Ultra-fast excited state dynamics in green fluorescent protein: multiple states and proton transfer.

The green fluorescent protein (GFP) of the jellyfish Aequorea Victoria has attracted widespread interest since the discovery that its chromophore is generated by the autocatalytic, posttranslational cyclization and oxidation of a hexapeptide unit. This permits fusion of the DNA sequence of GFP with that of any protein whose expression or transport can then be readily monitored by sensitive fluorescence methods without the need to add exogenous fluorescent dyes. The excited state dynamics of GFP were studied following photo-excitation of each of its two strong absorption bands in the visible using fluorescence upconversion spectroscopy (about 100 fs time resolution). It is shown that excitation of the higher energy feature leads very rapidly to a form of the lower energy species, and that the excited state interconversion rate can be markedly slowed by replacing exchangeable protons with deuterons. This observation and others lead to a model in which the two visible absorption bands correspond to GFP in two ground-state conformations. These conformations can be slowly interconverted in the ground state, but the process is much faster in the excited state. The observed isotope effect suggests that the initial excited state process involves a proton transfer reaction that is followed by additional structural changes. These observations may help to rationalize and motivate mutations that alter the absorption properties and improve the photo stability of GFP.

Deciphering the mechanism for the assembly of aromatic polyketides by a bacterial polyketide synthase.

Aromatic polyketides are assembled by a type 11 (iterative) polyketide synthase (PKS) in bacteria. Understanding the enzymology of such enzymes should provide the information needed for the synthesis of novel polyketides through the genetic engineering of PKSs. Using a previously described cell-free system [B.S. & C.R.H. (1993) Science 262, 1535-1540], we studied a PKS enzyme whose substrate is not directly available and purified the TcmN polyketide cyclase from Streptomyces glaucescens. TcmN is a bifunctional protein that catalyzes the regiospecific cyclization of the Tcm PKS-bound linear decaketide to Tcm F2 and the 0-methylation of Tcm D3 to Tcm B3. In the absence of TcmN, the decaketide formed by the minimal PKS consisting of the TcmJKLM proteins undergoes spontaneous cyclization to form some Tcm F2 as well as SEK15 and many other aberrant shunt products. Addition of purified TcmN to a mixture of the other Tcm PKS components both restores and enhances Tcm F2 production. Interestingly, Tcm F2 but none of the aberrant products was bound tightly to the PKS. The results described support the notion that the polyketide cyclase, not the minimal PKS, dictates the regiospecificity for the cyclization of the linear polyketide intermediate. Furthermore, because the addition of TcmN to the TcmJKLM proteins results in a significant increase of the total yield of decaketide, interactions among the individual components of the Tcm PKS complex must give rise to the optimal PKS activity.

Identifying functional domains within terpene cyclases using a domain-swapping strategy.

Cyclic terpenes and terpenoids are found throughout nature. They comprise an especially important class of compounds from plants that mediate plant- environment interactions, and they serve as pharmaceutical agents with antimicrobial and anti-tumor activities. Molecular comparisons of several terpene cyclases, the key enzymes responsible for the multistep cyclization of C10, C15, and C20 allylic diphosphate substrates, have revealed a striking level of sequence similarity and conservation of exon position and size within the genes. Functional domains responsible for a terminal enzymatic step were identified by swapping regions approximating exons between a Nicotiana tabacum 5-epi-aristolochene synthase (TEAS) gene and a Hyoscyamus muticus vetispiradiene synthase (HVS) gene and by characterization of the resulting chimeric enzymes expressed in bacteria. While exon 4 of the TEAS gene conferred specificity for the predominant reaction products of the tobacco enzyme, exon 6 of the HVS gene conferred specificity for the predominant reaction products of the Hyoscyamus enzyme. Combining these two functional domains of the TEAS and HVS genes resulted in a novel enzyme capable of synthesizing reaction products reflective of both parent enzymes. The relative ratio of the TEAS and HVS reaction products was also influenced by the source of exon 5 present in the new chimeric enzymes. The association of catalytic activities with conserved but separate exonic domains suggests a general means for generating additional novel terpene cyclases.

The effects of sequence context on DNA curvature.

