The catalytic domain of MMP‐1 studied through tagged lanthanides

Pseudocontact shifts (pcs) and paramagnetic residual dipolar couplings (rdc) provide structural information that can be used to assess the adequacy of a crystallographic structure to represent the solution structure of a protein. This can be done by attaching a lanthanide binding tag to the protein. There are cases in which only local rearrangements are sufficient to match the NMR data and cases where significant secondary structure or domain rearrangements from the solid state to the solution state are needed. We show that the two cases are easily distinguishable. Whereas the use of solution restraints in the latter case is described in the literature, here we deal with how to obtain a better model of the solution structure in a case (the catalytic domain of the matrix metalloproteinase MMP‐1) of the former class.

[1]  P. Keizers,et al.  Design, synthesis, and evaluation of a lanthanide chelating protein probe: CLaNP-5 yields predictable paramagnetic effects independent of environment. , 2008, Journal of the American Chemical Society.

[2]  Ivano Bertini,et al.  Perspectives in paramagnetic NMR of metalloproteins. , 2008, Dalton transactions.

[3]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[4]  C. Luchinat,et al.  Backbone-only protein solution structures with a combination of classical and paramagnetism-based constraints: a method that can be scaled to large molecules. , 2004, Chemphyschem : a European journal of chemical physics and physical chemistry.

[5]  D. Blow,et al.  The detection of sub‐units within the crystallographic asymmetric unit , 1962 .

[6]  G. Otting,et al.  A dipicolinic acid tag for rigid lanthanide tagging of proteins and paramagnetic NMR spectroscopy. , 2008, Journal of the American Chemical Society.

[7]  D. McRee,et al.  A visual protein crystallographic software system for X11/Xview , 1992 .

[8]  S. Grzesiek,et al.  DOTA-M8: An extremely rigid, high-affinity lanthanide chelating tag for PCS NMR spectroscopy. , 2009, Journal of the American Chemical Society.

[9]  G. Clore,et al.  Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small alpha/beta protein: a unified picture of high probability, fast atomic motions in proteins. , 2006, Journal of molecular biology.

[10]  G Marius Clore,et al.  Improving the accuracy of NMR structures of RNA by means of conformational database potentials of mean force as assessed by complete dipolar coupling cross-validation. , 2003, Journal of the American Chemical Society.

[11]  N. Dixon,et al.  Site‐Specific Labelling of Proteins with a Rigid Lanthanide‐Binding Tag , 2006, Chembiochem : a European journal of chemical biology.

[12]  A Vagin,et al.  An approach to multi-copy search in molecular replacement. , 2000, Acta crystallographica. Section D, Biological crystallography.

[13]  Maxim V. Petoukhov,et al.  Conformational space of flexible biological macromolecules from average data. , 2010, Journal of the American Chemical Society.

[14]  Ivano Bertini,et al.  13C direct detected NMR increases the detectability of residual dipolar couplings. , 2006, Journal of the American Chemical Society.

[15]  I. Bertini,et al.  Accurate solution structures of proteins from X-ray data and a minimal set of NMR data: calmodulin-peptide complexes as examples. , 2009, Journal of the American Chemical Society.

[16]  A. Bax,et al.  Measurement of J and dipolar couplings from simplified two-dimensional NMR spectra. , 1998, Journal of magnetic resonance.

[17]  P. Güntert Automated NMR structure calculation with CYANA. , 2004, Methods in molecular biology.

[18]  M. Gochin,et al.  Protein structure refinement based on paramagnetic NMR shifts: Applications to wild‐type and mutant forms of cytochrome c , 1995, Protein science : a publication of the Protein Society.

[19]  D. Svergun,et al.  Interdomain Flexibility in Full-length Matrix Metalloproteinase-1 (MMP-1)* , 2009, Journal of Biological Chemistry.

[20]  P. Keizers,et al.  Increased paramagnetic effect of a lanthanide protein probe by two-point attachment. , 2007, Journal of the American Chemical Society.

[21]  V S Lamzin,et al.  Automated refinement of protein models. , 1993, Acta crystallographica. Section D, Biological crystallography.

[22]  I. Bertini,et al.  NMR Spectroscopy of Paramagnetic Metalloproteins , 2005, Chembiochem : a European journal of chemical biology.

[23]  G. Clore,et al.  How much backbone motion in ubiquitin is required to account for dipolar coupling data measured in multiple alignment media as assessed by independent cross-validation? , 2004, Journal of the American Chemical Society.

