Publications of MoRe Members

 

2013

L. Gelens, L. Hill, A. Vandervelde, J. Danckaert & R. Loris (2013) A general model for toxin-antitoxin module dynamics can explain persister cell formation in E. coli. PLoS Comput. Biol. 9, e1003190.

S. Hadzi, A. Garcia-Pino, S. Martinez-Rodriguez, K. Verschueren, M. Christensen-Dalsgaard, K. Gerdes, J. Lah & R. Loris (2013) Crystallization of the HigBA2 toxin-antitoxin complex from Vibrio cholerae. Acta Crystallogr. F. 69, 1052-9.

J.L. Ortega Roldan, S. Casares, M.R. Jensen, N. Cardenes, J. Bravo, M. Blackledge, A.I. Azuaga & N.A.J. van Nuland (2013) Distinct ubiquitin binding modes exhibited by SH3 domains: Molecular determinants and functional implications. PLoS One 8, e73018.

S. Vanwetswinkel, N.A.J. van Nuland & A.N. Volkov (2013) Paramagnetic properties of the low- and high-spin states of yeast cytochrome c peroxidase. J. Biomol. NMR 57, 21-6.

M.G.K. Ghequire, E. De Canck, P. Wattiau, I. Van Winge, R. Loris, T. Coenye & R. De Mot (2013) Antibacterial activity of a lectin-like Burkholderia cenocepacia protein. MicrobiologyOpen 2, 566-75.

L. Rubio, R. Huculeci, L. Buts, S. Vanwetswinkel, T. Lenaerts & N.A.J. van Nuland (2013) 1H, 13C, and 15N backbone and side-chain chemical shift assignments of the free and bound forms of the human PTPN11 second SH2 domain. Biomol. NMR Assign., in press.

M.A. Ceregido, A. Garcia-Pino, J.L. Ortega-Roldan, S. Casares, O. López Mayorga, J. Bravo, N.A.J. van Nuland & A.I. Azuaga (2013) Multimeric and differential binding of CIN85/CD2AP with two atypical proline-rich sequences from CD2 and Cbl-b. FEBS Journal 280, 3399-415.

A.N. Volkov & N.A.J. van Nuland (2013) Solution NMR study of the yeast cytochrome c peroxidase - cytochrome c interaction. J. Biomol. NMR 56, 255-63.

A.N. Volkov, A. Wohlkonig, S.H. Soror & N.A.J. van Nuland (2013) Expression, purification, characterization, and solution nuclear magnetic resonance study of highly deuterated yeast cytochrome c peroxidase with enhanced solubility. Biochemistry 52, 2165-75.

M.G.K. Ghequire, A. Garcia-Pino, E.K.M. Lebbe, S. Spaepen, R. Loris & R. De Mot (2013) Structural determinants for activity and specificity of the bacterial toxin LlpA. PLoS Pathogens 9, e1003199.

S. De Gieter, R. Loris, N.A.J. van Nuland & A. Garcia-Pino (2013) 1H, 13C, and 15N backbone and sidechain chemical shift assignments of the toxin Doc in the unbound state. Biomol. NMR Assign., in press.

P. Guerry, L. Salmon, L. Mollica, J.L. Ortega Roldan, P. Markwick, N.A.J. van Nuland, J.A. McCammon & M. Blackledge (2013) Mapping the population of protein confromational energy sub-states from NMR dipolar couplings. Angew. Chem. Int. Ed. 52, 3181-5.

A. Vuchelen, E. Pardon, J. Steyaert, B. Gamain, R. Loris, N.A.J. van Nuland & S. Ramboarina (2013) Production, crystallisation and X-ray diffraction analysis of two nanobodies against the Duffy Binding like (DBL) domain DBL6e-FCR3 of the Plasmodium falciparum VAR2CSA protein. Acta Crystallogr. F. 69, 270-4.

I. Drobnak, N. De Jonge, S. Haesaerts, G. Vesnaver, R. Loris & J. Lah (2013) Energetic basis of uncoupling folding from binding for an intrinsically disordered protein. J. Am. Chem. Soc. 135, 1288-94.

 

2012

M.G.K. Ghequire, W. Li, P. Proost, R. Loris, T. Coenye & R. De Mot (2012) Plant lectin-like antibacterial proteins from phytopathogens Pseudomonas syringae and Xanthomonas citri. Environ.Microbiol.Rep 4, 373-80.

D.M. Shah, E. AB, T. Diercks, M.A.S. Hass, N.A.J. van Nuland & G.D. Siegal (2012) Rapid protein-ligand co-structures from sparse NOE data. J. Med. Chem. 55, 10786-90.

