Staff Profile

Education and Research positions

1995-1996: Postdoctoral research fellow, Inorganic chemistry, University of Oxford, Oxford, UK

1997: Postdoctoral research fellow, Physical Chemistry, University of Granada, Granada, Spain

1998-1999: Postdoctoral research fellow, Inorganic Chemistry, University of Oxford, Oxford, UK

2000-2004: Postdoctoral research fellow, Cell Biology, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA

Academic positions

2004-2009: Assistant Professor, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA

2009-2012: Associate Professor, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA (tenure awarded in 2012)

2013- : Professor in Membrane Protein Structural Biology, NUBI (formerly Institute for Cellular and Molecular Biosciences), Newcastle University, UK

Awards

2005: Elected a PEW scholar in the Biomedical Sciences.

2013: Royal Society Wolfson Research Merit Award

2019-2025: Wellcome Trust Investigator Award

2025-2030: ERC Advanced Grant

Current Grants

BBSRC BB/Y010655/1: Understanding outer membrane protein complex assembly in the Bacteroidetes (2025-2027).

ERC AdG 2024: In and OUT: In with the good, out with the bad: understanding small molecule influx and efflux in

gut Bacteroides (2025-2030).

I joined the Biosciences Institute (formerly Institute of Cellular and Molecular Biosciences) at Newcastle University in January 2013. Prior to coming to the UK, I was a faculty member within the Program in Molecular Medicine at UMass Medical School in Worcester, Massachusetts (USA). The main focus of my research is to understand how small molecules are transported across the outer membrane (OM) of Gram-negative bacteria. For this, we determine the three-dimensional structures of bacterial integral OM proteins and complexes via cryo-EM. Those structures are then used, in combination with functional data obtained from biochemical experiments, to propose transport models that can be tested experimentally.

At the moment, our research on OM proteins is funded by the BBSRC and the ERC and is focused on studying influx and efflux processes in members of the Bacteroides, the most abundant microbial genus in the human gut:

The human gut microbiome has a profound influence on many aspects of human health. While very diverse at the species level, this community is dominated by just two bacterial phyla, the Gram-positive Firmicutes and the Gram-negative Bacteroidetes. The Bacteroides genus belongs to the Bacteroidetes phylum and is the most abundant genus within the gut of western world populations. Due to their abundance and their well-established ability to break down dietary glycans that are inaccessible to the host, Bacteroides are keystone species that shape the human gut microbiome. However, to thrive within the gut, Bacteroides need to take up many small molecules besides glycans, and noxious compounds such as bile acids and antibiotics need to be removed from the cell. Both processes are crucial for fitness within the highly competitive environment of the human gut, and depend critically on lipoproteins, channels and transporters residing in the outer membrane (OM).

We will identify and characterise OM influx and efflux processes in gut Bacteroides via a multi-disciplinary approach including structural biology, proteomics and metabolomics. Compared to Proteobacteria in which these processes have been studied in detail, OM influx and efflux in the phylogenetically distant Bacteroides is largely terra incognita. Based on what we do know, it is clear that the OM and OM proteins of Bacteroides are very different from those of well-studied bacterial model systems. By delivering a step-change in our understanding, this research will not only result in groundbreaking new knowledge of the "ins and outs" of arguably the most important microbial genus in the gut but should also provide directions for gut microbiota manipulation to better human health.

Another long-standing research interest of the lab is how we can exploit important OM proteins for the design and delivery of novel antibiotics against Gram-negative bacteria.

BGM2061

practical membrane protein purification (BGM2061)

