ISSN:
1432-1017
Keywords:
Key words Vicinal coupling constants
;
Polypeptide φ angles
;
Karplus parameters
;
Least-squares optimization
;
Back-calculation of coupling constants
Source:
Springer Online Journal Archives 1860-2000
Topics:
Biology
,
Physics
Notes:
Abstract Quantitative φ-dihedral angle determinations of non-glycine and non-proline residues in Desulfovibrio vulgaris flavodoxin are carried out on the exclusive basis of 3 J coupling constants. In total 124 3 JHNH α , 123 3 JHNC ′i , 118 3 JHNC β , 117 3 JC′ i–1Hα , 109 3 JC′ i–1C′i , and 103 3 JC′ i–1Hβ values form the experimental basis for translating J coupling data into geometry information using various combinations of Karplus parameters given in the literature. In addition, each backbone torsional angle φ is adjusted assuming different models of local geometry, either a rigid torsion, a Gaussian distribution centered at a distinct angle, or a two-site jump model. Numerical optimization is followed by a statistical significance evaluation to assess the results. It is found that experimental coupling constants of most of the residues involved in secondary structure elements agree best with those predicted from rigid local conformations. For dihedral angles in loop regions, mobility effects are not negligible, and a single torsion (Glu 42) is likely to adopt two distinct adjustments. However, α-helix conformations with –60° 〈 φ 〈 –45° give rise to an alternate solution with φ≈+170° with similar statistical significance when using the four traditionally determined proton-involved 3 J couplings. This ambiguity is efficiently avoided only when taking advantage of the complete data set comprising six available experimental 3 J coupling constants and of the degeneracy intrinsic to the Karplus relation. The optimized φ conformations are compared with reference values from the crystal structure of flavodoxin.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1007/s002490050139
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