Bert Poolman

Summary

Affiliation: University of Groningen
Country: The Netherlands

Publications

  1. ncbi request reprint Lateral diffusion of membrane proteins
    Sivaramakrishnan Ramadurai
    Department of Biochemistry, Groningen Biomolecular science and Biotechnology Institute and Zernike Institute of Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    J Am Chem Soc 131:12650-6. 2009
  2. ncbi request reprint How do membrane proteins sense water stress?
    Bert Poolman
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh, Groningen, The Netherlands
    Mol Microbiol 44:889-902. 2002
  3. ncbi request reprint Transporters and their roles in LAB cell physiology
    Bert Poolman
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    Antonie Van Leeuwenhoek 82:147-64. 2002
  4. ncbi request reprint Bacterial osmosensing: roles of membrane structure and electrostatics in lipid-protein and protein-protein interactions
    Bert Poolman
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology and Materials Science Center plus, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    Biochim Biophys Acta 1666:88-104. 2004
  5. ncbi request reprint Substrate-induced conformational changes in the membrane-embedded IIC(mtl)-domain of the mannitol permease from Escherichia coli, EnzymeII(mtl), probed by tryptophan phosphorescence spectroscopy
    Gertjan Veldhuis
    Department of Biochemistry and Biophysical Chemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    J Biol Chem 280:35148-56. 2005
  6. pmc Stoichiometry and substrate affinity of the mannitol transporter, EnzymeIImtl, from Escherichia coli
    Gertjan Veldhuis
    Department of Biochemistry and Biophysical Chemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
    Biophys J 89:201-10. 2005
  7. pmc Engineering of ion sensing by the cystathionine beta-synthase module of the ABC transporter OpuA
    Nik A B N Mahmood
    Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, and Zernike Institute for Advanced Materials and Centre for Synthetic Biology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    J Biol Chem 284:14368-76. 2009
  8. ncbi request reprint Identification of the dimer interface of the lactose transport protein from Streptococcus thermophilus
    Eric R Geertsma
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
    J Mol Biol 332:1165-74. 2003
  9. pmc The oligomeric state and stability of the mannitol transporter, EnzymeII(mtl), from Escherichia coli: a fluorescence correlation spectroscopy study
    Gertjan Veldhuis
    Department of Biochemistry and Biophysical Chemistry, Groningen Biomolecular Science and Biotechnology Institute and Materials Science Centreplus, University of Groningen, The Netherlands
    Protein Sci 15:1977-86. 2006
  10. doi request reprint Quaternary structure of SecA in solution and bound to SecYEG probed at the single molecule level
    Ilja Kusters
    Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
    Structure 19:430-9. 2011

Collaborators

Detail Information

Publications85

  1. ncbi request reprint Lateral diffusion of membrane proteins
    Sivaramakrishnan Ramadurai
    Department of Biochemistry, Groningen Biomolecular science and Biotechnology Institute and Zernike Institute of Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    J Am Chem Soc 131:12650-6. 2009
    ....
  2. ncbi request reprint How do membrane proteins sense water stress?
    Bert Poolman
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh, Groningen, The Netherlands
    Mol Microbiol 44:889-902. 2002
    ....
  3. ncbi request reprint Transporters and their roles in LAB cell physiology
    Bert Poolman
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    Antonie Van Leeuwenhoek 82:147-64. 2002
    ..The mechanosensitive channels have been best studied in organisms other than LAB, but the presence of similar systems in LAB, and their conservation of structure, suggest that the postulated functions and mechanisms generally hold...
  4. ncbi request reprint Bacterial osmosensing: roles of membrane structure and electrostatics in lipid-protein and protein-protein interactions
    Bert Poolman
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology and Materials Science Center plus, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    Biochim Biophys Acta 1666:88-104. 2004
    ..7 mV for monovalent ions. The osmosensing mechanism is qualitatively described as an "ON/OFF switch" representing thermally relaxed and electrostatically locked protein conformations...
