Biomaterial Database

A structure of sperm whale myoglobin at a nitrogen gas pressure of 145 atmospheres. 1988

R F Tilton, and G A Petsko

Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139.

A structure of sperm whale metmyoglobin under a nitrogen gas pressure of 145 atm (2200 psi) has been solved by X-ray diffraction using data to 2.0-A resolution. The perturbation of the gas pressure on the overall structure of the protein is minimal with a root mean square deviation of backbone atoms between the pressurized and unpressurized structures of 0.22 A. Additional electron density is observed, however, in two cavities of the protein molecule. The density is interpreted as a nitrogen molecule bound in the proximal cavity and as a water molecule hydrogen bonded in a separate cavity (cavity 3). In addition, alternate conformations are observed for three internal residues (Leu-135, Phe-138, and Ile-142) that border these cavities. These alternate conformations are not observed in atmospheric pressure structures and are presumed due to the effects of pressure and/or gas binding. The appearance of these alternate conformations implies a repacking of the protein interior and produces a new distribution of cavity spaces. The profile of the Debye-Waller factors for the pressurized structure is similar to that for the room pressure except for a small increase in the distal region (residues 61-69) of the protein.

UI	MeSH Term	Description	Entries
D008958	Models, Molecular	Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.	Molecular Models,Model, Molecular,Molecular Model
D009211	Myoglobin	A conjugated protein which is the oxygen-transporting pigment of muscle. It is made up of one globin polypeptide chain and one heme group.
D009584	Nitrogen	An element with the atomic symbol N, atomic number 7, and atomic weight [14.00643; 14.00728]. Nitrogen exists as a diatomic gas and makes up about 78% of the earth's atmosphere by volume. It is a constituent of proteins and nucleic acids and found in all living cells.
D011312	Pressure	A type of stress exerted uniformly in all directions. Its measure is the force exerted per unit area. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)	Pressures
D011487	Protein Conformation	The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).	Conformation, Protein,Conformations, Protein,Protein Conformations
D003196	Computer Graphics	The process of pictorial communication, between human and computers, in which the computer input and output have the form of charts, drawings, or other appropriate pictorial representation.	Computer Graphic,Graphic, Computer,Graphics, Computer
D000818	Animals	Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA.	Animal,Metazoa,Animalia
D014907	Whales	Large marine mammals of the order CETACEA. In the past, they were commercially valued for whale oil, for their flesh as human food and in ANIMAL FEED and FERTILIZERS, and for baleen. Today, there is a moratorium on most commercial whaling, as all species are either listed as endangered or threatened.	Beaked Whales,Berardius,Caperea,Dwarf Sperm Whale,Giant Bottle-Nosed Whales,Goose-Beaked Whale,Gray Whale,Mesoplodon,Narwhals,Pygmy Right Whale,Pygmy Sperm Whale,Right Whale, North Atlantic,Right Whale, Southern,Ziphiidae,Ziphius,Eschrichtius robustus,Eubalaena australis,Grey Whale,Monodon monoceros,North Atlantic Right Whale,Beaked Whale,Bottle-Nosed Whale, Giant,Bottle-Nosed Whales, Giant,Dwarf Sperm Whales,Giant Bottle Nosed Whales,Giant Bottle-Nosed Whale,Goose Beaked Whale,Goose-Beaked Whales,Gray Whales,Grey Whales,Narwhal,Pygmy Right Whales,Pygmy Sperm Whales,Right Whale, Pygmy,Right Whales, Pygmy,Right Whales, Southern,Southern Right Whale,Southern Right Whales,Sperm Whale, Dwarf,Sperm Whale, Pygmy,Sperm Whales, Dwarf,Sperm Whales, Pygmy,Whale,Whale, Grey,Whale, Southern Right,Whales, Grey,Whales, Southern Right
D014961	X-Ray Diffraction	The scattering of x-rays by matter, especially crystals, with accompanying variation in intensity due to interference effects. Analysis of the crystal structure of materials is performed by passing x-rays through them and registering the diffraction image of the rays (CRYSTALLOGRAPHY, X-RAY). (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)	Xray Diffraction,Diffraction, X-Ray,Diffraction, Xray,Diffractions, X-Ray,Diffractions, Xray,X Ray Diffraction,X-Ray Diffractions,Xray Diffractions