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https://www.readbyqxmd.com/read/28723063/using-cooperatively-folded-peptides-to-measure-interaction-energies-and-conformational-propensities
#1
Maziar S Ardejani, Evan T Powers, Jeffery W Kelly
The rates and equilibria of the folding of biopolymers are determined by the conformational preferences of the subunits that make up the sequence of the biopolymer and by the interactions that are formed in the folded state in aqueous solution. Because of the centrality of these processes to life, quantifying conformational propensities and interaction strengths is vitally important to understanding biology. In this Account, we describe our use of peptide model systems that fold cooperatively yet are small enough to be chemically synthesized to measure such quantities...
July 19, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28718643/correction-to-chemical-dynamic-thermodynamic-resolution-and-s-r-interconversion-of-unprotected-unnatural-tailor-made-%C3%AE-amino-acids
#2
Shuni Wang, Shengbin Zhou, Jiang Wang, Yong Nian, Aki Kawashima, Hiroki Moriwaki, José L Aceña, Vadim A Soloshonok, Hong Liu
No abstract text is available yet for this article.
July 18, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28714902/fluorescence-modulation-of-green-fluorescent-protein-using-fluorinated-unnatural-amino-acids
#3
Jordan K Villa, Hong-Anh Tran, Megha Vipani, Stephanie Gianturco, Konark Bhasin, Brent L Russell, Elizabeth J Harbron, Douglas D Young
The ability to modulate protein function through minimal perturbations to amino acid structure represents an ideal mechanism to engineer optimized proteins. Due to the novel spectroscopic properties of green fluorescent protein, it has found widespread application as a reporter protein throughout the fields of biology and chemistry. Using site-specific amino acid mutagenesis, we have incorporated various fluorotyrosine residues directly into the fluorophore of the protein, altering the fluorescence and shifting the pKa of the phenolic proton associated with the fluorophore...
July 16, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28677608/conformational-study-of-the-3-6-dihydro-2h-1-4-oxazin-2-one-fragment-in-8-tert-butyl-7-methoxy-8-methyl-9-oxa-6-azaspiro-4-5-decane-2-10-dione-stereoisomers
#4
Ewa Żesławska, Anna Jakubowska, Wojciech Nitek
Unnatural cyclic α-amino acids play an important role in the search for biologically active compounds and macromolecules. Enantiomers of natural amino acids with a D configuration are not naturally encoded, but can be chemically synthesized. The crystal structures of two enantiomers obtained by a method of stereoselective synthesis, namely (5R,8S)-8-tert-butyl-7-methoxy-8-methyl-9-oxa-6-azaspiro[4.5]decane-2,10-dione, (1), and (5S,8R)-8-tert-butyl-7-methoxy-8-methyl-9-oxa-6-azaspiro[4.5]decane-2,10-dione, (2), both C14H21NO4, were determined by X-ray diffraction...
July 1, 2017: Acta Crystallographica. Section C, Structural Chemistry
https://www.readbyqxmd.com/read/28672107/a-toolbox-of-fluorescent-probes-for-parallel-imaging-reveals-uneven-location-of-serine-proteases-in-neutrophils
#5
Paulina Kasperkiewicz, Yoav Altman, Maximiliano D'Angelo, Guy S Salvesen, Marcin Drag
Neutrophils, the front line defenders against infection, express four serine proteases (NSPs) that play roles in the control of cell signaling pathways, defense against pathogens, and whose imbalance leads to pathological conditions. Dissecting the roles of individual NSPs in humans is problematic because neutrophils are end stage cells with a short half life and minimal ongoing protein synthesis. To gain insight into the regulation of NSPs activity we have generated a small molecule chemical toolbox consisting of activity-based probes with different fluorophore detecting groups with minimal wavelength overlap, and highly selective natural and unnatural amino acid recognition sequences...
