NMR paper NMR secondary structure of the plasminogen activator protein staphylokinase.

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[NMR paper] NMR secondary structure of the plasminogen activator protein staphylokinase.

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NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

Chemical shifts re-referencing:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

Quality Control Check

NMR spectrum prediction:

FANDAS

MestReS

V-NMR

Flexibility from structure:

Backbone S2

Methyl S2

B-factor

Molecular dynamics:

Gromacs

Amber

Antechamber

Chemical shifts prediction:

From structure:

Shiftx2

Sparta+

Camshift

CH3shift- Methyl

ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

From sequence:

Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

Format conversion & validation:

CCPN

From NMR-STAR 3.1

Validate NMR-STAR 3.1

NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

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08-22-2010, 03:03 PM

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NMR secondary structure of the plasminogen activator protein staphylokinase.

NMR secondary structure of the plasminogen activator protein staphylokinase.

Related Articles NMR secondary structure of the plasminogen activator protein staphylokinase.

J Biomol NMR. 1997 Apr;9(3):273-86

Authors: Ohlenschläger O, Ramachandran R, Flemming J, Gührs KH, Schlott B, Brown LR

Staphylokinase (Sak) is a 15.5 kDa protein secreted by several strains of Staphylococcus aureus. Due to its ability to convert plasminogen, the inactive proenzyme of the fibrinolytic system, into plasmin, Sak is presently undergoing clinical trials for blood clot lysis in the treatment of thrombovascular disorders. With a view to developing a better understanding of the mode of action of Sak, we have initiated a structural investigation of Sak via multidimensional heteronuclear NMR spectroscopy employing uniformly 15N- and 15N, 13C-labelled Sak. Sequence-specific resonance assignments have been made employing 15N-edited TOCSY and NOE experiments and from HNCACB, CBCA(CO)NH, HBHA-(CBCACO) NH and CC(CO)NH sets of experiments. From an analysis of the chemical shifts, 3JHNH alpha scalar coupling constants, NOEs and HN exchange data, the secondary structural elements of Sak have been characterized.

PMID: 9204556 [PubMed - indexed for MEDLINE]

Source: PubMed

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