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https://www.readbyqxmd.com/read/28073163/hydrocarbon-stapled-lipopeptides-exhibit-selective-antimicrobial-activity
#1
Zachary B Jenner, Christopher M Crittenden, Martín Gonzalez, Jennifer S Brodbelt, Kerry A Bruns
Antimicrobial peptides (AMPs) occur widely in nature and have been studied for their therapeutic potential. AMPs are of interest due to the large number of possible chemical structural combinations using natural and unnatural amino acids, with varying effects on their biological activities. Using physicochemical properties from known naturally occurring amphipathic cationic AMPs, several hydrocarbon-stapled lipopeptides (HSLPs) were designed, synthesized, and tested for antimicrobial properties. Peptides were chemically modified by N-terminal acylation, C-terminal amidation, and some were hydrocarbon stapled by intramolecular olefin metathesis...
January 10, 2017: Biopolymers
https://www.readbyqxmd.com/read/28068458/synthetic-muc1-glycopeptide-bearing-%C3%AE-galnac-thr-as-tn-antigen-isomer-induces-antibodies-production-against-tumor-cells
#2
Vanessa Leiria Campo, Thalita Riul, Leandro Bortot, Maristela Martins-Teixeira, Marcelo Marchiori, Emanuela Iaccarino, Menotti Ruvo, Marcelo Dias-Baruffi, Ivone Carvalho
This study presents the synthesis of the novel protected O-glycosyl amino acids βGalNAc-SerOBn (1) and βGalNAc-ThrOBn (2) as mimetics of the natural Tn antigen (αGalNAc-Ser/Thr), along with the solid-phase assembly of the glycopeptides NHAcSer-Ala-Pro-Asp-Thr[αGalNAc]-Arg-Pro-Ala-Pro-Gly-BSA (3-BSA) and NHAcSer-Ala-Pro-Asp-Thr[βGalNAc]-Arg-Pro-Ala-Pro-Gly-BSA (4-BSA), bearing αGalNAc-Thr or βGalNAc-Thr, as mimetics of MUC1 tumor mucin glycoproteins. According to ELISA tests, mice immunizations with βGalNAc-glycopeptide 4-BSA induced higher sera titers (1:320000) if compared to immunizations with αGalNAc-glycopeptide 3-BSA (1:40000)...
January 9, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28068088/a-200-mev-uphill-thermodynamic-landscape-for-radical-transport-in-escherichia-coli-ribonucleotide-reductase-determined-using-fluorotyrosine-substituted-enzymes
#3
Kanchana R Ravichandran, Alexander T Taguchi, Yifeng Wei, Cecilia Tommos, Daniel G Nocera, JoAnne Stubbe
Escherichia coli class Ia ribonucleotide reductase (RNR) converts ribonucleotides to deoxynucleotides. A diferric-tyrosyl radical (Y122•) in one subunit (β2) generates a transient thiyl radical in another subunit (α2) via long-range radical transport (RT) through aromatic amino acid residues (Y122 ⇆ [W48] ⇆ Y356 in β2 to Y731 ⇆ Y730 ⇆ C439 in α2). Equilibration of Y356•, Y731•, and Y730• was recently observed using site specifically incorporated unnatural tyrosine analogs; however, equilibration between Y122• and Y356• has not been detected...
October 19, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28060353/efficient-and-site-specific-antibody-labeling-by-strain-promoted-azide-alkyne-cycloaddition
#4
Sanggil Kim, Wooseok Ko, Hyunji Park, Hyun Soo Lee
There are currently many chemical tools available to introduce chemical probes into proteins to study their structure and function. A useful method is protein conjugation by genetically introducing an unnatural amino acid containing a bioorthogonal functional group. This report describes a detailed protocol for site-specific antibody conjugation. The protocol includes experimental details for the genetic incorporation of an azide-containing amino acid, and the conjugation reaction by strain-promoted azide-alkyne cycloaddition (SPAAC)...
