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PubMed1987

Ribonuclease structure and catalysis: crystal structure of sulfate-free native ribonuclease A at 1.5-A resolution.

The structure of native bovine pancreatic ribonuclease A, without the inhibitory sulfate anion normally bound at the active site, has been determined by X-ray diffraction at 1.53-A resolution. Treatment of a crystal of ribonuclease containing sulfate with an alkaline buffer released most of the sulfate anions. On return to active pH, few of the side chains moved, and the backbone structure remained unchanged. The active site conformation was essentially unchanged except for the replacement of the sulfate anion by a water molecule, which is hydrogen-bonded to histidine-12 and to another water, and for a small movement of the side chain of lysine-41. Histidines-12 and -119, the catalytic basic and acidic residues, have not moved. Thus the distance between them, and the presence of an intervening water, prohibits the possibility of their being hydrogen-bonded together. The structure has been refined by restrained least squares to an R factor of 0.17. Analysis of individual atomic temperature factors indicates that the molecule has become less rigid in general but that some regions were particularly affected by loss of the sulfate, while others were relatively unaffected. The active site geometry of native ribonuclease A supports the original in-line mechanism of Rabin and co-workers and is in disagreement with the adjacent mechanism of Witzel and co-workers.

Models, Molecular↗
PubMed2004

A model of voltage gating developed using the KvAP channel crystal structure.

Having inspected the crystal structure of the complete KvAP channel protein, we suspect that the voltage-sensing domain is too distorted to provide reliable information about its native tertiary structure or its interactions with the central pore-forming domain. On the other hand, a second crystal structure of the isolated voltage-sensing domain may well correspond to a native open conformation. We also observe that the paddle model of gating developed from these two structures is inconsistent with many experimental results, and suspect it to be energetically unrealistic. Here we show that the isolated voltage-sensing domain crystal structure can be docked onto the pore domain portion of the full-length KvAP crystal structure in an energetically favorable way to create a model of the open conformation. Using this as a starting point, we have developed rather conventional models of resting and transition conformations based on the helical screw mechanism for the transition from the open to the resting conformation. Our models are consistent with both theoretical considerations and experimental results.

Amino Acid Sequence↗
PubMed1996

Synthetic Strategies To Obtain V-P-O Open Frameworks Containing Organic Species as Structural Directing Agents. Crystal Structure of the V(IV)-Fe(III) Bimetallic Phosphate [H(3)N(CH(2))(2)NH(3)](2)[H(3)N(CH(2))(2)NH(2)][Fe(III)(H(2)O)(2)(V(IV)O)(8)(OH)(4)(HPO(4))(4)(PO(4))(4)].4H(2)O.

A general synthetic approach to rationalize the solution preparative chemistry of oxovanadium phosphates containing organic species as structural directing agents is presented. Careful attention is payed to the hydrolysis and condensation processes involving the ionic species in solution, and a simple restatement of the partial charge model (PCM) has been used in order to organize the experimental results. The structure of a new V(IV)-Fe(III) bimetallic oxovanadium phosphate, [H(3)N(CH(2))(2)NH(3)](2)[H(3)N(CH(2))(2)NH(2)] [Fe(III)(H(2)O)(2)(V(IV)O)(8)(OH)(4)(HPO(4))(4)(PO(4))(4)].4H(2)O, has been determined by X-ray single crystal diffraction methods. This compound crystallizes in the monoclinic system, space group P2(1)/n and the cell dimensions are as follows: a = 14.383(3) Å, b = 10.150(2) Å, c = 18.355(4) Å, and beta = 90.39(3) degrees (Z = 2). The existence of a complex intercrossing channel system, including a very large channel of 18.4 Å of diameter (in which both water molecules and ethylenediamine species are located), is the more interesting feature of this structure. Thermal decomposition, including the dehydration/rehydration process, has been studied by thermal analysis and variable temperature X-ray powder diffraction techniques. A complementary SEM study of the different intermediate decomposition products is presented.

