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Banerjee Rajat R Department of Microbiology, Center for RNA Biology, Ohio State University, Columbus, OH 43210, - - 2010
The role of tRNA in translating the genetic code has received considerable attention over the last 50 years, and we now know in great detail how particular amino acids are specifically selected and brought to the ribosome in response to the corresponding mRNA codon. Over the same period, it has ...
Francklyn Christopher S CS Cell and Molecular Biology Program, University of Vermont, Burlington, VT 05405, United States. - - 2010
During protein synthesis, tRNA serves as the intermediary between cognate amino acids and their corresponding RNA trinucleotide codons. Aminoacyl-tRNA is also a biosynthetic precursor and amino acid donor for other macromolecules. AA-tRNAs allow transformations of acidic amino acids into their amide-containing counterparts, and seryl-tRNA(Ser) donates serine for antibiotic synthesis. Aminoacyl-tRNA ...
Vagt Toni - - 2010
Phage display technology has been applied to screen for preferred interaction partners of fluoroalkyl-substituted amino acids from the pool of the 20 canonical amino acids. A parallel, heterodimeric alpha-helical coiled coil was designed such that one peptide strand contained one of three different fluorinated amino acids within the hydrophobic core. ...
Hohenester Ulli Martin - - 2010
Bioanalytical techniques were preferentially developed for the investigation of phosphohydroxyamino acids in the past and there is a wealth of information on the detection of serine, threonine and tyrosine phosphorylation in functional proteomics. However, similarly important for protein regulation and signalling is the phosphorylation of other amino acids such as ...
Al?as Miriam - - 2010
Alpha helices are useful scaffolds to build biologically active peptides. The intrinsic stability of an alpha-helix is a key feature that can be successfully designed, and it is governed by the constituting amino acid residues. Their individual contributions to helix stability are given, according to Lifson-Roig theory, by their w ...
Gao Rong R Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, - - 2010
The changeabilities of individual modules of aminoacyl-tRNAs are poorly understood, despite the relevance for evolution, translational accuracy and incorporation of unnatural amino acids (AAs). Here, we dissect the effect of successive changes in four domains of Ala-tRNA(3)(Ala) on translation in a purified system. Incorporating five AAs, not one, was necessary ...
Kino Kuniki - - 2010
L-Amino acid ligase catalyzes dipeptide synthesis from unprotected L-amino acids in an ATP-dependent manner. We have purified a new L-amino acid ligase, RizA, which synthesizes dipeptides whose N-terminus is Arg, from Bacillus subtilis NBRC3134, a microorganism that produces a rhizocticin peptide antibiotic. It was suggested that RizA is probably involved ...
Nesterov Alexander - - 2010
Today, lithographic methods enable combinatorial synthesis of >50,000 oligonucleotides per cm(2), an advance that has revolutionized the whole field of genomics. A similar development is expected for the field of proteomics, provided that affordable, very high-density peptide arrays are available. However, peptide arrays lag behind oligonucleotide arrays. This is mainly ...
Muthusamy Karen - - 2010
The 37-amino acid polypeptide islet amyloid polypeptide (IAPP), or amylin, is found as amyloid aggregates in the islets of Langerhans in patients with type II diabetes. Herein, we report an efficient microwave assisted solid phase peptide synthesis of amylin (IAPP). The most efficient synthesis used double and triple couplings and ...
Muttenthaler Markus - - 2010
This study evaluated the acidic lability of the acetamidomethyl (Acm), trimethylacetamidomethyl (Tacm), and the p-nitrobenzyl (pNB) as protecting groups for cysteine and selenocysteine (Sec) during the tert-butyloxycarbonyl (Boc)-chemistry solid-phase peptide synthesis of oxytocin (OT). Two novel Sec building blocks (Nalpha-tert-butyloxycarbonyl-Se(acetamidomethyl)-L-selenocysteine (Boc-L-Sec(Acm)-OH) and Nalpha-tert-butyloxycarbonyl-S(4-nitrobenzyl)-L-selenocysteine (Boc-L-Sec(pNB)-OH)) were developed for this study. Six ...
Seligmann Hervé - - 2010
Accurate amino acid insertion during peptide elongation requires tRNAs loaded by cognate amino acids and that anticodons match codons. However, tRNA misloading does not necessarily cause misinsertions: misinsertion is avoided when anticodons mismatch codons coding for misloaded amino acids. Occasional compensation of misacylation by codon-anticodon mismatch necessarily occurs. Putatively, occasional ...
Darlington L Gail - - 2010
Of the major components of the kynurenine pathway for the oxidative metabolism of tryptophan, most attention has focussed on the N-methyl-D-aspartate (NMDA) receptor agonist quinolinic acid, and the glutamate receptor blocker kynurenic acid. However, there is increasing evidence that the redox-active compound 3-hydroxyanthranilic acid may also have potent actions on ...
