Bert van den Berg’s Publications

  1. Silale, A, Zhu, Y, Witwinowski, J, Smith, RE, Newman, KE, Bhamidimarri, SP et al.. Dual function of OmpM as outer membrane tether and nutrient uptake channel in diderm Firmicutes. Nat Commun. 2023;14 (1):7152. doi: 10.1038/s41467-023-42601-y. PubMed PMID:37932269 PubMed Central PMC10628300.
  2. Abellon-Ruiz, J, Jana, K, Silale, A, Frey, AM, Baslé, A, Trost, M et al.. BtuB TonB-dependent transporters and BtuG surface lipoproteins form stable complexes for vitamin B12 uptake in gut Bacteroides. Nat Commun. 2023;14 (1):4714. doi: 10.1038/s41467-023-40427-2. PubMed PMID:37543597 PubMed Central PMC10404256.
  3. White, JBR, Silale, A, Feasey, M, Heunis, T, Zhu, Y, Zheng, H et al.. Outer membrane utilisomes mediate glycan uptake in gut Bacteroidetes. Nature. 2023;618 (7965):583-589. doi: 10.1038/s41586-023-06146-w. PubMed PMID:37286596 .
  4. Rietjens, RGJ, Wang, G, van der Velden, AIM, Koudijs, A, Avramut, MC, Kooijman, S et al.. Phosphatidylinositol metabolism of the renal proximal tubule S3 segment is disturbed in response to diabetes. Sci Rep. 2023;13 (1):6261. doi: 10.1038/s41598-023-33442-2. PubMed PMID:37069341 PubMed Central PMC10110589.
  5. Silale, A, van den Berg, B. TonB-Dependent Transport Across the Bacterial Outer Membrane. Annu Rev Microbiol. 2023;77 :67-88. doi: 10.1146/annurev-micro-032421-111116. PubMed PMID:36944260 .
  6. van den Berg, B, Silale, A, Baslé, A, Brandner, AF, Mader, SL, Khalid, S et al.. Structural basis for host recognition and superinfection exclusion by bacteriophage T5. Proc Natl Acad Sci U S A. 2022;119 (42):e2211672119. doi: 10.1073/pnas.2211672119. PubMed PMID:36215462 PubMed Central PMC9586334.
  7. Bhamidimarri, SP, Young, TR, Shanmugam, M, Soderholm, S, Baslé, A, Bumann, D et al.. Acquisition of ionic copper by the bacterial outer membrane protein OprC through a novel binding site. PLoS Biol. 2021;19 (11):e3001446. doi: 10.1371/journal.pbio.3001446. PubMed PMID:34762655 PubMed Central PMC8610252.
  8. Gray, DA, White, JBR, Oluwole, AO, Rath, P, Glenwright, AJ, Mazur, A et al.. Insights into SusCD-mediated glycan import by a prominent gut symbiont. Nat Commun. 2021;12 (1):44. doi: 10.1038/s41467-020-20285-y. PubMed PMID:33398001 PubMed Central PMC7782687.
  9. Somboon, K, Doble, A, Bulmer, D, Baslé, A, Khalid, S, van den Berg, B et al.. Uptake of monoaromatic hydrocarbons during biodegradation by FadL channel-mediated lateral diffusion. Nat Commun. 2020;11 (1):6331. doi: 10.1038/s41467-020-20126-y. PubMed PMID:33303757 PubMed Central PMC7728783.
  10. Amornloetwattana, R, Robinson, RC, Soysa, HSM, van den Berg, B, Suginta, W. Chitoporin from Serratia marcescens: recombinant expression, purification and crystallization. Acta Crystallogr F Struct Biol Commun. 2020;76 (Pt 11):536-543. doi: 10.1107/S2053230X20013874. PubMed PMID:33135672 PubMed Central PMC7605108.
  11. Madej, M, White, JBR, Nowakowska, Z, Rawson, S, Scavenius, C, Enghild, JJ et al.. Structural and functional insights into oligopeptide acquisition by the RagAB transporter from Porphyromonas gingivalis. Nat Microbiol. 2020;5 (8):1016-1025. doi: 10.1038/s41564-020-0716-y. PubMed PMID:32393857 PubMed Central PMC7610489.
  12. Vergalli, J, Bodrenko, IV, Masi, M, Moynié, L, Acosta-Gutiérrez, S, Naismith, JH et al.. Porins and small-molecule translocation across the outer membrane of Gram-negative bacteria. Nat Rev Microbiol. 2020;18 (3):164-176. doi: 10.1038/s41579-019-0294-2. PubMed PMID:31792365 .
