChemBioChem, 22, 1656–16. https://doi.org/10.1002/cbic.202000834
  • Casalino L et al (2021) "AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics". The International Journal of High Performance Computing  Applications, https://doi.org/10.1177/10943420211006452

 

2020

  • Somboon K, Doble A, Bulmer D, Baslé A, Khalid S, van den Berg B. (2020) “Uptake of monoaromatic hydrocarbons during biodegradation by FadL channel-mediated lateral diffusion”. Nat Commun, 11, 6331. https://doi.org/10.1038/s41467-020-20126-y
  • Shearer J, Marzinek JR, Bond PJ, Khalid S. (2020) “Molecular dynamics simulations of bacterial outer membrane lipid extraction: Adequate sampling?” J. Chem. Phys., 153, 044122. https://doi.org/10.1063/5.0017734
  • Khalid S, Newstead S. (2020) “A Computational Swiss Army Knife Approach to Unraveling the Secrets of Proton Movement through SERCA.” Biophys. J., 119(5), 890-891. https://doi.org/10.1016/j.bpj.2020.07.028
  • Gault J, Liko I, Landreh M, Shutin D, Bolla JR, Jefferies D, Agasid M, Yen HY, Ladds MJGW, Lane DP, Khalid S, Mullen C, Remes PM, Huguet R, McAlister G, Goodwin M, Viner R, Syka JEP, Robinson CV. (2020) “Combining native and ‘omics’ mass spectrometry to identify endogenous ligands bound to membrane proteins.” Nat. Methods, 17, 505-508. https://doi.org/10.1038/s41592-020-0821-0 
  • Du D, Neuberger A, Orr MW, Newman CE, Hsu PC, Samsudin F, Szewczak-Harris A, Ramos LM, Debela M, Khalid S, Storz G, Luisi BF. (2020) “Interactions of a Bacterial RND Transporter with a Transmembrane Small Protein in a Lipid Environment.” Structure, 28(6), 625-634. https://doi.org/10.1016/j.str.2020.03.013
  • Szczepaniak J, Holmes P, Rajasekar K, Kaminska R, Samsudin F, Inns PG, Rassam P, Khalid S, Murray SM, Redfield C, Kleanthous C. (2020) “The lipoprotein Pal stabilises the bacterial outer membrane during constriction by a mobilisation-and-capture mechanism.” Nat. Commun, 11, 1305. https://doi.org/10.1038/s41467-020-15083-5
  • Roman-Trufero M, Ito CM, Pedebos C, Magdalou I, Wang YF, Karimi MM, Moyon B, Webster Z, di Gregorio A, Azuara V, Khalid S, Speck C, Rodriguez T, Dillon N. (2020) “Evolution of an Amniote-Specific Mechanism for Modulating Ubiquitin Signaling via Phosphoregulation of the E2 Enzyme UBE2D3.” Mol Biol Evol, 37(7), 1986-2001. https://doi.org/10.1093/molbev/msaa060
  • Jefferies D, Khalid S. (2020) “Atomistic and Coarse-grained Simulations of Membrane Proteins: A Practical Guide.” Methods, 185, 15-27. https://doi.org/10.1016/j.ymeth.2020.02.007
  • Im W, Khalid S. (2020) “Molecular Simulations of Gram-negative Bacterial Membranes Come of age.” Annu. Rev. Phys. Chem., 71(1), 171-188. https://doi.org/10.1146/annurev-physchem-103019-033434
  • Jefferies D, Khalid S. (2020) “To Infect or Not to Infect: Molecular Determinants of Bacteria Outer Membrane Internalization by Host Membranes.” J. Mol. Biol, 432(4), 1251-1264. https://doi.org/10.1016/j.jmb.2020.01.008
  • Rouse SL, Khalid S.  (2020) “Simulation of Subcellular Structures.” Curr Opin Struc Biol, 61, 167-172. https://doi.org/10.1016/j.sbi.2019.12.017

