4 research outputs found
A Continuous, Fluorogenic Sirtuin 2 Deacylase Assay: Substrate Screening and Inhibitor Evaluation
Sirtuins are important regulators
of lysine acylation, which is implicated in cellular metabolism and
transcriptional control. This makes the sirtuin class of enzymes interesting
targets for development of small molecule probes with pharmaceutical
potential. To achieve detailed profiling and kinetic insight regarding
sirtuin inhibitors, it is important to have access to efficient assays.
In this work, we report readily synthesized fluorogenic substrates
enabling enzyme-economical evaluation of SIRT2 inhibitors in a continuous
assay format as well as evaluation of the properties of SIRT2 as a
long chain deacylase enzyme. Novel enzymatic activities of SIRT2 were
thus established in vitro, which warrant further investigation, and
two known inhibitors, suramin and SirReal2, were profiled against
substrates containing ε-<i>N</i>-acyllysine modifications
of varying length
Correction to A Continuous, Fluorogenic Sirtuin 2 Deacylase Assay: Substrate Screening and Inhibitor Evaluation
Correction to A
Continuous, Fluorogenic Sirtuin 2 Deacylase Assay: Substrate Screening
and Inhibitor Evaluatio
An NAD<sup>+</sup>‑Dependent Sirtuin Depropionylase and Deacetylase (Sir2La) from the Probiotic Bacterium <i>Lactobacillus acidophilus</i> NCFM
Sirtuins, a group
of NAD<sup>+</sup>-dependent deacylases, have
emerged as the key connection between NAD<sup>+</sup> metabolism and
aging. This class of enzymes hydrolyzes a range of ε-<i>N</i>-acyllysine PTMs, and determining the repertoire of catalyzed
deacylation reactions is of high importance to fully elucidate the
roles of a given sirtuin. Here we have identified and produced two
potential sirtuins from the probiotic bacterium <i>Lactobacillus
acidophilus</i> NCFM. Screening more than 80 different substrates,
covering 26 acyl groups on five peptide scaffolds, demonstrated that
one of the investigated proteins, Sir2La, is a <i>bona fide</i> NAD<sup>+</sup>-dependent sirtuin, catalyzing hydrolysis of acetyl-,
propionyl-, and butyryllysine. Further substantiating the identity
of Sir2La as a sirtuin, known sirtuin inhibitors, nicotinamide and
suramin, as well as a thioacetyllysine compound inhibit the deacylase
activity in a concentration-dependent manner. On the basis of steady-state
kinetics, Sir2La showed a slight preference for propionyllysine (Kpro)
over acetyllysine (Kac). For nonfluorogenic peptide substrates, the
preference is driven by a remarkably low <i>K</i><sub>M</sub> (280 nM vs 700 nM, for Kpro and Kac, respectively), whereas <i>k</i><sub>cat</sub> was similar (21 × 10<sup>–3</sup> s<sup>–1</sup>). Moreover, while NAD<sup>+</sup> is a prerequisite
for Sir2La-mediated deacylation, Sir2La has a very high <i>K</i><sub>M</sub> for NAD<sup>+</sup> compared to the expected levels
of the dinucleotide in <i>L. acidophilus</i>. Sir2La is
the first sirtuin from Lactobacillales and of the Gram-positive bacterial
subclass of sirtuins to be functionally characterized. The ability
to hydrolyze propionyl- and butyryllysine emphasizes the relevance
of further exploring the role of other short-chain acyl moieties as
PTMs
Identification and Characterization of Second-Generation Invader Locked Nucleic Acids (LNAs) for Mixed-Sequence Recognition of Double-Stranded DNA
The
development of synthetic agents that recognize double-stranded
DNA (dsDNA) is a long-standing goal that is inspired by the promise
for tools that detect, regulate, and modify genes. Progress has been
made with triplex-forming oligonucleotides, peptide nucleic acids,
and polyamides, but substantial efforts are currently devoted to the
development of alternative strategies that overcome the limitations
observed with the classic approaches. In 2005, we introduced Invader
locked nucleic acids (LNAs), i.e., double-stranded probes that are
activated for mixed-sequence recognition of dsDNA through modification
with “+1 interstrand zippers” of 2′-<i>N</i>-(pyren-1-yl)Âmethyl-2′-amino-α-l-LNA monomers.
Despite promising preliminary results, progress has been slow because
of the synthetic complexity of the building blocks. Here we describe
a study that led to the identification of two simpler classes of Invader
monomers. We compare the thermal denaturation characteristics of double-stranded
probes featuring different interstrand zippers of pyrene-functionalized
monomers based on 2′-amino-α-l-LNA, 2′-<i>N</i>-methyl-2′-amino-DNA, and RNA scaffolds. Insights
from fluorescence spectroscopy, molecular modeling, and NMR spectroscopy
are used to elucidate the structural factors that govern probe activation.
We demonstrate that probes with +1 zippers of 2′-<i>O</i>-(pyren-1-yl)Âmethyl-RNA or 2′-<i>N</i>-methyl-2′-<i>N</i>-(pyren-1-yl)Âmethyl-2′-amino-DNA monomers recognize
DNA hairpins with similar efficiency as original Invader LNAs. Access
to synthetically simple monomers will accelerate the use of Invader-mediated
dsDNA recognition for applications in molecular biology and nucleic
acid diagnostics