  13. Kesireddy, A, Pothula, KR, Lee, J, Patel, DS, Pathania, M, van den Berg, B et al.. Modeling of Specific Lipopolysaccharide Binding Sites on a Gram-Negative Porin. J Phys Chem B. 2019;123 (27):5700-5708. doi: 10.1021/acs.jpcb.9b03669. PubMed PMID:31260306 .
  14. Bhamidimarri, SP, Zahn, M, Prajapati, JD, Schleberger, C, Söderholm, S, Hoover, J et al.. A Multidisciplinary Approach toward Identification of Antibiotic Scaffolds for Acinetobacter baumannii. Structure. 2019;27 (2):268-280.e6. doi: 10.1016/j.str.2018.10.021. PubMed PMID:30554842 .
  15. Abellón-Ruiz, J, Zahn, M, Baslé, A, van den Berg, B. Crystal structure of the Acinetobacter baumannii outer membrane protein Omp33. Acta Crystallogr D Struct Biol. 2018;74 (Pt 9):852-860. doi: 10.1107/S205979831800904X. PubMed PMID:30198896 .
  16. Samanta, S, Bodrenko, I, Acosta-Gutiérrez, S, D'Agostino, T, Pathania, M, Ghai, I et al.. Getting Drugs through Small Pores: Exploiting the Porins Pathway in Pseudomonas aeruginosa. ACS Infect Dis. 2018;4 (10):1519-1528. doi: 10.1021/acsinfecdis.8b00149. PubMed PMID:30039960 .
  17. Acosta-Gutiérrez, S, Ferrara, L, Pathania, M, Masi, M, Wang, J, Bodrenko, I et al.. Getting Drugs into Gram-Negative Bacteria: Rational Rules for Permeation through General Porins. ACS Infect Dis. 2018;4 (10):1487-1498. doi: 10.1021/acsinfecdis.8b00108. PubMed PMID:29962203 .
  18. Pathania, M, Acosta-Gutierrez, S, Bhamidimarri, SP, Baslé, A, Winterhalter, M, Ceccarelli, M et al.. Unusual Constriction Zones in the Major Porins OmpU and OmpT from Vibrio cholerae. Structure. 2018;26 (5):708-721.e4. doi: 10.1016/j.str.2018.03.010. PubMed PMID:29657131 .
  19. Bolam, DN, van den Berg, B. TonB-dependent transport by the gut microbiota: novel aspects of an old problem. Curr Opin Struct Biol. 2018;51 :35-43. doi: 10.1016/ PubMed PMID:29550504 .
  20. Aunkham, A, Zahn, M, Kesireddy, A, Pothula, KR, Schulte, A, Baslé, A et al.. Structural basis for chitin acquisition by marine Vibrio species. Nat Commun. 2018;9 (1):220. doi: 10.1038/s41467-017-02523-y. PubMed PMID:29335469 PubMed Central PMC5768706.
  21. Abellón-Ruiz, J, Kaptan, SS, Baslé, A, Claudi, B, Bumann, D, Kleinekathöfer, U et al.. Structural basis for maintenance of bacterial outer membrane lipid asymmetry. Nat Microbiol. 2017;2 (12):1616-1623. doi: 10.1038/s41564-017-0046-x. PubMed PMID:29038444 .
  22. Glenwright, AJ, Pothula, KR, Bhamidimarri, SP, Chorev, DS, Baslé, A, Firbank, SJ et al.. Structural basis for nutrient acquisition by dominant members of the human gut microbiota. Nature. 2017;541 (7637):407-411. doi: 10.1038/nature20828. PubMed PMID:28077872 PubMed Central PMC5497811.
  23. Arunmanee, W, Pathania, M, Solovyova, AS, Le Brun, AP, Ridley, H, Baslé, A et al.. Gram-negative trimeric porins have specific LPS binding sites that are essential for porin biogenesis. Proc Natl Acad Sci U S A. 2016;113 (34):E5034-43. doi: 10.1073/pnas.1602382113. PubMed PMID:27493217 PubMed Central PMC5003275.
  24. 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. Biophys J. 2016;110 (3):600-611. doi: 10.1016/j.bpj.2015.12.027. PubMed PMID:26840725 PubMed Central PMC4744173.
  25. Zahn, M, Bhamidimarri, SP, Baslé, A, Winterhalter, M, van den Berg, B. Structural Insights into Outer Membrane Permeability of Acinetobacter baumannii. Structure. 2016;24 (2):221-31. doi: 10.1016/j.str.2015.12.009. PubMed PMID:26805524 .