BGM2062

BGM3064

• Articles

  • Silale A, Madej M, Mikruta K, Frey AM, Hart AJ, Basle A, Scavenius C, Enghild JJ, Trost M, Hirt RP, van den Berg B. Structure of a distinct β-barrel assembly machinery complex in the Bacteroidota. Nature Microbiology 2025, epub ahead of print.
  • Parr RJ, Santin YG, Ratkeviciute G, Caulton SG, Radford P, Gurvic D, Jenkins M, Doyle MT, Mead L, Silale A, van den Berg B, Knowles TJ, Sockett RE, Stansfeld PJ, Laloux G, Lovering AL. A porin-like protein used by bacterial predators defines a wider lipid-trapping superfamily. Nature Communications 2025, 16, 6213.
  • White JBR, Silale A, Feasey M, Heunis T, Zhu Y, Zheng H, Gajbhiye A, Firbank S, Baslé A, Trost M, Bolam DN, van den Berg B, Ranson NA. Outer membrane utilisomes mediate glycan uptake in gut Bacteroidetes. Nature 2023, 618(7965), 583-589.
  • Silale A, Zhu Y, Witwinowski J, Smith RE, Newman KE, Bhamidimarri SP, Basle A, Khalid S, Beloin C, Gribaldo S, van den Berg B. Dual function of OmpM as outer membrane tether and nutrient uptake channel in diderm Firmicutes. Nature Communications 2023, 14, 7152.
  • Abellon-Ruiz J, Jana K, Silale A, Frey AM, Baslé A, Trost M, Kleinekathöfer U, van den Berg B. BtuB TonB-dependent transporters and BtuG surface lipoproteins form stable complexes for vitamin B₁₂ uptake in gut Bacteroides. Nature Communications 2023, 14, 4714.
  • van den Berg B, Silale A, Baslé A, Brandner AF, Mader SL, Khalid S. Structural basis for host recognition and superinfection exclusion by bacteriophage T5. Proc Natl Acad Sci U S A 2022, 119(42), e2211672119.
  • Putnam EE, Abellon-Ruiz J, Killinger BJ, Rosnow JJ, Wexler AG, Folta-Stogniew E, Wright AT, van den Berg B, Goodman AL. Gut Commensal Bacteroidetes Encode a Novel Class of Vitamin B12-Binding Proteins. mBio 2022, 13(2), e02845-21.
  • Ling EM, Baslé A, Cowell IG, van den Berg B, Blower TR, Austin CA. A comprehensive structural analysis of the ATPase domain of Human DNA topoisomerase II Beta bound to AMPPNP, ADP and the bisdioxopiperazine, ICRF193. Structure 2022, 30(8), 1129-1145.e3.
  • Gray DA, White JBR, Oluwole AO, Rath P, Glenwright AJ, Mazur A, Zahn M, Baslé A, Morland C, Evans SL, Cartmell A, Robinson CV, Hiller S, Ranson NA, Bolam DN, vandenBerg B. Insights into SusCD-mediated glycan import by a prominent gut symbiont. Nature Communications 2021, 12(1), 44.
  • Bhamidimarri SP, Young TR, Shanmugam M, Soderholm S, Baslé A, Bumann D, van den Berg B. Acquisition of ionic copper by the bacterial outer membrane protein OprC through a novel binding site. PLOS Biology 2021, 19(11), e3001446.
  • Somboon K, Doble A, Bulmer D, Baslé A, Khalid S, van den Berg B. Uptake of monoaromatic hydrocarbons during biodegradation by FadL channel-mediated lateral diffusion. Nature Communications 2020, 11, 6331.
  • Madej M, White JBR, Nowakowska Z, Rawson S, Scavenius C, Enghild JJ, Bereta GP, Pothula K, Kleinekathoefer U, Baslé A, Ranson NA, Potempa J, van den Berg B. Structural and functional insights into oligopeptide acquisition by the RagAB transporter from Porphyromonas gingivalis. Nature Microbiology 2020, 5, 1016-1025.
  • Meekrathok P, Stubbs KA, Aunkham A, Kaewmaneewat A, Kardkuntod A, Bulmer DM, van den Berg B, Suginta W. NAG-thiazoline is a potent inhibitor of the Vibrio campbellii GH20 β-N-Acetylglucosaminidase. The FEBS Journal 2020, 287(22), 4982-4995.
  • van den Berg B, Lister S, Rutherford JC. Ammonium transceptors: Novel regulators of fungal development. PLoS Pathogens 2019, 15(11).
  • Bhamidimarri SP, Zahn M, Prajapati JD, Schleberger C, Soderholm S, Hoover J, West J, Kleinekathofer U, Bumann D, Winterhalter M, van den Berg B. A Multidisciplinary Approach toward Identification of Antibiotic Scaffolds for Acinetobacter baumannii. Structure 2019, 27(2), 268-280.e6.
  • Pathania M, Acosta-Gutierrez S, Bhamidimarri SP, Basle A, Ceccarelli M, Winterhalter M, van den Berg B. Unusual constriction zones in the major porins OmpU and OmpT from Vibrio cholerae. Structure 2018, 26(5), 708-721.
