5UE5

proMMP-7 with heparin octasaccharide bound to the catalytic domain


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
13D 1H-15N NOESY300 uM [U-99% 15N] proMMP-7, 450 uM heparin dp893% H2O/7% D2O180 mM6.61 atm310Bruker AVANCE III 800
2TROSY-detected titration300 uM [U-99% 15N] proMMP-7, 450 uM heparin dp893% H2O/7% D2O180 mM6.61 atm310Bruker AVANCE III 800
3PREs by PROJECT-CPMG TROSY300 uM [U-99% 2H/15N] proMMP-7, 450 uM heparin dp8-TEMPO93% H2O/7% D2O180 mM6.61 atm310Bruker AVANCE III 800
4solvent PREs, 1H relaxation detected via TROSY300 uM [U-99% 2H/15N] proMMP-7, 450 uM heparin dp493% H2O/7% D2O180 mM6.61 atm310Bruker AVANCE III 800
53D HNCACB300 uM [U-100% 13C; U-100% 15N; U-80% 2H] proMMP-793% H2O/7% D2O30 mM6.61 atm310Bruker AVANCE III 800
63D CBCA(CO)NH300 uM [U-100% 13C; U-100% 15N; U-80% 2H] proMMP-793% H2O/7% D2O30 mM6.61 atm310Bruker AVANCE III 800
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE III800
NMR Refinement
MethodDetailsSoftware
torsion angle dynamics15000 steps of refinement. Explicit distance restraints to the TEMPO spin-labeled reducing end of heparin dp8 were obtained from the PREs (T2) using an equation from Battiste and Wagner (2000, Biochemistry) simplified by WHTC greater than1 to the form r equal to 4KTC/T2 given by Koppisetti et al. (2014, Nature Comms.). The rotational correlation time TC of the protein-heparin complexes was obtained from amide 15N cross-correlation rates nxy (Liu and Prestegard, 2008, J. Magn. Reson.) interpreted by the spectral density expression used in the TRACT approach (Lee et al., 2006. J. Magn. Reson.). Upper bounds were set at 15% above the distance estimate. An intermolecular NOE from an arginine backbone amide from 2H/15N-labeled enzyme to the anomeric proton H1 of GlcNS6S 5 or 7 had an upper bound of 6 A. Lower bounds were implicitly at van der Waals distance. Ambiguous distance restraints from any residue of heparin dp8 to explicit protein amide groups were applied on the basis of amide chemical shift perturbations from heparin dp8 or protection of amides by heparin dp4 from line broadening by Gd.EDTA with deltaT2 greater than 37/sec. Ambiguous distance restraints from any residue of heparin dp8 to lysine amino or arginine ureido groups were also applied on the basis of mutations that impaired activation of proMMP-7 by heparin dp16. The combination of the intermolecular distance restraints from the explicit PRE and NOE measurements and the ambiguous sources were used to dock coordinates of heparin dp8 with the NMR solution structure of human proMMP-7 of Prior et al. (2015, Structure). To enable molecular flexibility widely through the proMMP-7 and heparin dp8 chains while maintaining the structural integrity of the proMMP-7 during the restrained docking simulations, CYANA 2.1 (Guntert and Buchner, 2015, J. Biomol. NMR) was utilized in concert with the intramolecular proMMP-7 NOE-derived distance restraints and chemical shift-derived dihedral restraints of the NMR structure (Prior et al., 2015, Structure). CYANA topology files describing the sugar monomers were derived from topology files curated by the Automated Topology Builder (Malde et al., 2011, J. Chem. Theory Comput.) and based on accession number 9804 for 2-O-sulfo-alpha-L-idopyranuronic acid (IDS or IdoA2S) and 9778 for N,O6-disulfo-glucosamine (SGN or GlcNS6S). The globally flexible docking simulations required the proMMP-7 polypeptide to be linked to the calcium and zinc ions and heparin dp8 chains via tethers of non-interacting pseudoatoms. With this tethering and flexible structural integrity enforced, the carbohydrate chains were docked with the intermolecular distance restraintsSYBYL
NMR Ensemble Information
Conformer Selection Criteriastructures with the least restraint violations
Conformers Calculated Total Number200
Conformers Submitted Total Number16
Representative Model1 (target function)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
2structure calculationCYANA2.1Guntert, Mumenthaler and Wuthrich
3data analysisSparkyGoddard
4chemical shift assignmentAnalysisCCPN
5processingTopSpinBruker Biospin
1refinementSYBYLX 2.1.1Tripos / Certara