July 3, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28671456/picalculax-improved-prediction-of-isoelectric-point-for-modified-peptides
#6
Esben J Bjerrum, Jan H Jensen, Jakob L Tolborg
The isoelectric point of a peptide is a physicochemical property that can be accurately predicted from the sequence of the peptide when the peptide is built from natural amino acids. Peptides can however have chemical modifications, such as phosphorylations, amidations, and unnatural amino acids, which can result in erroneous predictions if not accounted for. Here we report on an open source program, pICalculax, which in an extensible way can handle pI calculations of modified peptides. Tests on a database of modified peptides and experimentally determined pI values show an improvement in pI predictions when taking the modifications into account...
July 21, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28657738/genetic-code-expansion-in-zebrafish-embryos-and-its-application-to-optical-control-of-cell-signaling
#7
Jihe Liu, James Hemphill, Subhas Samanta, Michael Tsang, Alexander Deiters
Site-specific incorporation of unnatural amino acids into proteins provides a powerful tool to study protein function. Here we report genetic code expansion in zebrafish embryos and its application to the optogenetic control of cell signaling. We genetically encoded four unnatural amino acids with a diverse set of functional groups, which included a photocaged lysine that was applied to the light-activation of luciferase and kinase activity. This approach enables versatile manipulation of protein function in live zebrafish embryos, a transparent and commonly used model organism to study embryonic development...
June 28, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28641210/comparative-analysis-of-polyspecificity-of-the-endogenous-trna-synthetase-of-different-expression-host-towards-photocrosslinking-amino-acids-using-an-in-silico-approach
#8
Nadarajan Saravanan Prabhu, Hyungdon Yun
Photo-induced covalent crosslinking has emerged as the powerful strategy for analyzing and characterizing the protein-protein interaction and mapping protein 3D conformations. In the last decades, a number of photocrosslinking amino acids have been reported but only a few have been efficiently utilized for photocrosslinking purposes. Recently, incorporation of diazirine containing photoactivatable analogs such as photo-methionine, photo-leucine, photo-isoleucine and photo-lysine into target proteins were accomplished in live cells (Human A549cells, HEK 293) by depleting corresponding natural amino acid and supplementing these analogs in the medium...
June 8, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28637867/full-length-cellular-beta-secretase-has-a-trimeric-subunit-stoichiometry-and-its-sulfur-rich-transmembrane-interaction-site-modulates-cytosolic-copper-compartmentalization
#9
Filip Liebsch, Mark R P Aurousseau, Tobias Bethge, Hugo McGuire, Silvia Scolari, Andreas Herrmann, Rikard Blunck, Derek Bowie, Gerd Multhaup
The beta-secretase (BACE1) initiates processing of the amyloid precursor protein (APP) into Aβ peptides, which have been implicated as central players in the pathology of Alzheimer disease. BACE1 has been described as a copper-binding protein and its oligomeric state as being monomeric, dimeric, and/or multimeric, but the native cellular stoichiometry has remained elusive. Here, by using single-molecule fluorescence and in vitro cross-linking experiments with photo-activatable unnatural amino acids, we show that full-length BACE1, independently of its subcellular localization, exists as trimers in human cells...
June 21, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28636281/aryl-and-heteroaryl-substituted-phenylalanines-as-ampa-receptor-ligands
#10
Ewa Szymańska, Paulina Chałupnik, Tommy N Johansen, Birgitte Nielsen, Ana Maria Cuñado Moral, Darryl S Pickering, Anna Więckowska, Katarzyna Kieć-Kononowicz
A series of racemic unnatural amino acids was rationally designed on the basis of recently published X-ray structures of the GluA2 LBD with bound phenylalanine-based antagonists. Twelve new diaryl- or aryl/heteroaryl-substituted phenylalanine derivatives were synthesized and evaluated in vitro in radioligand binding assays at native rat ionotropic glutamate receptors. The most interesting compound in this series, (RS)-2-amino-3-(3'-hydroxy-5-(1H-pyrazol-4-yl)-[1,1'-biphenyl]-3-yl)propanoic acid 7e, showed the binding affinity of 4...
