The Influence of Chemical Change on Protein Dynamics: A Case Study with Pyruvate Formate-Lyase

Pyruvate formate-lyase (PFL) catalyzes the reversible conversion of pyruvate and coenzyme A (CoA) into formate and acetyl-CoA in two half-reactions. For the second half-reaction to take place, the S-H group of CoA must enter the active site of the enzyme to retrieve a protein-bound acetyl group. However, CoA is bound at the protein surface, whereas the active site is buried in the protein interior, some 20-30 Å away. The PFL system was therefore subjected to a series of extensive molecular dynamics simulations (in the μs range) and a host of advanced analysis procedures. Models representing PFL before and after the first half-reaction were used to examine the possible effect of enzyme acetylation. All simulated structures were found to be relatively stable compared to the initial crystal structure. Although the adenine portion of CoA remained predominantly bound at the protein surface, the binding of the S-H group was significantly more labile. A potential entry channel for CoA, which would allow the S-H group to reach the active site, was identified and characterized. The channel was found to be associated with accentuated fluctuations and a higher probability of being in an open state in acetylated systems. This result suggests that the acetylation of the enzyme assumes a prominent functional role, whereby the formation of the acyl intermediate serves to initiate a subtle signaling cascade that influences the protein dynamics and facilitates the entry of the second substrate.

Facile Synthetic Access to Glycopeptide Antibiotic Precursor Peptides for the Investigation of Cytochrome P450 Action in Glycopeptide Antibiotic Biosynthesis

The glycopeptide antibiotics are an important class of complex, medically relevant peptide natural products. Given that the production of such compounds all stems from in vivo biosynthesis, understanding the mechanisms of the natural assembly system--consisting of a nonribosomal-peptide synthetase machinery (NRPS) and further modifying enzymes--is vital. In order to address the later steps of peptide biosynthesis, which are catalyzed by Cytochrome P450s that interact with the peptide-producing nonribosomal peptide synthetase, peptide substrates are required: these peptides must also be in a form that can be conjugated to carrier protein domains of the nonribosomal peptide synthetase machinery. Here, we describe a practical and effective route for the solid phase synthesis of glycopeptide antibiotic precursor peptides as their Coenzyme A (CoA) conjugates to allow enzymatic conjugation to carrier protein domains. This route utilizes Fmoc-chemistry suppressing epimerization of racemization-prone aryl glycine derivatives and affords high yields and excellent purities, requiring only a single step of simple solid phase extraction for chromatographic purification. With this, comprehensive investigations of interactions between various NRPS-bound substrates and Cytochrome P450s are enabled.

TOCCATA: a customized carbon total correlation spectroscopy NMR metabolomics database

A customized metabolomics NMR database, TOCCATA, is introduced, which uses (13)C chemical shift information for the reliable identification of metabolites, their spin systems, and isomeric states. TOCCATA, whose information was derived from the BMRB and HMDB databases and the literature, currently contains 463 compounds and 801 spin systems, and it can be used through a publicly accessible web server. TOCCATA allows the identification of metabolites in the submillimolar concentration range from (13)C-(13)C total correlation spectroscopy experiments of complex mixtures, which is demonstrated for an Escherichia coli cell lysate, a carbohydrate mixture, and an amino acid mixture, all of which were uniformly (13)C-labeled.

Rapid and simple ribozymic aminoacylation using three conserved nucleotides

Selection-amplification finds new RNA enzymes (ribozymes) among randomized RNAs with flanking unvaried sequences (primer complements). Precise removal of 3'-primer before reaction selected aminoacylation from PheAMP in three cycles, yielding active RNAs (k(cat) = 12-20 min(-1)) using only three conserved nucleotides, acting independently of divalent ions. This unusually simple RNA active site encouraged study of the reaction via molecular mechanics-based free energy minimization. On this basis, we suggest a chemical path for RNA-catalyzed transaminoacylation. Site modeling also predicted new features, L-stereoselectivity, 2'-regioselectivity, independence of amino acid side chain, and phosphorylated activating group, that were subsequently verified. The same selection also showed that RNA aminoacylation from adenylate is simpler than from CoA thioester, potentially rationalizing translational activation by adenylates. The simplicity of this active site suggests a general route to small ribozymes.

