PubMed Health⌕ Search

Biomedical subjects

Silvano Geremia

Publications and source records attributed to Silvano Geremia.

11 recordsLinked to original sources
PubMed2003

Guest encapsulation in a water-soluble molecular capsule based on ionic interactions.

We report on the synthesis and characterization of a water-soluble molecular capsule based on multiple ionic interactions. The assembly has been studied by means of 1H NMR, ESI-MS spectroscopy, and isothermal titration calorimetry (ITC), showing an association constant in water, Ka, of 3.3 x 104 M-1. The achieved water solubility of the system opens the possibility of using this supramolecular assembly for molecular recognition in pure water. Encapsulation studies have been performed and are reported in this Communication.

Journal Article↗
PubMed2003

Phasing protein structures using the group-subgroup relation.

Diffraction data from two non-isomorphous crystals (forms 1 and 2) of an artificial protein with a four-helix bundle motif, di-Co(II)-DF1-L13A, have been collected using synchrotron radiation. The phase of form 1 has been assigned using the group and minimal non-isomorphic supergroup relation between the space group of the previously determined di-Mn(II)-DF1-L13G structure and the space group of this form. This unconventional method of solving the phase problem has also been tested with form 2 using a reverse relation. The structure of the latter form has been solved using the group and maximal non-isomorphic subgroup relation with the space group of form 2 of the analogous dimanganese protein. This application has shown that this phasing method can be used for solving the protein structures of polymorphic crystals as an alternative to the molecular-replacement method.

Amino Acid Motifs↗
PubMed2003

Crystal chemistry and binding of NO2, SCN and SeCN to Co in cobalamins.

Results of the accurate crystal structure determination of NO(2)Cbl.2LiCl (1), NO(2)Cbl.NaCl (2), NCSCbl (3) and NCSeCbl (4), based on synchrotron diffraction data collected at 100 K, are described. The nitro group in (1) was found to be disordered with two orientations that differ by a rotation of approximately 60 degrees about the Co-NO(2) bond, whereas in (2) the nitro group has only one orientation. The first X-ray structural determination of a cobalamin with a Co-Se bond is reported. Comparison of the axial distances indicates that SeCN has a bond length of 2.384 (3) A and that the trans influence on the Co-N bond is only slightly greater than that of SCN. The crystals of the thiocyanate cobalamin contain both the S- and N-bonded coordination isomers in a 3:2 ratio. The structural features of the Co-S bond in cobalamins are discussed. The crystal chemistry of cobalamins is discussed in terms of packing of roughly spherical molecules. The unit-cell parameters can be used to group the cobalamins' crystal structures in different arrays intermediate between distorted hexagonal close packing and primitive hexagonal arrangements. The structural features of cobalamins, and of cobaloximes that have the same axial fragment as the cobalamins, are reviewed and discussed in terms of the cis influence of the equatorial ligand.

Crystallization↗
PubMed2002

Two-point self-coordination of a dizinc(II) bispyridylporphyrin ruthenium complex leading selectively to a discrete molecular assembly: solution and solid-state characterization.

The dizinc(II) bispyridylporphyrin ruthenium complex trans,cis,cis[RuCl2(CO)2(Zn.4'-cisDPyP)2] (1Zn, 4'-cisDPyP = 5,10-bis(4'-pyridyl)-15,20-diphenylporphyrin) features two donor (the uncoordinated 4'-N(py) atoms) and two acceptor (the Zn atoms) sites and is thus a building block suited for two-point coordination. 1H NMR spectroscopy indicates that 1Zn self-assembles in solution through Zn-4'-N(py) interactions to yield selectively a highly symmetrical discrete species, in which all donor and all acceptor sites of 1Zn are mutually saturated. Single-crystal X-ray analysis established that this adduct is a dimeric species, (1Zn)2, with a global S4 symmetry, in which the four porphyrins have a propeller-like arrangement. The dimeric species (1Zn)2 is a meso form derived from the combination of two 1Zn units with opposite helical chirality. The geometry of this highly symmetrical tetraporphyrin assembly in solution, as determined by NMR spectroscopy, is essentially the same as that found in the solid state. Thus 1Zn is an unprecedented example of metal-containing self-complementary building block that selectively recognizes itself through four Zn-N(py) interactions, and thus yields a very stable and symmetrical dimeric species, (1Zn)2, that features four porphyrins and six metal atoms (two Ru and four Zn).

