Sequence-specific 1H NMR assignments and structural characterization of bovine seminal fluid protein PDC-109 domain b

Keith L. Constantine, Vasudevan Ramesh, László Bányai, L. Bányai, M. Trexler, L. Patthy

Research output: Article

30 Citations (Scopus)

Abstract

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 1H 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 Val2 CH3γ,γ′ groups and from seven CHβ,β′ geminal pairs has been accomplished by analysis of 3Jαβ coupling constants in conjunction with patterns of cross-peak intensities observed in two-dimensional nuclear Overhauser effect (NOESY) spectra. Analysis of NOESY and 3JαNH data reveals a small antiparallel β-sheet involving stretches containing residues 25-28 and 39-42, a cis-proline residue (Pro4), antiparallel strands consisting of residues 1-3, 5-7, and 10-13, and an aromatic cluster composed of Tyr7, Trp26, and Tyr33. The results of distance geometry and restrained molecular dynamics calculations indicate that the global fold of the PDC-109 b domain, a type II module related to those found in fibronectin, is somewhat different from that predicted by modeling the structure on the basis of homology between type II 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.

Original languageEnglish
Pages (from-to)1663-1672
Number of pages10
JournalBiochemistry
Volume30
Issue number6
Publication statusPublished - 1991

Fingerprint

Kringles
Molecular Dynamics Simulation
Fibronectins
Proline
Fatty Acids
Binding Sites
Nuclear magnetic resonance
Ligands
Amino Acids
Fluids
Proteins
Molecular dynamics
Geometry
Proton Magnetic Resonance Spectroscopy
Experiments

ASJC Scopus subject areas

  • Biochemistry

Cite this

Sequence-specific 1H NMR assignments and structural characterization of bovine seminal fluid protein PDC-109 domain b. / Constantine, Keith L.; Ramesh, Vasudevan; Bányai, László; Bányai, L.; Trexler, M.; Patthy, L.

In: Biochemistry, Vol. 30, No. 6, 1991, p. 1663-1672.

Research output: Article

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AU - Constantine, Keith L.

AU - Ramesh, Vasudevan

AU - Bányai, László

AU - Bányai, L.

AU - Trexler, M.

AU - Patthy, L.

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AB - 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 1H 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 Val2 CH3γ,γ′ groups and from seven CHβ,β′ geminal pairs has been accomplished by analysis of 3Jαβ coupling constants in conjunction with patterns of cross-peak intensities observed in two-dimensional nuclear Overhauser effect (NOESY) spectra. Analysis of NOESY and 3JαNH data reveals a small antiparallel β-sheet involving stretches containing residues 25-28 and 39-42, a cis-proline residue (Pro4), antiparallel strands consisting of residues 1-3, 5-7, and 10-13, and an aromatic cluster composed of Tyr7, Trp26, and Tyr33. The results of distance geometry and restrained molecular dynamics calculations indicate that the global fold of the PDC-109 b domain, a type II module related to those found in fibronectin, is somewhat different from that predicted by modeling the structure on the basis of homology between type II 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.

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