C75 is converted to C75-CoA in the hypothalamus, where it inhibits carnitine palmitoyltransferase 1 and decreases food intake and body weight

Central nervous system administration of C75 produces hypophagia and weight loss in rodents identifying C75 as a potential drug against obesity and type 2 diabetes. However, the mechanism underlying this effect is unknown. Here we show that C75-CoA is generated chemically, in vitro and in vivo from C75 and that it is a potent inhibitor of carnitine palmitoyltranferase 1 (CPT1), the rate-limiting step of fatty-acid oxidation. Three-D docking and kinetic analysis support the inhibitory effect of C75-CoA on CPT1. Central nervous system administration of C75 in rats led to C75-CoA production, inhibition of CPT1 and lower body weight and food intake. Our results suggest that inhibition of CPT1, and thus increased availability of fatty acids in the hypothalamus, contribute to the pharmacological mechanism of C75 to decrease food intake.

Iso-coenzyme A

Iso-coenzyme A is an isomer of coenzyme A in which the monophosphate is attached to the 2'-carbon of the ribose ring. Although iso-CoA was first reported in 1959 (Moffatt, J. G., and Khorana, H. G. (1959) J. Am. Chem. Soc. 81, 1265-1265) to be a by-product of the chemical synthesis of CoA, relatively little attention has been focused on iso-CoA or on acyl-iso-CoA compounds in the literature. We now report structural characterizations of iso-CoA, acetyl-iso-CoA, acetoacetyl-iso-CoA, and beta-hydroxybutyryl-iso-CoA using mass spectrometry (MS), tandem MS, and homonuclear and heteronuclear NMR analyses. Although the 2'-phosphate isomer of malonyl-CoA was recently identified in commercial samples, previous characterizations of iso-CoA itself have been based on chromatographic analyses, which ultimately rest on comparisons with the degradation products of CoA and NADPH or have been based on assumptions regarding enzyme specificity. We describe a high performance liquid chromatography methodology for separating the isomers of several CoA-containing compounds. We also report here the first examples of iso-CoA-containing compounds acting as substrates in enzymatic acyl transfer reactions. Finally, we describe a simple synthesis of iso-CoA from CoA, which utilizes beta-cyclodextrin to produce iso-CoA with high regioselectivity, and we demonstrate a plausible mechanism that accounts for the existence of iso-CoA isomers in commercial preparations of CoA-containing compounds. We anticipate that these results will provide methodology and impetus for investigating iso-CoA compounds as potential pseudo-substrates or inhibitors of the >350 known CoA-utilizing enzymes.

Isolation and identification of two isomeric forms of malonyl-coenzyme A in commercial malonyl-coenzyme A

Two isomers of malonyl-coenzyme A (malonyl-CoA) were detected in a commercial preparation of malonyl-CoA. These compounds were separated by preparative high-performance liquid chromatography (HPLC) and characterized by HPLC/ultraviolet (UV)/mass spectrometry. Both compounds had a UV absorbance maximum at 259-260 nm. Both compounds underwent negative electrospray ionization to produce a [M-H](-)quasi-molecular ion at m/z 852 and both compounds underwent collision-induced dissociation to produce a characteristic fragment at m/z 808, all consistent with the structure of malonyl-CoA. Nuclear magnetic resonance spectrometry showed that the two chromatographically distinguishable malonyl-CoAs are structural isomers: the major component is the naturally occurring malonyl-CoA and the contaminant is 3'-dephospho- 2'-phospho-coenzyme A.

Investigating the role of the geminal dimethyl groups of coenzyme A: synthesis and studies of a didemethyl analogue

An analogue 2 of coenzyme A (CoA) has been prepared in which the geminal methyl groups are replaced with hydrogens. An NMR titration study was conducted and shifts in frequency of protons in the pantetheine portion of the molecule upon titration of the adenine base were observed as has been previously reported with CoA. These studies indicate that the geminal dimethyl groups are not essential for adoption of a partially folded conformation in solution. Based on 1H-1H coupling constants, the distribution of conformations about the carbon-carbon bonds in the region of the methyl deletion were estimated. The results suggest that the conformer distribution is similar to that of CoA, but with small increases in population of the anti conformers. A simple model compound containing the didemethyl pantoamide moiety was prepared and subjected to similar conformational analysis. The coupling constants and predicted conformer distribution were almost identical to that of the CoA analogue, indicating that the conformer distribution is controlled by local interactions and not influenced by interactions between distant parts of the CoA molecule. The acetyl derivative of 2 was a fairly good substrate for the acetyl-CoA utilizing enzymes carnitine acetyltransferase, chloramphenicol acetyltransferase, and citrate synthase, with 1.3- to 10-fold increased Km values and 2.5- to 11-fold decreases in Vmax. The combined results indicate that the geminal dimethyl groups of CoA have modest effects on function and minimal effects on conformation.