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PubMed2006

Biosynthesis of sespendole.

Sespendole is the first reported fungal metabolite having an indolosesquiterpene core structure. The biosynthesis of sespendole was studied here by feeding experiments with [13C]acetate, [15N]anthranilic acid and [13C]tryptophan. The data suggested that a farnesyl residue derived from the mevalonate pathway and an anthranilate-derived indole-3-glycerol phosphate residue are condensed, and then cyclization occurs along with rearrangement to form the indolosesquiterpene core.

Acetates↗
PubMed2000

Highly versatile solid phase synthesis of biofunctional 4-aryl-3,4-dihydropyrimidines using resin-bound isothiourea building blocks and multidirectional resin cleavage.

A series of pharmacologically active, functionalized 4-aryl-3,4-dihydropyrimidine-5-carboxylates (DHPMs) are prepared by a versatile novel solid phase approach. In the key step, a polymer-bound thiouronium salt is condensed with unsaturated 1-ketoesters. The resulting polymer bound 1,4-dihydropyrimidines are cleaved from the resin employing multidirectional resin cleavage strategies.

Nuclear Magnetic Resonance, Biomolecular↗
PubMed1996

Lipopeptide conjugates: biomolecular building blocks for receptor activating membrane-mimetic structures.

A simple method for the derivatization of phospholipid subunits with short peptide sequences is presented. Amphiphilic conjugates of distearoylphosphatidylethanolamine (DSPE) and the minimal human thrombin-receptor peptide agonist SFLLRN were synthesized via coupling of the bromoacetyl derivative of DSPE (PEBr) with a thiol-terminated decapeptide of SFLLRN. Bromoderivatization of DSPE was performed by condensation of bromoacetic acid and DSPE, with an overall yield of 40%. Coupling of PEBr and the unprotected thiol-terminated decapeptide was performed in chloroform/methanol/water in the presence of triethylamine and afforded 25.5% of the lipopeptide. The compound was characterized by TLC, 1H-NMR (600 MHz) and mass spectrometry. Lipopeptide bioactivity was confirmed by a platelet aggregation assay. The EC50 of the all-L amino acid lipopeptide was 38 +/- 3 microM. The all-D conjugate was inactive. Model receptor-activating systems, including well-ordered assemblies of amphiphilic phospholipid-peptide conjugates, represent the first step in the construction of bioactive surfaces for tissue engineering based on a membrane-mimetic approach.

Bromine Compounds↗
PubMed2005

Nucleation and the transition state of the SH3 domain.

We present a verified computational model of the SH3 domain transition state (TS) ensemble. This model was built for three separate SH3 domains using experimental phi-values as structural constraints in all-atom protein folding simulations. While averaging over all conformations incorrectly considers non-TS conformations as transition states, quantifying structures as pre-TS, TS, and post-TS by measurement of their transmission coefficient ("probability to fold", or p(fold)) allows for rigorous conclusions regarding the structure of the folding nucleus and a full mechanistic analysis of the folding process. Through analysis of the TS, we observe a highly polarized nucleus in which many residues are solvent-exposed. Mechanistic analysis suggests the hydrophobic core forms largely after an early nucleation step. SH3 presents an ideal system for studying the nucleation-condensation mechanism and highlights the synergistic relationship between experiment and simulation in the study of protein folding.

Models, Molecular↗
PubMed2001

Biosynthesis of vitamin B(6) in yeast: incorporation pattern of glucose.

Two yeasts, Saccharomyces cerevisiae ATCC 7752 and Candida utilis ATCC 9256, were incubated in the presence of variously multiply (13)C-labeled samples of D-glucose. The (13)C incorporation pattern within pyridoxamine dihydrochloride, established by (13)C NMR spectroscopy, differed from that which had previously been found within pyridoxine, isolated from Escherichia coli. Thus, the origin of the carbon skeleton of vitamin B(6) in yeast differs substantially from its origin in E. coli. In particular, in yeast the distribution of (13)C within the C(5) chain C-2',2,3,4,4' of pyridoxamine corresponds to the distribution of (13)C within the C(5) chain C-1,2,3,4,5 of the ribose component of cytidine. It follows that the C(5) chains of pyridoxamine and of ribose originate from a common glucose-derived pentulose or pentose intermediate. By contrast, in E. coli the C(5) chain of pyridoxine is derived from 1-deoxy-D-xylulose 5-phosphate which, in turn, originates by condensation of pyruvic acid with glyceraldehyde 3-phosphate.