2019

  • Jefferies D, Shearer J, Khalid S. (2019) “Role of O-Antigen in Response to Mechanical Stress of the E. coli Outer Membrane: Insights from Coarse-Grained MD Simulations.” J. Phys. Chem. B, 123(17), 3567-3575. https://doi.org/10.1021/acs.jpcb.8b12168
  • Shearer J, Jefferies D, Khalid S. (2019) “Outer Membrane Proteins OmpA, FhuA, OmpF, EstA, BtuB, and OmpX Have Unique Lipopolysaccharide Fingerprints.” J. Chem. Theory Comput., 15(4), 2608-2619. https://doi.org/10.1021/acs.jctc.8b01059
  • Boags A, Samsudin F, Khalid S. (2019) “Details of hydrophobic entanglement between small molecules and Braun’s lipoprotein within the cavity of the bacterial chaperone LolA.” Sci. Rep., 9(1), 3717. https://doi.org/10.1038/s41598-019-40170-z
  • Samsudin F, Khalid S. (2019) “Movement of Arginine through OprD: The Energetics of Permeation and the Role of Lipopolysaccharide in Directing Arginine to the Protein.” J. Phys. Chem. B, 123(13), 2824-2832. https://doi.org/10.1021/acs.jpcb.9b00063
  • Boags AT, Samsudin F, Khalid S. (2019) “Binding from Both Sides: TolR and Full-Length OmpA Bind and Maintain the Local Structure of the E. coli Cell Wall.” Structure, 27(4), 713-724. https://doi.org/10.1016/j.str.2019.01.001
  • Mitra M, Asad M, Kumar S, Yadav K, Chaudhary S, Bhavesh NS, Khalid S, Thukral L, Bajaj A. (2019) “Distinct Intramolecular Hydrogen Bonding Dictates Antimicrobial Action of Membrane-Targeting Amphiphiles.” J. Phys. Chem. Lett., 10(4), 754-760. https://doi.org/10.1021/acs.jpclett.8b03508
  • Khalid S, Piggot TJ, Samsudin F. (2019) “Atomistic and Coarse Grain Simulations of the Cell Envelope of Gram-Negative Bacteria: What Have We Learned?” Acc. Chem. Res,, 52(1), 180-188. https://doi.org/10.1021/acs.accounts.8b00377

 

2018

  • Chorev DS, Baker LA, Wu D, Beilsten-Edmands V, Rouse SL, Zeev-Ben-Mordehai T, Jiko C, Samsudin F, Gerle C, Khalid S, Stewart AG, Matthews SJ, Grünewald K, Robinson CV. (2018) “Protein assemblies ejected directly from native membranes yield complexes for mass spectrometry.” Science, 362(6416), 829-834. https://doi.org/10.1126/science.aau0976
  • Friedman R, Khalid S, Aponte-Santamaría C, Arutyunova E, Becker M, Boyd KJ, Christensen M, Coimbra JTS, Concilio S, Daday C, van Eerden FJ, Fernandes PA, Gräter F, Hakobyan D, Heuer A, Karathanou K, Keller F, Lemieux MJ, Marrink SJ, May ER, Mazumdar A, Naftalin R, Pickholz M, Piotto S, Pohl P, Quinn P, Ramos MJ, Schiøtt B, Sengupta D, Sessa L, Vanni S, Zeppelin T, Zoni V, Bondar AN, Domene C. (2018) “Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology.” J. Membr. Biol., 251(5-6), 609-631. https://doi.org/10.1007/s00232-018-0050-y
  • Saunders GM, Bruce Macdonald HE, Essex JW, Khalid S. (2018) “Prediction of the closed conformation and insights into the mechanism of the membrane protein LpxR.” Biophys. J., 115(8), 1445-1456. https://doi.org/10.1016/j.bpj.2018.09.002
  • Punekar AS, Samsudin F, Lloyd AJ, Dowson CG, Scott DJ, Khalid S, Roper DI. (2018) “The role of the jaw subdomain of peptidoglycan glycosyltransferases for lipid II polymerization.” Cell Surf, 2, 54-66. https://doi.org/10.1016/j.tcsw.2018.06.002
  • Haynes T, Smith IPS, Wallace EJ, Trick JL, Sansom MSP, Khalid S. (2018) “Electric-field driven Translocation of ssDNA through hydrophobic nanopores.” ACS Nano, 12(8), 8208-8213. https://doi.org/10.1021/acsnano.8b03365
  • Housden NG, Rassam P, Lee S, Samsudin F, Kaminska R, Sharp C, Goult JD, Francis ML, Khalid S, Bayley H, Kleanthous C. (2018) “Directional Porin Binding of Intrinsically Disordered Protein Sequences Promotes Colicin Epitope Display in the Bacterial Periplasm.” Biochemistry, 57(29), 4374-4381. https://doi.org/10.1021/acs.biochem.8b00621
  • Huber RG, Berglund NA, Kargas V, Marzinek JK, Holdbrook DA, Khalid S, Piggot TJ, Schmidtchen A, Bond PJ. (2018) “A Thermodynamic Funnel Drives Bacterial Lipopolysaccharide Transfer in the TLR4 Pathway.” Structure, 26(18), 1151-1161. https://doi.org/10.1016/j.str.2018.04.007
  • Shearer J, Khalid S. (2018) “Communication between the leaflets of asymmetric membranes revealed from coarse-grain molecular dynamics simulations.” Sci. Rep., 8(1), 1805. https://doi.org/10.1038/s41598-018-20227-1