Recent experiments have exposed significant discrepancies between experimental data and predictive models for DNA structure. These results strongly suggest that DNA structural parameters incorporated in the models are not always sufficient to account for the influence of sequence context and of specific ion effects. In an attempt to evaluate these two effects, we have investigated repetitive DNA sequences with the sequence motif GAGAG.CTCTC located in different helical phasing arrangements with respect to poly(A) tracts and GGGCCC.GGGCCC sequence motifs. Methods used are ligase-mediated cyclization and gel mobility experiments along with DNase I cutting and chemical probe studies. The results provide new evidence for curvature in poly(A) tracts. They also show that the sequence context in which bending and flexible sequence elements are found is an important aspect of sequence-dependent DNA conformation. Although dinucleotide models generally have good predictive power, this work demonstrates that in some instances sequence elements larger than the dinucleotide must be taken into account, and hence it provides a starting point for the appropriate modification and refinement of existing structural models for DNA.

Fos and Jun do not bend the AP-1 recognition site.

We have used a solution-based DNA cyclization assay and a gel-phasing method to show that contrary to previous reports [Kerppola, T. K. & Curran, T. (1991) Cell 66, 317-326], basic region leucine zipper proteins Fos and Jun do not significantly bend their AP-1 recognition site. We have constructed two sets of DNA constructs that contain the 7-bp 5'-TGACTCA-3' AP-1 binding site, from either the yeast or the human collagenase gene, which is well separated from and phased by 3-4 helical turns against an A tract-directed bend. The cyclization probabilities of DNAs with altered phasings are not significantly affected by Fos-Jun binding. Similarly, Fos-Jun and Jun-Jun bound to differently phased DNA constructs show insignificant variations in gel mobilities. Both these methods independently indicate that Fos and Jun bend their AP-1 target site by <5 degrees, an observation that has important implications in understanding their mechanism of transcriptional regulation.

Potent, structurally constrained agonists and competitive antagonists of corticotropin-releasing factor.

Predictive methods, physicochemical measurements, and structure activity relationship studies suggest that corticotropin-releasing factor (CRF; corticoliberin), its family members, and competitive antagonists (resulting from N-terminal deletions) usually assume an alpha-helical conformation when interacting with the CRF receptor(s). To test this hypothesis further, we have scanned the whole sequence of the CRF antagonist [D-Phe12,Nle21,38]r/hCRF-(12-41) (r/hCRF, rat/human CRF; Nle, norleucine) with an i-(i + 3) bridge consisting of the Glu-Xaa-Xaa-Lys scaffold. We have found astressin [cyclo(30-33)[D-Phe12,Nle21,38,Glu30,Lys33]r/ hCRF(12-41)] to be approximately 30 times more potent than [D-Phe12,Nle21,38]r/hCRF-(12-41), our present standard, and 300 times more potent than the corresponding linear analog in an in vitro pituitary cell culture assay. Astressin has low affinity for the CRF binding protein and high affinity (Ki = 2 nM) for the cloned pituitary receptor. Radioiodinated [D-125I-Tyr12]astressin was found to be a reliable ligand for binding assays. In vivo, astressin is significantly more potent than any previously tested antagonist in reducing hypophyseal corticotropin (ACTH) secretion in stressed or adrenalectomized rats. The cyclo(30-33)[Ac-Pro4,D-Phe12,Nle21,38,Glu30,Lys33++ +]r/hCRF-(4-41) agonist and its linear analog are nearly equipotent, while the antagonist astressin and its linear form vary greatly in their potencies. This suggests that the lactam cyclization reinstates a structural constraint in the antagonists that is normally induced by the N terminus of the agonist.