Journal Article↗
PubMed2002

Cleavage of the iron-methionine bond in c-type cytochromes: crystal structure of oxidized and reduced cytochrome c(2) from Rhodopseudomonas palustris and its ammonia complex.

The three-dimensional structures of the native cytochrome c(2) from Rhodopseudomonas palustris and of its ammonia complex have been obtained at pH 4.4 and pH 8.5, respectively. The structure of the native form has been refined in the oxidized state at 1.70 A and in the reduced state at 1.95 A resolution. These are the first high-resolution crystal structures in both oxidation states of a cytochrome c(2) with relatively high redox potential (+350 mV). The differences between the two oxidation states of the native form, including the position of internal water molecules, are small. The unusual six-residue insertion Gly82-Ala87, which precedes the heme binding Met93, forms an isolated 3(10)-helix secondary structural element not previously observed in other c-type cytochromes. Furthermore, this cytochrome shows an external methionine residue involved in a strained folding near the exposed edge of the heme. The structural comparison of the present cytochrome c(2) with other c-type cytochromes has revealed that the presence of such a residue, with torsion angles phi and psi of approximately -140 and -130 degrees, respectively, is a typical feature of this family of proteins. The refined crystal structure of the ammonia complex, obtained at 1.15 A resolution, shows that the sulphur atom of the Met93 axial ligand does not coordinate the heme iron atom, but is replaced by an exogenous ammonia molecule. This is the only example so far reported of an X-ray structure with the heme iron coordinated by an ammonia molecule. The detachment of Met93 is accompanied by a very localized change in backbone conformation, involving mainly the residues Lys92, Met93, and Thr94. Previous studies under typical denaturing conditions, including high-pH values and the presence of exogenous ligands, have shown that the detachment of the Met axial ligand is a basic step in the folding/unfolding process of c-type cytochromes. The ammonia adduct represents a structural model for this important step of the unfolding pathway. Factors proposed to be important for the methionine dissociation are the strength of the H-bond between the Met93 and Tyr66 residues that stabilizes the native form, and the presence in this bacterial cytochrome c(2) of the rare six-residue insertion in the helix 3(10) conformation that increases Met loop flexibility.

Alanine↗
PubMed1999

Solution and Solid State Structure of a Canted, Side-to-Face, Bis(porphyrin) Adduct.

The coordination chemistry of meso-pyridyl/phenyl porphyrins (PyPs) toward metallo-porphyrins with substitutionally labile axial ligands has been exploited for the self-assembling of ordered arrays of pigments. PyPs are particularly versatile bulding blocks: the peripheral N atom can be either in the 4'-position (4'PyPs) or in the 3'-position (3'PyPs), and they can provide connections to as many as four metal centers by coordination of the pyridyl groups. While 4'PyPs lead to arrays of perpendicularly linked, side-to-face, porphyrins, 3'PyPs yield the corresponding canted analogues. Even though several perpendicular arrays have been described, the examples of canted adducts are few and all very recent. We report here a detailed X-ray structure of the new adduct of two axially ligated canted porphyrins [Ru(TPP)(CO)(3'MPyP)] (1) (TPP = tetraphenylporphyrin, 3'MPyP = 5-(3'-pyridyl)-10,15,20-triphenylporphyrin) as well as its thorough spectroscopic characterization in solution, including the dynamic (1)H NMR investigation of the NH tautomeric exchange process. 1 crystallizes in the monoclinic space group P2(1)/a, Z = 4, with a = 13.508(1) Å, b = 29.972(1) Å, c = 19.084(1) Å, and beta = 96.03(1) degrees. The structural and spectroscopic data of 1 assume a strategic importance among axially ligated pyridylporphyrin systems, since they can be fruitfully compared to those of perpendicular analogues. The importance of a comparative investigation of the canted and perpendicular arrays of porphyrins is readily understood: it might help understanding how relevant physicochemical properties, such as photoinduced long-range electron or energy transfer processes, depend on the mutual orientation of the pigments in the 3-dimensional architecture while the other parameters in the supramolecular array (number of macrocycles, distance between them) are maintained substantially unchanged.

Journal Article↗
PubMed1998

Stereochemistry of Ruthenium Bis-chelate Disulfoxide Complexes. A Molecular Mechanics Investigation.