  5. ncbi request reprint Substrate-induced conformational changes in the membrane-embedded IIC(mtl)-domain of the mannitol permease from Escherichia coli, EnzymeII(mtl), probed by tryptophan phosphorescence spectroscopy
    Gertjan Veldhuis
    Department of Biochemistry and Biophysical Chemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    J Biol Chem 280:35148-56. 2005
    ..The observations are discussed in context of the current mechanistic and structural model of EII(mtl)...
  6. pmc Stoichiometry and substrate affinity of the mannitol transporter, EnzymeIImtl, from Escherichia coli
    Gertjan Veldhuis
    Department of Biochemistry and Biophysical Chemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
    Biophys J 89:201-10. 2005
    ..The dependency could be simulated assuming that >50% of the binding sites were occupied with a ligand that shows an affinity for EnzymeIImtl in the same range as mannitol...
  7. pmc Engineering of ion sensing by the cystathionine beta-synthase module of the ABC transporter OpuA
    Nik A B N Mahmood
    Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, and Zernike Institute for Advanced Materials and Centre for Synthetic Biology, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    J Biol Chem 284:14368-76. 2009
    ....
  8. ncbi request reprint Identification of the dimer interface of the lactose transport protein from Streptococcus thermophilus
    Eric R Geertsma
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
    J Mol Biol 332:1165-74. 2003
    ..The four regions of the protein located at the dimer interface are close to the extracellular ends of transmembrane segments V and VIII and the intracellular ends of transmembrane segments VI and VII...
  9. pmc The oligomeric state and stability of the mannitol transporter, EnzymeII(mtl), from Escherichia coli: a fluorescence correlation spectroscopy study
    Gertjan Veldhuis
    Department of Biochemistry and Biophysical Chemistry, Groningen Biomolecular Science and Biotechnology Institute and Materials Science Centreplus, University of Groningen, The Netherlands
    Protein Sci 15:1977-86. 2006
    ....
  10. doi request reprint Quaternary structure of SecA in solution and bound to SecYEG probed at the single molecule level
    Ilja Kusters
    Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
    Structure 19:430-9. 2011
    ..A structural model for the dimeric assembly of SecA while bound to SecYEG is proposed based on the crystal structures of the Thermotoga maritima SecA-SecYEG and the Escherichia coli SecA dimer...
  11. pmc The structural basis for peptide selection by the transport receptor OppA
    Ronnie P A Berntsson
    Biochemistry Department, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
    EMBO J 28:1332-40. 2009
    ..lactis is auxotrophic for branched chain amino acids and favours proline-rich caseins as a source of amino acids. We propose a new mechanism for peptide selection based on amino-acid composition rather than sequence...
  12. doi request reprint Evolved Lactococcus lactis strains for enhanced expression of recombinant membrane proteins
    Daniel M Linares
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    J Mol Biol 401:45-55. 2010
    ..The generality and simplicity of our approach allow rapid improvements of protein production yields by directed evolution in a high-throughput way...
  13. ncbi request reprint The first cytoplasmic loop of the mannitol permease from Escherichia coli is accessible for sulfhydryl reagents from the periplasmic side of the membrane
    Elisa B Vervoort
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    J Mol Biol 346:733-43. 2005
    ..These and other results suggest that the predicted loop between TM2 and TM3 may fold back into the membrane and form part of the translocation path...
  14. pmc Ligand binding and crystal structures of the substrate-binding domain of the ABC transporter OpuA
    Justina C Wolters
    Biochemistry Department, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre, University of Groningen, Groningen, The Netherlands
    PLoS ONE 5:e10361. 2010
    ..In this study, the ligand binding characteristics of purified OpuA in a detergent-solubilized state and of its substrate-binding domain produced as soluble protein (OpuAC) was characterized...
  15. ncbi request reprint Functional diversity of tandem substrate-binding domains in ABC transporters from pathogenic bacteria
    Faizah Fulyani
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    Structure 21:1879-88. 2013
    ..We succeeded in converting a low-affinity SBD into a high-affinity receptor and vice versa. Our data indicate that a small number of residues that reside in the binding pocket constitute the major affinity determinants of the SBDs...
