Peer-reviewed articles

2017

Samsudin F, Boags A, Piggot TJ, Khalid S. (2017), “Braun’s Lipoprotein Facilitates OmpA Interaction with the Escherichia coli Cell Wall”. Biophys J (online).

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. (online)

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

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

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

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

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

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

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): 3446-51

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.

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):3303-14

Berg B, Chembath A, Jefferies D, Basle A, Khalid S, Rutherford J (2016) “Structural basis for Mep2 ammonium transceptor activation by phosphorylation”. Nature Communications 7, 11337.

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”, Biochim Biophysica Acta, 1858(10):2549-57

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.” Angewandte Chemie, 54(41):11952-5

Parkin J, Chavent M and Khalid S (2015) “Molecular Dynamics simulations of Gram-negative bacteria: a vignette of some recent successes” Biophys J, 109(3):461-8

Manara R.A,  Wallace E.J and Khalid S (2015) ” DNA sequencing with MspA: Molecular Dynamics simulations reveal free energy differences between sequencing and non-sequencing mutants” Scientific Reports, 5:12783.

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 Memb. Biol., 248(4):611-40

Ashworth Briggs; Gomes; Elhussein; Collier; Findlow; Khalid; McCormick; Williamson (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. Biochim Biophysica Acta, 1848(8):1671-7

Berglund N, Bond PJ, Jefferies D, PiggotTJ,  Sessions R, , Khalid, S (2015) ““Interaction of The Antimicrobial Peptide Polymyxin B1 with Both Membranes of E. coli: A Molecular Dynamics Study” PLoS Comp Biol, 11(4):e1004180

Turlan C, Strahl H, Khalid S, Bond P.J, Kebalo J-M, Peyron P, Poljak L, Bouvier M, Hamoen L, Luisi B.F, Carpousis A.J. (2015) “Membrane recognition and dynamics of the RNA Degradosome” PLoS Genetics, 11(2):e1004961

Gray A, Harlen O.G, Harris S.A, Khalid S, Leung,Y.M., Lonsdale R, Mulholland A.J. Pearson R.A, Read D.J, and 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. Cryst. D, 71(Pt 1):162-72

Manara R.A, Guy A.T, Wallace E.J and Khalid S (2015) ” Free-Energy Calculations Reveal the Subtle Differences in the Interactions of DNA Bases with alpha-Hemolysin” Journal of Chem. Theory and Comput. 11(2):810-6

Manara R.A, Tomasio S and 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

Khalid S, Berglund N.A, Holdbrook D.A. Leung Y.M and Parkin J. (2015) “The Membranes of Gram-negative Bacteria: Progress in Molecular Modelling and Simulation”, Biochem Soc Trans, 43(2):162-7

2014

Parkin J and Khalid S (2014) “Atomistic molecular dynamics simulations enable prediction of the arginine permeation pathway through OccD1 from Pseudomonas aeruginosa.”, Biophysical Journal, 107 (8): 1853-61

Leung Y.M, Holdbrook D.A, Piggot T.J and 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):460-8

2013

Piggot T.J, Holdbrook D.A and 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): 284-93

Holdbrook D.A. Piggot T.J. Sansom M.S.P and 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): 715-23

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 J Biophysics, 41 (2): 199-207

Piggot T.J, Piñeiro A and Khalid S, (2012) “Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study”, Journal of Chemical Theory and Computation. 8 (11): 4593–4609

Guy, A.T, Piggot T.J. and Khalid S, (2012) “Single-Stranded DNA within Nanopores: Conformational Dynamics and Implications for Sequencing; a Molecular Dynamics Simulation Study”, Biophysical Journal, 103(5):1028-36

Piggot T.J, Holdbrook D.A, 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):13381-8

2011

Bond P.J, Guy A.T , Heron A, Bayley H and Khalid S (2011), “Molecular dynamics simulations of DNA within a nanopore: arginine-phosphate tethering and a binding/sliding mechanism for translocation”. Biochemistry. 50(18):3777-83.