A.N. Volkov & N.A.J. van Nuland (2012) Electron transfer interactome of cytochrome c. PLoS Comput. Biol. 8, e1002807.

M.G.K. Ghequire, R. Loris & R. De Mot (2012) MMBL proteins: from lectin to bacteriocin. Biochem. Soc. Trans. 40, 1553-59.

A. Vandersteen*, E. Hubin*, R. Sarroukh, G. De Baets, J. Schymkowitz, F. Rousseau, V. Subramaniam, V. Raussens, H. Wenschuh, D. Wildemann & K.A. Broersen (2012) A comparative analysis of the aggregation behavior fo amyloid-b peptide variants. FEBS Lett. 586, 4088-93 (*contributed equally).

J.F. Doreleijers, A.W. Sousa da Silva, E. Krieger, S.B. Nabuurs, C.A.E.M. Spronk, T.J. Stevens, W.F. Vranken, G. Vriend & G.W. Vuister (2012) CING: an integrated residue-based structure validation program suite. J. Biomol. NMR 54, 267-83.

K. Van Laer, L. Buts, N. Foloppe, D. Vertommen, K. Van Belle, K. Wahni, G. Roos, L. Nilsson, L.M. Mateos, M. Rawat, N.A.J. van Nuland & J. Messens (2012) Mycoredoxin-1 is one of the missing links in the oxidative stress defense mechanism of Mycobacteria. Mol. Microbiol. 86, 787-804.

M. Szpakowska, V. Fievez, K. Arumugan, N. van Nuland, J.C. Schmit & A. Chevigne (2012) Function and diversity of the N-terminal domain of human chemokine receptors. Biochem. Pharmacol. 84, 1366-80.

S. Martinez-Rodriguez, A. Garcia-Pino, F.J. Las Heras-Vazquez, J.M. Clemente-Jimenez, F. Rodriguez-Vico, J.M. Garcia-Ruiz, R. Loris & J.A. Gavira (2012) Mutational and structural analysis of L-N-carbamoylase: new insights into a peptidase M20/M25/M40 family member. J. Bacteriol. 194, 5759-68.

A.W. Sousa da Silva & W.F. Vranken (2012) ACPYPE - AnteChamber PYthon Parser interfacE. BMC Res. Notes 5, 367.

E. Baranova, R. Fronzes, A. Garcia-Pino, N. Van Gerven, D. Papapostolou, G. Péhau-Arnaudet, E. Pardon, J. Steyaert, S. Howorka & H. Remaut (2012) SbsB structure and lattice reconstruction unveil Ca(2+)-triggered S-layer assembly. Nature 487, 119-22.

L. Salmon, L. Pierce, A. Grimm, J.L. Ortega Roldan, L. Mollica, M.R. Jensen, N. van Nuland, P.R.L. Markwick, J.A. McCammon & M. Blackledge (2012) Multi-timescale conformational dynamics of the SH3 domain of CD2-associated protein using NMR spectroscopy and accelerated molecular dynamics. Angew. Chem. Int. Ed. 41, 6103-6.

N. De Jonge, M. Simic, L. Buts, K. Roelants, A. Garcia-Pino,  Y. Sterckx, H. De Greve, J. Lah & R. Loris (2012) Alternative interactions define gyrase specificity in the CcdB family. Mol. Microbiol. 84, 965-78.

Y. Sterckx, A. Garcia-Pino, S. Haesaerts, T. Jové, L. Geerts, V. Sakellaris, L. Van Melderen & R. Loris (2012) The ParE2-PaaA2 toxin-antitoxin complex from Escherichia coli O157 forms a heterododecamer in solution and in the crystal. Acta Crystallogr. F. 68, 724-9.

A. Sahakyan, A. Cavalli, W.F. Vranken & M. Vendruscolo (2012) Protein structure validation using side-chain chemical shifts. J.Phys.Chem.B 116, 4754-9.

C. Camilloni, A. De Simone, W.F. Vranken & M. Vendruscolo (2012) Determination of secondary structure populations in disordered states of proteins using NMR chemical shifts. Biochemistry 51, 2224-31.

R. Huculeci, L. Buts, T. Lenaerts, N.A.J. van Nuland & A. Garcia-Pino (2012) Purification, crystallization and preliminary X-ray diffraction analysis of the Fyn SH2 domain and its complex with a phosphotyrosine peptide. Acta Crystallogr. F. 68, 359-64.

A.N. Volkov, S. Vanwetswinkel, K. Van de Water & N.A.J. van Nuland (2012) Redox-dependent conformational changes in eukaryotic cytochromes revealed by paramagnetic NMR spectroscopy. J. Biomol. NMR. 52, 245-56. 