December 23, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28059571/presynaptic-calmodulin-targets-lessons-from-structural-proteomics
#5
Noa Lipstein, Melanie Göth, Christine Piotrowski, Kevin Pagel, Andrea Sinz, Olaf Jahn
Calmodulin (CaM) is a highly conserved Ca(2+)-binding protein that is exceptionally abundant in the brain. In the presynaptic compartment of neurons, CaM transduces changes in Ca(2+) concentration into the regulation of synaptic transmission dynamics. Areas covered: We review selected literature including published CaM interactor screens and outline established and candidate presynaptic CaM targets. We present a workflow of biochemical and structural proteomic methods that were used to identify and characterize the interactions between CaM and Munc13 proteins...
January 6, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28052530/ligand-enabled-%C3%AE-c-h-arylation-of-%C3%AE-amino-acids-without-installing-exogenous-directing-groups
#6
Gang Chen, Zhe Zhuang, Gen-Cheng Li, Tyler G Saint-Denis, Yi Hsiao, Candice L Joe, Jin-Quan Yu
Herein we report acid-directed β-C(sp(3) )-H arylation of α-amino acids enabled by pyridine-type ligands. This reaction does not require the installation of an exogenous directing group, is scalable, and enables the preparation of Fmoc-protected unnatural amino acids in three steps. The pyridine-type ligands are crucial for the development of this new C(sp(3) )-H arylation.
January 3, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28045249/rationally-designed-peptides-and-peptidomimetics-as-inhibitors-of-amyloid-%C3%AE-a%C3%AE-aggregation-potential-therapeutics-of-alzheimer-s-disease
#7
Deepti Goyal, Suniba Shuaib, Sukhmani Mann, Bhupesh Goyal
Alzheimer's disease (AD) is a progressive neurodegenerative disease with no clinically accepted treatment to cure or halt its progression. The worldwide effort to develop peptide-based inhibitors of amyloid-β (Aβ) aggregation can be considered an unplanned combinatorial experiment. An understanding of what has been done and achieved may advance our understanding of AD pathology and the discovery of effective therapeutic agents. We review here the history of such peptide-based inhibitors, including those based on the Aβ sequence and those not derived from that sequence, containing both natural and unnatural amino acid building blocks...
January 3, 2017: ACS Combinatorial Science
https://www.readbyqxmd.com/read/28045057/conformational-transition-of-fgfr-kinase-activation-revealed-by-site-specific-unnatural-amino-acid-reporter-and-single-molecule-fret
#8
Louis Perdios, Alan R Lowe, Giorgio Saladino, Tom D Bunney, Nethaji Thiyagarajan, Yuriy Alexandrov, Christopher Dunsby, Paul M W French, Jason W Chin, Francesco Luigi Gervasio, Edward W Tate, Matilda Katan
Protein kinases share significant structural similarity; however, structural features alone are insufficient to explain their diverse functions. Thus, bridging the gap between static structure and function requires a more detailed understanding of their dynamic properties. For example, kinase activation may occur via a switch-like mechanism or by shifting a dynamic equilibrium between inactive and active states. Here, we utilize a combination of FRET and molecular dynamics (MD) simulations to probe the activation mechanism of the kinase domain of Fibroblast Growth Factor Receptor (FGFR)...
January 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28034744/extended-substrate-specificity-and-first-potent-irreversible-inhibitor-activity-based-probe-design-for-zika-virus-ns2b-ns3-protease
#9
Wioletta Rut, Linlin Zhang, Paulina Kasperkiewicz, Marcin Poreba, Rolf Hilgenfeld, Marcin Drąg
Zika virus is spread by Aedes mosquitoes and is linked to acute neurological disorders, especially to microcephaly in newborn children and Guillan-Barré Syndrome. The NS2B-NS3 protease of this virus is responsible for polyprotein processing and therefore considered an attractive drug target. In this study, we have used the Hybrid Combinatorial Substrate Library (HyCoSuL) approach to determine the substrate specificity of ZIKV NS2B-NS3 protease in the P4-P1 positions using natural and a large spectrum of unnatural amino acids...