  16. pmc Structural divergence of paralogous S components from ECF-type ABC transporters
    Ronnie P A Berntsson
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    Proc Natl Acad Sci U S A 109:13990-5. 2012
    ..Solitary BioY (in the absence of the ECF module) is monomeric in detergent solution and binds D-biotin with a high affinity but does not transport the substrate across the membrane...
  17. pmc Dual-color fluorescence-burst analysis to probe protein efflux through the mechanosensitive channel MscL
    Geert van den Bogaart
    Biochemistry Department, Groningen Biomolecular Science and Biotechnology Institute and Materials Science Centre, University of Groningen, Groningen, The Netherlands
    Biophys J 92:1233-40. 2007
    ..For MscL, reconstituted in large unilamellar vesicles, we show that insulin, bovine pancreas trypsin inhibitor, and other compounds smaller than 6.5 kDa can pass through MscL, whereas larger macromolecules cannot...
  18. pmc Probing receptor-translocator interactions in the oligopeptide ABC transporter by fluorescence correlation spectroscopy
    Mark K Doeven
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
    Biophys J 94:3956-65. 2008
    ..ATP-hydrolysis would complete the peptide translocation and reset the transporter for another catalytic cycle. Implications in terms of a general transport mechanism for ABC importers and exporters are discussed...
  19. pmc Distribution, lateral mobility and function of membrane proteins incorporated into giant unilamellar vesicles
    Mark K Doeven
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute and Materials Science Centre, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    Biophys J 88:1134-42. 2005
    ..In addition, we show that sucrose slows down the lateral mobility of fluorescent lipid analogs, possibly due to hydrogen-bonding with the lipid headgroups, leading to larger complexes with reduced mobility...
  20. pmc Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes
    Lars V Schäfer
    Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
    Proc Natl Acad Sci U S A 108:1343-8. 2011
    ....
  21. doi request reprint Structural basis for the enhanced activity of cyclic antimicrobial peptides: the case of BPC194
    Jacek T Mika
    Department of Biochemistry and Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
    Biochim Biophys Acta 1808:2197-205. 2011
    ..The results provide a chemical rationale for enhanced activity in certain cyclic antimicrobial peptides and can be used as a guideline for design of novel antimicrobial peptides...
  22. pmc The response of Lactococcus lactis to membrane protein production
    Ravi K R Marreddy
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
    PLoS ONE 6:e24060. 2011
    ....
  23. pmc Efficient overproduction of membrane proteins in Lactococcus lactis requires the cell envelope stress sensor/regulator couple CesSR
    Joao P C Pinto
    Groningen Biomolecular Sciences and Biotechnology Institute, Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands
    PLoS ONE 6:e21873. 2011
    ....
  24. pmc Cystathionine β-synthase (CBS) domains 1 and 2 fulfill different roles in ionic strength sensing of the ATP-binding cassette (ABC) transporter OpuA
    Akira Karasawa
    Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, Netherlands Proteomics Centre and Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
    J Biol Chem 286:37280-91. 2011
    ....
  25. ncbi request reprint Specificity and selectivity determinants of peptide transport in Lactococcus lactis and other microorganisms
    Mark K Doeven
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    Mol Microbiol 57:640-9. 2005
    ..Besides reviewing the current data on binding specificity and transport selectivity of peptide transporters in L. lactis, the possible implications for peptide utilization by other bacterial species are discussed...
  26. doi request reprint Dual-color fluorescence-burst analysis to study pore formation and protein-protein interactions
    Geert van den Bogaart
    Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    Methods 46:123-30. 2008
    ..In addition, DCFBA can be used to quantitatively measure the binding of proteins to liposomes and to membrane proteins. In this paper, we provide an overview of the method and discuss the experimental details of DCFBA...
  27. ncbi request reprint The binding specificity of OppA determines the selectivity of the oligopeptide ATP-binding cassette transporter
    Mark K Doeven
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
    J Biol Chem 279:32301-7. 2004
    ....
  28. doi request reprint Quantitative analysis of membrane protein transport across the nuclear pore complex
    Anne C Meinema
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
    Traffic 14:487-501. 2013
    ..We propose that also during passive efflux, the unfolded linker facilitates the passage of extralumenal domains through the central channel of the NPC...
