Conformational properties of native sperm whale apomyoglobin in solution

• Published in: Protein science Vol. 8; no. 7; pp. 1484 - 1491
• Main Authors: LECOMTE, JULIETTE T.J., SUKITS, STEVEN F., BHATTACHARYA, SHIBANI, FALZONE, CHRISTOPHER J.
• Format: Journal Article
• Language: English
• Published: Bristol Cambridge University Press 01-07-1999; Cold Spring Harbor Laboratory Press
• Subjects: Animals; ANS; apomyoglobin; Apoproteins - chemistry; Magnetic Resonance Spectroscopy; Models, Molecular; myoglobin; Myoglobin - chemistry; NMR; partially folded protein; Protein Conformation; Solutions; Whales; NMR; partially folded protein; apomyoglobin; ANS; myoglobin
• ISSN: 0961-8368; 1469-896X
• DOI: 10.1110/ps.8.7.1484

Apomyoglobin from sperm whale is often used for
studies of ligand binding, protein folding, and protein
stability. In an effort to describe its conformational
properties in solution, homonuclear and heteronuclear (13C
and 15N) NMR methods were applied to the protein
in its native state. Assignments were confirmed for nuclear
Overhauser effects (NOEs) involving side chain and backbone
protons in the folded regions of the structure. These NOEs
were used to derive distance restraints. The shifts induced
by the hydrophobic dye 8-anilino-1-naphthalenesulfonic
acid (ANS) were inspected in the regions remote from its
binding site and served as an indicator of conformational
flexibility. 3JαH-NH
values were obtained to assess dihedral angle averaging
and to provide additional restraints. A family of structures
was calculated with X-PLOR and an ab initio simulated annealing
protocol using holomyoglobin as a template. Where the structure
appeared well defined by chemical shift, line width, ANS
perturbation, and density of NOEs, the low resolution model
of apomyoglobin provides a valid approximation for the
structure. The new model offers an improved representation
of the folded regions of the protein, which encompass the
A, B, E, helices as well as parts of the G and H helices.
Regions that are less well defined at this stage of calculations
include the CD corner and the end of the H-helix. The EF-F-FG
segment remains uncharacterized.