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PubMed1990

Cardiotoxin VII4 from Naja mossambica mossambica. The refined crystal structure.

The crystal structure of cardiotoxin VII4 from Naja mossambica mossambica was refined to 2.5 A resolution. Fifty ordered solvent sites were localized and included in the refinement. The final R factor is 0.197 (lambda/(2sin theta) less than 5 A; F greater than 3 sigma). The three-dimensional structure is characterized by two beta-sheets. Of particular interest is the two-stranded beta-sheet in the N-terminal region. This shows a large right-handed twist and, though strongly connected to the core of the molecule, and in particular to the C-terminal end, protrudes out of the bulk of the molecule. The segment of four amino acid residues connecting the two strands of this sheet is particularly exposed. It contains an invariant proline residue that has probably an important structural role, and is completely hydrophobic. Two other conserved hydrophobic zones were identified; the largest extends over the second and third loops, on one side only of the molecule. All side-chains of invariant hydrophobic character (except proline residues) belong to one of these three zones. Also discussed are the dimeric assembly and the rather loose packing in the crystal. The three-dimensional structure is compared with that of short and long alpha-neurotoxins. Comparison with two-dimensional nuclear magnetic resonance results on the 68% homologous cardiotoxin CT X IIb shows an excellent overall agreement. A few differences are probably genuine.

Amino Acid Sequence↗
PubMed1995

Crystal structure of desulforedoxin from Desulfovibrio gigas determined at 1.8 A resolution: a novel non-heme iron protein structure.

The crystal structure of desulforedoxin from Desulfovibrio gigas, a new homo-dimeric (2 x 36 amino acids) non-heme iron protein, has been solved by the SIRAS method using the indium-substituted protein as the single derivative. The structure was refined to a crystallographic R-factor of 16.9% at 1.8 A resolution. Native desulforedoxin crystals were grown from either PEG 4K or lithium sulfate, with cell constants a = b = 42.18 A, c = 72.22 A (for crystals grown from PEG 4K), and they belong to space group P3(2)21. The indium-substituted protein crystallized isomorphously under the same conditions. The 2-fold symmetric dimer is firmly hydrogen bonded and folds as an incomplete beta-barrel with the two iron centers placed on opposite poles of the molecule. Each iron atom is coordinated to four cysteinyl residues in a distorted tetrahedral arrangement. Both iron atoms are 16 A apart but connected across the 2-fold axis by 14 covalent bonds along the polypeptide chain plus two hydrogen bonds. Desulforedoxin and rubredoxin share some structural features but show significant differences in terms of metal environment and water structure, which account for the known spectroscopic differences between rubredoxin and desulforedoxin.

Amino Acid Sequence↗
PubMed2002

Crystal structure of the cyclomaltohexaose (alpha-cyclodextrin) complex with isosorbide dinitrate. Guest-modulated channel-type structure.

The crystal structure of the 2:1 complex of cyclomaltohexaose (alpha-cyclodextrin, alpha-CD) with isosorbide dinitrate was determined by single-crystal X-ray analysis. In the crystal with the space group C2, two cyclomaltohexaose molecules form a head-to-head dimer with the secondary hydroxy-group sides facing each other. The dimer unit is stacked along the crystallographic c-axis to form a channel-type structure. The isosorbide dinitrate molecule is encapsulated in the cylindrical cavity of the cyclomaltohexaose dimer. The dimeric structure exhibits pseudo twofold symmetry, and the guest molecule is disordered on the local symmetry axis. The isosorbide moiety is located at the center of the dimer cavity, and the nitrate groups penetrate into the cyclomaltohexaose rings. The guest molecule modulates the dimer structure to attain the most stable accommodation into the cavity. The cyclomaltohexaose molecules are laterally shifted away from each other to create the cavity fitted to the shape of the guest molecule. As the result, the intermolecular hydrogen bonds between secondary hydroxy-groups are not fully formed, but the dimeric structure is stabilized by the interaction with the guest molecule.