R.N. Abskharon, S. Ramboarina, H. El Hassan, W. Gad, M.I. Apostol, G. Giachin, G. Legname, J. Steyaert, J. Messens, S.H. Soror & A. Wohlkonig (2012) A novel expression system for production of soluble prion proteins in E. coli. Microb. Cell Fact. 11, 6.

A. Rosato, J.M. Aramini, C. Arrowsmith, A. Bagaria, D. Baker, A. Cavalli, J.F. Doreleijers, A. Eletsky, A. Giachetti, P. Guerry, A. Gutmanas, P. Güntert, Y. He, T. Herrmann, Y.J. Huang, V. Jaravine, H.R. Jonker, M.A. Kennedy, O.F. Lange, G. Liu, T.E. Malliavin, R. Mani, B. Mao, G.T. Montelione, M. Nilges, P. Rossi, G. van der Schot, H. Schwalbe, T.A. Szyperski, M. Vendruscolo, R. Vernon, W.F. Vranken, S. de Vries, G.W. Vuister, B. Wu, Y. Yang & A.M.J.J. Bonvin (2012) Blind testing of routine, fully automated determination of protein structures from NMR data. Structure 20, 227-36.

J.F. Doreleijers, W.F. Vranken, C. Schulte, J.L. Markley, E.L. Ulrich, G. Vriend & G.W. Vuister (2012) NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB. Nucleic Acids Res. 40, D519-24.

S. Velankar, Y. Alhroub, C. Best, S. Caboche, M.J. Conroy, J.M. Dana, M.A. Fernandez Montecelo, G. van Ginkel, A. Golovin, S.P. Gore, A. Gutmanas, P. Haslam, P.M. Hendrickx, E. Heuson, M. Hirshberg, M. John, I. Lagerstedt, S. Mir, L.E. Newman, T.J. Oldfield, A. Patwardhan, L. Rinaldi, G. Sahni, E. Sanz-García, S. Sen, R. Slowley, A. Suarez-Uruena, G.J. Swaminathan, M.F. Symmons, W.F. Vranken, M. Wainwright & G.J. Kleywegt (2012) PDBe: Protein Data Bank in Europe. Nucleic Acids Res. 40, D445-52.

 

2011

M. Azarkan, S. Martinez-Rodriguez, L. Buts, D. Baeyens-Volant & A. Garcia-Pino (2011) The plasticity of the β-trefoil fold constitutes an evolutionary platform for protease inhibition. J. Biol. Chem. 286, 43726-34.

M.R. Jensen, J.L. Ortega-Roldan, L. Salmon, N.A.J. van Nuland & M. Blackledge (2011) Characterizing weak protein-protein complexes by NMR residual dipolar couplings. Eur. Biophys. J. 40, 1371-81.

F. Collard, D. Vertommen, S. Constantinescu, L. Buts & E. Van Schaftingen (2011) Molecular identification of β-citrylglutamate hydrolase as glutamate carboxypeptidase 3. J. Biol. Chem. 286, 38220-38230.

A.B. Sahakyan, W.F. Vranken, A. Cavalli & M. Vendruscolo (2011) Using side-chain aromatic proton chemical shifts for a quantative analysis of protein structures. Angew. Chem. Int. Edit. 50, 9620-3.

 A.N. Volkov, P. Nicholls & J.A.R. Worrall (2011) The complex of cytochrome c and cytochrome c peroxidase: the end of the road? Biochim. Biophys. Acta 1807, 1482-503.

A.B. Sahakyan, W.F. Vranken, A. Cavalli & M. Vendruscolo (2011) Structure-based prediction of methyl chemical shifts in proteins. J.Biomol.NMR 50, 331-46.

K. Van de Water, S.H. Soror, A. Wohlkonig, N.A.J. van Nuland & A.N. Volkov (2011) Crystallization and preliminary X-ray diffraction analysis of kanamycin-binding beta-lactamase in complex with its ligand. Acta Crystallogr. F. 67, 703-6.

L. Salmon, J.L. Ortega-Roldan, E. Lescop, A. Licinio, N.A.J. van Nuland, M. Ringkjobing-Jensen & M. Blackledge (2011) Structure, dynamics and kinetics of weak protein-protein complexes from NMR spin relaxation measurements of titrated solutions. Angew. Chem. Int. Edit. 50, 3755-9.

J.L. Ortega-Roldan, M. Blackledge, N.A.J. van Nuland & A.I. Azuaga (2011)    Solution structure, dynamics and thermodynamics of the three SH3 domains of CD2AP. J. Biomol. NMR 50, 103-17.

R. Huculeci, L. Buts, T. Lenaerts & N.A.J. van Nuland (2011) 1H, 13C and 15N backbone and side-chain chemical shift assignment of the Fyn SH2 domain and its complex with a phosphotyrosine peptide. Biomol. NMR Assign. 5, 181-4.