December 26, 2016: Antiviral Research
https://www.readbyqxmd.com/read/27994761/gossypol-with-hydrophobic-linear-esters-exhibits-enhanced-antitumor-activity-as-an-inhibitor-of-antiapoptotic-proteins
#10
Yuzhi Lu, Shuangchan Wu, Yuan Yue, Si He, Jun Li, Jun Tang, Wei Wang, Hai-Bing Zhou
A series of gossypol Schiff bases that were derived from unnatural linear amino acid methyl esters were identified and found to be much more potent than gossypol and ABT-199 in terms of anticancer activity. This is the first example of gossypol Schiff bases with increased activity. The investigation of the Schiff base side chain of gossypol revealed that the unique anticancer effect was achieved by the introduction of hydrophobic ester groups. The optimized products showed low micromolar pan antitumor activities against NCI-60 tumor cell lines, which is promising for further drug development...
December 8, 2016: ACS Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/27994746/turning-a-substrate-peptide-into-a-potent-inhibitor-for-the-histone-methyltransferase-setd8
#11
Russell A Judge, Haizhong Zhu, Anup K Upadhyay, Pierre M Bodelle, Charles W Hutchins, Maricel Torrent, Violeta L Marin, Wenyu Yu, Masoud Vedadi, Fengling Li, Peter J Brown, William N Pappano, Chaohong Sun, Andrew M Petros
SETD8 is a histone H4-K20 methyltransferase that plays an essential role in the maintenance of genomic integrity during mitosis and in DNA damage repair, making it an intriguing target for cancer research. While some small molecule inhibitors for SETD8 have been reported, the structural binding modes for these inhibitors have not been revealed. Using the complex structure of the substrate peptide bound to SETD8 as a starting point, different natural and unnatural amino acid substitutions were tested, and a potent (Ki 50 nM, IC50 0...
December 8, 2016: ACS Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/27992783/orthogonal-spin-labeling-using-click-chemistry-for-in-vitro-and-in-vivo-applications
#12
Svetlana Kucher, Sergei Korneev, Swati Tyagi, Ronja Apfelbaum, Dina Grohmann, Edward A Lemke, Johann P Klare, Heinz-Jürgen Steinhoff, Daniel Klose
Site-directed spin labeling for EPR- and NMR spectroscopy has mainly been achieved exploiting the specific reactivity of cysteines. For proteins with native cysteines or for in vivo applications, an alternative coupling strategy is required. In these cases click chemistry offers major benefits by providing a fast and highly selective, biocompatible reaction between azide and alkyne groups. Here, we establish click chemistry as a tool to target unnatural amino acids in vitro and in vivo using azide- and alkyne-functionalized spin labels...
December 2, 2016: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/27987323/translation-system-engineering-in-escherichia-coli-enhances-non-canonical-amino-acid-incorporation-into-proteins
#13
Rui Gan, Jessica G Perez, Erik D Carlson, Ioanna Ntai, Farren J Isaacs, Neil L Kelleher, Michael C Jewett
The ability to site-specifically incorporate noncanonical amino acids (ncAAs) into proteins has made possible the study of protein structure and function in fundamentally new ways, as well as the synthesis of unnatural polymers. However, the task of site-specifically incorporating multiple ncAAs into proteins with high purity and yield continues to present a challenge. At the heart of this challenge lies the lower efficiency of engineered orthogonal translation system components compared to their natural counterparts (e...
December 17, 2016: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/27966891/combining-sense-and-nonsense-codon-reassignment-for-site-selective-protein-modification-with-unnatural-amino-acids
#14
Zhenling Cui, Sergey Mureev, Mark E Polinkovsky, Zhong Guo, Zakir Tnimov, Thomas Durek, Alun Jones, Kirill Alexandrov
Incorporation of unnatural amino acids (uAAs) via codon reassignment is a powerful approach for introducing novel chemical and biological properties to synthesized polypeptides. However, the site-selective incorporation of multiple uAAs into polypeptides is hampered by the limited number of reassignable nonsense codons. This challenge is addressed in the current work by developing Escherichia coli in vitro translation system depleted of specific endogenous tRNAs. The translational activity in this system is dependent on the addition of synthetic tRNAs for the chosen sense codon...