Journal Article↗
PubMed2006

Crystal structure of a highly acidic neurotoxin from scorpion Buthus tamulus at 2.2A resolution reveals novel structural features.

The crystal structure of a highly acidic neurotoxin from the scorpion Buthus tamulus has been determined at 2.2A resolution. The amino acid sequence determination shows that the polypeptide chain has 64 amino acid residues. The pI measurement gave a value of 4.3 which is one of the lowest pI values reported so far for a scorpion toxin. As observed in other alpha-toxins, it contains four disulphide bridges, Cys12-Cys63, Cys16-Cys36, Cys22-Cys46, and Cys26-Cys48. The crystal structure reveals the presence of two crystallographically independent molecules in the asymmetric unit. The conformations of two molecules are identical with an r.m.s. value of 0.3A for their C(alpha) tracings. The overall fold of the toxin is very similar to other scorpion alpha-toxins. It is a betaalphabetabeta protein. The beta-sheet involves residues Glu2-Ile6 (strand beta1), Asp32-Trp39 (strand beta3) and Val45-Val55 (strand beta4). The single alpha-helix formed is by residues Asn19-Asp28 (alpha2). The structure shows a trans peptide bond between residues 9 and 10 in the five-membered reverse turn Asp8-Cys12. This suggests that this toxin belongs to classical alpha-toxin subfamily. The surface features of the present toxin are highly characteristic, the first (A-site) has residues, Phe18, Trp38 and Trp39 that protrude outwardly presumably to interact with its receptor. There is another novel face (N-site) of this neurotoxin that contains several negatively charged residues such as, Glu2, Asp3, Asp32, Glu49 and Asp50 which are clustered in a small region of the toxin structure. On yet another face (P-site) in a triangular arrangement, with respect to the above two faces there are several positively charged residues, Arg58, Lys62 and Arg64 that also protrude outwardly for a potentially potent interaction with other molecules. This toxin with three strong features appears to be one of the most toxic molecules reported so far. In this sense, it may be a new subclass of neurotoxins with the largest number of hot spots.

Amino Acid Sequence↗
PubMed2003

Insights into peptide nucleic acid (PNA) structural features: the crystal structure of a D-lysine-based chiral PNA-DNA duplex.

Peptide nucleic acids (PNAs) are oligonucleotide analogues in which the sugar-phosphate backbone has been replaced by a pseudopeptide skeleton. They bind DNA and RNA with high specificity and selectivity, leading to PNA-RNA and PNA-DNA hybrids more stable than the corresponding nucleic acid complexes. The binding affinity and selectivity of PNAs for nucleic acids can be modified by the introduction of stereogenic centers (such as D-Lys-based units) into the PNA backbone. To investigate the structural features of chiral PNAs, the structure of a PNA decamer containing three D-Lys-based monomers (namely H-GpnTpnApnGpnAdlTdlCdlApnCpnTpn-NH2, in which pn represents a pseudopeptide link and dl represents a D-Lys analogue) hybridized with its complementary antiparallel DNA has been solved at a 1.66-A resolution by means of a single-wavelength anomalous diffraction experiment on a brominated derivative. The D-Lys-based chiral PNA-DNA (LPD) heteroduplex adopts the so-called P-helix conformation. From the substantial similarity between the PNA conformation in LPD and the conformations observed in other PNA structures, it can be concluded that PNAs possess intrinsic conformational preferences for the P-helix, and that their flexibility is rather restricted. The conformational rigidity of PNAs is enhanced by the presence of the chiral centers, limiting the ability of PNA strands to adopt other conformations and, ultimately, increasing the selectivity in molecular recognition.

Base Sequence↗
PubMed1995

Structure determination of the biliverdin apomyoglobin complex: crystal structure analysis of two crystal forms at 1.4 and 1.5 A resolution.