V. Zorzini, S. Haesaerts, Z. Fu, N. Donegan, A. Cheung, N.A.J. van Nuland & R. Loris (2011) Crystallization of the Staphylococcus aureus MazF mRNA interferase. Acta Crystallogr. F. 67, 386-9.

A.N. Volkov, H. Barrios, M. Mathonet, C. Evrard, M. Ubbink, J.P. Declercq, P. Soumillion & J. Fastrez (2011) Engineering an allosteric binding site for aminoglycosides into the TEM-1 beta-lactamase. ChemBioChem 12, 904-13. 

V. Zorzini, S. Haesaerts, A. Cheung, R. Loris & N.A.J. van Nuland (2011) 1H, 13C, and 15N backbone and side-chain chemical shift assignment of the staphylococcal MazF mRNA interferase. Biomol. NMR Assign. 5, 157-60.

A. Bernard, W.F. Vranken, B. Bardiaux, M. Nilges & T. Malliavin (2011) Bayesian estimation of NMR restraint potential and weight: a validation on a representative set of protein structures. Proteins 79, 1525-37.

C.W. von der Lieth, A. Ardá Freire, D. Blank, M.P. Campbell, A. Ceroni, D.R. Damerell, A. Dell, R.A. Dwek, B. Ernst, R. Fogh, M. Frank, H. Geyer, R. Geyer, M.J. Harrison, K. Henrick, S. Herget, W.E. Hull, J. Ionides, H.J. Joshi, J.P. Kamerling, B.R. Leeflang, T. Lütteke, M. Lundborg, K. Maass, A. Merry, R. Ranzinger, J. Rosen, L. Royle, P.M. Rudd, S. Schloissnig, R. Stenutz, W.F. Vranken, G. Widmalm & S.M. Haslam (2011) EUROCarbDB: An open-access platform for glycoinformatics. Glycobiology 21, 493-502.

S. Velankar, Y. Alhroub, A. Alili, C. Best, H.C. Boutselakis, S. Caboche, M.J. Conroy, A. W. Sousa Da Silva, J.M. Dana, A. Golovin, S. Gore, A. Gutmanas, P. Haslam, M. Hirshberg, M. John, I. Lagerstedt, S. Mir, L. E. Newman, T. Oldfield, C.J. Penkett , J. Pineda-Castillo, L. Rinaldi, G. Sahni, S. Sawka, S. Sen, R. Slowley, A. Suarez-Uruena, G.J. Swaminathan, M.F. Symmons, G. van Ginkel, W.F. Vranken, M. Wainwright & G.J. Kleywegt (2011) PDBe: Protein Data Bank in Europe. Nucleic Acids Res. 39, D402-10.

 

2010

J. Yuan, Y. Sterckx, L.A. Mitchenall, A. Maxwell, R. Loris & M.K. Waldor (2010) Vibrio cholerae ParE2 poisons DNA gyrase via a mechanism distinct from other gyrase inhibitors. J. Biol. Chem. 285, 40397-408.

A.N. Volkov, M. Ubbink & N.A.J. van Nuland (2010) Mapping the encounter state of a transient protein complex by PRE NMR spectroscopy. J. Biomol. NMR 48, 225-36.

A.N. Volkov, Q. Bashir, J.A.R. Worrall, G.M. Ullmann & M. Ubbink (2010) Shifting the equilibrium between the encounter state and the specific form of a protein complex by interfacial point mutations. J. Am. Chem. Soc. 132, 11487-95.

A. Garcia-Pino, S. Balasubramanian, L. Wyns, E. Gazit, H. De Greve, R.D. Magnuson, D. Charlier, N.A.J. van Nuland & R. Loris (2010) Allostery and intrinsic disorder mediate transcription regulation by conditional cooperativity. Cell 142, 101-11.

R. Hallez, D. Geeraerts, Y. Sterckx, N. Mine, R. Loris & L. Van Melderen (2010) New toxins homologous to ParE belonging to three-component toxin-antitoxin systems in Escherichia coli O157:H1. Mol. Microbiol. 76, 719-32.

K. Remans, K. Pauwels, P. van Ulsen, L. Buts, P. Cornelis, J. Tommassen, S.N. Savvides, K. Decanniere & P. Van Gelder (2010) Hydrophobic Surface Patches on LolA of Pseudomonas aeruginosa Are Essential for Lipoprotein Binding. J. Mol. Biol. 401, 921-30.

A. Garcia-Pino, Y. Sterckx, G. Vandenbussche & R. Loris (2010) Purification and crystallization of Phd, the antitoxin of the phd/doc operon. Acta Crystallogr. F 66, 167-71.