  29. ncbi request reprint Substrate specificity and ionic regulation of GlnPQ from Lactococcus lactis. An ATP-binding cassette transporter with four extracytoplasmic substrate-binding domains
    Gea K Schuurman-Wolters
    Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
    J Biol Chem 280:23785-90. 2005
    ..The regulation of GlnPQ conforms to an electrostatic switch in which protein domain(s) and low molecular weight electrolytes participate...
  30. pmc Importance of a hydrophobic pocket for peptide binding in lactococcal OppA
    Ronnie P A Berntsson
    Biochemistry Department, Groningen Biomolecular Sciences and Biotechnology Center, NPC and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    J Bacteriol 193:4254-6. 2011
    ..Two crystal structures of OppA with different nonapeptides now indeed show binding in different registers...
  31. doi request reprint Domain complementation studies reveal residues critical for the activity of the mannitol permease from Escherichia coli
    Erwin P P Vos
    Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    Biochim Biophys Acta 1788:581-6. 2009
    ..The involvement of specific residue positions in the oligomeric functioning of a sugar-translocating EII protein has not been presented before...
  32. doi request reprint Long unfolded linkers facilitate membrane protein import through the nuclear pore complex
    Anne C Meinema
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
    Science 333:90-3. 2011
    ..We propose an import mechanism for membrane proteins in which an unfolded linker slices through the NPC scaffold to enable binding between the transport factor and the FG domains in the center of the NPC...
  33. doi request reprint Effect of iTRAQ labeling on the relative abundance of peptide fragment ions produced by MALDI-MS/MS
    Tejas Gandhi
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
    J Proteome Res 11:4044-51. 2012
    ..This information will be useful for the development of improved method-specific intensity-based protein identification algorithms...
  34. pmc Evaluation of pulsed-FRAP and conventional-FRAP for determination of protein mobility in prokaryotic cells
    Jacek T Mika
    Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, Netherlands Proteomics Centre and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
    PLoS ONE 6:e25664. 2011
    ..In this study, we have evaluated two of these methods: pulsed-FRAP and "conventional"-FRAP...
  35. pmc On the mechanism of pore formation by melittin
    Geert van den Bogaart
    Department of Biochemistry, the Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, 9747AG The Netherlands
    J Biol Chem 283:33854-7. 2008
    ..The direct insertion of melittin leads to pore formation, whereas the parallel conformation is inactive and prevents other melittin molecules from inserting, hence preventing pore formation...
  36. pmc Amino acid accumulation limits the overexpression of proteins in Lactococcus lactis
    Ravi K R Marreddy
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
    PLoS ONE 5:e10317. 2010
    ..In this study, we employed a proteomic approach to understand the difference in expression levels for various multidomain membrane proteins in L. lactis cells grown in complex and synthetic media...
  37. ncbi request reprint The activity of the lactose transporter from Streptococcus thermophilus is increased by phosphorylated IIA and the action of beta-galactosidase
    Eric R Geertsma
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
    Biochemistry 44:15889-97. 2005
    ..The proposed mode of regulation thus proceeds via a mechanism opposite to the inducer exclusion type of regulation in gram-negative bacteria, where transporters are inhibited by binding of the unphosphorylated form of IIA(Glc)...
  38. ncbi request reprint The ATP/substrate stoichiometry of the ATP-binding cassette (ABC) transporter OpuA
    Jason S Patzlaff
    Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    J Biol Chem 278:29546-51. 2003
    ..ADP is an inhibitor, but accumulation of ADP was negligible in the assays with inside-out-oriented OpuA, and potential effects of the ATP/ADP ratio on the ATP/substrate stoichiometry determinations could be eliminated...
  39. pmc Influence of hydrophobic mismatch and amino acid composition on the lateral diffusion of transmembrane peptides
    Sivaramakrishnan Ramadurai
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre, and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
    Biophys J 99:1447-54. 2010
    ..The specific lipid headgroup composition of the membrane has a much less pronounced impact on the diffusion of the peptides than does the hydrophobic thickness...
