Antibody-catalyzed decarboxylation and aldol reactions using a primary amine molecule as a functionalized small nonprotein component

Catalytic antibody 27C1 bears binding sites for both a substrate- and a functionalized small nonprotein component in the active site. We investigated the possibility of exploiting imine and enamine intermediates using a primary amine molecule into the active site of antibody 27C1. The antibody catalyzed β-keto acid decarboxylation with a rate enhancement (k_cat/K_m/k_uncat) of 140,000, as well as highly regioselective cross-aldol reactions of ketones and p-nitrobenzaldehyde. These studies provide new strategies for the generation of catalytic antibodies possessing binding sites for functionalized components.     

The molecular mechanism of acylation stimulating protein regulation of adipophilin and perilipin expression: involvement of phosphoinositide 3-kinase and phospholipase C

The novel adipokine acylation stimulating protein (ASP) is involved in lipid metabolism and obesity‐related disorders. Adipophilin and perilipin, two members of the lipid droplet protein family, participate not only in fat storage within adipocytes, but also in ectopic lipid deposition in the form of cytoplasmic triglyceride (TG) droplets within many types of mammalian cells. During differentiation to mature adipocytes, mechanisms controlling the synthesis and turnover of these lipid droplet proteins are only partially understood, the mechanisms regulating gene/protein expression as yet unidentified. In our previous study, ASP has been shown to regulate adipophilin and perilipin expression to facilitate TG synthesis during 3T3‐L1 cell differentiation. Our aim in this study was to provide insight into the physiological importance of phosphoinositide 3‐kinase (PI3K) and phospholipase C (PLC) in ASP‐triggered alteration of adipophilin and perilipin expression. We found that acute (2.5 h) inhibition of PLC or PI3K results in a decrease in mRNA and protein of perilipin and adipophilin at any time during differentiation. The fact that there is such a rapid change even with mRNA levels suggests a rapid turnover of both mRNA and protein independent of a direct ASP effect. Also, the presence of these inhibitors blocked the ASP stimulatory effects with a maximal decrease in gene and protein expression of adipophilin (?45% and ?60%, respectively, P < 0.01) and perilipin (?96% and ?63%, respectively, P < 0.01 and P < 0.05). These findings provide further understanding of the adipogenic properties of ASP in adipocytes. J. Cell. Biochem. 112: 1622–1629, 2011. © 2011 Wiley‐Liss, Inc.     

A new,robust, and nonradioactive approach for exploring N-myristoylation

Myristoyl-CoA (CoA):protein N-myristoyltransferase (NMT) catalyzes protein modification through covalent attachment of a C14 fatty acid (myristic acid) to the N-terminal glycine of proteins, thus promoting protein-protein and protein-membrane interactions. NMT is essential for the viability of numerous human pathogens and is also up-regulated in several tumors. Here we describe a new, nonradioactive, ELISA-based method for measuring NMT activity. After the NMT-catalyzed reaction between a FLAG-tagged peptide and azido-dodecanoyl-CoA (analog of myristoyl-CoA), the resulting azido-dodecanoyl-peptide-FLAG was coupled to phosphine-biotin by Staudinger ligation, captured by plate-bound anti-FLAG antibodies and detected by streptavidin-peroxidase. The assay was validated with negative controls (including inhibitors), corroborated by HPLC analysis, and demonstrated to function with fresh or frozen tissues. Recombinant murine NMT1 and NMT2 were characterized using this new method. This versatile assay is applicable for exploring recombinant NMTs with regard to their activity, substrate specificity, and possible inhibitors as well as for measuring NMT-activity in tissues.     

Understanding the acylation mechanisms of active-site serine penicillin-recognizing proteins: a molecular dynamics simulation study

Beta-lactam antibiotics inhibit enzymes involved in the last step of peptidoglycan synthesis. These enzymes, also identified as penicillin-binding proteins (PBPs), form a long-lived acyl-enzyme complex with beta-lactams. Antibiotic resistance is mainly due to the production of beta-lactamases, which are enzymes that hydrolyze the antibiotics and so prevent them reaching and inactivating their targets, and to mutations of the PBPs that decrease their affinity for the antibiotics. In this study, we present a theoretical study of several penicillin-recognizing proteins complexed with various beta-lactam antibiotics. Hybrid quantum mechanical/molecular mechanical potentials in conjunction with molecular dynamics simulations have been performed to understand the role of several residues, and pK(a) calculations have also been done to determine their protonation state. We analyze the differences between the beta-lactamase TEM-1, the membrane-bound PBP2x of Streptococcus pneumoniae, and the soluble DD-transpeptidase of Streptomyces K15.     