 

2017

  • Hsu PC, Samsudin F, Shearer J, Khalid S. (2017) “It Is Complicated: Curvature, Diffusion, and Lipid Sorting within the Two Membranes of Escherichia coli.” J. Phys. Chem. Lett., 8(22), 5513-5518. https://doi.org/10.1021/acs.jpclett.7b02432
  • Samsudin F, Boags A, Piggot TJ, Khalid S. (2017) “Braun’s Lipoprotein Facilitates OmpA Interaction with the Escherichia coli Cell Wall.” Biophys. J., 113(7), 1496-1504. https://doi.org/10.1016/j.bpj.2017.08.011
  • Hsu PC, Bruininks BMH, Jefferies D, Cesar Telles de Souza P, Lee J, Patel DS, Marrink SJ, Qi Y, Khalid S, Im W. (2017) “CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides.” J. Comput. Chem., 38(27), 2354-2363. https://doi.org/10.1002/jcc.24895
  • Boags A, Hsu PC, Samsudin F, Bond PJ, Khalid S. (2017) “Progress in Molecular Dynamics Simulations of Gram-Negative Bacterial Cell Envelopes.” J. Phys. Chem. Lett., 8(11), 2513-2518. https://doi.org/10.1021/acs.jpclett.7b00473
  • Graham JA, Essex JW, Khalid S. (2017) “PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories.” J. Chem. Inf. Model., 57(4), 650-656. https://doi.org/10.1021/acs.jcim.7b00096
  • Jefferies D, Hsu PC, Khalid S. (2017) “Through the Lipopolysaccharide Glass: A Potent Antimicrobial Peptide Induces Phase Changes in Membranes.” Biochemistry, 56(11), 1672-1679. https://doi.org/10.1021/acs.biochem.6b01063

 

2016

  • Samsudin F, Ortiz-Suarez ML, Piggot TJ, Bond PJ, Khalid S. (2016) “OmpA: a Flexible Clamp for Bacterial Cell Wall Attachment.” Structure, 24(12), 2227-2235. https://doi.org/10.1016/j.str.2016.10.009
  • Hsu P-C, Jefferies D, Khalid S. (2016) “Molecular Dynamics Simulations Predict the Pathways via Which Pristine Fullerenes Penetrate Bacterial Membranes.” J. Phys. Chem. B, 120(43), 11170-11179. https://doi.org/10.1021/acs.jpcb.6b06615
  • Ortiz-Suarez ML, Samsudin F, Piggot TJ, Bond PJ, Khalid S. (2016) “The Full-Length OmpA dimer: Structure, Function and Membrane Interactions Predicted by Atomistic Molecular Dynamics Simulations.” Biophys. J., 111(8), 1692-1702. https://doi.org/10.1016/j.bpj.2016.09.009
  • Carpenter TS, Parkin J, Khalid S. (2016) “The Free Energy of Small Solute Permeation through the E. coli Outer Membrane has a Distinctly Asymmetric Profile.” J. Phys. Chem. Lett., 7(17), 3446-3451. https://doi.org/10.1021/acs.jpclett.6b01399
  • Holbrook DA, Huber RG, Piggot TJ, Bond PJ, Khalid S. (2016) “Dynamics of Crowded Vesicles: Local and Global Responses to Membrane Composition.” PLoS ONE, 11(6), e0156963. https://doi.org/10.1371/journal.pone.0156963
  • Witzke S, Petersen M, Carpenter TS, 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. https://doi.org/10.1021/acs.biochem.5b01315 
  • Berg B, Chembath A, Jefferies D, Basle A, Khalid S, Rutherford J. (2016) “Structural basis for Mep2 ammonium transceptor activation by phosphorylation.” Nat. Commun, 7, 11337. https://doi.org/10.1038/ncomms11337
  • Lee SC, Khalid S, Pollock NL, Knowles TJ, Edler K, Rothnie AJ, R T Thomas O, Dafforn TR. (2016) “Encapsulated membrane proteins: A simplified system for molecular simulation.” BBA Biomembranes, 1858(10), 2549-2557. https://doi.org/10.1016/j.bbamem.2016.02.039 