Carbohydrate Conformation↗
PubMed1993

Crystal structure of a Z-DNA hexamer d(CGCICG) at 1.7 A resolution: inosine.cytidine base-pairing, and comparison with other Z-DNA structures.

The crystal structure of the deoxyhexamer, d(CGCICG), has been determined and refined to a resolution of 1.7A. The DNA hexamer crystallises in space group P2(1)2(1)2(1) with unit cell dimensions of a = 18.412 +/- .017 A, b = 30.485 +/- .036A, and c = 43.318 +/- .024 A. The structure has been solved by rotation and translation searches and refined to an R-factor of 0.148 using 2678 unique reflections greater than 1.0 sigma (F) between 10.0-1.7 A resolution. Although the crystal parameters are similar to several previously reported Z-DNA hexamers, this inosine containing Z-DNA differs in the relative orientation, position, and crystal packing interactions compared to d(CGCGCG) DNA. Many of these differences in the inosine form of Z-DNA can be explained by crystal packing interactions, which are responsible for distortions of the duplex at different locations. The most noteworthy features of the inosine form of Z-DNA as a result of such distortions are: (1) sugar puckers for the inosines are of C4'-exo type, (2) all phosphates have the Zl conformation, and (3) narrower minor grove and compression along the helical axis compared to d(CGCGCG) DNA. In addition, the substitution of guanosine by inosine appears to have resulted in Watson-Crick type base-pairing between inosine and cytidine with a potential bifurcated hydrogen bond between inosine N1 and cytidine N3 (2.9 A) and O2 (3.3-3.A).

Base Composition↗
PubMed1997

RNA structure: crystal clear?

Structured RNAs play an essential role in chromosome maintenance, RNA processing, protein biosynthesis, and protein transport. To understand RNA function in these diverse biological systems, the rules for RNA folding and recognition must be learned. Recent crystal structures of hammerhead ribozymes, a group I intron domain, and RNA duplexes provide new insights into the principles of RNA folding and function.

Animals↗
PubMed1999

Peptide recognition by two HLA-A2/Tax11-19-specific T cell clones in relationship to their MHC/peptide/TCR crystal structures.

The crystal structures of two human TCRs specific for a HTLV-I Tax peptide bound to HLA-A2 were recently determined, for the first time allowing a functional comparison of TCRs for which the MHC/peptide/TCR structures are known. Extensive amino acid substitutions show that the native Tax residues are optimal at each peptide position. A prominent feature of the TCR contact surface is a deep pocket that accommodates a tyrosine at position 5 of the peptide. For one of these TCRs, this pocket is highly specific for aromatic residues. In the other TCR structure, this pocket is larger, allowing many different residues to be accommodated. The CTL clones also show major differences in the specificity for several other peptide residues, including side chains that are not directly contacted by the TCR. Despite the specificity of these clones, peptides that are distinct at five or six positions from Tax11-19 induce CTL activity, indicating that substantial changes of the peptide surface are tolerated. Human peptides with limited sequence homology to Tax11-19 represent partial TCR agonists for these CTL clones. The distinct functional properties of these CTL clones highlight structural features that determine TCR specificity and cross-reactivity for MHC-bound peptides.

Amino Acid Sequence↗
PubMed1998

Basis for monomer stabilization in Rhodopseudomonas palustris cytochrome c' derived from the crystal structure.

