Three-dimensional Crystal Structures Research Articles

High Resolution Structures of Holo and Apo Formate Dehydrogenase

Three-dimensional crystal structures of holo (ternary complex enzyme-NAD-azide) and apo NAD-dependent dimeric formate dehydrogenase (FDH) from the methylotrophic bacterium Pseudomonas sp. 101 have been refined to R factors of 11·7% and 14·8% at 2·05 and 1·80 Å resolution, respectively. The estimated root-mean-square error in atomic co-ordinates is 0·11 Å for holo and 0·18 Å for apo. X-ray data were collected from single crystals using an imaging plate scanner and synchrotron radiation. In both crystal forms there is a dimer in the asymmetric unit. Both structures show essentially 2-fold molecular symmetry. NAD binding causes movement of the catalytic domain and ordering of the C terminus, where a new helix appears. This completes formation of the enzyme active centre in holo FDH. NAD is bound in the cleft separating the domains and mainly interacts with residues from the co-enzyme binding domain. In apo FDH these residues are held in essentially the same conformation by water molecules occupying the NAD binding region. An azide molecules is located the point of catalysis, the C4 atom of the nicotinamide moiety of NAD, and overlaps with the proposed formate binding. There is an extensive channel running from the active site to the protein surface and this is supposed to be used by substrate to reach the active centre after NAD has already bound. The structure of the active site and a hypothetical catalytic mechanism are discussed. Sequence homology of FDH with other NAD-dependent formate dehydrogenases and some d -specific dehydrogenases is discussed on the basis of the FDH three-dimensional structure.

A crystallographic molecular lattice builder applied to model lipid bilayers

It is often desirable for noncrystallographers to generate graphical models of three-dimensional crystal structures based on published coordinates of the atoms that make up the crystallographic unit cells. This type of visualization is particularly important for small-molecule crystals, such as lipid crystals, where one may be interested in investigating interactions between the individual molecules in addition to their conformations. BILAYER BUILDER is a program that generates a portion of the entire crystal structure from the coordinates of the molecules in a single unit cell. It gives users of small desktop computers, such as the Apple Macintosh, the capability to generate and examine model crystal structures with a molecular graphics display program. BILAYER BUILDER stores the crystal coordinates in a Brookhaven Protein Data Bank file format for possible use in a variety of applications on many different computers. Initially, it was written for use with lipid crystals and bilayers but may be used for building an assortment of molecular crystals.

Comparison of .alpha.-lactalbumin and lysozyme using vibrational circular dichroism. Evidence for a difference in crystal and solution structures

The conformation of the milk protein alpha-lactalbumin has been studied using vibrational circular dichroism (VCD) and compared to parallel studies on lysozyme. These proteins have been shown by Acharya et al. [(1989) J. Mol. Biol. 208, 99-127] to have very similar three-dimensional crystal structures. However, their VCD spectra in D2O solution are quite different. The VCD of lysozyme in D2O more resembles that of alpha-lactalbumin in 33% propanol/D2O, under which conditions alpha-lactalbumin has conformationally transformed to a structure with increased helical fraction. These results can be seen to be consistent with UVCD and resolution-enhanced FTIR spectra of alpha-lactalbumin and lysozyme in both D2O and H2O environments. The solvent sensitivity of the alpha-lactalbumin spectra and hence of its conformation contrasted with the lack of such sensitivity for lysozyme suggest that the alpha-lactalbumin crystal structure represents a conformation different from that which is dominant in aqueous solution.

Structural and evolutionary relationships between retroviral and eukaryotic aspartic proteinases

