Identification of covalently bound fatty acids on acylated proteins immobilized on nitrocellulose paper

Nucleic Acids Analysis

Nucleic acids are natural biopolymers of nucleotides that store, encode, transmit and express genetic information, which play central roles in diverse cellular events and diseases in living things. The analysis of nucleic acids and nucleic acids-based analysis have been widely applied in biological studies, clinical diagnosis, environmental analysis, food safety and forensic analysis. During the past decades, the field of nucleic acids analysis has been rapidly advancing with many technological breakthroughs. In this review, we focus on the methods developed for analyzing nucleic acids, nucleic acids-based analysis, device for nucleic acids analysis, and applications of nucleic acids analysis. The representative strategies for the development of new nucleic acids analysis in this field are summarized, and key advantages and possible limitations are discussed. Finally, a brief perspective on existing challenges and further research development is provided.

Chemical and genetic probes for analysis of protein palmitoylation

Reversible protein palmitoylation is one of the most important posttranslational modifications that has been implicated in the regulation of protein signaling, trafficking, localizing and enzymatic activities in cells and tissues. In order to achieve a precise understanding of mechanisms and functions of protein palmitoylation as well as its roles in physiological processes and disease progression, it is necessary to develop techniques that can qualitatively and quantitatively monitor the dynamic protein palmitoylation in vivo and in vitro. This review will highlight recent advances in both chemical and genetic encoded probes that have been developed for accurate analysis of protein palmitoylation, including identification and quantification of acyl moieties and palmitoylated proteins, localization of amino acid residues on which acyl moieties are attached, and imaging of cellular distributions of palmitoylated proteins. The role of major techniques of fluorescence microscopy and mass spectrometry in facilitating the analysis of protein palmitoylation will also be explored.

Exogenous myristic acid acylates proteins in cultured rat hepatocytes

Fatty acid acylation is a functionally important modification of proteins. In the liver, however, acylated proteins remain largely unknown. This work was aimed at investigating fatty acid acylation of proteins in cultured rat hepatocytes. Incubation of these cells with [9,10-3H] myristic acid followed by two-dimensional electrophoresis separation of the delipidated cellular proteins and autoradiography evidenced the reproducible and selective incorporation of radioactivity from the precursor into 18 well-resolved proteins in the 10--120 kDa range and the 4--7 pH range. Radiolabeling of these proteins resulted from covalent linkage to the precursor [9,10-3H] myristic acid or to its elongation product, palmitic acid. The majority of the covalent linkages between the proteins and the fatty acids were broken by base hydrolysis, which indicated that the linkage was of thioester or ester-type. Only one of the studied proteins was attached to myristic acid via an amide linkage which resisted the basic treatment but was broken by acid hydrolysis. After incubation with [9,10-3H] palmitic acid, only two proteins previously detected with myristic acid were radiolabeled. Finally, the identified acylated proteins may be grouped into two classes: proteins involved in signal transduction (the alpha subunit of a heterotrimeric G protein and several small G proteins) and cytoskeletal proteins (cytokeratins, actin).

Novel acylation of poxvirus A-type inclusion proteins

Myristylation is one of several post-translational modifications that occur on vaccinia virus (VV) proteins. Previously, time course labeling of VV-infected cells with myristic acid had indicated that five late proteins (17, 25, 36, 38 and 92 kDa) are myristylated. Four of these proteins were mapped to the E7R, L1R, AI6L and G9R open-reading frames, respectively, because of the predicted presence of the N-myristyltransferase recognition sequence (M-G-X-X-X-S/T/A) at their amino termini. In contrast, computer analyses of large (80-100 kDa) VV open reading frames did not reveal any predicted species with this N-terminal motif. By immunoprecipitation with monospecific sera and transient expression of cloned gene products, the myristylated 92-kDa protein has been demonstrated to be the A-type inclusion protein encoded by the Western Reserve (WR) strain of VV. Labeling of cowpox virus (CPV) infected cells with myristic acid indicated that the 160-kDa A-type inclusion protein appears to be myristylated as well. Both the VV 92-kDa and the CPV 160-kDa A-type inclusion proteins labeled with myristic acid were stable to hydroxylamine treatment, suggesting an amide linkage between the fatty acid and the acceptor protein. HPLC analysis confirmed that the 92-kDa protein was in fact myristylated. This data suggests that poxvirus ATI proteins may be subject to a novel type of internal myristylation modification, and the roles such modifications may play in the replication cycles of these viruses is discussed.

Use of derivatization to improve the chromatographic properties and detection selectivity of physiologically important carboxylic acids

In this review, tagging techniques with reagents used for ultraviolet-visible (UV-Vis), fluorescent (FL), chemiluminescent (CL) and electrochemical detection (ED) for higher carboxylic acids in HPLC are evaluated in terms of the tagging reactions, handling, flexibility, stability of the reagents and the corresponding derivatives, sensitivity and selectivity. Emphasis is given to the applications of these tagging techniques to biologically important carboxylic acids of relatively high molecular mass including free fatty acids, prostaglandins, leukotrienes and thromboxanes etc. Some typical examples are described. Although RIA and GC-MS are powerful techniques for the highly sensitive determination of carboxylic acids, tagging for these techniques is not included in this review because recent progress in tagging methods has been mainly concerned with HPLC detection.