The crystal structure of an unusual monomeric cytochrome c' from Rhodopseudomonas palustris (RPCP) has been determined at 2.3 A resolution. RPCP has the four-helix (helices A, B, C and D) bundle structure similar to dimeric cytochromes c'. However the amino acid composition of the surface of helices A and B in RPCP is remarkably different from that of the dimeric cytochromes c'. This surface forms the dimer interface in the latter proteins. RPCP has seven charged residues on this surface contrary to the dimeric cytochromes c', which have only two or three charged groups on the corresponding surface. Moreover, hydrophobic residues on this surface of RPCP are two to three times fewer than in dimeric cytochromes c'. As a result of the difference in amino acid composition, the A-B surface of RPCP is rather hydrophilic compared with dimeric cytochromes c'. We thus suggest that RPCP is monomeric in solution because of the hydrophilic nature of the A-B surface. The amino acid composition of the A-B surface is similar to that of Rhodobacter capsulatus cytochrome c' (RCCP), which is an equilibrium admixture of monomer and dimer. The charge distribution of the A-B surface in RCCP, however, is considerably different from that of RPCP. Due to the difference, RCCP can form dimers by both ionic and hydrophobic interactions. These dimers are quite different from those in proteins which form strong dimers such as in Chromatium vinosum, Rhodospirillum rubrum, Rhodospirillum molischianum and Alcaligenes. Cytochrome c' can be classified into two types. Type 1 cytochromes c' have hydrophobic A-B surfaces and they are globular. The A-B surface of type 2 cytochromes c' is hydrophilic and they take a monomeric or flattened dimeric form.

Amino Acid Sequence↗
PubMed2005

Targeting the DNA minor groove with fused ring dicationic compounds: comparison of in silico screening and a high-resolution crystal structure.

The crystal structure of the DNA minor groove biphenyl benzimidazole diamidine ligand DB819 has been determined, bound to the DNA sequence d(CGCGAATTCGCG)(2), at a resolution of 1.36 Angstrom. Conditions for reliable in silico docking that reproduce the observed position of the ligand in the minor groove have been determined.

Crystallography, X-Ray↗
PubMed2002

Design, synthesis and evaluation of peptide libraries as potential anti-HIV compounds, via inhibition of gp120/cell membrane interactions, using the gp120/cd4/fab17 crystal structure.

The crystal structure of a gp120/CD4/Fab17b complex was analysed leading to the design of several peptide libraries in the hope of obtaining novel gp120/cell membrane receptor interaction inhibitors, especially inhibitors of gp120/CD4 and gp120/chemokine receptor interactions. Syntheses of tri- and tetra- and pentapeptides were performed via a solid phase synthesis methodology using a Rink Amide MBHA resin and a Fmoc strategy giving C-terminal amide form peptides. Compounds were assayed against C8166 cells infected by HIV-1 IIIB and screened using a gp120 binding assay and the FIGS reporter gene assay.

Anti-HIV Agents↗
PubMed1993

Crystal structure of human immunodeficiency virus (HIV) type 2 protease in complex with a reduced amide inhibitor and comparison with HIV-1 protease structures.

The crystal structure of HIV-2 protease in complex with a reduced amide inhibitor [BI-LA-398; Phe-Val-Phe-psi (CH2NH)-Leu-Glu-Ile-amide] has been determined at 2.2-A resolution and refined to a crystallographic R factor of 17.6%. The rms deviation from ideality in bond lengths is 0.018 A and in bond angles is 2.8 degrees. The largest structural differences between HIV-1 and HIV-2 proteases are located at residues 15-20, 34-40, and 65-73, away from the flap region and the substrate binding sites. The rms distance between equivalent C alpha atoms of HIV-1 and HIV-2 protease structures excluding these residues is 0.5 A. The shapes of the S1 and S2 pockets in the presence of this inhibitor are essentially unperturbed by the amino acid differences between HIV-1 and HIV-2 proteases. The interaction of the inhibitor with HIV-2 protease is similar to that observed in HIV-1 protease structures. The unprotected N terminus of the inhibitor interacts with the side chains of Asp-29 and Asp-30. The glutamate side chain of the inhibitor forms hydrogen bonds with the main-chain amido groups of residues 129 and 130.

Amino Acid Sequence↗
PubMed1997

Crystal structure of 3-isopropylmalate dehydrogenase from the moderate facultative thermophile, Bacillus coagulans: two strategies for thermostabilization of protein structures.