[24]  L. Kay,et al.  Orienting domains in proteins using dipolar couplings measured by liquid-state NMR: differences in solution and crystal forms of maltodextrin binding protein loaded with beta-cyclodextrin. , 2000, Journal of molecular biology.

[25]  G. Otting,et al.  3-Mercapto-2,6-pyridinedicarboxylic acid: a small lanthanide-binding tag for protein studies by NMR spectroscopy. , 2010, Chemistry.

[26]  J. Prestegard,et al.  NMR evidence for slow collective motions in cyanometmyoglobin , 1997, Nature Structural Biology.

[27]  P. Domaille,et al.  ULTRA-HIGH FIELD NMR SPECTROSCOPY: OBSERVATION OF PROTON-PROTON DIPOLAR COUPLING IN PARAMAGNETIC BIS(TOLYLTRIS(PYRAZOLYL)BORATO)COBALT(II) , 1981 .

[28]  M. Ubbink,et al.  Conformation of pseudoazurin in the 152 kDa electron transfer complex with nitrite reductase determined by paramagnetic NMR. , 2008, Journal of molecular biology.

[29]  I. Bertini,et al.  Paramagnetism-based NMR restraints provide maximum allowed probabilities for the different conformations of partially independent protein domains. , 2007, Journal of the American Chemical Society.

[30]  Ivano Bertini,et al.  NMR-validated structural model for oxidized Rhodopseudomonas palustris cytochrome c556 , 2004, JBIC Journal of Biological Inorganic Chemistry.

[31]  Andrea Giachetti,et al.  Paramagnetism-Based Restraints for Xplor-NIH , 2004, Journal of biomolecular NMR.

[32]  A. Rosato,et al.  Partial Orientation of Oxidized and Reduced Cytochrome b5 at High Magnetic Fields: Magnetic Susceptibility Anisotropy Contributions and Consequences for Protein Solution Structure Determination , 1998 .

[33]  Andrea Giachetti,et al.  Combining in silico tools and NMR data to validate protein-ligand structural models: application to matrix metalloproteinases. , 2005, Journal of medicinal chemistry.

[34]  P. Keizers,et al.  Intermolecular dynamics studied by paramagnetic tagging , 2009, Journal of biomolecular NMR.

[35]  A. Leslie Molecular data processing , 1992 .

[36]  I. Bertini,et al.  Moving the frontiers in solution and solid-state bioNMR , 2011 .

[37]  J. Prestegard,et al.  Structure determination of a Galectin‐3–carbohydrate complex using paramagnetism‐based NMR constraints , 2008, Protein science : a publication of the Protein Society.

[38]  Oliver F. Lange,et al.  Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution , 2008, Science.

[39]  P. Keizers,et al.  Validation of a lanthanide tag for the analysis of protein dynamics by paramagnetic NMR spectroscopy. , 2010, Journal of the American Chemical Society.

[40]  Ad Bax,et al.  Solution structure of Ca2+–calmodulin reveals flexible hand-like properties of its domains , 2001, Nature Structural Biology.

[41]  Rui Zhang,et al.  Data Reduction , 2009, Encyclopedia of Database Systems.

[42]  A. Bax,et al.  Are proteins even floppier than we thought? , 1997, Nature Structural Biology.

[43]  Ivano Bertini,et al.  Magnetic susceptibility in paramagnetic NMR , 2002 .

[44]  M G Rossmann,et al.  The molecular replacement method. , 1990, Acta crystallographica. Section A, Foundations of crystallography.

[45]  K. Ogura,et al.  Two-point anchoring of a lanthanide-binding peptide to a target protein enhances the paramagnetic anisotropic effect , 2009, Journal of biomolecular NMR.

[46]  R. Powers,et al.  Assignments, secondary structure and dynamics of the inhibitor-free catalytic fragment of human fibroblast collagenase , 1997, Journal of biomolecular NMR.

[47]  G L Gilliland,et al.  Combining experimental information from crystal and solution studies: joint X-ray and NMR refinement. , 1992, Science.

[48]  P. Keizers,et al.  A solution model of the complex formed by adrenodoxin and adrenodoxin reductase determined by paramagnetic NMR spectroscopy. , 2010, Biochemistry.

[49]  J H Prestegard,et al.  Nuclear magnetic dipole interactions in field-oriented proteins: information for structure determination in solution. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[50]  G. Murshudov,et al.  Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.

[51]  A. Vagin,et al.  MOLREP: an Automated Program for Molecular Replacement , 1997 .