June 21, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28634827/highly-functionalized-cyclic-%C3%AE-amino-acid-moieties-as-promising-scaffolds-in-peptide-research-and-drug-design
#11
REVIEW
Loránd Kiss, István M Mándity, Ferenc Fülöp
Peptide-based drug research has received high attention in the field of medicinal chemistry over the past decade. For drug design, to improve proteolytic stability, it is desirable to include unnatural building blocks, such as conformationally restricted β-amino acid moieties, into the peptide sequence. Accordingly, the synthesis and incorporation of such conformationally rigid systems into novel type of peptides has gained large interest. Our research group has designed highly efficient methods for the construction of potential antimicrobial peptides...
May 30, 2017: Amino Acids
https://www.readbyqxmd.com/read/28608946/genetic-encoding-of-photocaged-tyrosines-with-improved-light-activation-properties-for-the-optical-control-of-protease-function
#12
Ji Luo, Jessica Torres-Kolbus, Jihe Liu, Alexander Deiters
We genetically encoded three new caged tyrosine analogues with improved photochemical properties by using an engineered pyrrolysyl-tRNA synthetase/tRNACUA pair in bacterial and mammalian cells. We applied the new tyrosine analogues to the photoregulation of firefly luciferase by caging its key tyrosine residue, Tyr340, and observed excellent off-to-on light switching. This reporter was then used to evaluate the activation rates of the different light-removable protecting groups in live cells. We identified the nitropiperonyl caging group as an excellent compromise between incorporation efficiency and photoactivation properties...
June 13, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28605379/voltage-clamp-fluorometry-in-xenopus-oocytes-using-fluorescent-unnatural-amino-acids
#13
Tanja Kalstrup, Rikard Blunck
Voltage-Clamp Fluorometry (VCF) has been the technique of choice to investigate the structure and function of electrogenic membrane proteins where real-time measurements of fluorescence and currents simultaneously report on local rearrangements and global function, respectively(1). While high-resolution structural techniques such as cryo-electron microscopy or X-ray crystallography provide static images of the proteins of interest, VCF provides dynamic structural data that allows us to link the structural rearrangements (fluorescence) to dynamic functional data (electrophysiology)...
May 27, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28603976/%C3%AE-imino-esters-in-organic-synthesis-recent-advances
#14
Bagher Eftekhari-Sis, Maryam Zirak
α-Imino esters are useful precursors for the synthesis of a variety of types of natural and unnatural α-amino acid derivatives, with a wide range of biological activities. Due to the adjacent ester group, α-imino esters are more reactive relative to other types of imines and undergo different kinds of reactions, including organometallics addition, metal catalyzed vinylation and alkynylation, aza-Henry, aza-Morita-Baylis-Hillman, imino-ene, Mannich-type, and cycloaddition reactions, as well as hydrogenation and reduction...
June 12, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28576486/construction-of-an-inducible-stable-cell-line-for-efficient-incorporation-of-unnatural-amino-acids-in-mammalian-cells
#15
Ziwei Zhang, Huan Xu, Longlong Si, Yi Chen, Bo Zhang, Yan Wang, Yiming Wu, Xueying Zhou, Lihe Zhang, Demin Zhou
The genetic incorporation of unnatural amino acids (Uaas) with defined properties into proteins at designated sites represents an extremely powerful tool for protein engineering. However, the efficient incorporation of Uaas in response to the amber stop codon in mammalian cells remains a substantial challenge due to the competition from release factor 1(RF1). Addressing this challenge will greatly broaden the power and scope of this technology. Here, we chose the eRF1 mutant, which can selectively enhance Uaa incorporation in response to the amber codon without increasing the readthrough of the opal and ochre codons...
May 31, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28566650/a-convenient-method-for-preparation-of-%C3%AE-imino-carboxylic-acid-derivatives-and-application-to-the-asymmetric-synthesis-of-unnatural-%C3%AE-amino-acid-derivative
#16
Tsubasa Inokuma, Takahisa Jichu, Kodai Nishida, Akira Shigenaga, Akira Otaka
We describe herein a manganese(IV) oxide-mediated oxidation of N-p-methoxyphenyl (PMP)-protected glycine derivatives for the synthesis of α-imino carboxylic acid derivatives. Using this methodology, utilization of unstable glyoxic acid derivatives was avoided. Furthermore, using this methodology we synthesized novel α-imino carboxylic acid derivatives such as α-imino phenyl ester, perfluoroalkyl etsers, imides, and thioester. The asymmetric Mannich reaction of those novel imine derivatives with 1,3-dicarbonyl compound is also described, and the novel α-imino imide gave improved chemical yield and stereoselectivity compared with those obtained by the use of the conventional α-imino ester-type substrate...