The crystal structure of 3-isopropylmalate dehydrogenase from the moderate facultative thermophile Bacillus coagulans (BcIPMDH) has been determined by the X-ray method. BcIPMDH is a dimeric enzyme composed of two identical subunits, each of which takes an open alpha/beta structure with 11 alpha-helices and 14 beta-strands. The polypeptide is folded into two domains. The first domain is composed of residues 1-101 and 257-356, and the second domain, of residues 102-256. The latter domains of the two subunits are associated with one another by a dyad axis to make the dimer, locally forming a beta-sheet and a four-helix bundle. As compared with the structure of the enzyme from the extreme thermophile Thermus thermophilus (TtIPMDH), a new short beta-sheet (residues 329-330 and 340-341) absent in TtIPMDH is formed by the insertion of 5 residues in BcIPMDH. In terms of determinants for thermostabilization, both consistent and inconsistent changes were found between the two enzymes. The regions including inconsistent changes are formed by different usages of the determinants for stabilizing the loops at different levels. Those in BcIPMDH contain some structural redundancies in length of amino acid sequence and flexibility of residues, which seem to be unnecessary for the enzymatic reaction. Such redundancies are also found in the primary structure of the enzyme of the mesophile Bacillus subtilis, but these parts are more stabilized in BcIPMDH by hydrogen bonds and salt bridges. On the other hand, TtIPMDH is stabilized by reducing such redundant parts. This contrast suggests that different strategies may be preferred for thermostabilization, depending on temperature.

3-Isopropylmalate Dehydrogenase↗
PubMed1999

Crystal structures of

The crystal structures of [18]aneN(6)H(2)K[Co(CN)(6)].4H(2)O [potassium dihydrogen hexacyanocobaltate-1,4,7,10,13,16-hexaazacyclooctadecane-water (1/1/4)], [16]aneN(4)H(2)K[Co(CN)(6)] [potassium dihydrogen hexacyanocobaltate-1,5,9,13-tetraazacyclohexadecane (1/1)] and [12]aneN(4)H(3)[Co(CN)(6)].2H(2)O [trihydrogen hexacyanocobaltate-1,4,7,10-tetraazacyclododecane-water (1/1/2)] have been determined. For these supercomplexes, the [Co(CN)(6)](3-) binding with protonated polyammonium macrocycles is dominant in the binding competition between K(+) and [Co(CN)(6)](3-). It is suggested that the binding of [Co(CN)(6)](3-) with protonated polyammonium macrocycles is independent of the cavity size of the macrocycle, whereas that of K(+) is size-match selective. For [18]aneN(6)H(2)K[Co(CN)(6)].4H(2)O, the formation of a two-dimensional lamella may be derived from a chain-like arrangement of four-, five- and eight-membered rings in the network through the mutual balance between electrostatic and hydrogen-bonding interactions. [16]aneN(4)H(2)K[Co(CN)(6)] is a novel example demonstrating the anchoring of cobalticyanide through hydrogen-bonding interactions inside a zeolite-type cavity in the three-dimensional network formed by K(+) and the macrocycles through Coulombic interactions. Also, a three-dimensional network was formed mainly through hydrogen-bonding interactions between [Co(CN)(6)](3-), protonated macrocycles and water molecules in [12]aneN(4)H(3)[Co(CN)(6)].2H(2)O.

Journal Article↗
PubMed2004

Characterization and crystal structure of cadmium(II) halide complexes with amino acids and their derivatives VI. The comparison of crystal structures of cadmium(II) halide complexes with three kinds of piperidine carboxylic acids.