  40. ncbi request reprint Protein mobility and diffusive barriers in Escherichia coli: consequences of osmotic stress
    Geert van den Bogaart
    Biochemistry Department, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, The Netherlands
    Mol Microbiol 64:858-71. 2007
    ..Also, lowering the osmolality from 0.6 Osm back to 0.15 Osm restored the mobility of GFP. The implications of these findings in terms of heterogeneities and diffusive barriers inside the cell are discussed...
  41. pmc Lateral diffusion of membrane proteins: consequences of hydrophobic mismatch and lipid composition
    Sivaramakrishnan Ramadurai
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre and the Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh, Groningen, The Netherlands
    Biophys J 99:1482-9. 2010
    ..We conclude that the hydrophobic thickness of the bilayer is a major determinant of molecule diffusion in membranes, but protein-specific properties may lead to deviations from the Saffman-Delbrück model...
  42. ncbi request reprint Biochemistry. A missing link in membrane protein evolution
    Bert Poolman
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands
    Science 315:1229-31. 2007
  43. doi request reprint Apex peptide elution chain selection: a new strategy for selecting precursors in 2D-LC-MALDI-TOF/TOF experiments on complex biological samples
    Tejas Gandhi
    Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
    J Proteome Res 9:5922-8. 2010
    ..Consequently, reduced sample depletion allowed further selection of lower signal-to-noise ratio precursor ions, leading to a larger number of identified unique peptides...
  44. doi request reprint The structural basis of modularity in ECF-type ABC transporters
    Guus B Erkens
    University of Groningen, Groningen Biomolecular Science and Biotechnology Institute, Groningen, The Netherlands
    Nat Struct Mol Biol 18:755-60. 2011
    ..Based on these findings, we propose a general transport mechanism for ECF transporters...
  45. doi request reprint Evolved Escherichia coli strains for amplified, functional expression of membrane proteins
    Nadia Gul
    Department of Biochemistry, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre and Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    J Mol Biol 426:136-49. 2014
    ..We propose that (partial) removal of the transcriptional silencing mechanism changes the levels of proteins essential for the functional overexpression of membrane proteins. ..
  46. doi request reprint On the role of individual subunits in MscL gating: "all for one, one for all?"
    Jacek T Mika
    Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    FASEB J 27:882-92. 2013
    ..This suggests the presence of supplementary mechanisms other than only the hydrophobic gate for MscL opening and closing and/or insufficient expansion of the channel by hydrophobic gating in the absence of applied membrane tension...
  47. pmc Structure and mode of peptide binding of pheromone receptor PrgZ
    Ronnie P A Berntsson
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre, University of Groningen, 9747 AG Groningen, The Netherlands
    J Biol Chem 287:37165-70. 2012
    ..Comparison of PrgZ with homologous oligopeptide-binding proteins (AppA and OppA) explains the high specificity of PrgZ for hydrophobic heptapeptides versus the promiscuity of peptide binding in the homologous proteins...
  48. pmc Hydrophobic gating of mechanosensitive channel of large conductance evidenced by single-subunit resolution
    Jan Peter Birkner
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, 9747 AG Groningen, The Netherlands
    Proc Natl Acad Sci U S A 109:12944-9. 2012
    ..Such a minimal change in the pore environment seems ideal for a fast and energy-efficient response to changes in the membrane tension...
  49. doi request reprint Functional characterization of amphipathic α-helix in the osmoregulatory ABC transporter OpuA
    Nadia Gul
    Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, Netherlands Proteomics Centre and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    Biochemistry 51:5142-52. 2012
    ..We show that the amphipathic α-helix of OpuA is necessary for high activity of OpuA but is not critical for the biogenesis of the protein or the ionic regulation of transport...
  50. ncbi request reprint A karyopherin acts in localized protein synthesis
    Liesbeth M Veenhoff
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
    Cell Cycle 9:1281-5. 2010
    ..In this report, we reflect on the possible mechanisms by which Kap104p links these events and hypothesize on a possible function of the localized protein synthesis...
  51. ncbi request reprint Ion specificity and ionic strength dependence of the osmoregulatory ABC transporter OpuA
    N A B Nik Mahmood
    Membrane Enzymology Group, Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute and Materials Science Centre, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    J Biol Chem 281:29830-9. 2006
    ..Our data lend new support for the contention that the CBS module in OpuA constitutes the ionic strength sensor whose activity is modulated by the C-terminal anionic tail...