Three-dimensional crystal structures of the homologous retroviral proteinases from Rous sarcoma virus (RSV PR) and from human immunodeficiency virus (HIV-1 PR) are to a large extent similar and bear close resemblance to the six known structures of the bilobal fungal and mammalian aspartic proteinases. Systematic three-dimensional structural superpositions were carried out between the retroviral and the eucaryotic aspartic proteinases. Both retroviral enzymes were found to be similarly related to their fungal and mammalian counterparts. The most strongly conserved parts correspond to those regions in the N- and C-domains of the eucaryotic enzymes that are related by the interdomain dyad and consist of a combination of secondary structural elements that form the psi loop-alpha helix motif at the active sites of the aspartic proteinases. The retroviral proteinase monomer exhibits nearly the same degree of structural equivalence to the N- and C-domains of the eucaryotic enzymes. In light of the deduced structural relationships between HIV-1 PR and RSV PR, sequence alignments were performed for a number of retroviral proteinases from different subfamilies. There are three highly conserved amino acid sequence stretches, of which two belong to the psi loop-alpha helix motif, that bear moderate sequence similarity with the eucaryotic enzymes. The third conserved sequence stretch among the retroviral proteinases belongs to the flap and bears no resemblance to the flap sequences in the eucaryotic enzymes. The interdomain antiparallel beta sheet in the cellular enzymes differs from the intersubunit beta sheet in the number, arrangement, and directionality of strands, suggesting the possibility of convergent evolution.(ABSTRACT TRUNCATED AT 250 WORDS)

Coordination chemistry of lithium ion: a crystal and molecular structure review

There has been much recent interest in lithium and lithium ionophores. This growing interest in lithium is mainly due to the actual and potential applications of Li[sup +] in science, medicine, and technology. In the present review article, a tabulation is given, based on X-ray crystallographic data, of the bond lengths, geometry, coordination numbers, and solvent of crystallization of Li[sup +] complexes. The data included in the review extend from the earliest publications through February 1990. The authors have attempted in the text to draw the reader's attention to the various parameters involved in lithium-ligand interaction such as ligand coordination sites, ligand conformation changes, stereochemical arrangement of ligand binding sites, counterion effects, and solvent effects. In addition, discussion is included of lithium selective ionophores and of the involvement of Li[sup +] in biological cycles. Appropriate examples taken from the tables of data are used to illustrate the text. The compounds included in the review are listed by formula and abbreviation in Charts 1--18. The approach the authors chose for this review is a structural one, centered on the examination of the three-dimensional crystal structures of lithium salts and complexes. The basic assumption is that the structures of these lithium complexes more » in the solid state resemble their structures in solution, and that similar structure-selectivity relationships exist, at least to some extent, in both media. 190 refs. « less

Three-dimensional structures of substituted benzylphenyl ethers

Forty nine three-dimensional crystal structures of a benzylphenyl ether fragment retrieved from the Cambridge Structural Database were confronted with computed conformational maps of the fragment. Due to the symmetry the number of analyzed fragments rose to 98. When an endocyclic torsion angle of a phenyl ring deviates from 0° the adjacent torsion angle is deformed in opposite direction compensating thus the deviation from planarity. The shape of the fragment is mainly controlled by torsion angles τ1 = C-C-O-CH2, τ2 = C-O-CH2-C, and τ3 = O-CH2-C-C. The attachment of both phenyl rings to the -CH2-O- moiety is not symmetrical and the deformation depends on the value of the τ3 angle. In the crystal, the fragment prefers conformation with τ1 around 0°, τ2 around 180° and with broad bimodal distribution of τ3 around 0° and ±90° despite the fact that energetically equivalent regions exist in the potential energy maps for τ2 values near 60° and 300° and that many crystal structures with τ3 around 0° lie in higher energetical regions than those with τ3 around 90°. Thus a significant difference between the crystal and simulated gas phase conformations was observed supporting the hypothesis that crystals prefer flatter and more storable molecular conformations.

Escherichia coli aspartate carbamoyltransferase: the probing of crystal structure analysis via site-specific mutagenesis

Crystal structures are known for aspartate carbamoyltransferase (ATCase) in the T and R states, with and without the allosteric activator adenosine triphosphate (ATP) or inhibitor cytidine triphosphate (CTP). Visual inspection of X-ray crystal structures does not provide all of the information necessary for the determination of structure--function relationships in protein molecules. This problem is compounded because the crystalline states of the molecule may introduce effects due to crystal packing, restricted flexibility and less than optimum enzymatic conditions. Therefore, alternative techniques are required to test mechanisms conjectured from three-dimensional crystal structures of proteins. The technique of site-specific mutagenesis allows the researcher to test structure--function models based on three-dimensional structures and to obtain further insight into characteristics of the enzyme. Site-specific mutagenesis has been used to probe residues believed to be critical in the structure and function of ATCase. Selection of residues to be mutated has depended extensively on three-dimensional crystal structures of the enzyme. To date, 48 site-specific mutations at 37 different amino acid sites have been published. Although a total of 118 mutants at 58 different sites has been communicated to our laboratory, only published mutants will be considered in this review. In this paper, we compile for the first time, review, and analyze the site-specific mutants of ATCase. Site-specific mutagenesis of proteins has become a powerful technique in modern-day molecular biology, especially in studying a molecule as large as aspartate carbamoyltransferase. In this review, the role of site-specific mutagenesis of ATCase is discussed and improvements in the analysis are suggested.