Piñeiro A, Bond P.J, and 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):1746-52

2010 and earlier

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

Kurze A, Michie K.A, Dixon S.E, Mishra A, Itoh T, Khalid S, Strmecki L, Shirahige K, Haering C H, Löwe J and Nasmyth K, (2010), “A positively charged channel within the Smc1/Smc3 hinge required for sister chromatid cohesion”. Embo J. 30(2):364-78

Holdbrook HA , Leung YM, Piggot TJ, Marius P, Williamson PT and Khalid S, (2010), “Stability and Membrane Orientation of the Fukutin Transmembrane Domain: A Combined Multiscale Molecular Dynamics and Circular Dichroism Study”. Biochemistry. 49(51):10796-802

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.Letters. 17(11):1313-27

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):12119-25.

Mishra, A, Hu B., Kurze, A., Beckouët, B., Farcas, A., Dixon, S.E., Katou,Y., Khalid, S., Shirahige, K., Nasmyth, K.A. (2010) Both interaction surfaces within cohesin’s hinge domain are essential for its stable association with chromatin. Curr. Biology. 20(4):279-89

Ainalem, M.A, Campbell, R.A, Khalid, S., Gillams, R.J, Rennie, A.R., Nylander T., (2010) On the Ability of PAMAM Dendrimers and Dendrimer/DNA Aggregates to Penetrate POPC Model Biomembranes. J Phys Chem B. 114(21):7229-44

Johnston, J.M., Khalid, S., and Sansom, M.S.P. (2008) Conformational dynamics of the mitochondrial ADP/ATP carrier: A simulation study. Mol. Memb. Biol. 25:506-517

Khalid, S., Bond, P.J., Holyoake, J., Hawtin, R.W. and Sansom, M.S.P. (2008) DNA and lipid bilayers: self assembly and insertion. J. Roy. Soc. Interface 5: S241-S250

Carpenter T, Bond PJ, Khalid S, Sansom MS. (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, M.S.P. and Bayley, H. (2008) OmpG: engineering a quiet pore for biosensing Proc. Natl. Acad. Sci. USA. 105: 6272-6277

Scott, K.A., Bond, P.J., Ivetac, A., Chetwynd, A.P., Khalid, S., and Sansom, M.S.P. (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”, Biochimica et Biophysica Acta, 1778,1871-80

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

*Carpenter T, *Khalid S , Sansom MSP, “A Multidomain Outer Membrane Protein from Pasteurella Multocida: Modelling and Simulation Studies of PmOmpA”, (2007) Biochimica et Biophysica Acta, 1768, 2831-40

Peberdy J, Malina J, Khalid S , Hannon MJ, Rodger A, “Influence of hydrophobic surface groups on DNA binding of bimetallo helicates”, Journal of Inorganic Biochemistry, (in press)

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

J.M.C.A. Kerchoffs, J.C. Peberdy, I. Meistermann, L.J. Childs, C.J. Isaac, C.R. Pearmund, V. Reudegger, S. Khalid, N.A. Alcock, M.J. Hannon, A. Rodger, (2007), “Enantiomeric Resolution of Supramolecular Helicates with Different Surfaces Topographies”, Dalton Trans.,21, 734-742

Khalid and M. S. P. Sansom, (2006),“Molecular Dynamics Simulations of a Bacterial Autotransporter: NalP From Neisseria meningitidis”, Molecular Membrane Biology, 23, 499-508

Khalid, M. J. Hannon, A. Rodger and P. M. Rodger, (2007),“Shape effects on the activity of synthetic major-groove binding ligands”, Journal of Molecular Graphics & Modelling, 25, 794-800

Khalid, P. J. Bond, S. S. Deol and M. S. P. Sansom (2006), “Modelling and Simulations of a Bacterial Outer Membrane Protein: OprF from P. aeruginosa”, Proteins: Structure, Functions and Bioinformatics, 63, 6-15

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

Khalid, P. M. Rodger and A. Rodger, (2005), “Theoretical Aspects of the Enantiomeric Resolution of Supramolecular Cylinders With Different Surface Topologies on Cellulose Columns”, Journal of Liquid Chromatography and Related Technologies, 28, 2995-3003.

Khalid and P. M. Rodger, (2004) “Molecular Dynamics Simulations of DNA and its Complexes “, Progress in Reaction Kinetics & Mechanism, 29, 167-186

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

Lukac, A. J. Clark, S. Khalid, A. Rodger, A Snedden, and P. M. Rodger, (2002), “Chiral Discrimination in Mobile Phases for HPLC” Journal of Molecular Liquids, 98-99, 411-423, Sp Iss.

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