Depalmitoylation of rhodopsin with hydroxylamine

Intrinsic membrane proteins that to date have been investigated with respect to the function of palmitoylation are the beta-adrenergic receptor, rhodopsin, the alpha 2A-adrenergic receptor, and the influenza virus spike glycoprotein. As described above, the studies have led to differing conclusions with respect to the influence of palmitoylation on physiological activity. The basis of the differences remains unclear, but it may relate at least in part to the membrane environment of the protein during these studies, that is, the presence of a native membrane, the membrane composition of the expression cell line (in the case of mutant proteins), or the absence of membrane (in the case of detergent-purified proteins). For example, in the case of rhodopsin, the composition of the ROS disk membrane differs from that of the rod plasma membrane, and presumably also from the plasma membranes of cell lines in which mutant rhodopsins are expressed. Variation in membrane composition is known to have marked effects on the ability of rhodopsin to mediate the photic activation of PDE. Thus, although Karnik et al. clearly demonstrated the absence of an absolute requirement for palmitate in activating transducin, the influence of detergent on tertiary protein structure may have masked the full effect of the elimination of palmitate on the transducin-activating property of rhodopsin. Alternatively, the differing results obtained in the studies of rhodopsin could be a consequence of differences in amino acid sequences of the proteins studied. The precise functional role of the palmitate groups of rhodopsin remains an important question for further research. It was suggested by Ovchinnikov et al. that the hydrolysis of covalently bound palmitate might occur during the process of rhodopsin bleaching, but more recent data argue against this hypothesis. Experiments using synthetic peptides (representing cytoplasmic loop regions of rhodopsin) to identify the sites of interaction of R* and transducin provide support for an alternative possibility, namely, that palmitoylation and the resulting cytoplasmic loop play a role in the coupling of rhodopsin with transducin. The finding that the binding of transducin to R* occurs independently of the presence of palmitate argues against an essential requirement of palmitoylation on the binding step itself. However, available data indicate an enhancement, by depalmitoylation, of light-dependent GTPase activity in ROS preparations, although not in assays of unpalmitoylated, purified mutant rhodopsins (see above).(ABSTRACT TRUNCATED AT 400 WORDS)

Evidence for multiple species of vaccinia virus-encoded palmitylated proteins

When cells were infected with vaccinia virus in the presence of [3H]palmitic acid, radiolabel was incorporated into six viral proteins with apparent molecular weights of 92, 41, 37, 26, 17, and 14 kDa, all of which are expressed at late times during the infection cycle. The [3H]palmitate-labeled fatty acid moieties from the modified proteins were isolated, converted to p-nitrophenacyl derivatives, and subjected to reverse phase HPLC analysis which confirmed the identity of the fatty acid group as palmitic acid. Furthermore, the radiolabeled palmitate-protein bonds were sensitive to treatment with neutral hydroxylamine, suggesting that association of the fatty acid moieties with these proteins occurs via a thioester linkage. Previous studies by other investigators have identified the 37-kDa protein as the major antigen present in the outer membrane of extracellular enveloped virions, and demonstrated that the protein is modified by palmitic acid but is not glycosylated (G. Hiller and K. Weber J. Virol. (1985) 55, 651-659). Growth of vaccinia virus in the presence of tunicamycin indicated that the 41- and 26-kDa palmitylated proteins were also subject to modification by glycosylation, whereas like the 37-kDa protein, the 92-, 17-, and 14-kDa species did not appear to be glycosylated. Subcellular fractionation studies provided evidence that all of the viral palmitylated proteins were membrane-associated. Extraction of purified vaccinia virus with NP-40 and DTT demonstrated that the palmitylated proteins were associated with one of the viral membranes rather than the core of the virion. Viewing these results together with the previous reports of myristylated VV proteins (Franke et al. J. Virol. (1989) 63, 4285-4291), suggests that acylation of VV proteins represents a major modification pathway utilized by VV proteins during the assembly of progeny virions.

Low-energy collision-induced dissociation of protonated polyamino alcohol derivatives of peptides and N-terminal blocked peptides

This investigation reports the low-energy collision-induced dissociation of the protonated molecules of polyamino alcohols, formed by chemical reduction of synthetic peptides and N-terminal blocked peptides, in order to evaluate its potential for peptide sequence determination. The --CH2--NH-- cleavage with charge retention on the N-terminus was prominent, and the entire sequence of ions produced in this manner was observed. Some of the sequence ions arising from --CH2--NH-- cleavage accompanied by migration of two hydrogens, and --NH--C alpha H-- cleavage with charge retention on the C-terminus, also occurred prominently. In addition, a great number of internal fragment ions were produced in relatively high abundance; these provided supplementary sequence information and were, in some cases, critical in determining the sequence. The usefulness of this method was exemplified by its application to the sequence determination of bacterial lipopeptides.