  • Suginta W, Sritho N, Ranok A, Bulmer DM, Kitaoku Y, van den Berg B, Fukamizo T. Structure and function of a novel periplasmic chitooligosaccharide-binding protein from marine Vibrio bacteria. Journal of Biological Chemistry 2018, 293(14), 5150-5159.
  • Aunkham A, Zahn M, Kesireddy A, Pothula KR, Schulte A, Basle A, Kleinekathofer U, Suginta W, van den Berg B. Structural basis for chitin acquisition by marine Vibrio species. Nature Communications 2018, 9(1), 220.
  • Abellon-Ruiz J, Zahn M, Basle A, van den Berg B. Crystal structure of the Acinetobacter baumannii outer membrane protein Omp33. Acta Crystallographica Section D: Structural Biology 2018, 74(9), 852-860.
  • Glenwright AJ, Pothula KR, Bhamidimarri SP, Chorev DS, Baslé A, Firbank SJ, Zheng H, Robinson CV, Winterhalter M, Kleinekathöfer U, Bolam DN, van den Berg B. Structural basis for nutrient acquisition by dominant members of the human gut microbiota. Nature 2017, 541, 407-411.
  • Abellón-Ruiz J, Kaptan SS, Baslé A, Claudi B, Bumann D, Kleinekathöfer U, van den Berg B. Structural basis for maintenance of bacterial outer membrane lipid asymmetry. Nature Microbiology 2017, 2, 1616-1623.
  • Zahn M, Bhamidimarri SP, Basle A, Winterhalter M, van den Berg B. Structural Insights into Outer Membrane Permeability of Acinetobacter baumannii. Structure 2016, 24(2), 221-231.
  • van den Berg B, Chembath A, Jefferies D, Basle A, Khalid S, Rutherford JC. Structural basis for Mep2 ammonium transceptor activation by phosphorylation. Nature Communications 2016, 7, 11337.
  • Bhamidimarri SP, Prajapati JD, van den Berg B, Winterhalter M, Kleinekathöfer U. Role of Electroosmosis in the Permeation of Neutral Molecules: CymA and Cyclodextrin as an Example. Biophysical Journal 2016, 110(3), 600-611.
  • Arunmanee W, Pathania M, Solovyova AS, Le Brun AP, Ridley H, Baslé A, van den Berg B, Lakey JH. Gram-negative trimeric porins have specific LPS binding sites that are essential for porin biogenesis. Proceedings of the National Academy of Sciences of the USA 2016, 113(34), E5034-E5043.
  • Modi N, Ganguly S, Bárcena-Uribarri I, Benz R, van den Berg B, Kleinekathöfer U. Structure, Dynamics, and Substrate Specificity of the OprO Porin from Pseudomonas aeruginosa. Biophysical Journal 2015, 109(7), 1429-1438.
  • Zahn M, D'Agostino T, Eren E, Baslé A, Ceccarelli M, van den Berg B. Small-Molecule Transport by CarO, an Abundant Eight-Stranded β-Barrel Outer Membrane Protein from Acinetobacter baumannii. Journal of Molecular Biology 2015, 427(14), 2329-2339.
  • Cheneke BR, van den Berg B, Movileanu L. Quasithermodynamic contributions to the fluctuations of a protein nanopore. ACS Chemical Biology 2015, 10(3), 784–794.
  • van den Berg B, Prathyusha BS, Dahyabhai PJ, Kleinekathöfer U, Winterhalter M. Outer-membrane translocation of bulky small molecules by passive diffusion. Proceedings of the National Academy of Sciences of the United States of America 2015, 112(23), E2991-E2999.
  • van den Berg B, Bhamidimarri SP, Winterhalter M. Crystal structure of a COG4313 outer membrane channel. Scientific Reports 2015, 5, 11927.
  • Eren E, Parkin J, Adelanwa A, Cheneke B, Movileanu L, Khalid S, van den Berg B. Towards understanding of outer membrane uptake of small molecules by Pseudomonas aeruginosa. Journal of Biological Chemistry 2013, 288(17), 12042-120453.
  • Malaby AW, van den Berg B, Lambright DG. Structural basis for membrane recruitment and allosteric activation of cytohesin family Arf GTPase exchange factors. Proc Natl Acad Sci USA 2013, 110(35), 14213-14218.
  • Malaby AW, vandenBerg B, Lambright DG. Structural basis for membrane recruitment and allosteric activation of cytohesin family Arf GTPase exchange factors. Proc Natl Acad Sci U S A 2013, 110, 14213-14218. In Preparation.
  • Eren E, Vijayaraghavan J, Liu J, Cheneke BR, Touw DS, Lepore BW, Indic M, Movileanu L, van den Berg B. Substrate specificity within a family of outer membrane carboxylate channels. PLoS Biology 2012, 10(1), e1001242.
  • van den Berg B. Structural basis for outer membrane sugar uptake in pseudomonads. Journal of Biological Chemistry 2012, 287(49), 41044-41052.
