Gene/Protein Disease Symptom Drug Enzyme Compound
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CheY, the excitatory response regulator in the chemotaxis system of Escherichia coli, can be modulated by two covalent modifications: phosphorylation and acetylation. Both modifications have been detected in vitro only. The role of CheY acetylation is still obscure, although it is known to be involved in chemotaxis and to occur in vitro by two mechanisms--acetyl-CoA synthetase-catalyzed transfer of acetyl groups from acetate to CheY and autocatalyzed transfer from AcCoA. Here, we succeeded in detecting CheY acetylation in vivo by three means--Western blotting with a specific anti-acetyl-lysine antibody, mass spectrometry, and radiolabeling with [(14)C]acetate in the presence of protein-synthesis inhibitor. Unexpectedly, the level and rate of CheY acetylation in vivo were much higher than that in vitro. Thus, before any treatment, 9-13% of the lysine residues were found acetylated, depending on the growth phase, meaning that, on average, essentially every CheY molecule was acetylated in vivo. This high level was mainly the outcome of autoacetylation. Addition of acetate caused an incremental increase in the acetylation level, in which acetyl-CoA synthetase was involved too. These findings may have far-reaching implications for the structure-function relationship of CheY.
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PMID:In vivo acetylation of CheY, a response regulator in chemotaxis of Escherichia coli. 1823 27

Gold colloids functionalized with amino acids provide a scaffold for effective DNA binding with subsequent condensation. Particles with lysine and lysine dendron functionality formed particularly compact complexes and provided highly efficient gene delivery without any observed cytotoxicity. Nanoparticles functionalized with first generation lysine dendrons (NP-LysG1) were approximately 28-fold superior to polylysine in reporter gene expression. These amino acid-based nanoparticles were responsive to intracellular glutathione levels, providing a tool for controlled release and concomitant expression of DNA.
ACS Nano 2008 Nov 25
PMID:Efficient gene delivery vectors by tuning the surface charge density of amino acid-functionalized gold nanoparticles. 1920 85

We present a method providing synchronized measurements using the two techniques: quartz crystal microbalance with dissipation (QCM-D) monitoring and localized surface plasmon resonance (LSPR). This was achieved by letting a thin gold film perforated with short-ranged ordered plasmon-active nanoholes act as one of the electrodes of a QCM-D crystal. This enabled transmission-mode optical spectroscopy to be used to temporally resolve colorimetric changes of the LSPR active substrate induced upon biomolecular binding events. The LSPR response could thus be compared with simultaneously obtained changes in resonance frequency, Deltaf, and energy dissipation, DeltaD, of the QCM-D device. Since the LSPR technique is preferentially sensitive to changes within the voids of the nanoholes, while the QCM-D technique is preferentially sensitive to reactions on the planar region between the holes, a surface chemistry providing the same binding kinetics on both gold and silica was used. This was achieved by coating the substrate with poly(L-lysine)-graft-poly(ethylene glycol) (PLL-g-PEG), which was shown to bind in the same manner on silica and gold modified with a carboxyl-terminated thiol. In this way, the combined setup provided new information about structural changes upon PLL-g-PEG adsorption. We also demonstrate subsequent binding of NeutrAvidin and an immunoreaction utilizing biotin-modified IgG. The combined information from the synchronized measurements was also used in a new way to estimate the sensing volume of the LSPR sensor.
ACS Nano 2008 Oct 28
PMID:Synchronized quartz crystal microbalance and nanoplasmonic sensing of biomolecular recognition reactions. 1920 65

We perform in this paper a kinetic study of the photoelectrochemical responses of nanoporous thin photoactive films. The films were fabricated by by a layer-by-layer assembly of positively charged polyelectrolytes (poly-l-Lysine, pLys) and negatively charged semiconductor nanoparticles (NPs) on a carboxylic acid terminated alkanethiol-modified gold electrode. Two types of NPs were used to build uniform films: cadmium selenide (CdSe) and cadmium selenide/cadmium sulfide core/shell (CdSe@CdS). Large photocathodic and photoanodic currents were recorded for CdSe and CdSe@CdS sensitized films, respectively. A theoretical model of the photocurrent responses was developed to analyze the kinetics of photoinduced processes and coupled reactions, showing that the multilayer films behave as homogeneous nanoporous semiconducting photoelectrodes.
ACS Nano 2008 May
PMID:Nanoporous photocathode and photoanode made by multilayer assembly of quantum dots. 1920 96

Aqueous dispersible detonation nanodiamonds (NDs) with a diameter of 2-8 nm were assembled into a closely packed ND multilayer nanofilm with positively charged poly-L-lysine via the layer-by-layer deposition technique. The innate biocompatibility of the NDs in both free-floating and thin-film forms was confirmed via cellular gene expression examination by real-time polymerase chain reaction as well as MTT and DNA fragmentation assays. The highly biologically amenable ND nanofilm was successfully integrated with therapeutic molecules, and the functionality of the composite drug-ND material was assessed via interrogation of the suppression of inflammatory cytokine release. Knockdown of lipopolysaccharide-mediated inflammation was observed through the potent attenuation of tumor necrosis factor-alpha, interleukin-6, and inducible nitric oxide synthase levels following ND nanofilm interfacing with RAW 264.7 murine macrophages. Furthermore, basal cytokine secretion levels were assessed to examine innate material biocompability, revealing unchanged cellular inflammatory responses which strongly supported the relevance of the NDs as effective treatment platforms for nanoscale medicine. In addition to the easy preparation, robustness, and fine controllability of the film structures, these hybrid materials possess enormous potential for biomedical applications such as localized drug delivery and anti-inflammatory implant coatings and devices, as demonstrated in vitro in this work.
ACS Nano 2008 Feb
PMID:Protein-mediated assembly of nanodiamond hydrogels into a biocompatible and biofunctional multilayer nanofilm. 1920 20