N. De Jonge, W. Hohlweg, A. Garcia-Pino, M. Respondek, L. Buts, S. Haesaerts, J. Lah, K. Zangger & R. Loris (2010) Structural and thermodynamic characterization of Vibrio fischeri CcdB. J. Biol. Chem. 285, 5606-13.

I. Van Molle, K. Moonens, A. Garcia-Pino, L. Buts, M. De Kerpel, L. Wyns, J. Bouckaert & H. De Greve (2010) Structural and thermodynamic characterization of pre- and postpolymerization states in the F4 fimbrial subunit FaeG. J. Mol. Biol. 394, 957-67.

Q. Bashir, A.N. Volkov, G.M. Ullmann & M. Ubbink (2010) Visualization of the encounter ensemble of the transient electron transfer complex of cytochrome c and cytochrome c peroxidase. J. Am. Chem. Soc. 132, 241-7.

C.J. Penkett, G. van Ginkel, S. Velankar, J. Swaminathan, E. Ulrich, S. Mading, T.J. Stevens, R.H. Fogh, A. Gutmanas, G.J. Kleywegt, K. Henrick & W.F. Vranken (2010) Straightforward and complete deposition of NMR data to the PDBe. J. Biomol. NMR 48, 85-92.

W. Rieping & W.F. Vranken (2010) Validation of Archived chemical Shifts through atomic COordinates (VASCO). Proteins 78, 2482-9.

R.H. Fogh, W. Boucher, J.M.C. Ionides, W.F. Vranken, T.J. Stevens & E.D. Laue (2010) MEMOPS: Data modelling and automatic code generation. J. Integr. Bioinform. 7, 123.

S. Velankar, C. Best, B. Beuth, H.C. Boutselakis, N. Cobley, A. Da Silva, D. Dimitropoulos, A. Golovin, M. Hirshberg, M. John, E. Krissinel, R. Newman, T. Oldfield, A. Pajon, C. Penkett, J. Pineda-Castillo, G. Sahni, S. Sen, R. Slowley, A. Suarez-Uruena, J. Swaminathan, G. van Ginkel, W.F. Vranken, K. Henrick & G.J. Kleywegt (2010) PDBe: Protein Data Bank in Europe. Nucleic Acids Res. 38, D308-17.

 

2009

N. De Jonge, A. Garcia-Pino, L. Buts, S. Haesaerts, D. Charlier, K. Zangger, L. Wyns, H. De Greve & R. Loris (2009) Rejuvenation of CcdB-poisoned gyrase by an intrinsically disordered protein domain. Mol. Cell 35, 154-63.

M. Respondek, L. Buts, N. De Jonge, S. Haesaerts, R. Loris, L. Van Melderen, L. Wyns & K. Zangger (2009) Sequence-specific 1H, 15N and 13C resonance assignments of the 23.7 kDa homodimeric toxin CcdB from Vibrio fischeri. Biomol. NMR Assign. 3, 145-7.

I. Drobnak, A. Korencic, R. Loris, I. Marianovsky, G. Glaser, A. Jamnik, G. Vesnaver & J. Lah (2009) Energetics of MazG unfolding in correlation with its structural features. J. Mol. Biol. 392, 63-74.

M. Simic, N. De Jonge, R. Loris, G. Vesnaver & J. Lah (2009) Driving forces of gyrase recognition by the addiction toxin CcdB. J. Biol. Chem. 284, 20002-10.

A. Garcia-Pino, S. Martinez-Rodriguez, K. Wahni, L. Wyns, R. Loris & J. Messens (2009) Coupling of domain swapping to kinetic stability of a thioredoxin mutant. J. Mol. Biol. 385, 1590-9.

I. Van Molle, K. Moonens, L. Buts, A. Garcia-Pino, S. Panjikar, L. Wyns, H. De Greve & J. Bouckaert (2009) The F4 fimbrial chaperone FaeE is stable as a monomer that does not require self-capping of its pilin-interactive surfaces. Acta Crystallogr. D 65, 411-20.

D. Yu, A.N. Volkov & C. Tang (2009) Characterizing dynamic protein-protein interactions using differentially scaled paramagnetic relaxation enhancement. J. Am. Chem. Soc. 131, 17291-7.

A.N. Volkov, Q. Bashir, J.A.R. Worrall & M. Ubbink (2009) Binding hot spot in the weak protein complex of physiological redox partners yeast cytochrome c and cytochrome c peroxidase. J. Mol. Biol. 385, 1003-13.