Zaborske John M JM Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, - - 2010
When eukaryotic cells are deprived of amino acids, uncharged tRNAs accumulate and activate the conserved GCN2 protein kinase. Activated Gcn2p up-regulates the general amino acid control pathway through phosphorylation of the translational initiation factor eIF2. In Saccharomyces cerevisiae, Gcn2p is the only kinase that phosphorylates eIF2 to regulate translation through ...
Banerjee Jayati - - 2010
Collagen-mimetic peptides and lipopeptides are widely used as substrates for matrix degrading enzymes, as new biomaterials for tissue engineering, as drug delivery systems and so on. However, the preparation and subsequent purification of these peptides and their fatty-acid conjugates are really challenging. Herein, we report a rapid microwave-assisted, solid-phase synthetic ...
Guo Min M The Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, California 92037, - - 2009
Mistranslation arising from confusion of serine for alanine by alanyl-tRNA synthetases (AlaRSs) has profound functional consequences. Throughout evolution, two editing checkpoints prevent disease-causing mistranslation from confusing glycine or serine for alanine at the active site of AlaRS. In both bacteria and mice, Ser poses a bigger challenge than Gly. One ...
Bhatt Tarun Kumar TK Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Road, New Delhi, 110067, - - 2010
D-tyrosyl-tRNA(Tyr) deacylase (DTD) is an editing enzyme that removes D-amino acids from mischarged tRNAs. We describe an in-depth analysis of the malaria parasite Plasmodium falciparum DTD here. Our data provide structural insights into DTD complexes with adenosine and D-amino acids. Bound adenosine is proximal to the DTD catalysis site, and ...
Bertrand Maryl?ne - - 2009
Delivery of prebiotic molecules, such as amino acids and peptides, in meteoritic/micrometeoritic materials to early Earth during the first 500 million years is considered to be one of the main processes by which the building blocks of life arrived on Earth. In this context, we present a study in which ...
Claerhout Stijn - - 2010
A thorough comparative study to demonstrate the properties of a new microwave labile backbone amide linker is presented. A cyclic pentapeptide, cyclo(Trp-Gln-Gly-beta-Ala-Phe), was used as a model and synthesized following 16 different conditions. The new backbone amide linker is stable towards acid and base at r.t., and can be cleaved ...
Puthenveetil Sujiet S Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, - - 2009
Escherichia coli lipoic acid ligase (LplA) catalyzes ATP-dependent covalent ligation of lipoic acid onto specific lysine side chains of three acceptor proteins involved in oxidative metabolism. Our lab has shown that LplA and engineered mutants can ligate useful small-molecule probes such as alkyl azides ( Nat. Biotechnol. 2007 , 25 ...
Effraim Philip R PR Columbia University, New York, New York, - - 2009
The involvement of tRNA structural elements beyond the anticodon in aminoacyl-tRNA (aa-tRNA) selection by the ribosome has revealed that substrate recognition is considerably more complex than originally envisioned in the adaptor hypothesis. By combining recent breakthroughs in aa-tRNA synthesis and mechanistic and structural studies of protein synthesis, we have investigated ...
Ishibashi Yoshitaka - - 2009
By establishing both a highly efficient phosphonamidate formation and a RuCp-catalyzed cleavage of an allyl linker, the solid-phase synthesis of Fmoc-(GlyP(OBn))(6)-OH/DIEA, a protected form of a new type of unnatural peptide alpha-amino phosphonic acid oligomer (APO), has been realized.
Acosta Gerardo A - - 2009
This manuscript shows that ACN can be an excellent choice for the coupling of hindered amino acids as illustrated by the coupling of Fmoc-amino acids on free amino acids anchored on a BAL synthesis. Furthermore, ACN can be a good alternative for solid-phase peptide synthesis in the absence of DMF ...
Iwaoka Michio - - 2009
Molecular simulation by using force field parameters has been widely applied in the fields of peptide and protein research for various purposes. We recently proposed a new all-atom protein force field, called the SAAP force field, which utilizes single amino acid potentials (SAAPs) as the fundamental elements. In this article, ...
Vorobyev Aleksey - - 2009
We present mechanistic studies aimed at improving the understanding of the product ion formation rules in electron capture dissociation (ECD) of peptides and proteins in Fourier transform ion cyclotron resonance mass spectrometry. In particular, we attempted to quantify the recently reported general correlation of ECD product ion abundance (PIA) with ...
Zaborske John M JM Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, - - 2009
When cells are subjected to nutritional stress, uncharged tRNAs accumulate and activate Gcn2p phosphorylation of eukaryotic initiation factor-2 (eIF2) and the general amino acid control pathway. The Gcn2p regulatory domain homologous to histidyl-tRNA synthetases is proposed to bind to uncharged tRNA, directly contributing to activation of Gcn2p. Here we apply ...