  26. Modi, N, Ganguly, S, Bárcena-Uribarri, I, Benz, R, van den Berg, B, Kleinekathöfer, U et al.. Structure, Dynamics, and Substrate Specificity of the OprO Porin from Pseudomonas aeruginosa. Biophys J. 2015;109 (7):1429-38. doi: 10.1016/j.bpj.2015.07.035. PubMed PMID:26445443 PubMed Central PMC4601001.
  27. van den Berg, B, Bhamidimarri, SP, Winterhalter, M. Crystal structure of a COG4313 outer membrane channel. Sci Rep. 2015;5 :11927. doi: 10.1038/srep11927. PubMed PMID:26149193 PubMed Central PMC4493636.
  28. van den Berg, B, Prathyusha Bhamidimarri, S, Dahyabhai Prajapati, J, Kleinekathöfer, U, Winterhalter, M. Outer-membrane translocation of bulky small molecules by passive diffusion. Proc Natl Acad Sci U S A. 2015;112 (23):E2991-9. doi: 10.1073/pnas.1424835112. PubMed PMID:26015567 PubMed Central PMC4466742.
  29. Zahn, M, D'Agostino, T, Eren, E, Baslé, A, Ceccarelli, M, van den Berg, B et al.. Small-Molecule Transport by CarO, an Abundant Eight-Stranded β-Barrel Outer Membrane Protein from Acinetobacter baumannii. J Mol Biol. 2015;427 (14):2329-39. doi: 10.1016/j.jmb.2015.03.016. PubMed PMID:25846137 .
  30. van den Berg, B. Lateral gates: β-barrels get in on the act. Nat Struct Mol Biol. 2013;20 (11):1237-9. doi: 10.1038/nsmb.2709. PubMed PMID:24197163 .
  31. Eren, E, Parkin, J, Adelanwa, A, Cheneke, B, Movileanu, L, Khalid, S et al.. Toward understanding the outer membrane uptake of small molecules by Pseudomonas aeruginosa. J Biol Chem. 2013;288 (17):12042-53. doi: 10.1074/jbc.M113.463570. PubMed PMID:23467408 PubMed Central PMC3636890.
  32. van den Berg, B. Structural basis for outer membrane sugar uptake in pseudomonads. J Biol Chem. 2012;287 (49):41044-52. doi: 10.1074/jbc.M112.408518. PubMed PMID:23066028 PubMed Central PMC3510807.
  33. Liu, J, Wolfe, AJ, Eren, E, Vijayaraghavan, J, Indic, M, van den Berg, B et al.. Cation selectivity is a conserved feature in the OccD subfamily of Pseudomonas aeruginosa. Biochim Biophys Acta. 2012;1818 (11):2908-16. doi: 10.1016/j.bbamem.2012.07.009. PubMed PMID:22824298 PubMed Central PMC3424372.
  34. Cheneke, BR, Indic, M, van den Berg, B, Movileanu, L. An outer membrane protein undergoes enthalpy- and entropy-driven transitions. Biochemistry. 2012;51 (26):5348-58. doi: 10.1021/bi300332z. PubMed PMID:22680931 PubMed Central PMC3448022.
  35. Eren, E, van den Berg, B. Structural basis for activation of an integral membrane protease by lipopolysaccharide. J Biol Chem. 2012;287 (28):23971-6. doi: 10.1074/jbc.M112.376418. PubMed PMID:22645135 PubMed Central PMC3390672.
  36. Liu, J, Eren, E, Vijayaraghavan, J, Cheneke, BR, Indic, M, van den Berg, B et al.. OccK channels from Pseudomonas aeruginosa exhibit diverse single-channel electrical signatures but conserved anion selectivity. Biochemistry. 2012;51 (11):2319-30. doi: 10.1021/bi300066w. PubMed PMID:22369314 PubMed Central PMC3311111.
  37. Eren, E, Vijayaraghavan, J, Liu, J, Cheneke, BR, Touw, DS, Lepore, BW et al.. Substrate specificity within a family of outer membrane carboxylate channels. PLoS Biol. 2012;10 (1):e1001242. doi: 10.1371/journal.pbio.1001242. PubMed PMID:22272184 PubMed Central PMC3260308.
  38. Lepore, BW, Indic, M, Pham, H, Hearn, EM, Patel, DR, van den Berg, B et al.. Ligand-gated diffusion across the bacterial outer membrane. Proc Natl Acad Sci U S A. 2011;108 (25):10121-6. doi: 10.1073/pnas.1018532108. PubMed PMID:21593406 PubMed Central PMC3121852.
  39. 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):4987-97. doi: 10.1021/bi200454j. PubMed PMID:21548584 PubMed Central PMC3107985.