J.L. Ortega-Roldan, M.R. Jensen, B. Brutscher, A.I. Azuaga, M. Blackledge & N.A.J. van Nuland (2009). Accurate characterization of weak macromolecular interactions by titration NMR of residual dipolar couplings: application to the CD2AP SH3-C:ubiquitin complex. Nucleic Acids Res. 37, e70.

J.F. Doreleijers*, W.F. Vranken*, C. Schulte*, J. Lin, J. Wedell, C.J. Penkett, G.W. Vuister, G. Vriend, J.L. Markley & E.L. Ulrich (2009) The NMR Restraints Grid (NRG) at BMRB for 5,266 protein and nucleic acid PDB entries. J. Biomol. NMR 45, 389-96 (*joint first authors)

A. De Simone, A. Cavalli, S.-T. D. Hsu, W. Vranken & M. Vendruscolo (2009) Highly accurate determination of random coil chemical shifts of proteins from an analysis of loop regions in native states. J. Am. Chem. Soc. 131, 16332-3.

A. Rosato, A. Bagaria, D. Baker, B. Bardiaux, A. Cavalli, J.F. Doreleijers, A. Giachetti, P. Guerry, P. Güntert, T. Herrmann, Y.J. Huang, H.R. A. Jonker, B. Mao, T.E. Malliavin, G.T. Montelione, M. Nilges, S. Raman, G. van der Schot, W.F. Vranken, G.W. Vuister & A.M.J.J. Bonvin (2009) CASD-NMR: critical assessment of automated structure determination by NMR. Nat. Methods 6, 625-6.

W.F. Vranken & W. Rieping (2009) Relationship between chemical shift value and accessible surface area for all amino acid atoms. BMC Struct. Biol. 9, 20.

C.A. Laughton, M. Orozco & W. Vranken (2009) COCO: A simple tool to enrich the representation of conformational variability in NMR structures. Proteins 75, 206-16.

 

2008

S. Martinez-Rodriguez, A. Garcia-Pino, F.J. Las Heras-Vazquez, J.M. Clemente-Jimenez, F. Rodriguez-Vico, R. Loris, J.M. Garcia-Ruiz & J.M. Gavira (2008) Crystallization and preliminary crystallographic studies of the recombinant L-N-carbamoylase from Geobacillus stearothermophilus CECT43. Acta Crystallogr. F 64, 1135-8.

A. Garcia-Pino, M.H. Dao-Thi, E. Gazit, R.D. Magnuson & R. Loris (2008) Crystallization of Doc and the Phd-Doc toxin-antitoxin complex. Acta Crystallogr. F 64, 1034-8. 

A. Garcia-Pino, M. Christensen-Dalsgaard, L. Wyns, M.B. Yarmolinsky, R.D. Magnuson, K. Gerdes & R. Loris (2008) Doc of prophage P1 is inhibited by its antitoxin partner Phd through fold complementation. J. Biol. Chem. 283, 30821-7.

A.M. Candel, N.A.J. van Nuland, F.M. Martin-Sierra, J.C. Martinez & F. Conejero-Lara (2008) Analysis of the thermodynamics of binding of an SH3 domain to proline-rich peptides using a chimeric fusion protein. J. Mol. Biol. 377, 117-35.

N.A.J. van Nuland, C.M. Dobson & L. Regan (2008) Characterization of folding the four-helix bundle protein Rop by real-time NMR. Protein Eng. Des. Sel. 21, 165-70.

K. Henrick, Z. Feng, W.F. Bluhm, D. Dimitropoulos, J.F. Doreleijers, S. Dutta, J.L. Flippen-Anderson, J. Ionides, C. Kamada, E. Krissinel, C.L. Lawson, J.L. Markley, N.H. Nakamura, R. Newman, Y. Shimizu, J. Swaminathan, S. Velankar, J. Ory, E.L. Ulrich, W. Vranken, J. Westbrook, R. Yamashita, H. Yang, J. Young, M. Yousufuddin & H.M. Berman (2008) Remediation of the protein data bank archive. Nucleic Acids Res. 36, D426-33.

 

2007

A. Garcia-Pino, L. Buts, L. Wyns, A. Imberty, & R. Loris (2007) How a plant lectin recognizes high mannose oligosaccharides. Plant Physiol. 144, 1733-41.

G. Roos, A. Garcia-Pino, K. Van Belle, E. Brosens, K. Wahni, G. Vandenbussche, L. Wyns, R. Loris & J. Messens (2007) The conserved active site proline determines the reducing power of Staphylococcus aureus thioredoxin. J. Mol. Biol. 368, 800-11.

A.M.S. Duarte, C.J.A.M. Wolfs, N.A.J. van Nuland, M.A. Harrison, J.B.C. Findlay, C.P.M. Van Mierlo & M.A. Hemminga (2007) Structure and localization of an essential transmembrane segment of proton translocation channel of yeast H+-V-ATPase. BBA-Biomembranes 1768, 218-27.