A topological analysis of bis-chelate disulfoxide metal complexes is presented together with the results of molecular mechanics calculations on dichloro-1,2-bis(methylsulfinyl)ethane Ru(II) complexes. The goal of the work is to study the influence of the nonbonded atom interactions arising from linkage and cis-trans isomerism, combined with different arrangements of the sulfur chiral centers, on the strain energy of the compounds. The calculated strain energies show that the van der Waals and electrostatic interactions largely favor the S-bonding with respect to a mixed S,O-bonding and the cis isomers with respect to the trans isomers. Different arrangements of the chiral sulfur centers yield markedly different molecular energies; in general, meso ligands produce strain energies lower than racemic ligands. A "conformation discriminator" DeltaC has been introduced for the description of the ring conformations in the case of cycles characterized by marked inequalities of bond lengths and angles.

Journal Article↗
PubMed1998

Tyrosinase Models. Synthesis, Structure, Catechol Oxidase Activity, and Phenol Monooxygenase Activity of a Dinuclear Copper Complex Derived from a Triamino Pentabenzimidazole Ligand.

The dicopper(II) complex with the ligand N,N,N',N',N"-pentakis[(1-methyl-2-benzimidazolyl)methyl]dipropylenetriamine (LB5) has been synthesized and structurally characterized. The small size and the quality of the single crystal required that data be collected using synchrotron radiation at 276 K. [Cu(2)(LB5)(H(2)O)(2)][ClO(4)](4): platelet shaped, P&onemacr;, a = 11.028 Å, b = 17.915 Å, c = 20.745 Å, alpha = 107.44 degrees, beta = 101.56 degrees, gamma = 104.89 degrees, V = 3603.7 Å(3), Z = 2; number of unique data, I >/= 2sigma(I) = 3447; number of refined parameters = 428; R = 0.12. The ligand binds the two coppers nonsymmetrically; Cu1 is coordinated through five N donors and Cu2 through the remaining three N donors, while two water molecules complete the coordination sphere. Cu1 has distorted TBP geometry, while Cu2 has distorted SP geometry. Voltammetric experiments show quasireversible reductions at the two copper centers, with redox potential higher for the CuN(3) center (0.40 V) and lower for the CuN(5) center (0.17 V). The complex binds azide in the terminal mode at the CuN(3) center with affinity lower than that exhibited by related dinuclear polyaminobenzimidazole complexes where this ligand is bound in the bridging mode. The catechol oxidase activity of [Cu(2)(LB5)](4+) has been examined in comparison with that exhibited by [Cu(2)(L-55)](4+) (L-55 = alpha,alpha'-bis{bis[(1-methyl-2-benzimidazolyl)methyl]amino}-m-xylene) and [Cu(2)(L-66)](4+) (L-66 = alpha,alpha'-bis{bis[2-(1-methyl-2-benzimidazolyl)ethyl]amino}-m-xylene) by studying the catalytic oxidation of 3,5-di-tert-butylcatechol in methanol/aqueous buffer pH 5.1. Kinetic experiments show that [Cu(2)(L-55)](4+) is the most efficient catalyst (rate constant 140 M(-1) s(-1)), followed by [Cu(2)(LB5)](4+) (60 M(-1) s(-1)), in this oxidation, while [Cu(2)(L-66)](4+) undergoes an extremely fast stoichiometric phase followed by a slow and substrate-concentration-independent catalytic phase. The catalytic activity of [Cu(2)(L-66)](4+), however, is strongly promoted by hydrogen peroxide, because this oxidant allows a fast reoxidation of the dicopper(I) complex during turnover. The activity of [Cu(2)(LB5)](4+) is also promoted by hydrogen peroxide, while that of [Cu(2)(L-55)](4+) is little affected. The phenol monooxygenase activity of [Cu(2)(LB5)](2+) has been compared with that of [Cu(2)(L-55)](2+) and [Cu(2)(L-66)](2+) by studying the ortho hydroxylation of methyl 4-hydroxybenzoate to give methyl 3,4-dihydroxybenzoate. The LB5 complex is much more selective than the other complexes since its reaction produces only catechol, while the main product obtained with the other complexes is an addition product containing a phenol residue condensed at ring position 2 of the catechol.

Journal Article↗