 

2015

  • Clifton LA, Holt SA, Hughes AV, Daulton EL, Arunmanee W, Heinrich F, Khalid S, Jefferies D, Charlton TR, Webster JR, Kinane CJ, Lakey JH. (2015) “An Accurate In Vitro Model of the E. coli Envelope.” Angew. Chem., 54(41), 11952-11955. https://doi.org/10.1002/anie.201504287
  • Parkin J, Chavent M, Khalid S. (2015) “Molecular Dynamics simulations of Gram-negative bacteria: a vignette of some recent successes.” Biophys. J., 109(3), 461-468. https://doi.org/10.1016/j.bpj.2015.06.050
  • Manara RA,  Wallace EJ, Khalid S. (2015) “DNA sequencing with MspA: Molecular Dynamics simulations reveal free energy differences between sequencing and non-sequencing mutants.” Sci. Rep., 5, 12783. https://doi.org/10.1038/srep12783
  • Cournia Z, Allen TW, Andricioaei I, Antonny B, Baum D, Brannigan G, Buchete NV, Deckman JT, Delemotte L, Del Val C, Friedman R, Gkeka P, Hege HC, Hénin J, Kasimova MA, Kolocouris A, Klein ML, Khalid S, Lemieux MJ, Lindow N, Roy M, Selent J, Tarek M, Tofoleanu F, Vanni S, Urban S, Wales DJ, Smith JC, Bondar AN. (2015) “Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory.” J. Membr. Biol., 248(4), 611-640. https://doi.org/10.1007/s00232-015-9802-0
  • Esther L, Briggs A, Gomes RGB, Elhussein M, Collier W, Findlow IS, Khalid S, McCormick CJ, Williamson PTF. (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.” BBA Biomembranes, 1848(8), 1671-1677. https://doi.org/10.1016/j.bbamem.2015.04.015
  • Berglund N, Piggot TJ, Jefferies D, Sessions RB, Bond PJ, Khalid S. (2015) ““Interaction of The Antimicrobial Peptide Polymyxin B1 with Both Membranes of E. coli: A Molecular Dynamics Study.” PLoS Comput. Biol., 11(4), e1004180. https://doi.org/10.1371/journal.pcbi.1004180
  • Strahl H, Turlan C, Khalid S, Bond PJ, Kebalo JM, Peyron P, Poljak L, Bouvier M, Hamoen L, Luisi BF, Carpousis AJ. (2015) “Membrane recognition and dynamics of the RNA Degradosome” PLoS Gent., 11(2), e1004961. https://doi.org/10.1371/journal.pgen.1004961
  • Gray A, Harlen OG, Harris SA, Khalid S, Leung YM, Lonsdale R, Mulholland AJ, Pearson AR, Read DJ, Richardson RA. (2015) “In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation.” Acta Crystallogr. D, 71, 162-172. https://doi.org/10.1107/S1399004714026777
  • Manara RA, Guy AT, Wallace EJ, Khalid S. (2015) “Free-Energy Calculations Reveal the Subtle Differences in the Interactions of DNA Bases with alpha-Hemolysin.” J. Chem. Theory Comput., 11(2), 810-816. https://doi.org/10.1021/ct501081h
  • Manara RA, 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. https://doi.org/10.3390/nano5010144
  • Khalid S, Berglund NA, Holdbrook DA. Leung YM, Parkin J. (2015) “The Membranes of Gram-negative Bacteria: Progress in Molecular Modelling and Simulation.” Biochem. Soc. Trans., 43(2), 162-167. https://doi.org/10.1042/BST20140262

 

2014

Parkin J, Khalid S. (2014) “Atomistic molecular dynamics simulations enable prediction of the arginine permeation pathway through OccD1 from Pseudomonas aeruginosa.” Biophys. J., 107 (8), 1853-1861. https://doi.org/10.1016/j.bpj.2014.08.035

