Three-dimensional solution structure of Ca sup 2+ -loaded porcine calbindin D sub 9k determined by nuclear magnetic resonance spectroscopy

The three-dimensional solution structure of native, intact porcine calbindin D{sub 9k} has been determined by distance geometry and restrained molecular dynamics calculations using distance and dihedral angle constraints obtained from {sup 1}H NMR spectroscopy. The protein has a well-defined global...

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Bibliographic Details
Published in:Biochemistry (Easton) 1992-02, Vol.31:4
Main Authors: Akke, M., Drakenberg, T., Chazin, W.J.
Format: Article
Language:English
Subjects:
550201 - Biochemistry- Tracer Techniques
ALKALINE EARTH METAL COMPOUNDS
AMIDES
AMINO ACIDS
ANIMALS
AQUEOUS SOLUTIONS
ASPARAGINE
BASIC BIOLOGICAL SCIENCES
CALCIUM COMPOUNDS
CALMODULIN
CARBOXYLIC ACIDS
COHERENT SCATTERING
CRYSTALLOGRAPHY
DIFFRACTION
DISPERSIONS
DOMESTIC ANIMALS
GEOMETRY
MAGNETIC RESONANCE
MAMMALS
MATHEMATICS
MIXTURES
NUCLEAR MAGNETIC RESONANCE
ORGANIC ACIDS
ORGANIC COMPOUNDS
ORGANIC NITROGEN COMPOUNDS
PROTEINS
RESONANCE
SCATTERING
SOLUTIONS
SWINE
VERTEBRATES
X-RAY DIFFRACTION
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Summary:The three-dimensional solution structure of native, intact porcine calbindin D{sub 9k} has been determined by distance geometry and restrained molecular dynamics calculations using distance and dihedral angle constraints obtained from {sup 1}H NMR spectroscopy. The protein has a well-defined global fold consisting of four helices oriented in a pairwise antiparallel manner such that two pairs of helix-loop-helix motifs (EF-hands) are joined by a linker segment. The two EF-hands are further coupled through a short {beta}-type interaction between the two Ca{sup 2+}-binding loops. Overall, the structure is very similar to that of the highly homologous native, minor A form of bovine calbindin D{sub 9k} determined by X-ray crystallography. A model structure built from the bovine calbindin D{sub 9k} crystal structure shows several deviations larger than 2 {angstrom} from the experimental distance constraints for the porcine protein. These structural differences are efficiently removed by subjecting the model structure to the experimental distance and dihedral angle constraints in a restrained molecular dynamics protocol, thereby generating a model that is very similar to the refined distance geometry derived structures. The N-terminal residues of the intact protein that are absent in the minor A form appear to be highly flexible and do not influence the structure of other regions of the protein. This result is important because in validates the conclusions drawn from the wide range of studies that have been carried out on minor A forms rather than the intact calbindin D{sub 9k}.
ISSN:0006-2960
1520-4995
DOI:10.1021/bi00119a009