Sequence-specific sup 1 H NMR assignments and structural characterization of bovine seminal fluid protein PDC-109 domain b
- Carnegie Mellon Univ., Pittsburgh, PA (USA)
- Institute of Enzymology, Budapest (Hungary)
Sequence-specific resonance assignments for the isolated second or b domain of the bovine seminal fluid protein PDC-109 have been obtained from analysis of two-dimensional {sup 1}H NMR experiments recorded at 500 MHz. These assignments include the identification of all aromatic and most aliphatic amino acid resonances. Stereospecific assignment of resonances stemming from the Val{sup 2}CH{sub 3}{sup {gamma},{gamma}{prime}} groups and from seven CH{sup {beta},{beta}{prime}} geminal pairs has been accomplished by analysis of {sup 3}J{sub {alpha}{beta}} coupling constants in conjunction with patterns of cross-peak intensities observed in two-dimensional nuclear Overhauser effect (NOESY) spectra. Analysis of NOESY and {sup 3}J{sub {alpha}NH} data reveals a small antiparallel {beta}-sheet involving stretches containing residues 25-28 and 39-42, a cis-proline residue (Pro{sup 4}), antiparallel strands consisting of residues 1-3, 5-7, and 10-13, and an aromatic cluster composed of Tyr{sup 7}, Trp{sup 26}, and Tyr{sup 33}. The results of distance geometry and restrained molecular dynamics calculations indicate that the global fold of the PDC-109 b domain, a type 2 module related to those found in fibronectin, is somewhat different from that predicted by modeling the structure on the basis of homology between type 2 and kringle units. A shallow depression in the molecular surface which presents a solvent-exposed hydrophobic area-a potential ligand-binding site-is identified in the NMR-based models.
- OSTI ID:
- 5557547
- Journal Information:
- Biochemistry; (United States), Vol. 30:6; ISSN 0006-2960
- Country of Publication:
- United States
- Language:
- English
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Related Subjects
PROTEINS
NUCLEAR MAGNETIC RESONANCE
AMINO ACID SEQUENCE
CATTLE
PROTONS
STEREOCHEMISTRY
ANIMALS
BARYONS
DOMESTIC ANIMALS
ELEMENTARY PARTICLES
FERMIONS
HADRONS
MAGNETIC RESONANCE
MAMMALS
MOLECULAR STRUCTURE
NUCLEONS
ORGANIC COMPOUNDS
RESONANCE
RUMINANTS
VERTEBRATES
550201* - Biochemistry- Tracer Techniques