Leung YM, Holdbrook DA, Piggot TJ, Khalid S. (2014) “The NorM MATE transporter from N. gonorrhoeae: insights into drug and ion binding from atomistic molecular dynamics simulations.” Biophys. J., 107(2), 460-468. https://doi.org/10.1016/j.bpj.2014.06.005

 

2013

Piggot TJ, Holdbrook DA, Khalid S. (2013) “Conformational dynamics and membrane interactions of the E. coli outer membrane protein FecA: A molecular dynamics simulation study.” BBA Biomembranes, 1828(2), 284-293. https://doi.org/10.1016/j.bbamem.2012.08.021

Holdbrook DA, Piggot TJ, Sansom MSP, Khalid S. (2013) “Stability and membrane interactions of an autotransport protein: MD simulations of the Hia translocator domain in a complex membrane environment.” BBA Biomembranes, 1828(2), 715-723. https://doi.org/10.1016/j.bbamem.2012.09.002

Eren E, Parkin J, Adelanwa A, Cheneke B, Movileanu L, Khalid S, van den Berg B. (2013) “Towards understanding the outer membrane uptake of small molecules by Pseudomonas aeruginosa.” J. Biol. Chem., 288(17), 12042-12053. https://doi.org/10.1074/jbc.M113.463570

 

2012

Marius P, Leung YM, Piggot TJ, Khalid S, Williamson PT. (2012) “Probing the oligomeric state and interaction surfaces of Fukutin-I in dilauroylphosphatidylcholine bilayers.” Eur. Biophys. J., 41 (2), 199-207. https://doi.org/10.1007/s00249-011-0773-5

Piggot TJ, Piñeiro A, Khalid S. (2012) “Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study.” J. Chem. Theory Comput., 8(11), 4593-4609. https://doi.org/10.1021/ct3003157

Guy AT, Piggot TJ, Khalid S. (2012) “Single-Stranded DNA within Nanopores: Conformational Dynamics and Implications for Sequencing; a Molecular Dynamics Simulation Study.” Biophys. J., 103(5), 1028-1036. https://doi.org/10.1016/j.bpj.2012.08.012

Piggot TJ, Holdbrook DA, Khalid S. (2012) “Electroporation of the E. coli and S. aureus Membranes: Molecular Dynamics Simulations of Complex Bacterial Membranes.” J. Phys. Chem. B, 115(45), 13381-13388. https://doi.org/10.1021/jp207013v

 

2011

Bond PJ, Guy AT , Heron A, Bayley H, Khalid S. (2011) “Molecular dynamics simulations of DNA within a nanopore: arginine-phosphate tethering and a binding/sliding mechanism for translocation.” Biochemistry, 50(18), 3777-3783.

Piñeiro A, Bond PJ, Khalid S. (2011) “Exploring the conformational dynamics and membrane interactions of PorB from C. glutamicum: a multi-scale molecular dynamics simulation study.” BBA Biomembranes, 1808(6), 1746-1752.

 

2010 and earlier

Vohra S, Hall BA, Holdbrook HA , Khalid S, Biggin PC. (2010) “Bookshelf: a simple curation system for the storage of biomolecular simulation data.” Database, 2010, baq033.

Kurze A, Michie KA, Dixon SE, Mishra A, Itoh T, Khalid S, Strmecki L, Shirahige K, Haering CH, Löwe J, Nasmyth K. (2010) “A positively charged channel within the Smc1/Smc3 hinge required for sister chromatid cohesion.” EMBO J, 30(2), 364-378.

Holdbrook HA , Leung YM, Piggot TJ, Marius P, Williamson PT, 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.

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. Lett., 17(11), 1313-1327.

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, 26(14), 12119-12125.

Mishra, A, Hu B, Kurze A, Beckouët B, Farcas A, Dixon SE, Katou Y, Khalid S, Shirahige K, Nasmyth KA. (2010) “Both interaction surfaces within cohesin’s hinge domain are essential for its stable association with chromatin.” Curr. Biol., 20(4), 279-289.

Ainalem MA, 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,114(21), 7229-7244.

Johnston JM, Khalid S, Sansom MSP. (2008) “Conformational dynamics of the mitochondrial ADP/ATP carrier: A simulation study.” Mol. Memb. Biol, 25, 506-517.

