B. K. Vainshtein

Three-dimensional structure of catalase from Penicillium vitale at 2.0 Å resolution

The three-dimensional structure analysis of crystalline fungal catalase from Penicillium vitale has been extended to 2.0 A resolution. The crystals belong to space group P3(1)21, with the unit cell parameters of a = b = 144.4 A and c = 133.8 A. The asymmetric unit contains half a tetrameric molecule of 222 symmetry. Each subunit is a single polypeptide chain of approximately 670 amino acid residues and binds one heme group. The amino acid sequence has been tentatively determined by computer graphics model building (using the FRODO system) and comparison with the known sequence of beef liver catalase. The atomic model has been refined by the Hendrickson & Konnert (1981) restrained least-squares program against 68,000 reflections between 5 A and 2 A resolution. The final R-factor is 0.31 after 24 refinement cycles. The secondary and tertiary structure of the catalase has been analyzed.

Three-dimensional structure of catalase from Micrococcus lysodeikticus at 1.5 Å resolution

The three‐dimensional crystal structure of catalase from Micrococcus lysodeikticus has been solved by multiple isomorphous replacement and refined at 1.5 Å resolution. The subunit of the tetrameric molecule of 222 symmetry consists of a single polypeptide chain of about 500 amino acid residues and one haem group. The crystals belong to space group P42212 with unit cell parameters a = b = 106,7 Å, c = 106,3 Å, and there is one subunit of the tetramer. per asymmetric unit. The amino acid sequence has been tentatively determined by computer graphics model building and comparison with the known three‐dimensional structure of beef liver catalase and sequences of several other catalases. The atomic model has been refined by Hendrickson and Konnerts least‐squares minimisation against 94,315 reflections between 8 Å and 1.5 Å. The final model consists or 3,977 non‐hydrogen atoms of the protein and haem group, 426 water molecules and ones sulphate ion. The secondary and tertiary sructures of the bacterial catalase have been analyzed and a comparison with the structure of beef liver catalase has been made.

Structure of the Heme d of Penicillium vitale and Escherichia coli Catalases

A heme d prosthetic group with the configuration of a cis-hydroxychlorin -spirolactone has been found in the crystal structures of Penicillium vitale catalase and Escherichia coli catalase hydroperoxidase II (HPII). The absolute stereochemistry of the two heme d chiral carbon atoms has been shown to be identical. For both catalases the heme d is rotated 180 degrees about the axis defined by the α--meso carbon atoms, with respect to the orientation found for heme b in beef liver catalase. Only six residues in the heme pocket, preserved in P. vitale and HPII, differ from those found in the bovine catalase. In the crystal structure of the inactive N201H variant of HPII catalase the prosthetic group remains as heme b, although its orientation is the same as in the wild type enzyme. These structural results confirm the observation that heme d is formed from protoheme in the interior of the catalase molecule through a self-catalyzed reaction.

Atomic structure at 2.5 Å resolution of uridine phosphorylase from E. coli as refined in the monoclinic crystal lattice

Uridine phosphorylase from E. coli (Upase) has been crystallized using vapor diffusion technique in a new monoclinic crystal form. The structure was determined by the molecular replacement method at 2.5 Å resolution. The coordinates of the trigonal crystal form were used as a starting model and the refinement by the program XPLOR led to the R‐factor of 18.6%. The amino acid fold of the protein was found to be the same as that in the trigonal crystals. The positions of flexible regions were refined. The conclusion about the involvement in the active site is in good agreement with the results of the biochemical experiments.

The atomic structure of Carnation Mottle Virus capsid protein

The structure of the Carnation Mottle Virus (CMtV) capsid protein has been determinated at 3.2 Å resolution by the method of molecular replacement. Three‐dimensional data were collected from a small number of crystals (sp.g.I23, a = 382.6 Å) using the synchrotron radiation with an image plate as detector. The coordinates of Tomato Bushy Stunt Virus (TBSV) were used as a searching model. Refinement of the coordinates of 7,479 non‐hydrogen atoms performed by the program XPLOR, has led to an R‐factor of 18.3%. It was found that the amino acid chain fold of capsid protein is very similar to that in other icosahedral viruses. However, there are some differences in the contact regions between protein subunits and also the lack of the β‐annulus around the 3‐fold icosahedral axes. The structural and biochemical results lead us to consider an alternative assembly pathway.

Lattice Dynamics and Phase Transitions

Vibrations of atoms about their equilibrium position is one of the fundamental properties of the crystal lattice. The set of phenomena associated with such vibrations and describing their laws is called lattice dynamics. Lattice dynamics lies at the basis of the theory of thermal properties of crystals and the present- day concepts of the electrical and magnetic properties of crystals, light scattering in them, etc. For instance, the anharmonicity of atomic vibrations in the crystal lattice determines the ratio between the heat capacity, compressibility, and the coefficient of linear thermal expansion (the Gruneisen ratio). The concept of the thermal motion of atoms and the vibration anharmonicity is the foundation of the modern theory of phase transitions in crystals (ferroelectric ones, in partic- ular, see [4.1]). Here we shall only state the principal conclusions of the theory of crystal lattice dynamics and consider, on their basis, the heat capacity, thermal conductivity, and thermal expansion of crystals.

The Structure of Real Crystals

The regular, strictly periodic structure of the crystal discussed in the preceding chapters is just an idealized picture. In nature, even under conditions of ideal thermodynamic equilibrium, crystals must show various deviations from this structure, which are called crystal lattice defects. Equilibrium lattice defects should by no means be interpreted as crystal defects. They can be regarded as elementary excitations of the ground state of the crystal, being just as inherent in the crystal as phonons or electrons, etc. While phonons and electrons are elementary excitations in the phonon and electron subsystems of a crystal, which were considered in Chaps. 3,4, lattice defects are elementary excitations in the atomic subsystem of a crystal, whose ground state was described in Chap. 1.

Principal Types of Crystal Structures

At present more than a hundred thousand of crystal structures are known. They can be classified according to definite features of their enormous diversity. First of all, we shall consider the structures of elements in which different types of bonds are encountered, since these structures most prominently display the crystallo- chemical properties of the atoms of a given element; these properties are very often inherited by the structures formed by compounds of these atoms as well.

Band Energy Structure of Crystals

A number of physical phenomena in crystals are determined by their electron energy spectrum. Some phenomena are associated with the motion of electrons in the periodic field of the lattice and with their scattering on lattice vibrations. The optical, electrical, magnetic, galvanomagnetic, and other properties of crystals of dielectrics, semiconductors, and metals are intimately connected with the nature of the electron energy spectrum and the geometry of the isoenergetic surfaces of the electrons in the crystal, the peculiarities of vibrations of the lattice atoms, and the dispersion of the frequencies of these vibrations. This chapter discusses the energy spectrum of the electrons in a crystal.