Three-dimensional structure of ribonuclease T-1 complexed with an isosteric phosphonate substrate analogue of GpU: Alternate substrate binding modes and catalysis

The X-ray crystal structure of a complex between ribonuclease T-1 and guanylyl(3'-6')-6'-deoxyhomouridine (GpcU) has been determined at 2.0 Angstrom resolution. This Ligand is an isosteric analogue of the minimal RNA substrate, guanylyl(3'-5')uridine (GpU), where a methylene is substituted for the uridine 5'-oxygen atom. Two protein molecules are part of the asymmetric unit and both have a GpcU bound at the active site in the same manner. The protein-protein interface reveals an extended aromatic stack involving both guanines and three enzyme phenolic groups. A third GpcU has its guanine moiety stacked on His92 at the active site on enzyme molecule A and interacts with GpcU on molecule B in a neighboring unit via hydrogen bonding between uridine ribose 2'- and 3'-OH groups. None of the uridine moieties of the three GpcU molecules in the asymmetric unit interacts directly with the protein. GpcU-active-site interactions involve extensive hydrogen bonding of the guanine moiety at the primary recognition site and of the guanosine 2'-hydroxyl group with His40 and Glu58. on the other hand, the phosphonate group is weakly bound only by a single hydrogen bond with Tyr38, unlike ligand phosphate groups of other substrate analogues and 3'-GMP, which hydrogen-bonded with three additional active-site residues. Hydrogen bonding of the guanylyl 2'-OH group and the phosphonate moiety is essentially the same as that recently observed for a novel structure of a RNase T-1-3'-GMP complex obtained immediately after in situ hydrolysis of exo-(S-p)-guanosine 2',3'-cyclophosphorothioate [Zegers et al. (1998) Nature Struct. Biol. 5, 280-283]. It is likely that GpcU at the active site represents a nonproductive binding mode for GpU [:Steyaert, J., and Engleborghs (1995) fur. J. Biochem. 233, 140-144]. The results suggest that the active site of ribonuclease T-1 is adapted for optimal tight binding of both the guanylyl 2'-OH and phosphate groups (of GpU) only in the transition state for catalytic transesterification, which is stabilized by adjacent binding of the leaving nucleoside (U) group.

Inhibition of myotoxic activity of Bothrops asper myotoxin II by the anti-trypanosomal drug surarnin

Suramin, a synthetic polysulfonated compound, developed initially for the treatment of African trypanosomiasis and onchocerciasis, is currently used for the treatment of several medically relevant disorders. Suramin, heparin, and other polyanions inhibit the myotoxic activity of Lys49 phospholipase A(2) analogues both in vitro and in vivo, and are thus of potential importance as therapeutic agents in the treatment of viperid snake bites. Due to its conformational flexibility around the single bonds that link the central phenyl rings to the secondary amide backbone, the symmetrical suramin molecule binds by an induced-fit mechanism complementing the hydrophobic surfaces of the dimer and adopts a novel conformation that lacks C2 symmetry in the dimeric crystal structure of the suramin-Bothrops asper myotoxin II complex. The simultaneous binding of suramin at the surfaces of the two monomers partially restricts access to the nominal active sites and significantly changes the overall charge of the interfacial recognition face of the protein, resulting in the inhibition of myotoxicity. (c) 2005 Elsevier Ltd. All rights reserved.

Optical black holes in moving dielectrics

We study the optical paths of the light rays propagating inside a nonlinear moving dielectric medium. For rapidly moving dielectrics we show the existence of a distinguished surface which resembles, as far as the light propagation is concerned, the event horizon of a black hole. Our analysis clarifies the physical conditions under which electromagnetic analogues of gravitational black holes can eventually be obtained in laboratory.

Influence of N-Terminus Modifications on the Biological Activity, Membrane Interaction, and Secondary Structure of the Antimicrobial Peptide Hylin-a1

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Peptides based on CcdB protein as novel inhibitors of bacterial topoisomerases

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Mechanism of Action and Relationship Between Structure and Biological Activity of Ctx-Ha: A New Ceratotoxin-like Peptide from Hypsiboas albopunctatus

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Design and synthesis of peptides from bacterial ParE toxin as inhibitors of topoisomerases

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

SnO2 nanoparticles functionalized in amorphous silica and glass

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Febrifugine derivative antimalarial activity: quantum mechanical predictors

O desenvolvimento de linhagens resistentes de Plasmodium falciparum tem encorajado a busca por novas drogas antimalariais. A febrifugina é uma substância natural com alta atividade contra o P. falciparum que apresenta propriedade emética e toxicidade para o fígado tal que não permitem o seu uso clínico. A busca por análogos que possam ter uma performance clínica melhor é um tema de pesquisa atual. Nosso objetivo é investigar a estrutura eletrônica teórica de uma família de derivados da febrifugina empregando cálculos semi-empíricos de orbitais moleculares, procurando por índices eletrônicos que possam ajudar a modelar novos derivados mais eficientes. Os resultados teóricos mostram que para as moléculas mais seletivas existe um agrupamento dos valores de determinados índices em intervalos bem definidos. O modelo proposto para se obter alta seletividade foi testado com sucesso.