Crystal structure determinations of two orthorhombic (P2(1)2(1)2(1)) crystal modifications of the biliverdin apomyoglobin complex are described. The two structures were determined by X-ray diffraction at 100 K to a resolution of 1.5 A and 1.4 A. Both crystal forms were grown by hanging-drop techniques, using phosphate as precipitant. The structures were solved by molecular replacement and refined to final R-values of 19.4% and 21.2%. Both structures are very similar with respect to the binding site and the conformation of the biliverdin chromophore, which occurs in a (P) helical conformation. It is located within the heme pocket, very close in position and orientation to the heme binding site in myoglobin. Two water molecules not present in the crystal structure of myoglobin are sequestered within the heme pocket in the biliverdin-apomyoglobin complex, and they are engaged in hydrogen bonding to the biliverdin and to the protein. Comparison with structural results from an earlier NMR study of the same complex shows good agreement.

Apoproteins↗
PubMed2006

Novel cation [N(SO2NMe3)2]+ and its synthesis and crystal structure. Dichloride of imido-bis(sulfuric) acid HN(SO2Cl)2. Part 1. Crystal structures of KN(SO2Cl)2.(1/2)CH3CN, KN(SO2Cl)2.(1/6)CH2Cl2, and [PCl4][N(SO2Cl)2].

Several salts of bis(chlorosulfonyl)imide HN(SO2Cl)2 (1), namely, two solvates of its potassium salt, KN(SO2Cl)2.(1/2)CH3CN (1K1), KN(SO2Cl)2.(1/6)CH2Cl2 (1K2), and its tetrachlorophosphonium salt, [PCl4][N(SO2Cl)2] (2), were prepared and structurally characterized. The reaction of HN(SO2Cl)2 with Me3N gives the [N(SO2Cl)2]- salt of a novel cation, [N(SO2NMe3)2]+. This cation is analogous to the [HC(SO2NMe3)2]+ cation, but in contrast to the latter, it is fairly stable to hydrolysis. The salt [N(SO2NMe3)2]+[N(SO2Cl)2]- (3) can be converted into salts of other anions by being treated with diluted aqueous solutions of the respective acids, and thus NO3-, Cl-.H2O, SeO3(2-), CH3COO-, HSO4-, (COO)2(2-) salts were prepared. Treatment of 3 with concentrated HNO3 gave the [N(SO2NMe3)2]+ [O2NO-H-ONO2]- salt, and the addition of an HCl-acidified FeCl3 aqueous solution yielded the FeCl4- salt. Methanolysis resulted in the formation of MeOSO3- and [MeOSO2NSO2OMe]- salts. All salts have been characterized by chemical analysis, vibrational spectroscopy, and X-ray structure determinations.

Journal Article↗
PubMed2000

Synthesis, crystal structure, EXAFS, and magnetic properties of catena [mu-tris(1,2-bis(tetrazol-1-yl)propane-N1,N1')iron(II)] bis(perchlorate). First crystal structure of an iron(II) spin-crossover chain compound.

[Fe(btzp)3](ClO4)2 (btzp = 1,2-bis(tetrazol-1-yl)propane) represents the first structurally characterized Fe(II) linear chain compound exhibiting thermal spin crossover. It shows a very gradual spin transition (T1/2 = 130 K) which has been followed by magnetic susceptibility measurements and 57Fe Mössbauer spectroscopy. The structure has been solved at 200 and 100 K by single-crystal X-ray analysis. It crystallizes in the trigonal space group P3c1 with Z = 2 Fe(II) units at both temperatures. The molecular structure consists of chains running along the c axis in which the Fe(II) ions are linked by three N4,N4' coordinating bis(tetrazole) ligands. The main difference between the two forms appears to be in the Fe-N bond lengths, which are 2.164(4) A at 200 K and 2.038(4) A at 100 K. The Fe-Fe separations are 7.422(1) A at 200 K and 7.273(1) A at 100 K. The EXAFS results are consistent with the crystal structure. In both spin states, the FeN6 octahedron is almost regular within the EXAFS resolution. The Fe-N distance is found as 2.16(2) A at 300 K and 2.00(2) A at 40 K. The absence of the "7 A peak" in the EXAFS spectra of [Fe(btzp)3](ClO4)2, in contrast with what has been observed for the [Fe(4-R-1,2,4-triazole)3]-(anion)2 chain compounds, confirms that this peak can be used as the signature of a metal alignment only when it involves a strongly enhanced multiple scattering M-M-M path, with M-M spacing less than 4 A. Irradiation with green light at 5 K has led to the population of the metastable high-spin state for the iron(II) ion. The nature of the spin-crossover behavior has been discussed on the basis of the structural features.