A.M. Candel, F. Conejero-Lara, J.C. Martinez, N.A.J. van Nuland & M. Bruix (2007) The high-resolution NMR structure of a single-chain chimeric protein mimicking a SH3-peptide complex. FEBS Lett. 581, 687-92.

S. Casares, E. AB, H. Eshuis, O. Lopez-Mayorga, N.A.J. van Nuland & F. Conejero-Lara (2007) The high-resolution NMR structure of the R21A Spc-SH3:P41 complex: understanding the determinants of binding affinity by comparison with Abl-SH3. BMC Struct. Biol. 7, 22.

J.L. Ortega-Roldan, M.L. Romero-Romero, A. Ora, E. AB, O. Lopez-Mayorga, A.I. Azuaga & N.A.J. van Nuland (2007) The high-resolution NMR structure of the third SH3 domain of CD2AP. J. Biomol. NMR 39, 331-6.

W.F. Vranken (2007) A global analysis of NMR distance constraints from the PDB. J. Biomol. NMR 39, 303-14.

P. Feunou, S. Vanwetswinkel, F. Gaudray, M. Goldman, P. Matthys & M.Y. Braun (2007) Foxp3+CD25+ T regulatory cells stimulate IFN-gamma-independent CD152-mediated activation of tryptophan catabolism that provides dendritic cells with immune regulatory activity in mice unresponsive to staphylococcal enterotoxin BJ. Immunol. 179, 910-7.

 

2006

M. Azarkan, A. Garcia-Pino, R. Dibiani, L. Wyns, R. Loris & D. Baeyens-Volant (2006) Crystallization and preliminary X-ray analysis of a protease inhibitor from the latex of Carica papaya. Acta Crystallogr. F 62, 1239-42.

A. Garcia-Pino, L. Buts, L. Wyns & R. Loris (2006) Interplay between metal binding and cis/trans isomerization in legume lectins: structural and thermodynamic study of P. angolensis lectin. J. Mol. Biol. 361, 153-67.

L. Buts, A. Garcia-Pino, A. Imberty, N. Amiot, G.J. Boons, S. Beeckmans, W. Versées, L. Wyns & R. Loris (2006) Structural basis for the recognition of complex-type biantennary oligosaccharides by Pterocarpus angolensis lectin. FEBS J. 273, 2407-20.

L. Buts, A. Garcia-Pino, L. Wyns & R. Loris (2006) Structural basis of carbohydrate recognition by a Man(alpha1-2)Man-specific lectin from Bowringia milbraedii. Glycobiology 16, 635-40.

A.N. Volkov, J.A.R. Worrall, E. Holtzmann & M. Ubbink (2006) Solution structure and dynamics of the complex between cytochrome c and cytochrome c peroxidase determined by paramagnetic NMR. Proc. Natl. Acad. Sci. USA 103, 18945-50.

S. Tomaselli, V. Esposito, P. Vangone, N.A.J. van Nuland, A.M.J.J. Bonvin, R. Guerrini, T. Tancredi & D. Picone (2006) The alpha-to-beta conformational transition of Alzheimer's A-beta-(1-42) peptide in aqueous media is reversible: a step by step conformational analysis suggests the location of beta conformation seeding. ChemBioChem 7, 257-67.

N. Sibille, A. Favier, A.I. Azuaga, G. Ganshaw, R. Bott, A.M.J.J. Bonvin, R. Boelens & N.A.J. van Nuland (2006) Comparative NMR study on the impact of point mutations on protein stability of Pseudomonas mendocina lipase. Prot. Sci. 15, 1915-27.

R.H. Fogh*, W.F. Vranken*, W. Boucher, T.J. Stevens & E.D. Laue (2006) A nomenclature and data model to describe NMR experiments. J. Biomol. NMR 36, 147-55 (*joint first authors)

S. Albeck, P. Alzari, C. Andreini, L. Banci, I. M. Berry, I. Bertini, C. Cambillau, B. Canard, L. Carter, S. X. Cohen, J. M. Diprose, O. Dym, R. M. Esnouf, C. Felder, F. Ferron, F. Guillemot, R. Hamer, M. Ben Jelloul, R. A. Laskowski, T. Laurent, S. Longhi, R. Lopez, C. Luchinat, H. Malet, T. Mochel, R. J. Morris, L. Moulinier, T. Oinn, A. Pajon, Y. Peleg, A. Perrakis, O. Poch, J. Prilusky, A. Rachedi, R. Ripp, A. Rosato, I. Silman, D. I. Stuart, J. L. Sussman, J.-C. Thierry, J. D. Thompson, J. M. Thornton, T. Unger, B. Vaughan, W. Vranken, J. D. Watson, G. Whamond & K. Henrick (2006) SPINE bioinformatics and data-management aspects of high-throughput structural biology. Acta Crystallogr. D 62, 1184-95.