Alkene epoxidation with iodosylbenzene catalysed by polyionic manganese porphyrins electrostatically bound to counter-charged supports

Manganese(III) complexes of tetra-anionic and tetra-cationic porphyrins have been immobilised on counter-charged, surface-modified silica supports and on organic ion-exchange resins. The reactions of these supported manganese(III) porphyrin systems and analogous uncharged homogeneous systems have been examined using cyclooctene and (E)- and (Z)-4- methylpent-2-ene epoxidations, with iodosylbenzene (PhIO) as the oxygen donor.Comparisons using the manganese porphyrin systems as catalysts for the epoxidation of cyclooctene in acetonitrile reveal that, in low turnover reactions (maximum 136 turnovers), they all give an essentially quantitative yield of epoxide although the heterogeneous reactions are significantly slower than the homogeneous analogues. In large scale repeat-use experiments, however, the supported catalysts are clearly superior, giving markedly better yields.The epoxidations of (E)- and (Z)-4- methylpent-2-ene with all the catalysts show a very high stereoretention, with the (Z)-alkene reacting faster than the (E)-isomer. The sterically hindered manganese(III) 5,10,15,20-tetrakis(2,6-dichloro-3-sulfonatophenyl)porphyrin (MnTDCSPP) shows the highest selectivity for the (Z)-isomer; by contrast the supported manganese(III) 5,10,15,20-tetrakis[2,3,5,6-tetrafluoro-4-(trimethylammonio)phenyl]porphyrin on Dowex (MnTF(4)TMAPP-Dowex) reacts with the two alkenes at effectively the same rate.The mechanism of the epoxidations and the influence of the porphyrin ligand and support on the substrate selectivity are discussed.

Characterization and catalytic activity of iron(III) mono(4-N-methyl pyridyl)-tris(halophenyl) porphyrins in homogeneous and heterogeneous systems

The synthesis, characterization and catalytic activity of the cationic iron porphyrins Fe[M(4-N-MePy)TDCPP]Cl-2 and Fe[M(4-N-MePy)TFPP]Cl-2 in the epoxidation of (Z)-cyclooctene by PhIO in homogeneous solution and supported on silica gel (SG), imidazole propyl gel (IPG) or SG modified with 2-(4-sulfonatophenyl)ethyl groups (SiSO3) have been accomplished. When supported on IPG, both cationic FeP bind to the support via Fe-imidazole coordination. Fe[M(4-N-MePy)TDCPP]IPG contains a mixture of low-spin bis-coordinated (FeP)-P-III and high-spin mono-coordinated (FeP)-P-III species, whereas Fe[M(4-N-MePy)TFPP]IPG only contains high-spin mono-coordinated (FeP)-P-III. These FePIPG catalysts also contain (FeP)-P-II species, whose presence was confirmed by EPR spectroscopy using NO as a paramagnetic probe. Both cationic FePs coordinate to SG through Fe-O ligation and they are present as high-spin (FeP)-P-III species. The cationic FePs supported on SiSO3- are also high-spin (FeP)-P-III species and they bind to the support via electrostatic interaction between the 4-N-methylpyridyl groups and the SO3- groups present on the matrix. In homogeneous solution, both Fe[M(4-N-MePy)TDCPP]Cl-2 and Fe[M(4-N-MePy)TFPP]Cl-2 have similar catalytic activity to Fe(TDCPP)Cl and Fe(TFPP)Cl, leading to cis-epoxycyclooctane yields of 92%. When supported on inorganic matrices,both FePs lead to epoxide yields comparable to their homogeneous analogues and their anchoring enables catalyst recovery and re-use. Recycling of Fe[M(4-N-MePy)TDCPP]SiSO3- shows that this FeP maintains its activity in a second reaction. (C) 1999 Elsevier B.V. B.V. All rights reserved.

The absolute configuration of 1-(3 ',4 '-dihydroxycinnamoyl)cyclopentane-2,3-diol from the Amazonian tree Chimarrhis turbinata

An antioxidant, 1-(3',4'-dihydroxycinnamoyl) cyclopentane-2,3-diol [ or ( E)-2,3-dihydroxycyclopentyl-3-(3',4'-dihydroxyphenyl) acrylate ( 1)], and two known trans- and cis-chlorogenic acid methyl esters were isolated from the ethanolic extract of the leaves of Chimarrhis turbinata. The relative configuration of 1 was determined by NMR and by comparison of the circular dichroic spectrum ( CD) with those of the enantiomers of synthetic 3', 4'-dimethoxycinnamoyl analogues. The absolute configuration of one of the synthetic enantiomers was determined using the CD exciton chirality method. This established the structure of naturally occurring 1 as (E)- 2,3-dihydroxycyclopentyl- 3-(3', 4'-dihydroxyphenyl) acrylate.