Sais de diazônio: síntese e eletrorredução

Sais de diazônio são um classe de compostos amplamente usados em química orgânica. Sua aplicação abrange uma gama de sínteses desde corantes até reações de hetero-acoplamento para produção de fármacos, mas pouco é conhecido de sua redução eletroquímica para fins sintéticos. As metodologias empregadas na redução de sais de diazônio geralmente envolvem o uso de metais ou compostos capazes de transferir elétrons como Pd, Cu ou tetratiafulvaleno. Neste trabalho é descrita a redução eletroquímica de dois sais de diazônio: tetrafluoroborato de 2-(2-propen-1-ilóxi)benzenodiazônio (1) e tetrafluoroborato de 2-(2-propen-1-iltio)benzenodiazônio (2) usando três eletrodos: Pt, Hg e pó de grafite. Quando foi feita a eletrólise de (1) utilizando cátodo de Hg vários produtos foram formados envolvendo uma reação de ciclização intramolecular, porém não conseguimos separá-los pelos métodos cromatográficos. A eletrólise de (2) em condições experimentais similares conduziu a uma mistura complexa de produtos provavelmente devido a uma interação do Hg com o átomo de enxofre do substrato e seus produtos de redução. Usando o cátodo de Pt e sal (1) a reação não foi eficiente pois ocorria uma queda brusca da corrente, provavelmente devido ao bloqueio da superfície do eletrodo. Concernente ao eletrodo de pó de grafite, apenas alguns experimentos preliminares foram feitos, portanto uma análise de seu desemprenho é prematura.

Estudo da adição aldólica do éster terc-butílico da n-(difenilmetileno)glicina a alguns aldeídos aromáticos

As reações de adição aldólica entre a cetimina 1 e aldeídos aromáticos foram inicialmente efetuadas à temperatura ambiente, em sistema bifásico constituído por uma fase aquosa básica (KOH 10% ou NaOH 5% m/v) e por uma fase orgânica (aldeído), na ausência de solventes e de catalisadores, observando-se baixa conversão em produto. Porém, quando se utilizou o catalisador aliquat®-336, foi possível reduzir a concentração da base (NaOH 1%), com conversão total da imina em produto que, na maioria dos casos, era uma mistura de duas oxazolidinas isoméricas de estereoquímica cis e trans. Esses compostos puderam ser isolados e purificados por recristalização de etanol ou metanol. Em todas as reações efetuadas com benzaldeído, m-clorobenzaldeído e p-nitrobenzaldeído, não se observou excesso diastereomérico significativo. No entanto, as reações com p-clorobenzaldeído mostraram-se diastereosseletivas, conduzindo, à temperatura ambiente, quase que exclusivamente à oxazolidina de estereoquímica cis. A comparação entre o resultado de reações efetuadas a curto e longo tempo de reação, ou em diferentes temperaturas, permitiu concluir que o aldol de estereoquímica anti é o produto cinético, o qual se transforma lentamente na oxazolidina cis. O produto termodinâmico (aldol syn) cicliza rapidamente, não sendo observado nos espectros de RMN de H dos produtos brutos de reação, mas sim seu produto ciclizado, a oxazolidina trans. Tentativas de obter os produtos de reação com excesso enantiomérico, pelo emprego de catalisadores de transferência de fase assimétricos, não foram bem sucedidas.

Formação de ligação carbono-carbono através de compostos orgânicos de telúrio

Diversas classes de compostos orgânicos de telúrio foram exploradas neste trabalho. Inicialmente foi estudada a transmetalação entre teluretos alílicos e dibutil cianocupratos de lítio de ordem superior, levando aos respectivos cianocupratos alílicos de lítio. Estes, por sua vez, foram acoplados com triflatos vinílicos, importantes intermediários sintéticos preparados previamente a partir de teluretos vinílicos, levando a sistemas altamente insaturados em ótimos rendimentos (Esquema 1). (Ver no arquivo em PDF) Em seguida, foi explorada a reatividade de teluretos aromáticos frente a reagentes organometálicos. Cianocupratos arílicos, gerados a partir da transmetalação entre teluretos aromáticos com cianocupratos de lítio de ordem superior, foram adicionados a cetonas α,β -insaturadas, levando aos produtos de adição 1,4 em bons rendimentos (Esquema 2). (Ver no arquivo em PDF) Teluretos vinílicos funcionalizados de configuração Z também foram alvo de estudo visando a formação de ligação carbono-carbono. Reações de substituição entre estes teluretos e cianocupratos de lítio de ordem inferior levaram a cetonas e ésteres α,β- insaturados com estereoquímica defInida em ótimos rendimentos (Esquema 3). (Ver no arquivo em PDF) De agosto/20OJ a março/2004, a aluna realizou um estágio sanduíche na University of California, Santa Barbara, sob a orientação do Prof. Bruce H. Lipshutz, onde realizou estudos sobre a ciclização de Bergman, visando a síntese do fragmentobiarílico A-B da vancornicina. Diversas condições para a ciclização foram estudadas com um composto modelo (Esquema 4) (Ver no arquivo em PDF) e parte da síntese total do fragmento da vancomlcma, onde a ciclização seria a etapa-chave, foi realizada com sucesso (Esquema 5). (Ver no arquivo em PDF)