Three-dimensional structures of substituted diphenyl sulfides

Three-dimensional crystal structures of a diphenyl sulfide skeleton from various compounds were confronted with computed conformational map. Diphenyl sulfide fragments, 31 in total, were retrieved from the Cambridge Structural Database and four fragments were taken from our measurements. Due to the symmetry of the fragment, the number of analyzed fragments rose to 140. The main features of geometrical behaviour of the fragment can be summarized as follows: If an endocyclic torsion angle of a phenyl ring deviates from 0 °C, the adjacent torsion angle is deformed in opposite direction by the same value keeping thus the phenyl ring planar. Repulsion of phenyl rings enlarges a C-S-C bonding angle in all fragments and bends aside the phenyl ring from a symmetrical attachment which has torsion around a S-C bond near 0°. Torsion angles around the S-C bonds correlate with each other keeping approximately perpendicular orientation of the phenyl rings. The correspondence between experimental values of torsion angles and low energy regions of the molecular mechanics conformational map suggests that possible gas-phase and crystal conformations of the diphenyl sulfide molecule are the same. Ab initio calculations fully confirmed results of molecular mechanics and - along with the crystal conformations - justify further usage of molecular mechanics in computational modelling of diphenyl sulfides.

Three-dimensional crystal structures of Escherichia coli met repressor with and without corepressor.

The three-dimensional crystal structure of met repressor, in the presence or absence of bound corepressor (S-adenosylmethionine), shows a dimer of intertwined monomers, which do not have the helix-turn-helix motif characteristic of other bacterial repressor and activator structures. We propose that the interaction of met repressor with DNA occurs through either a pair of symmetry-related alpha-helices or a pair of beta-strands, and suggest a model for binding of several dimers to met operator regions.

Molecular mechanism of ATP synthesis in oxidative phosphorylation.

The experiments described in this paper may perhaps point the way towards a reaction mechanism for oxidative phosphorylation. However, we are not yet in a position to write a detailed chemical equation, supported by experimental evidence, for the mechanism of ATP synthesis. Continued pursuit of some of the implications of these experiments will be very much dependent on information presently unavailable. For example, it would be of great value to have three-dimensional X-ray crystal structures for F0 as well as F1. It will also be important to know the pathway of proton translocation through the ATPase complex. We shall surely require entirely new experimental tools to probe many of these questions.

The generation of possible crystal structures of primary amides

Procedures are outlined for generation of crystal structures of primary amide molecules by constructing the possible ways in which the molecules may pack. For each given one- or two-dimensional hydrogen-bonded array, ensembles of three-dimensional crystal structures are generated by considering the possible ways in which the arrays may be juxtaposed. Observed and generated hypothetical molecular arrangements are analysed to highlight both favourable and unfavourable features, par­ticularly in terms of close packing principles, the size and shape of the molecule, van der Waals and Coulomb interactions and N-H ∙ ∙ ∙ O bonding geometry.

Percolation and cluster distribution. I. Cluster multiple labeling technique and critical concentration algorithm

A new approach for the determination of the critical percolation concentration, percolation probabilities, and cluster size distributions is presented for the site percolation problem. The novel "cluster multiple labeling technique" is described for both two- and three-dimensional crystal structures. Its distinctive feature is the assignment of alternate labels to sites belonging to the same cluster. These sites are members of a simulated finite random lattice. An algorithm useful for the determination of the critical percolation concentration of a finite lattice is also presented. This algorithm is especially useful when applied in conjunction with the cluster multiple labeling technique. The basic features of this technique are illustrated by applying it to a small planar square lattice. Numerical results are given for a triangular subcrystal containing up to 9 000 000 sites. These results compare favorably with the exact value of the infinite lattice critical percolation concentration.