Six cadmium(II) halide complexes with dl-piperidine-2-carboxylic acid (DL-Hpipe-2), dl-piperidine-3-carboxylic acid (DL-Hpipe-3), and piperidine-4-carboxylic acid (Hpipe-4), have been prepared and characterized by means of IR and Raman spectra and thermal analysis. The crystal structures of [CdCl2(DL-Hpipe-2)(H2O)], [CdBr2(DL-Hpipe-3)], and [CdCl2(Hpipe-4)] have been determined by X-ray diffraction. These three complexes have one-dimensional polymer structures bridged by halide atoms. The crystal of [CdCl2(DL-Hpipe-2)(H2O)] is orthorhombic with the space group Pca2(1). The cadmium atom is in an octahedral geometry, ligated by a carboxyl oxygen atom, two bridging chlorine atoms, a terminal chlorine atom, a water molecule and a carboxyl oxygen atom of a neighboring molecule. The carboxyl oxygen atoms of DL-Hpipe-2 are coordinated to two cadmium atoms. The unit cell consists of two types of one-dimensional polymer structures: [CdCl2(D-Hpipe-2)(H2O)] and [CdCl2(L-Hpipe-2)(H2O)]. Therefore, it is better to write [CdCl2(DL-Hpipe-2)(H2O)] as [CdCl2(D-Hpipe-2)(H2O)][CdCl2(L-Hpipe-2)(H2O)]. The crystal structure of [CdBr2(DL-Hpipe-3)] is monoclinic with space group P2(1). The cadmium atom is in a distorted octahedral geometry ligated by two carboxyl oxygen atoms and four bridging bromine atoms. This complex consists of either D-Hpipe-3 or L-Hpipe-3. Therefore [CdBr2(DL-Hpipe-3)] is written as [CdBr2(D or L-Hpipe-3)]. The crystal of [CdCl2(Hpipe-4)] is monoclinic with space group P2(1)/n. The structure is similar to that of [CdBr2(D or L-Hpipe-3)].

Amino Acids↗
PubMed2006

Comparison of the crystal structures and magnetic properties of the low- and high-temperature forms of AgCuPO4: crystal structure determination, magnetic susceptibility measurements, and spin dimer analysis.

The crystal structure of the low-temperature form of AgCuPO4 (i.e., alpha-AgCuPO4) was determined by powder X-ray diffraction and was compared with that of the high-temperature form of AgCuPO4 (i.e., beta-AgCuPO4). The magnetic properties of the two forms were examined by measuring their magnetic susceptibilities and evaluating the relative strengths of their spin-exchange interactions on the basis of spin-dimer analysis. Both forms of AgCuPO4 have layers of Cu2P2O8 alternating with silver-atom double layers; beta-AgCuPO4 has two Cu2P2O8 layers per unit cell, while alpha-AgCuPO4 has one. The coordinate environment of each Cu2+ ion is close to being a distorted square pyramid in alpha-AgCuPO4, but it is close to being a distorted trigonal bipyramid in beta-AgCuPO4. The magnetic susceptibilities of alpha- and beta-AgCuPO4 are well simulated by an antiferromagnetic alternating-chain model, which leads to J/k(B) = -146.1 K and alphaJ/k(B) = -75.8 K for alpha-AgCuPO4, and J/k(B) = -82.6 K and alphaJ/k(B) = -31.7 K for beta-AgCuPO4 (with the convention in which the spin-exchange parameter between two adjacent spin sites is written as 2J). The spin gaps, delta/k(B), obtained from these parameters are 93.7 K for alpha-AgCuPO4 and 62.3 K for beta-AgCuPO4. The strongest spin exchange in both forms of AgCuPO4 comes from a super-superexchange path, and this interaction is stronger for alpha-AgCuPO4 than for beta-AgCuPO4 by a factor of approximately 2, in good agreement with the experiment. Our analysis supports the use of this model for beta-AgCuPO4 and indicates that the spin lattice of alpha-AgCuPO4 would be better described by a two-dimensional net made up of weakly interacting alternating chains.