Journal Article↗
PubMed2002

The Cambridge Structural Database: a quarter of a million crystal structures and rising.

The Cambridge Structural Database (CSD) now contains data for more than a quarter of a million small-molecule crystal structures. The information content of the CSD, together with methods for data acquisition, processing and validation, are summarized, with particular emphasis on the chemical information added by CSD editors. Nearly 80% of new structural data arrives electronically, mostly in CIF format, and the CCDC acts as the official crystal structure data depository for 51 major journals. The CCDC now maintains both a CIF archive (more than 73,000 CIFs dating from 1996), as well as the distributed binary CSD archive; the availability of data in both archives is discussed. A statistical survey of the CSD is also presented and projections concerning future accession rates indicate that the CSD will contain at least 500,000 crystal structures by the year 2010.

Journal Article↗
PubMed2005

Kinetic, stability, and structural changes in high-resolution crystal structures of HIV-1 protease with drug-resistant mutations L24I, I50V, and G73S.

The crystal structures, dimer stabilities, and kinetics have been analyzed for wild-type human immunodeficiency virus type 1 (HIV-1) protease (PR) and resistant mutants PR(L24I), PR(I50V), and PR(G73S) to gain insight into the molecular basis of drug resistance. The mutations lie in different structural regions. Mutation I50V alters a residue in the flexible flap that interacts with the inhibitor, L24I alters a residue adjacent to the catalytic Asp25, and G73S lies at the protein surface far from the inhibitor-binding site. PR(L24I) and PR(I50V), showed a 4% and 18% lower k(cat)/K(m), respectively, relative to PR. The relative k(cat)/K(m) of PR(G73S) varied from 14% to 400% when assayed using different substrates. Inhibition constants (K(i)) of the antiviral drug indinavir for the reaction catalyzed by the mutant enzymes were about threefold and 50-fold higher for PR(L24I) and PR(I50V), respectively, relative to PR and PR(G73S). The dimer dissociation constant (K(d)) was estimated to be approximately 20 nM for both PR(L24I) and PR(I50V), and below 5 nM for PR(G73S) and PR. Crystal structures of the mutants PR(L24I), PR(I50V) and PR(G73S) were determined in complexes with indinavir, or the p2/NC substrate analog at resolutions of 1.10-1.50 Angstrom. Each mutant revealed distinct structural changes relative to PR. The mutated residues in PR(L24I) and PR(I50V) had reduced intersubunit contacts, consistent with the increased K(d) for dimer dissociation. Relative to PR, PR(I50V) had fewer interactions of Val50 with inhibitors, in agreement with the dramatically increased K(i). The distal mutation G73S introduced new hydrogen bond interactions that can transmit changes to the substrate-binding site and alter catalytic activity. Therefore, the structural alterations observed for drug-resistant mutations were in agreement with kinetic and stability changes.

Crystallography, X-Ray↗
PubMed2003

Relations between 77Se NMR chemical shifts of (phenylseleno)-benzenes and their molecular structures derived from nine X-ray crystal structures.

An extensive library of 77Se chemical shifts have been generated from the NMR measurements on substituted (phenylseleno)benzenes, including 33 new compounds. The variation in chemical shifts cover 265 ppm ranging from 446 to 181 ppm. Crystal structures have been determined for nine selected representatives of the substituted (phenylseleno)-benzenes. The analysis of the crystal structures supported that through-space interactions between selenium and the ortho-substituent observed in the crystal structures also are likely to be present in solution. The variation in the 77Se NMR chemical shifts can be rationalised from the intramolecular interactions with the substituent in the ortho-position. Furthermore it appears that these ortho-effects are roughly additive, and that it is the actual interactions and not the resulting conformational constraints that are responsible for the variations in the 77Se NMR chemical shifts.