Candida↗
PubMed1998

Formation of a fluorescent adduct in the reaction of 2'-deoxyadenosine with a malonaldehyde-acetaldehyde condensation product.

Malonaldehyde (malondialdehyde, MDA) was reacted with 2'-deoxyadenosine in buffered aqueous solution. HPLC analyses of the reaction mixtures showed that, besides the two previously characterized N6-propenal (M1dA) and N6-oxazocinyl (M3dA) adenine adducts, a third compound eluting at longer retention time was formed. The compound generated a strong peak in the chromatogram recorded by a fluorescence detector. The new compound was isolated by preparative C18 chromatography, and its structure was characterized by UV absorbance, fluorescence emission, 1H and 13C NMR spectroscopy, and mass spectrometry. The product was identified as 9-(2'-deoxyribosyl)-6-(3,5-diformyl-4-methyl-1, 4-dihydro-1-pyridyl)purine (M2AA-dA). The yield of the product was 0.8% following 7 days of reaction at 37 degreesC and pH 4.6. Lower yields were obtained at higher pH conditions. By the addition of acetaldehyde, the yield increased about 10-fold at all studied pH conditions. The adduct was most likely formed by an initial condensation of two molecules of malonaldehyde with one molecule of acetaldehyde followed by reaction of the condensation product with the exocyclic amino group of 2'-deoxyadenosine. The identification of this adduct shows that acetaldehyde may react with DNA bases also through an initially formed malonaldehyde-acetaldehyde condensation product.

Acetaldehyde↗
PubMed2002

Solid-phase and solution-phase parallel synthesis of tetrahydro-isoquinolines via Pictet-Spengler reaction.

An efficient parallel synthesis of 6,7-dimethoxytetrahydroisoquinolines is reported. The key reaction step is 3,4-dimethoxyphenethylimines reacting with acid chlorides to form an N-acyliminium ion intermediate, which undergoes Pictet-Spengler condensation to give the desired products in >80% yield. Both solution-phase and solid-phase synthesis of 6,7-dimethoxytetrahydroisoquinolines are described.

Chromatography, High Pressure Liquid↗
PubMed2005

Simulation and experiment at high temperatures: ultrafast folding of a thermophilic protein by nucleation-condensation.

We used Phi-value analysis to characterise the transition state for folding of a thermophilic protein at the relatively high temperature of 325 K. PhiF values for the folding of the three-helix bundle, peripheral subunit binding domain from Bacillus stearothermophilus (E3BD) were determined by temperature-jump experiments in the absence of chemical denaturants. E3BD folded in microseconds through a highly diffuse transition state. Excellent agreement was observed between experiment and the results from eight (independent) molecular dynamics simulations of unfolding at 373 K. We used a combination of heteronuclear NMR experiments and molecular dynamics simulations to characterise the denatured ensemble, and found that it contained very little persistent, residual structure. However, those regions that adopt helical structure in the native state were found by simulation to be poised for helix formation in the denatured state. These regions also had significant structure in the transition state for folding. The overall folding pathway appears to be nucleation-condensation.

Bacterial Proteins↗
PubMed2003

Enantioselective total syntheses of slagenins A-C and their antipodes.

Full details of the total syntheses of slagenins A-C (1a-c) and their antipodes (2a-c), novel bromopyrrole alkaloids with a unique tetrahydrofuro[2,3-d]imidazolidin-2-one moiety, are described in which their absolute stereochemistry was established. The key step in the syntheses involves the efficient condensation of dihydrofuran-3-one or glyoxal with urea to construct the slagenin bicycle core.

Alkaloids↗
PubMed1991

Charged-particle transport in the condensed phase.

