X-Ray crystal structure and molecular dynamics simulations of silver hake parvalbumin (Isoform B)
Graduate School of Biomedical Sciences; Department of Biochemistry and Molecular Pharmacology
Medical Subject Headings
Animals; Binding Sites; Calcium-Binding Proteins; Crystallography, X-Ray; *Fishes; Hydrogen Bonding; Models, Molecular; Parvalbumins; Protein Conformation; Protein Isoforms; Solvents; Temperature
Life Sciences | Medicine and Health Sciences
Parvalbumins constitute a class of calcium-binding proteins characterized by the presence of several helix-loop-helix (EF-hand) motifs. In a previous study (Revett SP, King G, Shabanowitz J, Hunt DF, Hartman KL, Laue TM, Nelson DJ, 1997, Protein Sci 7:2397-2408), we presented the sequence of the major parvalbumin isoform from the silver hake (Merluccius bilinearis) and presented spectroscopic and structural information on the excised "EF-hand" portion of the protein. In this study, the X-ray crystal structure of the silver hake major parvalbumin has been determined to high resolution, in the frozen state, using the molecular replacement method with the carp parvalbumin structure as a starting model. The crystals are orthorhombic, space group C2221, with a = 75.7 A, b = 80.7 A, and c = 42.1 A. Data were collected from a single crystal grown in 15% glycerol, which served as a cryoprotectant for flash freezing at -188 degrees C. The structure refined to a conventional R-value of 21% (free R 25%) for observed reflections in the range 8 to 1.65 A [1 > 2sigma(I)]. The refined model includes an acetylated amino terminus, 108 residues (characteristic of a beta parvalbumin lineage), 2 calcium ions, and 114 water molecules per protein molecule. The resulting structure was used in molecular dynamics (MD) simulations focused primarily on the dynamics of the ligands coordinating the Ca2+ ions in the CD and EF sites. MD simulations were performed on both the fully Ca2+ loaded protein and on a Ca2+ deficient variant, with Ca2+ only in the CD site. There was substantial agreement between the MD and X-ray results in addressing the issue of mobility of key residues in the calcium-binding sites, especially with regard to the side chain of Ser55 in the CD site and Asp92 in the EF site.
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Citation: Protein Sci. 2000 Jan;9(1):73-82.
Protein science : a publication of the Protein Society
Richardson, Robert C.; King, Nancy M.; Harrington, Daniel John; Sun, Hongmao; Royer, William E.; and Nelson, Donald J., "X-Ray crystal structure and molecular dynamics simulations of silver hake parvalbumin (Isoform B)" (2000). GSBS Student Publications. 1042.