2017: Chemical & Pharmaceutical Bulletin
https://www.readbyqxmd.com/read/28533567/synthesis-and-incorporation-of-a-caged-tyrosine-amino-acid-possessing-a-bioorthogonal-handle
#17
Marshall S Padilla, Christopher A Farley, Lindsay E Chatkewitz, Douglas D Young
Reversing a bioconjugation in a spatial and temporal fashion has widespread applications, especially toward targeted drug delivery. We report the synthesis and incorporation of an unnatural amino acid with an alkyne modified dimethoxy-ortho-nitrobenzyl caging group. This unnatural amino acid can be utilized in a Glaser-Hay conjugation to generate a bioconjugate, but also is able to disrupt the bioconjugate when irradiated with light. These combined features allow for the preparation of bioconjugates with a high degree of site-specificity and allow for the separation of the two components if necessary...
October 19, 2016: Tetrahedron Letters
https://www.readbyqxmd.com/read/28522372/effective-antimicrobial-activity-of-a-peptide-mutant-cbf-14-2-against-penicillin-resistant-bacteria-based-on-its-unnatural-amino-acids
#18
Wei Kang, Hanhan Liu, Lingman Ma, Mengxiao Wang, Shanshan Wei, Pengbo Sun, Meiling Jiang, Min Guo, Changlin Zhou, Jie Dou
Broad spectrum activities, a unique mode of actions and rare resistant variants make antimicrobial peptide (AMP) a potential alternative to antibiotics. However, AMPs still have limitations in clinical development due to their physiological stability, toxicity and manufacturing costs. Cbf-14, derived from cathelicidin-BF has been proven to be effective against drug-resistant bacteria. Herein, a series of Cbf-14 mutants were designed to overcome these limitations. Design strategies included substitutions of lysine (Lys) or leucine (Leu) with similar residues such as ornithine (Orn) and norleucine (Ile), which are unnatural amino acids, to generate AMPs with enhanced therapeutic potential...
May 15, 2017: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28522266/site-specific-conjugation-of-fibroblast-growth-factor-2-fgf2-based-on-incorporation-of-alkyne-reactive-unnatural-amino-acid
#19
K W Swiderska, A Szlachcic, A Czyrek, M Zakrzewska, J Otlewski
Recent advances in site-specific protein modification include the increasingly popular incorporation of unnatural amino acid(s) using amber codon, a method developed by Schultz and coworkers. In this study, we employ this technique to introduce propargyllysine (PrK) in human fibroblast growth factor 2 (FGF2). Owing to an alkyne moiety in its side chain, PrK is compatible with Cu(I)-catalyzed azide-alkyne 1,3-dipolar cycloaddition (CuAAC). We successfully tested CuAAC-mediated conjugation of FGF2 with two compounds - a fluorophore carboxyrhodamine 110 or a cytotoxic drug monomethyl auristatin E (MMAE)...
May 5, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28507719/broad-substrate-tolerance-of-tubulin-tyrosine-ligase-enables-one-step-site-specific-enzymatic-protein-labeling
#20
Dominik Schumacher, Oliver Lemke, Jonas Helma, Lena Gerszonowicz, Verena Waller, Tina Stoschek, Patrick M Durkin, Nediljko Budisa, Heinrich Leonhardt, Bettina G Keller, Christian P R Hackenberger
The broad substrate tolerance of tubulin tyrosine ligase is the basic rationale behind its wide applicability for chemoenzymatic protein functionalization. In this context, we report that the wild-type enzyme enables ligation of various unnatural amino acids that are substantially bigger than and structurally unrelated to the natural substrate, tyrosine, without the need for extensive protein engineering. This unusual substrate flexibility is due to the fact that the enzyme's catalytic pocket forms an extended cavity during ligation, as confirmed by docking experiments and all-atom molecular dynamics simulations...
May 1, 2017: Chemical Science
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