M. Tagari, J. Tate, G. J. Swaminathan, R. Newman, A. Naim, W. Vranken, A. Kapopoulou, A. Hussain, J. Fillon, K. Henrick & S. Velankar (2006) E-MSD: improving data deposition and structure quality. Nucleic Acids Res. 34, D287-90.

 

2005

L. Buts, J. Lah, M.H. Dao-Thi, L. Wyns, & R. Loris (2005) Toxin-antitoxin modules as bacterial metabolic stress managers. Trends Biochem. Sci. 30 672-9.

A. Garcia-Pino, R. Loris, L. Wyns & L. Buts (2005) Crystallization and preliminary X-ray analysis of the Man(alpha1-2)Man-specific lectin from Bowringia milbraedii in complex with its carbohydrate ligand. Acta Crystallogr. F 61, 931-4.

R. Loris, A. Garcia-Pino, L. Buts, J. Bouckaert, S. Beeckmans, H. De Greve & L. Wyns (2005) Crystallization and crystal manipulation of the Pterocarpus angolensis seed lectin. Acta Crystallogr. D 61, 685-9.

A.N. Volkov, D. Ferrari, J.A.R. Worrall, A.M.J.J. Bonvin & M. Ubbink (2005) The orientations of cytochrome c in the highly dynamic complex with cytochrome b5 visualized by NMR and docking using HADDOCK. Prot. Sci. 14, 799-811.

C. Bernard, K. Houben, N.M. Derix, D. Marks, M.A. Van Der Horst, K.J. Hellingwerf, R. Boelens, R. Kaptein & N.A.J. van Nuland (2005) The solution structure of a transient photoreceptor intermediate: Delta-25 photoactive yellow protein. Structure 13, 953-62.

M.B. Ekkelenkamp, M. Hanssen, S.T.D. Hsu, A. De Jong, D. Milatovic, J. Verhoef & N.A.J. van Nuland (2005) Isolation and structural characterization of epilancin 15X, a novel lantibiotic from a clinical strain of Staphylococcus epidermidis. FEBS Lett. 579, 1917-22.

J.F. Doreleijers*, A.J. Nederveen*, W. Vranken*, A.M.J.J. Bonvin, R. Kaptein, J. Lin, J.L. Markley & E.L. Ulrich (2005) BioMagResBank databases DOCR and FRED with converted and filtered sets of experimental NMR constraints and coordinates from over 500 protein PDB structures. J. Biomol. NMR 32, 1-12 (* joint first authors)

W.F. Vranken, W. Boucher, T.J. Stevens, R.H. Fogh, A. Pajon, M. Llinas, E.L. Ulrich, J.L. Markley, J. Ionides & E.D. Laue (2005) The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59, 687-96.

A.J. Nederveen, J.F. Doreleijers, W. Vranken, Z. Miller, C.A.E.M. Spronk, S.B. Nabuurs, P. Güntert, M. Livny, J.L. Markley, M. Nilges, E.L. Ulrich, R. Kaptein & A.M.J.J. Bonvin (2005) RECOORD: a REcalculated COORdinates Database of 500+ proteins from the PDB using restraint data from the BioMagResBank. Proteins 59, 662-72.

R.H. Fogh, W. Boucher, W.F. Vranken, A. Pajon, T.J. Stevens, T.N. Bhat, J. Westbrook, J.M.C. Ionides & E.D. Laue (2005) A framework for scientific data modeling and automated software development. Bioinformatics 21, 1678-84.

A. Pajon, J. Ionides, J. Diprose, J. Fillon, R. Fogh, A.W. Ashton, H. Berman, W. Boucher, M. Cygler, E. Deulery, R. Esnouf, J. Janin, R. Kim, I. Krimm, C. Lawson, E. Oeuillet, A. Poupon, S. Raymond, T. Stevens, H. Van Tilbeurgh, J. Westbrook, P. Wood, E. Ulrich, W. Vranken, L. Xueli, E. Laue, D. Stuart & K. Henrick (2005) Design of a data model for developing laboratory information management and analysis systems for protein production. Proteins 58, 278-84.

S. Vanwetswinkel, R.J. Heetebrij, J. van Duynhoven, J.G. Hollander, D.V. Filippov, P.J. Hajduk & G. Siegal (2005) TINS, target immobilized NMR screening: an efficient and sensitive method for ligand discovery. Chem. Biol. 12, 207-16.

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