Journal Article↗
PubMed2005

Solvothermal syntheses of [Ln(en)3(H2O)x(mu(3-x)-SbS4)] (Ln = La, x = 0; Ln = Nd, x = 1) and [Ln(en)4]SbS4.0.5en (Ln = Eu, Dy, Yb): a systematic study on the formation and crystal structures of new lanthanide thioantimonates(V).

New lanthanide thioantimonate(V) compounds, [Ln(en)3(H2O)x(mu(3-x)-SbS4)] (en = ethylenediamine, Ln = La, x = 0, Ia; Ln = Nd, x = 1, Ib) and [Ln(en)4]SbS4.0.5en (Ln = Eu, IIa; Dy, IIb; Yb, IIc), were synthesized under mild solvothermal conditions by reacting Ln2O3, Sb, and S in en at 140 degrees C. These compounds were classified as two types according to the molecular structures. The crystal structure of type I (Ia and Ib) consists of one-dimensional neutral [Ln(en)3(H2O)x(mu(3-x)-SbS(4))]infinity (x = 0 or 1) chains, in which SbS4(3-) anions act as tridentate or bidentate bridging ligands to interlink [Ln(en)3]3+ ions, while the crystal structure of type II (IIa, IIb, and IIc) contains isolated [Ln(en)4]3+ cations, tetrahedral SbS4(3-) anions, and free en molecules. A systematic investigation of the crystal structures of the five lanthanide compounds, as well as two reported compounds, clarifies the relationship between the molecular structure and the entity of the lanthanide(III) series, such as the stability of the lanthanide(III)-en complexes, the coordination number, and the ionic radii of the metals.

Journal Article↗
PubMed2004

Packing motifs and magneto-structural correlations in crystal structures of metallo-tetrakis(1,2,5-thiadiazole)porphyrazine series, MTTDPz (M=H2, Fe, Co, Ni, Cu, Zn).

Single crystals of tetrakis(thiadiazole)porphyrazine and the corresponding metal(II) derivatives, MTTDPz (M=H2, Fe, Co, Ni, Cu, and Zn) were grown by sublimation under reduced pressure with continuous N2 gas flow. Their structures, obtained by X-ray crystallographic analysis, depend significantly on the central metal ion, and the M=Ni and Cu derivatives exhibit polymorphism. They can be classified into three forms, alpha, beta, and gamma. The alpha form (M=H2, Ni, and Cu) is composed of two-dimensional hexagonal close packing formed by side-by-side contacts between thiadiazole rings, whereas the beta form (M=Fe, Co, and Zn) crystallizes into a one-dimensional coordination polymer. The gamma form (M=Ni and Cu) consists of a ladder structure caused by pi stacking, similar to the beta form of phthalocyanine, and by side-by-side contacts between thiadiazole rings. Although the crystal structures of the MTTDPz series exhibited multi-dimensional network structures, magnetic measurements revealed relatively weak exchange interactions, probably reflecting the long distances between the metal ions.

Journal Article↗
PubMed1982

Conformation and structure of acidic dipeptides. Crystal structure of glycyl-L-aspartic acid dihydrate.

The crystal structure of the acidic dipeptide glycyl-L-aspartic acid dihydrate, Gly-L-Asp X 2H2O, C6H10N2O5 X 2H2O, has been determined by means of three-dimensional counter X-ray data. The dipeptide crystallizes in space group P212121 of the orthorhombic system with four formula units in a cell of dimensions of a = 9.611(4), b = 9.775(6), and c = 10.845(4)A. The structure was solved by direct methods and refined by least-squares methods to a final value of the weighted R-factor of 0.035 using all 1191 observed intensity data. The dipeptide occurs in the crystal as a zwitterion, with the glycyl N-terminus protonated and the aspartyl main chain carboxyl group deprotonated. The conformation about the peptide bond is fully trans extended, with an omega angle of -175.9 degrees. While there is extensive intermolecular hydrogen bonding in the crystals, there is no intramolecular hydrogen bonding either here or in the solid state structures of related dipeptides.

Dipeptides↗