  52. ncbi request reprint Functional interactions between the subunits of the lactose transporter from Streptococcus thermophilus
    Eric R Geertsma
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
    J Mol Biol 350:102-11. 2005
    ..In addition, analysis of in tandem fused LacS subunits containing one regulatory LacS-IIA domain showed that regulation is primarily an intramolecular event...
  53. pmc Selenomethionine incorporation in proteins expressed in Lactococcus lactis
    Ronnie P A Berntsson
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    Protein Sci 18:1121-7. 2009
    ..lactis for X-ray crystallography purposes. The crystal structure of ligand-free OppA was determined at 2.4 A resolution by a semiautomatic approach using selenium single-wavelength anomalous diffraction phasing...
  54. pmc Quality control of overexpressed membrane proteins
    Eric R Geertsma
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
    Proc Natl Acad Sci U S A 105:5722-7. 2008
    ..The method allows for rapid screening and, importantly, pinpointing the most likely bottlenecks in protein production...
  55. pmc Dual action of BPC194: a membrane active peptide killing bacterial cells
    Gemma Moiset
    Departments of Biochemistry and Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute GBB and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
    PLoS ONE 8:e61541. 2013
    ..We show that the cyclic antimicrobial peptides trigger both fusion and pore formation and that such large membrane perturbations have a similar mechanistic basis...
  56. pmc A sensor for intracellular ionic strength
    Esther Biemans-Oldehinkel
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    Proc Natl Acad Sci U S A 103:10624-9. 2006
    ..We present a model for the gating of membrane transport by ionic strength and propose a new role for CBS domains...
  57. pmc On the decrease in lateral mobility of phospholipids by sugars
    Geert van den Bogaart
    Biochemistry Department, Ultrafast Laser and Spectroscopy Laboratory, Groningen Biomolecular Science and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    Biophys J 92:1598-605. 2007
    ..Using coarse-grained molecular dynamics, we show that this increase in interactions can lead to a relatively large decrease in lateral phospholipid mobility...
  58. ncbi request reprint Lactococcus lactis uses MscL as its principal mechanosensitive channel
    Joost H A Folgering
    Department of Biochemistry, Groninger Biomolecular Sciences and Biotechnology Institute and Material Science Centreplus, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
    J Biol Chem 280:8784-92. 2005
    ..The data strongly suggest that L. lactis uses MscL as the main mechanosensitive solute release system to protect the cells under conditions of osmotic downshift...
  59. ncbi request reprint Functional analysis of detergent-solubilized and membrane-reconstituted ATP-binding cassette transporters
    Bert Poolman
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute and Materials Science Centre plus, University of Groningen, The Netherlands
    Methods Enzymol 400:429-59. 2005
    ..Also, we present simple methods, based on substrate binding or translocation, to follow the activity of the protein complexes in detergent-solubilized and/or membrane-reconstituted state(s)...
  60. pmc A method for site-specific labeling of multiple protein thiols
    Johanna M Kuiper
    Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
    Protein Sci 18:1033-41. 2009
    ..The average labeling efficiency was approximately 80% for the single thiol and 65-90% for the dithiol site...
  61. ncbi request reprint Production of membrane proteins in Escherichia coli and Lactococcus lactis
    Eric R Geertsma
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre, University of Groningen, The Netherlands
    Methods Mol Biol 601:17-38. 2010
    ..Here, we detail methodology to rapidly establish and optimize (membrane) protein expression in Escherichia coli and Lactococcus lactis...
  62. doi request reprint Membrane reconstitution of ABC transporters and assays of translocator function
    Eric R Geertsma
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    Nat Protoc 3:256-66. 2008
    ..The full protocol can be completed within 4-5 d...
  63. ncbi request reprint Lipid-mediated light activation of a mechanosensitive channel of large conductance
    Joost H A Folgering
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute and Materials Science Center, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    Langmuir 20:6985-7. 2004
    ..Light-induced isomerization of the azobenzene moiety of 4-Azo-5P from trans to cis was used to activate MscL...