Journal Article↗
PubMed1993

Evidence for crystal environment dominating base sequence effects on DNA conformation: crystal structures of the orthorhombic and hexagonal polymorphs of the A-DNA decamer d(GCGGGCCCGC) and comparison with their isomorphous crystal structures.

We have determined the structure of the A-DNA decamer d(GCGGGCCCGC) in two crystal forms, orthorhombic and hexagonal, at 1.7- and 1.8-A resolution, respectively. In the orthorhombic form, the fifth guanine residue has nearly trans-trans conformations for the alpha-gamma backbone torsions, as in the isomorphous orthorhombic structure d(CCCGGCCGGG) [Ramakrishnan, B., & Sundaralingam, M. (1993) J. Mol. Biol. 231, 431-444]. However, in the hexagonal form, the eighth cytosine residue adopts the trans-trans conformations for the backbone alpha-gamma torsions, as in the isomorphous hexagonal structure d(ACCGGCCGGT) [Frederick, C. A., Quigley, G. J., Teng, M.-K., Coll, M., van der Marel, G. A., van Boom, J. H., Rich, A., & Wang, A. H.-J. (1989) Eur. J. Biochem. 181, 295-307]. Even though the average helix and base-pair parameters are nearly the same in the two polymorphous crystal forms having the same sequence, many of the base-dependent local helix parameters are quite different. However, in the isomorphous crystal forms, in spite of the differing base sequences, the local helix and base-pair parameters of the duplexes are nearly the same. This indicates that, in crystals, the local conformation of a DNA structure is affected severely by the crystal packing environment rather than by the base sequence.

Base Sequence↗
PubMed2000

Structural studies on bioactive compounds. 30. Crystal structure and molecular modeling studies on the Pneumocystis carinii dihydrofolate reductase cofactor complex with TAB, a highly selective antifolate.

The crystal structure of the ternary complex of NADPH, the potent antifolate [2, 4-diamino-5-¿3-[3-(2-acetyloxyethyl)-3-benzyltriazen-1-yl]-4 -chloroph enyl¿-6-ethylpyrimidine] (TAB, 1) and Pneumocystis carinii dihydrofolate reductase (pcDHFR), refined to 2.1 A resolution, reveals that TAB binds similar to the antifolates trimethoprim and methotrexate. These data also reveal multiple conformations for the binding geometry of TAB with two preferred orientations of the acetyloxy and benzyl groups that results from a 180 degrees rotation about the N2-N3 triazenyl bond. The methyl of the acetyloxy and benzyl ring of TAB probes large hydrophobic regions of the p-aminobenzoyl folate binding pocket of the active site, in particular the region near Phe69, which is unique to the pcDHFR sequence. These results confirm prior molecular modeling investigations of the binding of TAB to pcDHFR that identified four low-energy binding geometries, two involving rotations about the terminal N(2)-N(3) triazenyl linkage and two involving atropisomerism about the pivotal pyrimethamine-phenyl bond. The primary differences in the molecular dynamics (MD) models and those observed in this crystal complex result from small conformational changes in active-site residues on energy minimization. However, two MD models place the acetyloxy and benzyl ring groups in a region of the active site between the cofactor-binding region and the p-aminobenzoyl folate pocket; an orientation never observed in any DHFR crystal structure to date. These conformers interact with solvent near the enzyme surface and are probably not observed due to the loss of specific hydrogen bonds with the enzyme. The high species pcDHFR selectivity of TAB could be the result of ligand flexibility that enables multiple binding orientations at the enzyme active site. Further modification of the acetyloxy region of TAB could increase its potency and selectivity for pcDHFR.

Binding Sites↗