  • Eren E, van den Berg B. Structural basis for activation of an integral membrane protease by lipopolysaccharide. Journal of Biological Chemistry 2012, 287(28), 23971-23976.
  • Liu J, Eren E, Vijayaraghavan J, Cheneke BR, Indic M, van den Berg B, Movileanu L. OccK channels from Pseudomonas aeruginosa exhibit diverse single-channel electrical signatures but conserved anion selectivity. Biochemistry 2012, 51(11), 2319-2330.
  • Liu J, Wolfe AJ, Eren E, Vijayaraghavan J, Indic M, van den Berg B, Movileanu L. Cation selectivity is a conserved feature in the OccD subfamily of Pseudomonas aeruginosa. Biochim Biophys Acta: Biomembranes 2012, 1818(11), 2908-2916.
  • Cheneke BR, Indic M, van den Berg B, Movileanu L. An outer membrane protein undergoes enthalpy- and entropy-driven transitions. Biochemistry 2012, 51(26), 5348-5358.
  • Lepore BW, Indic M, Pham H, Hearn EM, Patel DR, van den Berg B. Ligand-gated diffusion across the bacterial outer membrane. Proceedings of the National Academy of Sciences 2011, 108(25), 10121-10126.
  • Kulathila R, Kulathila R, Indic M, van den Berg B. Crystal structure of Escherichia coli CusC, the outer membrane component of a heavy metal efflux pump. PLoS One 2011, 6(1), e15610.
  • Cheneke BR, van den Berg B, Movileanu L. Analysis of Gating Transitions among the Three Major Open States of the OpdK Channel. Biochemistry 2011, 50(22), 4987-4997.
  • Touw DS, Patel DR, van den Berg B. The crystal structure of OprG from Pseudomonas aeruginosa, a potential channel for transport of hydrophobic molecules across the outer membrane. PLoS One 2010, 5(11), e15016.
  • van den Berg B. Going forward laterally: transmembrane passage of hydrophobic molecules through protein channel walls. Chembiochem 2010, 11(10), 1339-1343.
  • van den Berg B. Crystal structure of a full-length autotransporter. Journal of Molecular Biology 2010, 396(3), 627-633.
  • Eren E, Murphy M, Goguen J, van den Berg B. An active site water network in the plasminogen activator pla from Yersinia pestis. Structure 2010, 18(7), 809-818.
  • Hearn EM, Patel DR, Lepore BW, Indic M, van den Berg B. Transmembrane passage of hydrophobic compounds through a protein channel wall. Nature 2009, 458(7236), 367-370.
  • Hearn EM, Patel DR, van den Berg B. Outer-membrane transport of aromatic hydrocarbons as a first step in biodegradation. Proceedings of the National Academy of Sciences 2008, 105(25), 8601-8606.
  • Biswas S, Mohammad MM, Movileanu L, van den Berg B. Crystal structure of the outer membrane protein OpdK from Pseudomonas aeruginosa. Structure 2008, 16(7), 1027-1035.
  • Biswas S, Mohammad MM, Patel DR, Movileanu L, van den Berg B. Structural insight into OprD substrate specificity. Nat Struct Mol Biol 2007, 14(11), 1108-9.
  • Hong H, Patel DR, Tamm LK, van den Berg B. The outer membrane protein OmpW forms an eight-stranded beta-barrel with a hydrophobic channel. J Biol Chem 2006, 281(11), 7568-77.
  • Subbarao GV, van den Berg B. Crystal structure of the monomeric porin OmpG. J Mol Biol 2006, 360(4), 750-9.
  • Van den Berg B, Clemons WM Jr, Collinson I, Modis Y, Hartmann E, Harrison SC, Rapoport TA. X-ray structure of a protein-conducting channel. Nature 2004, 427(6969), 36-44.
  • van den Berg B, Black PN, Clemons WM Jr, Rapoport TA. Crystal structure of the long-chain fatty acid transporter FadL. Science 2004, 304(5676), 1506-1509.
  • Ye J, van den Berg B. Crystal structure of the bacterial nucleoside transporter Tsx. EMBO Journal 2004, 23(16), 3187-3195.

• Reviews

  • Silale A, van den Berg B. TonB-Dependent Transport Across the Bacterial Outer Membrane. Annual Review of Microbiology 2023, 77, 67-88.
  • Bolam DN, van den Berg B. TonB-dependent transport by the gut microbiota: novel aspects of an old problem. Current Opinion in Structural Biology 2018, 51, 35-43.
  • van den Berg B. Lateral gates: β-barrels get in on the act. Nature Structural and Molecular Biology 2013, 20(11), 1237-1239.
  • van den Berg B. The FadL family: unusual transporters for unusual substrates. Curr Opin Struct Biol 2005, 15(4), 401-7.
  • Osborne AR, Rapoport TA, van den Berg B. Protein translocation by the Sec61/SecY channel. Annu Rev Cell Dev Biol 2005, 529-50.