Wayne A. Hendrickson

Representation of phase probability distributions for simplified combination of independent phase information

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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.

Radiation damage in protein crystallography

Abstract A general model is derived to describe the rate of radiation damage in protein crystals. This model and some of its special cases are tested against the Blake and Phillips data on X-irradiation effects in myoglobin crystals. The results point to a sequential process of damage and suggest an improved method for correcting diffraction data for the effects of radiation damage.

Crystal structure analysis of sea lamprey hemoglobin at 2 Å resolution

Abstract The crystal structure of the predominant hemoglobin component of blood from the sea lamprey, Petromyzon marinus, has been determined by X-ray diffraction analysis. Crystals for this analysis were grown from cyanide methemoglobin V as crystal type D2. These crystals are in space group P212121 and have unit cell dimensions of a = 44.57 A , b = 96.62 A and c = 31.34 A . Isomorphous heavyatom derivatives were prepared by soaking crystals in solutions of Hg(CN)2, K2Hg(CNS)4 and KAu(CN)2. Diffracted intensities to as far as 2 A spacings were measured on a diffractometer. Phases were found by means of the isomorphous replacements and anomalous scattering, with supplementary information provided by the tangent formula. An atomic model was fitted to the final electron density map in a Richards optical comparator. The lamprey hemoglobin molecule is generally similar in structure to other globins, but differs in many details. Each molecule is in contact with ten neighboring molecules in the crystal lattice. The nature of the binding of the heavy atoms to lamprey hemoglobin has been interpreted.

Highly ordered crystals of the plant seed protein crambin.

Crystals of crambin, a plant seed protein of molecular weight 5000, diffract X-rays strongly to the interplanar spacing limit of 0.88 A. These diffraction data should allow a definition of atomic structure that is on a par with that typically obtained from crystals of small organic molecules. The crystals are in space group P21 and have unit cell dimensions a = 41.1 A, b = 18.7 A, c = 22·7 A, and β = 90.6 °. The asymmetric unit contains one protein molecule.

Atomic models for the polypeptide backbones of myohemerythrin and hemerythrin

Abstract A tentative atomic model, including the polypeptide backbone and side chains of residues in the active center, has been constructed for myohemerythrin. The model was built to fit a low resolution electron density map for this molecule while meeting several conditions for stereochemical reasonableness. An adaptation of this model serves also to explain an electron density map of octameric hemerythrin.

Crystal forms of lamprey hemoglobin and crystalline transitions between ligand states

Abstract Hemoglobin from the sea lamprey, Petromyzon marinus , has been crystallized in nine basic forms having polymeric asymmetric units containing 1, 6, 8, 10, 12 or 16 monomers. This polymorphism and further variations within some of the forms are particularly dependent on temperature, salt of crystallization and ligand state of the heme iron. Additional variations in a form result when the ligand state is changed within the crystal. All the crystal types so far acquired, whether by growth or by intracrystalline transition, have been catalogued. Crystalline transitions between ligand states tend to fall into two classes. In the first case, both the crystal lattice and the intensity distribution change only a little. The transition product is essentially isomorphous with its parent. In the second case, the lattice parameters change by as much as 10% and the diffracted intensity is distributed quite differently. Changes of the ligand state in the monomeric form of lamprey hemoglobin are always accomplished isomorphously; only the polymeric forms can undergo non-isomorphous transitions. Changes of ligand state are thought to effect in some subtle way the modification of potential polymerization sites on the monomer without appreciable alteration of the protein conformation. In crystals with monomeric asymmetric units such changes would have little effect on the diffraction pattern. However, if the affected sites were actual points of contact between the subunits of polymeric crystals then, within the constraints imposed by lattice forces, a re-arrangement of the subunits with attendant changes in the diffraction pattern could ensue.

The molecular architecture of oxygen-carrying proteins

Abstract Nature has evolved a diverse set of proteins that serve as oxygen carriers. These molecules differ from one another both in the character of their active sites and in the intricacy of their structural organization.

Crystals of myohemerythrin

Abstract Crystals have been grown of metazide myohemerythrin from the sipunculid Dendrostomum pyroides. The crystals are in space group P212121 and have unit cell dimensions of a = 41.6 A , b = 80.0 A and c = 37.8 A . An asymmetric unit contains a single myohemerythrin molecule.

Structural effects accompanying ligand change in crystalline lamprey hemoglobin

Abstract Crystals of lamprey hemoglobin in several states of ligation were prepared by intracrystalline reactions. X-ray diffraction data corresponding to a projection of the crystal structure were measured from the different ligand states: deoxy, carbonmonoxy, acid met, alkaline met, azomet and cyanomethemoglobin. These data were used to quantify the structural similarities between these ligand complexes. Structures of the low-spin complexes are all very similar, but the high-spin structures, particularly deoxyhemoglobin, differ quite considerably from the low-spin forms. The structural differences between deoxy and low-spin states are much greater in lamprey hemoglobin than in other monomeric globin. By contrast, these results are in qualitative agreement with observations on mammalian hemoglobin. A concentration of electron density changes in the CD and FG regions of the projected difference maps between deoxy and carbonmonoxyhemoglobin lends support to the suggestion that lamprey hemoglobin dimers may be analogous to the α 1 β 2 dimers of mammalian hemoglobin.