Dataset Information

Conformational properties of native sperm whale apomyoglobin in solution.

ABSTRACT: 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. 3JalphaH-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.

SUBMITTER: Lecomte JT

PROVIDER: S-EPMC2144374 | biostudies-other | 1999 Jul

REPOSITORIES: biostudies-other

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Conformational properties of native sperm whale apomyoglobin in solution.

Lecomte J T JT Sukits S F SF Bhattacharya S S Falzone C J CJ

Protein science : a publication of the Protein Society 19990701 7

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 in ...[more]

PMID: 10422837

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Project description:Herman Melville's novel Moby Dick was inspired by historical instances in which large sperm whales (Physeter macrocephalus L.) sank 19th century whaling ships by ramming them with their foreheads. The immense forehead of sperm whales is possibly the largest, and one of the strangest, anatomical structures in the animal kingdom. It contains two large oil-filled compartments, known as the "spermaceti organ" and "junk," that constitute up to one-quarter of body mass and extend one-third of the total length of the whale. Recognized as playing an important role in echolocation, previous studies have also attributed the complex structural configuration of the spermaceti organ and junk to acoustic sexual selection, acoustic prey debilitation, buoyancy control, and aggressive ramming. Of these additional suggested functions, ramming remains the most controversial, and the potential mechanical roles of the structural components of the spermaceti organ and junk in ramming remain untested. Here we explore the aggressive ramming hypothesis using a novel combination of structural engineering principles and probabilistic simulation to determine if the unique structure of the junk significantly reduces stress in the skull during quasi-static impact. Our analyses indicate that the connective tissue partitions in the junk reduce von Mises stresses across the skull and that the load-redistribution functionality of the former is insensitive to moderate variation in tissue material parameters, the thickness of the partitions, and variations in the location and angle of the applied load. Absence of the connective tissue partitions increases skull stresses, particularly in the rostral aspect of the upper jaw, further hinting of the important role the architecture of the junk may play in ramming events. Our study also found that impact loads on the spermaceti organ generate lower skull stresses than an impact on the junk. Nevertheless, whilst an impact on the spermaceti organ would reduce skull stresses, it would also cause high compressive stresses on the anterior aspect of the organ and the connective tissue case, possibly making these structures more prone to failure. This outcome, coupled with the facts that the spermaceti organ houses sensitive and essential sonar producing structures and the rostral portion of junk, rather than the spermaceti organ, is frequently a site of significant scarring in mature males suggest that whales avoid impact with the spermaceti organ. Although the unique structure of the junk certainly serves multiple functions, our results are consistent with the hypothesis that the structure also evolved to function as a massive battering ram during male-male competition.

Dataset Information

Conformational properties of native sperm whale apomyoglobin in solution.

Publications

Conformational properties of native sperm whale apomyoglobin in solution.

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