  40. 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. doi: 10.1371/journal.pone.0015610. PubMed PMID:21249122 PubMed Central PMC3017539.
  41. 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. doi: 10.1371/journal.pone.0015016. PubMed PMID:21124774 PubMed Central PMC2993939.
  42. van den Berg, B. Bacterial cleanup: lateral diffusion of hydrophobic molecules through protein channel walls. Biomol Concepts. 2010;1 (3-4):263-70. doi: 10.1515/bmc.2010.024. PubMed PMID:25962002 .
  43. 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):809-18. doi: 10.1016/j.str.2010.03.013. PubMed PMID:20637417 .
  44. van den Berg, B. Going forward laterally: transmembrane passage of hydrophobic molecules through protein channel walls. Chembiochem. 2010;11 (10):1339-43. doi: 10.1002/cbic.201000105. PubMed PMID:20533493 PubMed Central PMC3013500.
  45. van den Berg, B. Crystal structure of a full-length autotransporter. J Mol Biol. 2010;396 (3):627-33. doi: 10.1016/j.jmb.2009.12.061. PubMed PMID:20060837 .
  46. 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):367-70. doi: 10.1038/nature07678. PubMed PMID:19182779 PubMed Central PMC2658730.
  47. 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):1027-35. doi: 10.1016/j.str.2008.04.009. PubMed PMID:18611376 .
  48. Hearn, EM, Patel, DR, van den Berg, B. Outer-membrane transport of aromatic hydrocarbons as a first step in biodegradation. Proc Natl Acad Sci U S A. 2008;105 (25):8601-6. doi: 10.1073/pnas.0801264105. PubMed PMID:18559855 PubMed Central PMC2438428.
  49. 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. doi: 10.1038/nsmb1304. PubMed PMID:17952093 .
  50. Subbarao, GV, van den Berg, B. Crystal structure of the monomeric porin OmpG. J Mol Biol. 2006;360 (4):750-9. doi: 10.1016/j.jmb.2006.05.045. PubMed PMID:16797588 .
  51. 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. doi: 10.1074/jbc.M512365200. PubMed PMID:16414958 .
  52. van den Berg, B. The FadL family: unusual transporters for unusual substrates. Curr Opin Struct Biol. 2005;15 (4):401-7. doi: 10.1016/ PubMed PMID:16005205 .
  53. Ye, J, van den Berg, B. Crystal structure of the bacterial nucleoside transporter Tsx. EMBO J. 2004;23 (16):3187-95. doi: 10.1038/sj.emboj.7600330. PubMed PMID:15272310 PubMed Central PMC514505.
  54. 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):1506-9. doi: 10.1126/science.1097524. PubMed PMID:15178802 .
  55. van den Berg, BM, Beekhuizen, H, Willems, RJ, Mooi, FR, van Furth, R. Role of Bordetella pertussis virulence factors in adherence to epithelial cell lines derived from the human respiratory tract. Infect Immun. 1999;67 (3):1056-62. doi: 10.1128/IAI.67.3.1056-1062.1999. PubMed PMID:10024543 PubMed Central PMC96429.
  56. van den Berg, BM, Beekhuizen, H, Mooi, FR, van Furth, R. Role of antibodies against Bordetella pertussis virulence factors in adherence of Bordetella pertussis and Bordetella parapertussis to human bronchial epithelial cells. Infect Immun. 1999;67 (3):1050-5. doi: 10.1128/IAI.67.3.1050-1055.1999. PubMed PMID:10024542 PubMed Central PMC96428.
  57. Hazenbos, WL, van den Berg, BM, Geuijen, CW, Mooi, FR, van Furth, R. Binding of FimD on Bordetella pertussis to very late antigen-5 on monocytes activates complement receptor type 3 via protein tyrosine kinases. J Immunol. 1995;155 (8):3972-8. . PubMed PMID:7561105 .
  58. Hazenbos, WL, Geuijen, CA, van den Berg, BM, Mooi, FR, van Furth, R. Bordetella pertussis fimbriae bind to human monocytes via the minor fimbrial subunit FimD. J Infect Dis. 1995;171 (4):924-9. doi: 10.1093/infdis/171.4.924. PubMed PMID:7706820 .
  59. Hazenbos, WL, van den Berg, BM, van't Wout, JW, Mooi, FR, van Furth, R. Virulence factors determine attachment and ingestion of nonopsonized and opsonized Bordetella pertussis by human monocytes. Infect Immun. 1994;62 (11):4818-24. doi: 10.1128/iai.62.11.4818-4824.1994. PubMed PMID:7927760 PubMed Central PMC303192.
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