Paul Swapan Kumar - - 2009
The moc3 gene was screened out as an inducer of sexual differentiation in fission yeast Schizosaccharomyces pombe. We isolated a novel gene, named ers2, encoding mitochondrial glutamyl tRNA synthetase (mGluRS) as a Moc3 interacting element by the yeast two-hybrid system. Cytoplasmic glutamyl tRNA synthetase (cGluRS) also interacted with Moc3 in ...
Stokes Audrey L - - 2009
Many unnatural amino acid synthetases have been evolved to enable the site-specific in vivo incorporation of many useful functionalities into proteins. While these unnatural amino acid-tRNA synthetase-tRNA(CUA) pairs do not incorporate endogenous amino acids, their substrate specificity has not been assessed for other unnatural amino acids. Here we demonstrate that ...
Forster Anthony C AC Department of Pharmacology and Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, 2222 Pierce Ave., Nashville, TN 37232, USA. - - 2009
Aminoacyl-transfer RNAs contain four standardized units: amino acids, an invariant 3'-terminal CCA, trinucleotide anticodons and tRNA bodies. The degree of interchangeability of the three variable modules is poorly understood, despite its role in evolution and the engineering of translation to incorporate unnatural amino acids. Here, a purified translation system is ...
Kino Kuniki - - 2009
L-amino acid ligase catalyzes the formation of an alpha-peptide bond from unprotected L-amino acids in an ATP-dependent manner, and this enzyme is very useful in efficient peptide production. We performed enzyme purification to obtain a novel L-amino acid ligase from Bacillus subtilis NBRC3134, a microorganism producing peptide-antibiotic rhizocticin. Rhizocticins are ...
Niwa Nobuyoshi - - 2009
We have developed a new flexizyme (a flexible de novo tRNA acylation ribozyme) system, a pair of amino-derivatized benzyl thioester (ABT) and amino flexizyme (aFx). ABT bearing the ammonium ion was designed to render the acyl-donor substrates better water solubility. Although the previously reported flexizymes (eFx and dFx) did not ...
Huang Hai - - 2009
Three cDNA sequences encoding the gonadotropin subunits, common glycoprotein alpha subunit (GTHalpha), FSHbeta and LHbeta subunits were isolated from marbled eel. The cDNA of GTHalpha encodes 116 amino acids with a signal peptide of 24 amino acids and a mature peptide of 92 amino acids. The FSHbeta subunit consists of ...
Breitling Frank - - 2009
Lithographic methods allow for the combinatorial synthesis of >50,000 oligonucleotides per cm(2), and this has revolutionized the field of genomics. High-density peptide arrays promise to advance the field of proteomics in a similar way, but currently lag behind. This is mainly due to the monomer-by-monomer repeated consecutive coupling of 20 ...
Levengood Matthew R MR Department of Chemistry, University of Illinois at Urbana-Champaign, Howard Hughes Medical Institute, 600 S. Mathews Avenue, Urbana, IL 61801, - - 2009
Lantibiotics are peptide antimicrobial compounds that are characterized by the thioether-bridged amino acids lanthionine and methyllanthionine. For lacticin 481, these structures are installed in a two-step post-translational modification process by a bifunctional enzyme, lacticin 481 synthetase (LctM). LctM catalyzes the dehydration of Ser and Thr residues to generate dehydroalanine or ...
Bonnard Vanessa - - 2009
This communication introduces a new class of promising RNA ligands, named polyamide amino acids (PAA), which are able to bind a targeted bulged stem-loop RNA fragment (HIV-1 TAR RNA) with micromolar affinities and with specificity comparative to dsDNA and tRNA; both the affinity and the specificity of PAA for TAR ...
Kojima Naoshi - - 2009
Solid-support conjugation at the 5'-terminal primary amine of oligonucleotides is a convenient and powerful method for introducing various functional groups. However, conventional aliphatic amines do not necessarily provide conjugates with sufficient yields. To improve the modification efficacy, we used the amino-linker (aminoethoxycarbonyl)aminohexyl group (ssH-linker), for solid-support conjugation. In the ssH-linker ...
Zheng Anmin - - 2009
Precise theoretical predictions of NMR parameters are helpful for the spectroscopic identification of complicated biological molecules, especially for the carbon shielding tensors in amino acids. The (13)C shielding tensors of various crystalline amino acids and peptides have been calculated using the gauge-including projector augmented wave (GIPAW) method based on two ...
Martin Nathaniel I - - 2009
Lantibiotics are antimicrobial peptides containing the unique bis-amino acids lanthionine and beta-methyllanthionine. While previous syntheses of lanthionine have often involved the coupling of precursors derived from D-serine and L-cysteine, we here report an inverted strategy whereby D-cysteine and L-serine are employed as building blocks. This approach provides for a concise ...