  64. ncbi request reprint Two homologous oligopeptide binding protein genes (oppA) in Lactococcus lactis opp2 [corrected]
    Yolanda Sanz
    Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, NL 9751 NN, Haren, The Netherlands
    Int J Food Microbiol 97:9-15. 2004
    ..The differences in the ability to utilize this pentapeptide were not due to differences in expression levels but most likely reflect a different catalytic efficiency in oligopeptide utilization when AppA is used as ligand receptor...
  65. pmc Engineering covalent oligomers of the mechanosensitive channel of large conductance from Escherichia coli with native conductance and gating characteristics
    Joost H A Folgering
    Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
    Protein Sci 14:2947-54. 2005
    ..The in vivo data strongly suggest that pentameric MscL represents the functional state of the channel...
  66. ncbi request reprint Quaternary structure and function of transport proteins
    Liesbeth M Veenhoff
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4 9747 AG Groningen, The Netherlands
    Trends Biochem Sci 27:242-9. 2002
    ..This review evaluates knowledge of the functions that are associated with the oligomeric organization of secondary transport proteins, which are a major class of solute-translocation systems in all living species...
  67. pmc Proteomics of Saccharomyces cerevisiae Organelles
    Elena Wiederhold
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    Mol Cell Proteomics 9:431-45. 2010
    ....
  68. doi request reprint Purification and functional reconstitution of the bacterial protein translocation pore, the SecYEG complex
    Ilja Kusters
    Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
    Methods Mol Biol 619:131-43. 2010
    ..In addition, fluorescence based in vitro assays are described that allow monitoring translocation activity discontinuously and in real time...
  69. doi request reprint Design and synthesis of ATP-based nucleotide analogues and profiling of nucleotide-binding proteins
    Justina C Wolters
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    Bioconjug Chem 22:1345-53. 2011
    ..p-BABA-ATP and p-BAMBA-ATP both bind to ATP-binding cassette (ABC) proteins with at least 10-fold higher affinity than ATP. Several ABC transporters could be enriched using p-BABA-ATP or p-BAMBA-ATP...
  70. ncbi request reprint ABC transporter architecture and regulatory roles of accessory domains
    Esther Biemans-Oldehinkel
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    FEBS Lett 580:1023-35. 2006
    ..The regulatory domains add unique functions to the transporters allowing the systems to act as channel conductance regulators, osmosensors/regulators, and assemble into macromolecular complexes with specific properties...
  71. ncbi request reprint A structural classification of substrate-binding proteins
    Ronnie P A Berntsson
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
    FEBS Lett 584:2606-17. 2010
    ....
  72. ncbi request reprint High-throughput cloning and expression in recalcitrant bacteria
    Eric R Geertsma
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
    Nat Methods 4:705-7. 2007
    ..We demonstrated VBEx proof of principle for Lactococcus lactis, but the method can be adapted to all organisms for which plasmids are available...
  73. pmc On the role of the two extracytoplasmic substrate-binding domains in the ABC transporter OpuA
    Esther Biemans-Oldehinkel
    Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    EMBO J 22:5983-93. 2003
    ..These new insights on the functional role of the extracytoplasmic SBDs are discussed in the light of the current knowledge of substrate-binding-protein-dependent ABC transporters...
  74. ncbi request reprint Spatial organization of bacteriorhodopsin in model membranes. Light-induced mobility changes
    Nicoletta Kahya
    Ultrafast Laser and Spectroscopy Laboratory, Optical Sciences, Materials Science Centre, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    J Biol Chem 277:39304-11. 2002
    ..These observations are fully supported by freeze-fracture electron microscopy, and the size of the clusters during photoactivation was estimated to consist of two or three trimers...
  75. ncbi request reprint Oligomeric state of membrane transport proteins analyzed with blue native electrophoresis and analytical ultracentrifugation
    Esther H M L Heuberger
    Department of Biochemistry Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
    J Mol Biol 317:591-600. 2002
    ..Our data underscore the fact that the oligomeric state of many membrane transport proteins is dimeric...
