Postdoctoral Research Fellow (A*STAR Singapore)
Firdaus’ research focuses on the cell envelope of Gram-negative bacteria, specifically building a virtual model to understand the structure-function relationship of its molecular components and how they contribute towards protecting the bacteria from antibiotics. His recent work includes studying the molecular interactions between outer membrane protein A (OmpA) and Braun’s lipoprotein (BLP) with peptidoglycan cell wall in atomistic details. OmpA and BLP are two of the most abundant outer membrane proteins in E. coli, and understanding their contribution towards maintaining the integrity of the cell wall is imperative for development of novel antibiotics. Firdaus also built coarse-grain models of the inner membrane and outer membrane held together by the drug efflux pump complex, AcrAB-TolC. This pioneering work will enhance our understanding on protein-induced membrane curvature, lipid enrichment and diffusion, all of which are crucial physical properties of bacterial cell envelope.
This research mainly utilises atomistic and coarse-grain molecular dynamics (MD) simulations along with more advanced computational techniques such as molecular docking, steered MD, and umbrella sampling.
Firdaus completed his DPhil at the University of Oxford in 2015 under the supervision of Prof Mark Sansom and Dr Philip Fowler. The title of his thesis is “Improving Oral Drug Delivery: Computational Studies of Proton-Dependent Oligopeptide Transporters”.
- 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 spike glycoprotein.” Structure. https://doi.org/10.1016/j.str.2022.05.006
- Tan ZW*, Tee W*, Samsudin F, Guarnera E, Bond PJ, Berezovsky IN. (2022) “Allosteric perspective on the mutability and druggability of the SARS-CoV-2 Spike protein.” Structure, 30, 590–607. https://doi.org/10.1016/j.str.2021.12.011
- Chawla H, Jossi SE, Faustini SE, Samsudin F, Allen JD, Watanabe Y, Newby ML, Marcial-Juárez E, Lamerton RE, McLellan JS, Bond PJ, Richter AG, Cunningham AF, Crispin M. (2022) “Glycosylation and Serological Reactivity of an Expression-enhanced SARS-CoV-2 Viral Spike Mimetic.” J. Mol. Biol., 434(2). https://doi.org/10.1016/j.jmb.2021.167332
- Allen JD, Chawla H, Samsudin F, Zuzic L, Shivgan AT, Watanabe Y, He W, Callaghan S, Song G, Yong P, Brouwer PJM, Song Y, Cai Y, Duyvesteyn HME, Malinauskas T, Kint J, Pino P, Wurm MJ, Frank M, Chen B, Stuart DI, Sanders RW, Andrabi R, Burton DR, Li S, Bond PJ, Crispin M. (2021) “Site-Specific Steric Control of SARS-CoV-2 Spike Glycosylation.” Biochemistry, 60(27), 2153–2169. https://doi.org/10.1021/acs.biochem.1c00279
- Raghuvamsi PV, Tulsian NK, Samsudin F, Qian X, Purushotorman K, Yue G, Kozma MM, Hwa WY, Lescar J, Bond PJ, MacAry PA, Anand GS. (2021) “SARS-CoV-2 S protein:ACE2 interaction reveals novel allosteric targets.” eLife, 10:e63646. https://doi.org/10.7554/eLife.63646
- Samsudin F, Ken-EnGan S, Bond PJ. (2021) “The impact of Gag non-cleavage site mutations on HIV-1 viral fitness from integrative modelling and simulations.” Comput.Struct. Biotechnol. J., 19, 330-342. https://doi.org/10.1016/j.csbj.2020.12.022
- Petruk G*, Puthia M*, Petrlova J, Samsudin F, Strömdahl A, Cerps S, Uller L, Kjellström S, Bond PJ, Schmidtchen A. (2020) “SARS-CoV-2 spike protein binds to bacterial lipopolysaccharide and boosts proinflammatory activity.”J. Mol. Cell Biol., 12(12), 916–932. https://doi.org/10.1093/jmcb/mjaa067
- Petruk G, Petrlova J, Samsudin F, Giudice RD, Bond PJ, Schmidtchen A. (2020) “Concentration- and pH-Dependent Oligomerization of the Thrombin-Derived C-Terminal Peptide TCP-25.” Biomolecules, 10, 1572. https://doi.org/10.3390/biom10111572
- 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
- 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
- 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
- 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, Grunewald K, Robinson CV. (2018) “Protein assemblies ejected directly from native membranes yield complexes for mass spectrometry.” Science, 362, 829-834. https://doi.org/10.1126/science.aau0976
- Housden N, Rassam P, Lee S, Samsudin F, Kaminska R, Sharp C, Goult JD, Francis M-L, 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, 4374-4381. https://doi.org/10.1021/acs.biochem.8b00621
- 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.” The Cell Surface, 2, 54-66. https://doi.org/10.1016/j.tcsw.2018.06.002
- 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.” J. Phys. Chem. Lett., 8, 5513-551. 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, 1496-1504. https://doi.org/10.1016/j.bpj.2017.08.011
- Boags A*, Hsu P-C*, Samsudin F*, Bond PJ, Khalid S. (2017) “Progress in Molecular Dynamics Simulations of Gram-negative Bacterial Cell Envelopes.” J. Phys. Chem. Lett., 8, 2513-251. https://doi.org/10.1021/acs.jpclett.7b00473
- Samsudin F, Ortiz-Suarez ML, Piggot TJ, Bond PJ, Khalid S. (2016) “OmpA: a Flexible Clamp for Bacterial Cell Wall Attachment.” Structure, 24, 2227-2235. https://doi.org/10.1016/j.str.2016.10.009
- Ortiz-Suarez ML*, Samsudin F*, Piggot TJ, Bond PJ, Khalid S. (2016) “Full-Length OmpA: Structure, Function, and Membrane Interactions Predicted by Molecular Dynamics Simulations.” Biophys. J. 111, 1692-1702. https://doi.org/10.1016/j.bpj.2016.09.009
- Samsudin F, Parker JL, Sansom MSP, Newstead S, Fowler PW. (2016) “Accurate Prediction of Ligand Affinities for a Proton-Dependent Oligopeptide Transporter.” Cell Chem. Biol. 23, 299-309. https://doi.org/10.1016/j.chembiol.2015.11.015
- Beale JH*, Parker JL*, Samsudin F*, Barret AL, Senan A, Bird LE, Scott D, Owens RJ, Sansom MSP, Tucker SJ, Meredith D, Fowler PW, Newstead S. (2015) “Crystal Structures of the Extracellular Domain from PepT1 and PepT2 Provide Novel Insights into Mammalian Peptide Transport.” Structure, 23, 1889-1899. https://doi.org/10.1016/j.str.2015.07.016
*Authors contributed equally.
Agency for Science, Technology and Research (A∗STAR),