Arrangements of point charges having zero electric-field gradient

The general conditions are investigated under which an assembly of point charges will produce a zero electric-field gradient (ZEFG) at a reference point s0(0,0,0). It is shown that for equal charges it is necessary that they form a configuration of cubic or icosahedral symmetry about s0. Unequal charges must be located at the vertices of a centrosymmetric polyhedron of symmetry m3m, m3 or 53m in such a way that the sum of the charge values in a pair of charges related by the centre of symmetry of the polyhedron be the same for all the pairs. Configurations of this kind are self-dual (SD) with respect to interchange of vertices by inversion in the centre of symmetry of the polyhedron. Self-dual configurations containing two kinds of charges (SD2C) are listed for polyhedra of up to 20 vertices and enumerated for all the centrosymmetric cubic and icosahedral Archimedean polyhedra and their duals. The method of enumeration without construction is described. The conditions under which such discrete ZEFG configurations can be embedded in three-dimensional crystal structures to give ZEFG structures are also investigated and a number of examples of such embeddings are given. The potential usefulness of such structures as Mössbauer null matrices is briefly discussed.

Molecular complexes. Part XI. Crystal and molecular structure of the 1 : 1 complexes of 1,3,5-trinitrobenzene and bis-(N-t-butylsalicylideneiminato)-cobalt(II), -nickel(II), and -copper(II)

The three-dimensional crystal structures of the 1 : 1 complexes of 1,3,5-trinitrobenzene and bis-(N-t-butylsalicylideneiminato)-cobalt(II), -nickel(II), and -copper(II) have been determined. They are essentially isomorphous and have a structure formed from pairs of donor [bis-(N-t-butylsalicylideneiminato)metal(II)] and acceptor (1,3,5-trinitrobenzene) molecules. The 1,3,5-trinitrobenzene interacts with only one of the salicylideneiminato ligands of a given chelate. The co-ordination around the metal atom is a flattened MO2N2 tetrahedron with angles between the M, N(1), O(1) and M, N(2), O(2) planes of 81° 34′, 78° 51′, and 61° 36′ for the cobalt, nickel, and copper structures respectively. Inter-ligand steric strains increase with flattening but prevent the metal adopting square planar or octahedral co-ordinations.

The crystal structure of two of nine known crystalline forms of Cu(tetramine)(NCS)2

Three-dimensional X-ray crystal structures of two of nine known crystalline forms of copper 1,7-bis-(2-pyridyl)-2,6-diazaheptane dithiocyanate show that both are five-co-ordinate species of the type [Cu (tetramine)NCS]SCN, but with different conformations of the facultative quadridentate ligand.

Nature of the infrared absorption bands disappearing during the melting of polypropylene

THE infrared spectra of isotactic polypropylene (PP) contain a number of bands (e.g. 840, 998 and 1168 cm -1) which practically disappear from the spectra of melted samples. The literature does not contain a single viewpoint regarding the nature of these bands. Some authors [1, 2] consider these to be associated with the unilateral order existing along the polymer chain, i.e. that their presence in the spectrum is only indirectly connected with the existence of threedimensional crystal structures. Two facts speak in favour of this theory: 1. The bands are present in the spectra of smeetic PP [1] which, on the basis of X-ray data, is amorphous and apparently consists of stretched spirals not incorporated in crystalline bundles. 2. I t was found during the calculation of the isotactic PP vibration spectra [3, 4], carried out to isolate the molecular coils, that normal vibrations exist (which is normally a combination of deformation oscillations of CH3-, CH~and CH-groups with C--C main-chain valence oscillations), and that these have frequencies similar to those actually observed as disappearing from the spectrum on melting. There are other authors, however [5, 6], who think that these bands appear as a result of chain interactions in the PP crystals. Support for this assumption is the fact that tempered PP samples, earlier thought to have a smectic structure [1], actually contain very small 1)13 crystals so that the X-ray spectrum is strongly distorted by peak broadening and mutual overlap of these peaks [7]. I t must be pointed out, regardless of the various interpretations of the nature of these bands, that an essential conditions for their appearance in the spectrum is the presence of long, isotaetie coil segments in the PP molecule, which are normally able to form crystals. The disappearance of the particular bands during polymer melting seems to be associated with a shortening of the equilibrium length of the isotactic PP coil segment in the melt, so that it becomes insufficient for the realization of the bands due to the interaction of vibrations. The PP produced in the presence of stereospeeific catalysts is made up of statistical Dand L-stereo-isomeric polymer units. The probability of an iso-