Glycera dibranchiata hemoglobin. X-ray structure of carbonmonoxide hemoglobin at 1.5 A resolution.

The structure of carbonmonoxide Glycera hemoglobin has been determined to 1.5 A resolution by X-ray diffraction. The model, including ordered solvent, has been refined by the method of restrained least-squares to an R-value of 0.146. The positions of 1104 protein atoms and the oxygens of 155 water molecules have been determined with an estimated r.m.s. error of 0.10 to 0.13 A. The r.m.s. errors in protein geometry are 0.027 A for bond distances, 0.038 A for angle distances and 0.012 A for deviations of planar groups from their least-squares planes. The iron lies exactly in the plane of the heme nitrogens and the heme is very slightly domed toward the proximal side. The carbon-oxygen bond in the carbon monoxide ligand is bent 7.9 degrees away from the normal to the plane of the heme nitrogens. The ligand is in close contact with, and slightly removed from the heme normal by distal residues Leu 58(E7) and Val62(E11). Comparison of the CO structure with the 1.5 A deoxy structure shows that the majority of the rather small structural changes occurring upon ligation are mediated by movement of the heme due to shortening of the five iron to nitrogen bonds. There is very little empty space inside the molecule, and no direct channel from the solvent into the heme pocket; however, rotation of the side-chain of the distal leucine residue Leu 58(E6) could provide a ligand pathway.

The nucleosomal core histone octamer at 3.1 A resolution: a tripartite protein assembly and a left-handed superhelix.

The structure of the octameric histone core of the nucleosome has been determined by x-ray crystallography to a resolution of 3.1 A. The histone octamer is a tripartite assembly in which a centrally located (H3-H4)2 tetramer is flanked by two H2A-H2B dimers. It has a complex outer surface; depending on the perspective, the structure appears as a wedge or as a flat disk. The disk represents the planar projection of a left-handed proteinaceous superhelix with approximately 28 A pitch. The diameter of the particle is 65 A and the length is 60 A at its maximum and approximately 10 A at its minimum extension; these dimensions are in agreement with those reported earlier by Klug et al. [Klug, A., Rhodes, D., Smith, J., Finch, J. T. & Thomas, J. O. (1980) Nature (London) 287, 509-516]. The folded histone chains are elongated rather than globular and are assembled in a characteristic "handshake" motif. The individual polypeptides share a common central structural element of the helix-loop-helix type, which we name the histone fold.

Crystallization and preliminary X-ray diffraction studies on the mutT nucleoside triphosphate pyrophosphohydrolase of Escherichia coli.

The mutT nucleoside triphosphatase, which prevents AT----CG transversions during DNA replication, has been crystallized from ammonium sulfate utilizing a novel technique involving vapor diffusion in capillaries. X-ray diffraction analysis has revealed that the crystals are monoclinic, space group P2(1), with cell constants a = 34.14, b = 72.54, c = 56.38, and beta = 98.90. The Vm value of 2.31 A3/Da is consistent with two molecules of enzyme per asymmetric unit. The crystals are reasonably stable in the x-ray beam, and a data set to 2.5 A resolution has been collected for native protein. There is evidence that the crystals diffract to at least 2.1 A.

Glycera dibranchiata hemoglobin. Structure and refinement at 1.5 A resolution.

The coelomic cells of the common marine bloodworm Glycera dibranchiata contain several hemoglobin monomers and polydisperse polymers. We present the refined structure of one of the Glycera monomers at 1.5 A resolution. The molecular model for protein and ordered solvent for the deoxy form of the Glycera monomer has been refined to a crystallographic R-factor of 12.7% against an X-ray diffraction dataset at 1.5 A resolution. The positions of 1095 protein atoms have been determined with a maximum root-mean-square (r.m.s.) error of 0.13 A, and the r.m.s. deviation from ideal bond lengths is 0.015 A and from ideal bond angles is 1.0 degree. The r.m.s. deviation of planar groups from their least-squares planes is 0.007 A, and the r.m.s. deviation for torsion angles is 1.2 degrees for peptide groups and 16.8 degrees for side-chains. A total of 153 water molecules has been located, and they have been refined to a final average occupancy of 0.80. Multiple conformations have been found for five side-chains, and a change has been suggested for the sequence at five residues. The heme group is present in the "reverse" orientation that differs only in the positions of the vinyl beta-carbons from the "normal" orientation. The doming of the heme towards the proximal side, and the bond distances and angles of the heme and proximal histidine are typical of most deoxy globin structures. The substitution of leucine for the distal histidine residue (E7) creates an unusually hydrophobic heme pocket.

Crystals of Lumbricus erythrocruorin.

Lumbricus terrestris erythrocruorin, a 3.9 X 10(6) Mr respiratory protein, has been crystallized in four different forms. Despite the high molecular symmetry apparent from images in electron micrographs, only one crystal form expresses any molecular symmetry as crystallographic symmetry. The lattice parameters provide upper limits on the molecular dimensions of 267 A X 308 A X 172 A (1 A = 0.1 nm), which agree well with dimensions obtained from electron micrographs of negatively stained molecules. We have collected diffraction data to 5.5 A from type III crystals and have begun a structural analysis.

Cooperative dimeric and tetrameric clam haemoglobins are novel assemblages of myoglobin folds.

Cooperative functioning of many protein systems depends on communication between different subunits of those systems. Perhaps the best understood cooperative protein system is the vertebrate haemoglobin tetramer, in which the subunits share a similar tertiary structure (the myoglobin fold) with each other and with myoglobins and haemoglobins from at least four different animal phyla and leguminous plants. Blood clams have cooperative tetrameric haemoglobin. In view of previous reports concerning the role of dimers in the vertebrate tetramer, the clam haemoglobins represent a very interesting model system. We report here the low-resolution three-dimensional crystal structures of the dimeric and tetrameric cooperative haemoglobins from the blood clam Scapharca inaequivalvis. We find that clam haemoglobins are made of myoglobin-like subunits but their assembly to form dimers and tetramers is quite different from that of vertebrate haemoglobin. The arrangement of the subunits provides a simple structural explanation for haem-haem interaction in the dimer and tetramer.