Palladium and organocatalysis: an excellent recipe for asymmetric synthesis

The dual activation of simple substrates by the combination of organocatalysis and palladium catalysis has been successfully applied in a variety of different asymmetric transformations. Thus, the asymmetric a-allylation of carbonyl compounds, a-fluorination of acyl derivatives, decarboxylative protonation of β-dicarbonyl compounds, cyclization reactions of alkynyl carbonyl compounds and β-functionalization of aldehydes have been efficiently achieved employing this double-catalytic methodology.

Synthesis of γ-, δ-, and ε-Lactams by Asymmetric Transfer Hydrogenation of N-(tert-Butylsulfinyl)iminoesters

Highly enantiomerically enriched γ- and δ-lactams have been prepared by a simple and very efficient procedure that involves the asymmetric transfer hydrogenation of N-(tert-butylsulfinyl)iminoesters followed by desulfinylation of the nitrogen atom and spontaneous cyclization to the desired lactams during the basic workup procedure. Five- and six-membered ring lactams bearing aromatic, heteroaromatic, and aliphatic substituents have been obtained in very high yields and ee’s up to >99%. A slight modification of the procedure also allowed the preparation of ε-lactams in good yields and very high enantioselectivities. Both enantiomers of the final lactams could be prepared with equal efficiency by changing the absolute configuration of the sulfinyl chiral auxiliary.

Intramolecular Bromoamination of Conjugated N-Tosylaminodienes Using N-Bromosuccinimide. Synthesis of Bromoallyl-Substituted N-Heterocycles and Their Applications as Building Blocks

The bromonium-promoted cyclization of conjugated aminodienes is described. The reaction proceeds smoothly in the presence of N-bromosuccinimide as halonium promoter, and using N-tosyl-protected aminodienes as substrates, to give the corresponding halocyclization products in high yields and with high diastereoselectivities. It can be envisaged that the formation of these products is the result of an SN2′-type ring-opening of a terminal bromonium intermediate in a 5-exo-trig or 6-exo-trig cyclization mode. The presence of an allyl bromide moiety in the haloamination products makes these molecules highly attractive from a synthetic point of view, as it opens the way for further transformations. Thus, allylic substitution reactions with different nucleophiles (acetate, azide, cyanide, and malonate), palladium-catalysed Suzuki coupling, and silver-mediated bromine displacement reactions were carried out successfully.

Synthesis of Dihydroisobenzofurans via Palladium-Catalyzed Sequential Alkynylation/Annulation of 2-Bromobenzyl and 2-Chlorobenzyl Alcohols under Microwave Irradiation

The palladium-catalyzed synthesis of dihydroisobenzofurans has been performed by sequential Sonogashira cross-coupling/cyclization reactions between terminal alkynes and 2-(hydroxymethyl)bromo- and chlorobenzenes in methanol as solvent at 130 °C under microwave irradiation. A 4,4′-dichlorobenzophenone oxime-derived chloro-bridged palladacycle is an efficient pre-catalyst to perform this tandem process using 2-dicyclohexylphosphanyl-2′,4′,6′-triisopropylbiphenyl (Xphos) as ancillary ligand and potassium hydroxide as base in the absence of a copper cocatalyst. Under these conditions, functionalized 2-bromo- and 2-chlorobenzaldehydes are also suitable partners in the domino process affording phthalans in good yields. All the reactions can be performed under air and employing reagent-grade chemicals under low loading conditions (1 mol% Pd).