The use of fixed charge nanopores in practical applications requires tuning externally the electrostatic interaction between the charged groups and the ionic permeants in order to allow integrating a variety of functions on the same nanostructure. We design, produce, and characterize, theoretically and experimentally, a single-track amphoteric nanopore functionalized with lysine and histidine chains whose positive and negative charges are very sensitive to the external pH. This nanofluidic diode with amphoteric chains attached to the pore surface allows for a broad set of rectification properties supported by a single nanodevice. A definite plus is to functionalize these groups on a conical nanopore with well-defined, controlled structural asymmetry which gives virtually every rectification characteristic that may be required in practical applications. Nanometerscaled amphoteric pores are of general interest because of the potential applications in drug delivery systems, ion-exchange membranes for separation of biomacromolecules, antifouling materials with reduced molecular adsorption, and biochemical sensors.
ACS Nano 2009 Mar 24
PMID:A pH-tunable nanofluidic diode with a broad range of rectifying properties. 1922 30

Methods that introduce posttranslational modifications in a general, mild, and non-sequence-specific manner using biologically produced peptides have great utility for investigation of the functions of these modifications. In this study, the substrate promiscuity of a lantibiotic synthetase was exploited for the preparation of phosphopeptides, glycopeptides, and peptides containing analogs of methylated or acetylated lysine residues. Peptides attached to the C-terminus of the leader peptide of the lacticin 481 precursor peptide were phosphorylated on serine residues in a wide variety of sequence contexts by the R399M and T405A mutants of lacticin 481 synthetase (LctM). Serine residues located as many as 30 amino acids C-terminal to the leader peptide were phosphorylated. Wild-type LctM was shown to dehydrate these peptides to generate dehydroalanine-containing products that can be conveniently modified with external nucleophiles including thiosaccharides, 2-(dimethylamino)ethanethiol, and N-acetyl cysteamine, resulting in mimics of O-linked glycopeptides and acetylated and methylated lysines.
ACS Chem Biol 2009 May 15
PMID:Lacticin 481 synthetase as a general serine/threonine kinase. 1929 52

Natural polyphenols with previously demonstrated anticancer potential, epigallocatechin gallate (EGCG), tannic acid, curcumin, and theaflavin, were encased into gelatin-based 200 nm nanoparticles consisting of a soft gel-like interior with or without a surrounding LbL shell of polyelectrolytes (polystyrene sulfonate/polyallylamine hydrochloride, polyglutamic acid/poly-l-lysine, dextran sulfate/protamine sulfate, carboxymethyl cellulose/gelatin, type A) assembled using the layer-by-layer technique. The characteristics of polyphenol loading and factors affecting their release from the nanocapsules were investigated. Nanoparticle-encapsulated EGCG retained its biological activity and blocked hepatocyte growth factor (HGF)-induced intracellular signaling in the breast cancer cell line MBA-MD-231 as potently as free EGCG.
ACS Nano 2009 Jul 28
PMID:Layer-by-Layer-Coated Gelatin Nanoparticles as a Vehicle for Delivery of Natural Polyphenols. 1953 72

SIRT3 is a major mitochondrial NAD(+)-dependent protein deacetylase playing important roles in regulating mitochondrial metabolism and energy production and has been linked to the beneficial effects of exercise and caloric restriction. SIRT3 is emerging as a potential therapeutic target to treat metabolic and neurological diseases. We report the first sets of crystal structures of human SIRT3, an apo-structure with no substrate, a structure with a peptide containing acetyl lysine of its natural substrate acetyl-CoA synthetase 2, a reaction intermediate structure trapped by a thioacetyl peptide, and a structure with the dethioacetylated peptide bound. These structures provide insights into the conformational changes induced by the two substrates required for the reaction, the acetylated substrate peptide and NAD(+). In addition, the binding study by isothermal titration calorimetry suggests that the acetylated peptide is the first substrate to bind to SIRT3, before NAD(+). These structures and biophysical studies provide key insight into the structural and functional relationship of the SIRT3 deacetylation activity.
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PMID:Crystal structures of human SIRT3 displaying substrate-induced conformational changes. 1953 40

Post-translational modification of histones plays an integral role in regulation of genomic expression through modulation of chromatin structure and function. Chemical preparations of histones bearing these modifications allows for comprehensive in vitro mechanistic investigation into their action to deconvolute observations from genome-wide studies in vivo. Previously, we reported the semisynthesis of ubiquitylated histone H2B (uH2B) using two orthogonal expressed protein ligation reactions. Semisynthetic uH2B, when incorporated into nucleosomes, directly stimulates methylation of histone H3 lysine 79 (K79) by the methyltransferase, disruptor of telomeric silencing-like (Dot1L). Although recruitment of Dot1L to the nucleosomal surface by uH2B could be excluded, comprehensive mechanistic analysis was precluded by systematic limitations in the ability to generate uH2B in large scale. Here we report a highly optimized synthesis of ubiquitylated H2B bearing a G76A point mutation u(G76A)H2B, yielding tens of milligrams of ubiquitylated protein. u(G76A)H2B is indistinguishable from the native uH2B by Dot1L, allowing for detailed studies of the resultant trans-histone crosstalk. Kinetic and structure-activity relationship analyses using u(G76A)H2B suggest a noncanonical role for ubiquitin in the enhancement of the chemical step of H3K79 methylation. Furthermore, titration of the level of uH2B within the nucleosome revealed a 1:1 stoichiometry of Dot1L activation.
ACS Chem Biol 2009 Nov 20
PMID:Structure-activity analysis of semisynthetic nucleosomes: mechanistic insights into the stimulation of Dot1L by ubiquitylated histone H2B. 1979 66


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