Refinement of a molecular model for lamprey hemoglobin from Petromyzon marinus.

A molecular model for the protein and ambient solvent of the complex of cyanide with methemoglobin V from the sea lamprey Petromyzon marinus yields an R-factor of 0.142 against X-ray diffraction data to 2.0 A resolution. The root-mean-square discrepancies from ideal bond length and angle are, respectively, 0.014 A and 1.5 degrees. Atoms that belong to planar groups deviate by 0.012 A from planes determined by a least-squares procedure. The average standard deviation for chiral volumes, peptide torsion angle and torsion angles of side-chains are 0.150 A3, 2.0 degrees and 19.4 degrees, respectively. The root-mean-square variation in the thermal parameters of bonded atoms of the polypeptide backbone is 1.21 A2; the variation in thermal parameters for side-chain atoms is 2.13 A2. The model includes multiple conformations for 11 side-chains of the 149 amino acid residues of the protein. We identify 231 locations as sites of water molecules in full or partial occupancy. The sum of occupancy factors for these sites is approximately 154, representing 28% of the 550 molecules of water within the crystallographic asymmetric unit. The environment of the heme in the cyanide complex of lamprey methemoglobin resembles the deoxy state of the mammalian tetramer. In particular, the bond between atom NE2 of the proximal histidine and the Fe lies 5.1 degrees from the normal of the heme plane. In deoxy- and carbonmonoxyhemoglobins, the deviations from the normal to the heme plane are 7 to 8 degrees and 1 degree, respectively. Furthermore, the inequality in the distance of atom CD2 of the proximal histidine from the pyrrole nitrogen of ring-C of the heme (distance = 3.29 A) and CE1 from the pyrrole nitrogen of ring-A (distance = 3.06 A) is characteristic of deoxyhemoglobin, not carbonmonoxyhemoglobin, where these distances are equal. Finally, a hydrogen bond exists between carbonyl 111 and the hydroxyl of tyrosine 149. The corresponding hydrogen link in the mammalian tetramer is central to the T to R state transition and is present in deoxyhemoglobin but absent in carbonmonoxyhemoglobin. We suggest that the low affinity of oxygen for lamprey hemoglobin may be a consequence of these T-state geometries.

Refined crystal structure of deoxyhemoglobin S. I. Restrained least-squares refinement at 3.0-A resolution.

The crystal structure of deoxyhemoglobin S has been refined at 3.0-A resolution using the Hendrickson-Konnert restrained least-squares method. Comparison with the structure of deoxyhemoglobin A reveals a hingelike movement of the beta-chain A helices, which are involved in molecular contacts, toward the EF corners of their respective subunits. This movement brings the amino termini of the beta-chains closer to the molecular dyad. The A helices remain alpha-helical throughout their entire lengths. No other major structural difference is found between deoxyhemoglobin A and deoxyhemoglobin S.

Refined crystal structure of deoxyhemoglobin S. II. Molecular interactions in the crystal.

The refined crystal structure of deoxyhemoglobin S (Padlan, E. A., and Love, W. E. (1985) J. Biol. Chem. 260, 8272-8279) was used to analyze in detail the molecular interactions between hemoglobin tetramers in the crystal. The analysis confirms the close similarity and also the nonequivalence of the molecular interactions involving the two independent tetramers in the asymmetric unit of the crystal. The residue at the site of the hemoglobin S mutation, beta 6, is intimately involved in the lateral contacts between adjacent molecules. The molecular contacts in the crystals of deoxyhemoglobin S, deoxyhemoglobin A, and deoxyhemoglobin F were compared; some contacts involve the same regions of the molecule although the details of the interactions are very different. The effect of introducing an R state tetramer into the deoxyhemoglobin S strands was investigated using the known structure of carbon monoxyhemoglobin A. It was found that substituting a molecule of carbon monoxyhemoglobin A for one of the deoxyhemoglobin S tetramers results in extensive molecular interpenetration.

Crystallographic structure of the octameric histone core of the nucleosome at a resolution of 3.3 A.

The structure of the (H2A-H2B-H3-H4)2 histone octamer has been determined by means of x-ray crystallographic techniques at a resolution of 3.3 angstroms. The octamer is a prolate ellipsoid 110 angstroms long and 65 to 70 angstroms in diameter, and its general shape is that of a rugby ball. The size and shape are radically different from those determined in earlier studies. The most striking feature of the histone octamer is its tripartite organization, that is, a central (H3-H4)2 tetramer flanked by two H2A-H2B dimers. The DNA helix, placed around the octamer in a path suggested by the features on the surface of the protein, appears like a spring holding the H2A-H2B dimers at either end of the (H3-H4)2 tetramer.

Crystals of the octameric histone core of the nucleosome.

The undegraded core histone octamer has been crystallized in a form suitable for x-ray analysis. The hexagonal bipyramidal crystals reproducibly grow larger than 1.0 by 0.6 millimeter, X-ray reflections are observed from Bragg planes with spacings larger than 3.5 angstroms. The crystals have the symmetry of the space group P3l21 or its enantiomorph. There appears to be one histone octamer per asymmetric unit.

Location of amino acid residues in human deoxy hemoglobin.

A table has been compiled of the spatial disposition of the amino acid residues in the human deoxy hemoglobin tetramer. The table also indicates regions of possible contact between residues in each subunit and possible contacts between subunits.