Traditionally, studies of the biological effects of ionizing radiation have rested on the triumvirate: (gas-phase) radiation physics, biophysical modeling, and radiation biology. Two technical developments, the advent of supercomputing as a routine tool in quantum solid-state material science and molecular dynamics on the one hand, and molecular biology on the other hand, have created--perhaps for the first time-the possibility of directly linking a more realistic description of the radiation field to observable events at biomolecular level. It also becomes increasingly clear that the identification of specific molecular targets imposes a challenge to the radiation physics community to be equally specific in treating the energy--deposition stage of radiation action. In this paper: a) I review--and exemplify with results from our own work--the current status in Monte Carlo simulation of gas-phase material (particle transport and stochastic chemistry); b) examine the link between these essentially geometric representations of the track and the concept of "spatial distribution of energy deposition," a staple in radiation modeling; c) advocate an effort towards developing conceptually and calculationally, the field of solid-state microdosimetry; and d) describe methods based on semi-empirical Hamiltonians or quasi-particle techniques for obtaining the frequency-dependent and wave-vector-dependent dielectric response function for biomolecular crystalline systems, which are the main ingredients for describing charged-particle transport.

Mathematics↗
PubMed2002

Combined ab initio/empirical approach for optimization of Lennard-Jones parameters for polar-neutral compounds.

The study of small functionalized organic molecules in aqueous solution is a useful step toward gaining a basic understanding of the behavior of biomolecular systems in their native aqueous environment. Interest in studying amines and fluorine-substituted compounds has risen from their intrinsic physicochemical properties and their prevalence in biological and pharmaceutical compounds. In the present study, a previously developed approach which optimizes Lennard-Jones (LJ) parameters via the use of rare gas atoms combined with the reproduction of experimental condensed phase properties was extended to polar-neutral compounds. Compounds studied included four amines (ammonia, methylamine, dimethylamine, and trimethylamine) and three fluoroethanes (1-fluoroethane, 1,1-difluoroethane, and 1,1,1-trifluoroethane). The resulting force field yielded heats of vaporization and molecular volumes in excellent agreement with the experiment, with average differences less than 1%. The current amine CHARMM parameters successfully reproduced experimental aqueous solvation data where methylamine is more hydrophilic than ammonia, with hydrophobicity increasing with additional methylation on the nitrogen. For both the amines and fluoroethanes the parabolic relationship of the extent of methylation or fluorination, respectively, to the heats of vaporization were reproduced by the new parameters. The present results are also discussed with respect to the impact of parameterization approach to molecular details obtained from computer simulations and to the unique biological properties of fluorine in pharmaceutical compounds.

Amines↗
PubMedDate not supplied

Anachelin, the siderophore of the cyanobacterium Anabaena cylindrica CCAP 1403/2A.

A catecholate siderophore - anachelin - has been isolated from the cyanobacterium Anabaena cylindrica CCAP 1403/2A. The central part of the siderophore is a tripeptide consisting of L-Thr, D-Ser and L-Ser. Its C-terminus is linked amidically to a 1,1-dimethyl-3-amino-1,2,3,4-tetrahydro-7,8-dihydroxyquinolinium system and its N-terminus to 6-amino-3,5,7-trihydroxyheptanoic acid. The 7-hydroxyl group of the latter is esterified with salicylic acid whose carboxyl group is condensed with the 6-amino group to an oxazoline ring. Anachelin is the first genuine siderophore of a cyanobacterium whose structure has been elucidated.

Anabaena↗
PubMed2002

Direct assignment of the absolute configuration of a distinct class of deoxyribonucleoside cyclic N-acylphosphoramidites at phosphorus by M-GOESY nuclear magnetic resonance spectroscopy.

The determination of the absolute configuration of deoxyribonucleoside cyclic N-acylphosphoramidites at phosphorus toward the synthesis of P-stereodifined phosphorothioated oligodeoxyribonucleotides is easily accomplished with computer-assisted molecular modeling and M-GOESY NMR spectroscopy. Specifically, computer-modeling diasteromeric phosphoramidite 3 has identifed a proximal (2.55 A) through-space interaction between benzylic H-5 and sugar H-2' ', which can predictably be detected by M-GOESY NMR in SP-3 but not in RP-3 because of being too distant (5.85 A). Consistent with computer-assisted modeling predictions, M-GOESY NMR spectra of SP-3 and RP-3 revealed NOE signals generated from nuclei near the selectively excited H-2' ' that are common to both SP-3 and RP-3, namely those of H-2', H-4', H-3', and H-1'. In addition, a diagnostic NOE signal at 5.5 ppm (benzylic H-5) is, as predicted, only detected in SP-3 and thus provides an unequivocal assessment of the configuration of the diastereomer at phosphorus. M-GOESY NMR data also confirm that the condensation of deoxyribonucleoside cyclic N-acylphosphoramidites with base-activated nucleosidic or nucleotidic 5'-hydroxyls proceeds via a single nucleophilic event.