Khalid S, Bond PJ, Holyoake J, Hawtin RW, Sansom MSP. (2008) “DNA and lipid bilayers: self assembly and insertion.” J R Soc Interface, 5, S241-S250.

Carpenter T, Bond PJ, Khalid S, Sansom MSP. (2008) “Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel.” Biophys. J., 95, 3790-3801.

Chen M, Khalid S, Sansom MSP,  Bayley H. (2008) “OmpG: engineering a quiet pore for biosensing” Proc. Natl. Acad. Sci. USA, 105, 6272-6277.

Scott KA, Bond PJ, Ivetac A, Chetwynd AP, Khalid S, Sansom MSP. (2008) “Coarse-grained MD simulations of membrane protein/bilayer self-assembly.” Structure, 16, 621-630.

Khalid, P.J. Bond, T. Carpenter, M.S.P. Sansom, (2008), “OmpA: Gating and Dynamics Via Molecular Dynamics Simulations.” BBA Biomembranes, 1778, 1871-1880.

Bond PJ, Holyoake J, Ivetac A, Khalid S, Sansom MSP. (2007) “Coarse-grained molecular dynamics simulations of membrane proteins and peptides.” J. Struct. Biol., 157, 593-605.

Carpenter T, Khalid S , Sansom MSP. (2007) “A Multidomain Outer Membrane Protein from Pasteurella Multocida: Modelling and Simulation Studies of PmOmpA.” BBA Biomembranes, 1768, 2831-2840.

Peberdy J, Malina J, Khalid S, Hannon MJ, Rodger A. (2007) “Influence of hydrophobic surface groups on DNA binding of bimetallo helicates.” J. Inorg. Biochem., 101(11-12), 1937-1945.

Haider, Khalid S, Tucker SJ, Ashcroft FM, Sansom MSP. (2007) “Molecular Dynamics Simulations of Inwardly rectifying (Kir) Potassium Channels: A Comparative Study.” Biochemistry, 46, 3643-3652.

Kerchoffs JMCA, Peberdy JC, Meistermann I, Childs LJ, Isaac CJ, Pearmund CR, Reudegger V, Khalid S, Alcock NA, Hannon MJ, Rodger A. (2007) “Enantiomeric Resolution of Supramolecular Helicates with Different Surfaces Topographies.” Dalton Trans, 21, 734-742.

Khalid S, Sansom MSP. (2006) “Molecular Dynamics Simulations of a Bacterial Autotransporter: NalP From Neisseria meningitidis.” Mol. Membr. Biol, 23, 499-508.

Khalid S, Hannon MJ, Rodger A, Rodger PM. (2007) “Shape effects on the activity of synthetic major-groove binding ligands.” J. Mol. Graph. Model., 25, 794-800.

Khalid S, Bond PJ, Deol SS, Sansom MSP. (2006) “Modelling and Simulations of a Bacterial Outer Membrane Protein: OprF from P. aeruginosa.” Proteins, 63, 6-15.

Khalid S, Hannon MJ, Rodger A, Rodger PM. (2006) “Simulations of DNA Coiling Around a Synthetic Supramolecular Cylinder That Binds in the DNA Major Groove.” Chemistry, 24, 3493-3506.

Khalid S, Rodger PM, Rodger A. (2005) “Theoretical Aspects of the Enantiomeric Resolution of Supramolecular Cylinders With Different Surface Topologies on Cellulose Columns.” J. Liq. Chromatogr. Relat., 28, 2995-3003.

Khalid S, Rodger PM. (2004) “Molecular Dynamics Simulations of DNA and its Complexes.“ Prog. React. Kinet. Mech., 29, 167-186.

Meistermann I, Moreno V, Prieto MJ, Moldrheim E, Sletton E, Khalid S, Rodger PM, Peberdy JC, Isaac CJ, Rodger A, Hannon MJ. (2002) “Intramolecular DNA Coiling Mediated by Metallosupramolecular Cylinders: Differential Binding of P and M Helical Enantiomers.” Proc. Natl. Acad. Sci. USA, 99(8), 5069-5074.

Lukac R, Clark AJ, Khalid S, Rodger A, Snedden A, Rodger PM. (2002) “Chiral Discrimination in Mobile Phases for HPLC.” J. Mol. Liq., 98-99, 411-423, Sp Iss.