  76. ncbi request reprint Mapping of the dimer interface of the Escherichia coli mannitol permease by cysteine cross-linking
    Bart A van Montfort
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    J Biol Chem 277:14717-23. 2002
    ..In combination with the recently obtained projection structure of the IIC domain in two-dimensional crystals, a first proposal is made for alpha-helix packing in the mannitol permease...
  77. pmc The lipid dependence of melittin action investigated by dual-color fluorescence burst analysis
    Geert van den Bogaart
    Biochemistry Department, Groningen Biomolecular Science and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
    Biophys J 93:154-63. 2007
    ..Experiments with liposomes prepared from Escherichia coli lipid extracts and intact cells of Lactococcus lactis indicate that both mechanisms are physiologically relevant...
  78. pmc ABC transporters: one, two or four extracytoplasmic substrate-binding sites?
    Tiemen van der Heide
    Department of Biotehnology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
    EMBO Rep 3:938-43. 2002
    ..We also discuss the implications of multiple substrate-binding sites in close proximity to the translocator in terms of broadened substrate specificity and possible cooperative interactions between SBPs and the translocator...
  79. ncbi request reprint Combined in-gel tryptic digestion and CNBr cleavage for the generation of peptide maps of an integral membrane protein with MALDI-TOF mass spectrometry
    Bart A van Montfort
    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
    Biochim Biophys Acta 1555:111-5. 2002
    ..The fragments formed are predominantly below m/z 2500, which allows accurate mass measurement...
  80. doi request reprint Proteomic analysis of secreted membrane vesicles of archaeal Sulfolobus species reveals the presence of endosome sorting complex components
    Albert F Ellen
    Department of Molecular Microbiology Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
    Extremophiles 13:67-79. 2009
    ..These data suggest that the membrane vesicles in Sulfolobus sp. emerge from a specific budding process with similarity to the endosomal sorting pathway...
  81. ncbi request reprint Probing lipid mobility of raft-exhibiting model membranes by fluorescence correlation spectroscopy
    Nicoletta Kahya
    Experimental Biophysics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany
    J Biol Chem 278:28109-15. 2003
    ..Moreover, FCS data from ternary and binary mixtures have been used to build a ternary phase diagram, which shows areas of phase coexistence, transition points, and, importantly, how lipid dynamics varies between and within phase regions...
  82. ncbi request reprint In vitro functional characterization of BtuCD-F, the Escherichia coli ABC transporter for vitamin B12 uptake
    Elizabeth L Borths
    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
    Biochemistry 44:16301-9. 2005
    ....
  83. pmc The riboflavin transporter RibU in Lactococcus lactis: molecular characterization of gene expression and the transport mechanism
    Catherine M Burgess
    Alimentary Pharmabiotic Centre, Department of Microbiology and Biosciences Institute, National University of Ireland Cork, Western Road, Cork, Ireland
    J Bacteriol 188:2752-60. 2006
    ..The presented transport data are consistent with a uniport mechanism for riboflavin translocation and provide the first detailed molecular and functional analysis of a bacterial protein involved in riboflavin transport...
  84. ncbi request reprint Electrochemical structure of the crowded cytoplasm
    Jan J Spitzer
    IPM Emulsion Polymer Research, 6643 Lyndonville Drive, Charlotte, NC 28277 4616, USA
    Trends Biochem Sci 30:536-41. 2005
    ..The electrochemical gradients are brought about by cellular biochemical reactions and by extracellular stimuli. The cellular metabolism is thus vectorial not only across the membrane but also throughout the cytoplasm...
  85. ncbi request reprint Specificity of the second binding protein of the peptide ABC-transporter (Dpp) of Lactococcus lactis IL1403
    Yolanda Sanz
    Instituto de Agroqui mica y Tecnologi a de Alimentos C S I C, Apartado 73, 46100, Valencia, Burjasot, Spain
    FEMS Microbiol Lett 227:33-8. 2003
    ..Remarkably, the features (ii), (iii) and (iv) differ from those previously reported for DppA-His(6), suggesting that DppP-His(6) is a more versatile peptide-binding protein that could have additional functions...