The Acyl-Proteome of Syntrophus aciditrophicus Reveals Metabolic Relationships in Benzoate Degradation

Syntrophus aciditrophicus is a model syntrophic bacterium that degrades fatty and aromatic acids into acetate, CO₂, formate, and H₂ that are utilized by methanogens and other hydrogen-consuming microbes. S. aciditrophicus benzoate degradation proceeds by a multistep pathway with many intermediate reactive acyl-coenzyme A species (RACS) that can potentially N^ε-acylate lysine residues. Herein, we describe the identification and characterization of acyl-lysine modifications that correspond to RACS in the benzoate degradation pathway. The amounts of modified peptides are sufficient to analyze the post-translational modifications without antibody enrichment, enabling a range of acylations located, presumably, on the most extensively acylated proteins throughout the proteome to be studied. Seven types of acyl modifications were identified, six of which correspond directly to RACS that are intermediates in the benzoate degradation pathway including 3-hydroxypimeloylation, a modification first identified in this system. Indeed, benzoate-degrading enzymes are heavily represented among the acylated proteins. A total of 125 sites were identified in 60 proteins. Functional deacylase enzymes are present in the proteome, indicating a potential regulatory system/mechanism by which S. aciditrophicus modulates acylation. Uniquely, N^ε-acyl-lysine RACS are highly abundant in these syntrophic bacteria, raising the compelling possibility that post-translational modifications modulate benzoate degradation in this and potentially other, syntrophic bacteria. Our results outline candidates for further study of how acylations impact syntrophic consortia.     

Reaction design for evaluation of the substrate range of hydrolases

Biocatalytic acylation reactions involving 24 alcohols, 8 acyl donors and 6 hydrolases were analysed using an original method. The reaction outcome was determined by semi-automated semi-automated solid-phase microextraction and GC/MS (SPME-GC/MS) allowing rapid evaluation of the success rate of each enzyme. Using Candida antarctica Lipase B (CALB), in 36% of the cases (46 reactions) quantitative conversion of the starting alcohol was observed, with an average isolated yield of 96%. The platform was then used to screen other enzymes with the CALB non-reacting substrates, allowing the design and optimisation of some efficient enzymatic reactions. Modification of the odour profile of rose essential oils by enzymatic treatment was also carried out.     

Stabilization of conformationally dynamic helices by covalently attached acyl chains

Acylation of proteins is known to mediate membrane attachment and to influence subcellular sorting. Here, we report that acylation can stabilize secondary structure. Circular dichroism spectroscopy showed that N‐terminal attachment of acyl chains decreases the ability of an intrinsically flexible hydrophobic model peptide to refold from an α‐helical state to β‐sheet in response to changing solvent conditions. Acylation also stabilized the membrane‐embedded α‐helix. This increase of global helix stability did not result from decreased local conformational dynamics of the helix backbone as assessed by deuterium/hydrogen‐exchange experiments. We concluded that acylation can stabilize the structure of intrinsically dynamic helices and may thus prevent misfolding.     

Grafting of Aliphatic and Aromatic Probes on Bovine Serum Albumin: Influence on Its Structural and Physicochemical Characteristics

Bovine serum albumin was chosen as a model protein to study the effect of the functionalization of the -NH₂ of lysine residues with different carbon chains on the physical properties of proteins. Thus, BSA has been acylated and sulfonylated by means of anhydrides and sulfonyl chlorides, respectively. The secondary structures of modified BSA, studied by far-UV CD, showed very slight changes except after sulfamidation. However, near-UV CD and intrinsic fluorescence spectra revealed important conformational perturbations for proteins bearing long carbon chains. Furthermore, the binding of an apolar probe (ANS) to BSA revealed an improvement of surface hydrophobicity after modification. Meanwhile, Scatchard plot results indicate that only 20% of the hexanoyl carbon chains lie at the surface of the proteins. Solvent conditions should influence the exposure of these chains and consequently the surface hydrophobicity of proteins.