December 30, 2016: ACS Synthetic Biology
https://www.readbyqxmd.com/read/27966261/a-bifunctional-amino-acid-enables-both-covalent-chemical-capture-and-isolation-of-in-vivo-protein-protein-interactions
#15
Cassandra M Joiner, Meghan E Breen, James Clayton, Anna K Mapp
In vivo covalent chemical capture by using photoactivatable unnatural amino acids (UAAs) is a powerful tool for the identification of transient protein-protein interactions (PPIs) in their native environment. However, the isolation and characterization of the crosslinked complexes can be challenging. Here, we report the first in vivo incorporation of the bifunctional UAA BPKyne for the capture and direct labeling of crosslinked protein complexes through post-crosslinking functionalization of a bioorthogonal alkyne handle...
January 17, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27951650/incorporation-of-an-unnatural-amino-acid-as-a-domain-specific-fluorescence-probe-in-a-two-domain-protein
#16
Lena K Ries, Franz X Schmid, Philipp A M Schmidpeter
The biophysical analysis of multidomain proteins often is difficult because of overlapping signals from the individual domains. Previously, the fluorescent unnatural amino acid p-cyanophenylalanine has been used to study the folding of small single-domain proteins. Here we extend its use to a two-domain protein to selectively analyze the folding of a specific domain within a multidomain protein.
December 13, 2016: Biochemistry
https://www.readbyqxmd.com/read/27924490/site-specific-fluorescent-labeling-of-argonaute-for-fret-based-bio-assays
#17
Sarah Willkomm, Adrian Zander, Dina Grohmann
Deciphering the molecular mechanisms of eukaryotic Argonaute proteins is crucial for the understanding of RNA interference (RNAi), a posttranscriptional gene silencing process. Fluorescence-based single-molecule studies like single-molecule Förster resonance energy transfer (FRET) between a donor and acceptor dye represent a versatile tool to gain a mechanistic understanding of the structural dynamics of a biomolecular complex. Until today it was not possible to site-specifically introduce fluorophores into eukaryotic Argonaute...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27908261/n-chlorosuccinimide-mediated-oxidative-chlorination-of-thiols-to-n%C3%AE-protected-amino-alkyl-sulfonyl-azides-and-their-utility-in-the-synthesis-of-sulfonyl-triazole-acids
#18
K M Sharnabai, M Krishnamurthy, N R Sagar, L Santhosh, Sureshbabu V Vommina
An efficient oxidative chlorination of thiols to Nα-protected amino alkyl sulfonyl azides is delineated. The reaction involves in situ generation of sulfonyl chloride employing N-chlorosuccinimide and tetrabutylammonium chloride-water in acetonitrile, followed by the reaction with sodium azide. The protocol is simple, straight forward, mild and high yielding. Amino acids with simple as well as bifunctional side chains were used to obtain Nα-protected amino alkyl sulfonyl azides. Further, sulfonyl azides were utilized to synthesize unnatural amino acids via Cu(OAc)2...
November 30, 2016: Protein and Peptide Letters
https://www.readbyqxmd.com/read/27897371/structural-rearrangement-from-oligomer-to-fibril-detected-with-fret-in-a-designed-amphiphilic-peptide
#19
Heng Chi, Timothy A Keiderling
β-Sheet conformation is promoted in peptides with amphiphilic design, and stable β-turn formation is favored with the unnatural amino acid d-Pro followed by a flexible residue such as Gly. A 19-residue peptide (B3) was synthesized with alternating hydrophobic and hydrophilic residues connected by symmetrical d-Pro-Gly and Gly-d-Pro turns. B3 forms an oligomeric aggregate, rich in β-sheet conformation, that reversibly transforms into an unordered structure on heating, as evidenced by its temperature-dependent IR spectra...
January 17, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27894869/utilization-of-alkyne-bioconjugations-to-modulate-protein-function
#20
Johnathan C Maza, Christina A Howard, Megha A Vipani, Christopher R Travis, Douglas D Young
The ability to introduce or modify protein function has widespread application to multiple scientific disciplines. The introduction of unique unnatural amino acids represents an excellent mechanism to incorporate new functionality; however, this approach is limited by ability of the translational machinery to recognize and incorporate the chemical moiety. To overcome this potential limitation, we aimed to exploit the functionality of existing unnatural amino acids to perform bioorthogonal reactions to introduce the desired protein modification, altering its function...
January 1, 2017: Bioorganic & Medicinal Chemistry Letters
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