Models, Chemical↗
PubMed2006

Porphyrin synthesis in water provides new expanded porphyrins with direct bipyrrole linkages: isolation and characterization of two heptaphyrins.

The use of water for the porphyrin cyclization changes the products completely. Scandium-catalyzed aqueous condensation between pentafluorobenzaldehyde and pyrrole and subsequent oxidation provides novel expanded porphyrins with direct bipyrrole linkages, of which two novel heptaphyrins have been characterized by X-ray analyses.

Crystallography, X-Ray↗
PubMed2001

Protein folding from a highly disordered denatured state: the folding pathway of chymotrypsin inhibitor 2 at atomic resolution.

Previous experimental and theoretical studies have produced high-resolution descriptions of the native and folding transition states of chymotrypsin inhibitor 2 (CI2). In similar fashion, here we use a combination of NMR experiments and molecular dynamics simulations to examine the conformations populated by CI2 in the denatured state. The denatured state is highly unfolded, but there is some residual native helical structure along with hydrophobic clustering in the center of the chain. The lack of persistent nonnative structure in the denatured state reduces barriers that must be overcome, leading to fast folding through a nucleation-condensation mechanism. With the characterization of the denatured state, we have now completed our description of the folding/unfolding pathway of CI2 at atomic resolution.

Nuclear Magnetic Resonance, Biomolecular↗
PubMed1999

From snapshot to movie: phi analysis of protein folding transition states taken one step further.

Kinetic anomalies in protein folding can result from changes of the kinetic ground states (D, I, and N), changes of the protein folding transition state, or both. The 102-residue protein U1A has a symmetrically curved chevron plot which seems to result mainly from changes of the transition state. At low concentrations of denaturant the transition state occurs early in the folding reaction, whereas at high denaturant concentration it moves close to the native structure. In this study we use this movement to follow continuously the formation and growth of U1A's folding nucleus by phi analysis. Although U1A's transition state structure is generally delocalized and displays a typical nucleation-condensation pattern, we can still resolve a sequence of folding events. However, these events are sufficiently coupled to start almost simultaneously throughout the transition state structure.

Guanidine↗
PubMed2005

The discovery of glycated hemoglobin: a major event in the study of nonenzymatic chemistry in biological systems.

Glycated hemoglobins are minor components of human hemoglobin (Hb). These are formed nonenzymatically by condensation of glucose or other reducing sugars with alpha- and beta-chains of hemoglobin A. The subfraction HbA1c, a nonenzymatic glycation at the amino-terminal valines of the beta-chain, was identified by the author in the 1960s as a minor "abnormal fast-moving hemoglobin band" in diabetic patients during routine screening for hemoglobin variants. This finding later turned out to be an important biomolecular marker with clinical and pathological applications. Measurement of HbA1c in diabetic patients is an established procedure for evaluating long-term control of diabetes, and the introduction of this measurement represents an outstanding contribution to the quality of care of diabetic patients in this century. More importantly, HbA1c is the first example of in vivo nonenzymatic glycation of proteins, and its discovery opened new and still-growing avenues of research on Maillard reactions in biological systems, including the concept of advanced glycation/lipoxidation end products (AGEs/ALEs) and the development of diabetic complications and various diseases associated with aging. Although interest in the Maillard reaction is growing rapidly, much remains to be done in this field, including detection and characterization of all in vivo AGEs/ALEs, development and clinical applications of AGE inhibitors and breakers, as well as investigations into the possible roles of the Maillard reaction in regulatory biology and carcinogenesis.

Biochemistry↗