Gundala Chennakrishnareddy - - 2009
The synthesis of Bsmoc-N-methyl amino acids is presented. The first step involves p-toluenesulfonic acid (TsOH) catalysed condensation of a Bsmoc-amino acid with paraformaldehyde to furnish N-Bsmoc-5-oxazolidinone under MW irradiation. This intermediate is reduced to the corresponding N-methyl amino acid using triethylsilane (Et3SiH) and trifluoroacetic acid (TFA) at r.t. The N-methyl ...
Marinova Margarita - - 2009
Chick-pea (Cicer arietinum L.) cotyledons are unique source of aminopeptidase - 8-9 U/g cotyledons was observed using L-leucine-p-nitroanilide as substrate. The aminopeptidase was purified (65 kDa, pI 4.8 ) reaching a specific activity of 220 U/mg at pH 7.0-7.2 and 35-40 degrees C. The determined constant of specificity k(cat)/K(m) during ...
Zheng Gen - - 2009
DTD (D-Tyr-tRNA(Tyr) deacylase) is known to be able to deacylate D-aminoacyl-tRNAs into free D-amino acids and tRNAs and therefore contributes to cellular resistance against D-amino acids in Escherichia coli and yeast. We have found that h-DTD (human DTD) is enriched in the nuclear envelope region of mammalian cells. Treatment of ...
Rodin Andrei S - - 2009
The genetic code is brought into action by 20 aminoacyl-tRNA synthetases. These enzymes are evenly divided into two classes (I and II) that recognize tRNAs from the minor and major groove sides of the acceptor stem, respectively. We have reported recently that: (1) ribozymic precursors of the synthetases seem to ...
Lehmann Jean - - 2009
The origin of the genetic code in the context of an RNA world is a major problem in the field of biophysical chemistry. In this paper, we describe how the polymerization of amino acids along RNA templates can be affected by the properties of both molecules. Considering a system without ...
Chen Peng R PR Department of Chemistry, The Scripps Research Institute, 10550 Torry Pines Road, La Jolla, CA 92037, - - 2009
A shuttle system has been developed to genetically encode unnatural amino acids in mammalian cells using aminoacyl-tRNA synthetases (aaRSs) evolved in E. coli. A pyrrolysyl-tRNA synthetase (PylRS) mutant was evolved in E. coli that selectively aminoacylates a cognate nonsense suppressor tRNA with a photocaged lysine derivative. Transfer of this orthogonal ...
Pavlov Michael Y MY Department of Cell and Molecular Biology, Uppsala University, BMC, Box 596, 751 24 Uppsala, - - 2009
Proteins are made from 19 aa and, curiously, one N-alkylamino acid ("imino acid"), proline (Pro). Pro is thought to be incorporated by the translation apparatus at the same rate as the 19 aa, even though the alkyl group in Pro resides directly on the nitrogen nucleophile involved in peptide bond ...
Kaiser Jasper - - 2009
A series of cyclic enediyne-containing amino acids with ring sizes varying from 10 to 12 atoms have been prepared starting from propargylglycine and homopropargylglycine. Their reactivity towards Bergman cyclisation under elevated temperatures has been explored. The enediynes displayed marked differences in cyclisation half-lives depending on the olefinic substituent and the ...
Zhu Bin - - 2009
Aminoacyl-tRNA synthetases catalyze the formation of aminoacyl-tRNA in a two-step reaction starting with amino acid activation followed by aminoacyl group transfer to tRNA. To clear mistakes that occasionally occur, some of these enzymes carry out editing activities, acting on the misactivated amino acid (pretransfer editing) or after the transfer on ...
Haddoub Rose - - 2009
We have previously shown that dipeptides can be synthesised in high yields from amino acids using protease catalysis in aqueous media, if the amino component is immobilised on porous PEGA resin (a copolymer of polyethylene glycol and polyacrylamide). Here we explore the scope of this methodology for using protected and ...
Aryal Uma K - - 2008
Although widely used in proteomics research for the selective enrichment of phosphopeptides from protein digests, immobilized metal-ion affinity chromatography (IMAC) often suffers from low specificity and differential recovery of peptides carrying different numbers of phosphate groups. By systematically evaluating and optimizing different loading, washing, and elution conditions, we have developed ...
Lichtenstein Bruce R - - 2009
The synthesis of a naphthoquinone amino acid and its electrochemical characterization in a peptide is presented.
Theis Christoph - - 2008
Representative members of a group of linear, N-acylated polypeptide antibiotics (peptaibols) containing alpha-aminoisobutyric acid (Aib) and, in part, isovaline (Iva), as well as proteinogenic amino acids and a C-terminal-bonded 2-amino alcohol, were treated with anhydrous trifluoroacetic acid (TFA) at 37 degrees for 0.5-26 h. The resulting fragments were separated by ...
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