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https://www.readbyqxmd.com/read/28186733/utilizing-selenocysteine-for-expressed-protein-ligation-and-bioconjugations
#1
Jun Liu, Qingqing Chen, Sharon Rozovsky
Employing selenocysteine-containing protein fragments to form the amide bond between respective protein fragments significantly extends current capabilities of the widely used protein engineering method, expressed protein ligation. Selenocysteine-mediated ligation is noteworthy for its high yield and efficiency. However, it has so far been restricted to solid-phase synthesized seleno-peptides and thus constrained by where the selenocysteine can be positioned. Here we employ heterologously expressed seleno-fragments to overcome the placement and size restrictions in selenocysteine-mediated chemical ligation...
February 10, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28185915/targeting-kinase-signaling-pathways-with-constrained-peptide-scaffolds
#2
REVIEW
Laura E Hanold, Melody D Fulton, Eileen J Kennedy
Kinases are amongst the largest families in the human proteome and serve as critical mediators of a myriad of cell signaling pathways. Since altered kinase activity is implicated in a variety of pathological diseases, kinases have become a prominent class of proteins for targeted inhibition. Although numerous small molecule and antibody-based inhibitors have already received clinical approval, several challenges may still exist with these strategies including resistance, target selection, inhibitor potency and in vivo activity profiles...
February 6, 2017: Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/28184219/identification-of-bacterial-surface-antigens-by-screening-peptide-phage-libraries-using-whole-bacteria-cell-purified-antisera
#3
Yun-Fei Hu, Dun Zhao, Xing-Long Yu, Yu-Li Hu, Run-Cheng Li, Meng Ge, Tian-Qi Xu, Xiao-Bo Liu, Hua-Yuan Liao
Bacterial surface proteins can be good vaccine candidates. In the present study, we used polyclonal antibodies purified with intact Erysipelothrix rhusiopthiae to screen phage-displayed random dodecapeptide and loop-constrained heptapeptide libraries, which led to the identification of mimotopes. Homology search of the mimotope sequences against E. rhusiopthiae-encoded ORF sequences revealed 14 new antigens that may localize on the surface of E. rhusiopthiae. When these putative surface proteins were used to immunize mice, 9/11 antigens induced protective immunity...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28167892/selection-of-small-synthetic-antimicrobial-peptides-inhibiting-xanthomonas-citri-subsp-citri-causing-citrus-canker
#4
Jeahyuk Choi, Euiho Park, Se-Weon Lee, Jae-Wook Hyun, Kwang-Hyun Baek
Citrus canker disease decreases the fruit quality and yield significantly, furthermore, emerging of streptomycin-resistant pathogens threatens the citrus industry seriously because of a lack of proper control agents. Small synthetic antimicrobial peptides (AMPs) could be a promising alternative. Fourteen hexapeptides were selected by using positional scanning of synthetic peptide combinatorial libraries. Each hexapeptide showed different antimicrobial spectrum against Bacillus, Pseudomonas, Xanthomonas, and Candida species...
February 2017: Plant Pathology Journal
https://www.readbyqxmd.com/read/28165218/perfluoro-tert-butyl-homoserine-is-a-helix-promoting-highly-fluorinated-nmr-sensitive-aliphatic-amino-acid-detection-of-the-estrogen-receptor%C3%A2-coactivator-protein-protein-interaction-by-19-f-nmr
#5
Caitlin M Tressler, Neal J Zondlo
Highly fluorinated amino acids can stabilize proteins and complexes with proteins, via enhanced hydrophobicity, and provide novel methods for identification of specific molecular events in complex solutions, via selective detection by (19)F NMR and the absence of native (19)F signals in biological contexts. However, the potential applications of (19)F NMR in probing biological processes are limited both by the strong propensities of most highly fluorinated amino acids for the extended conformation and by the relatively modest sensitivity of NMR spectroscopy, which typically constrains measurements to mid-micromolar concentrations...
February 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/28164758/angiotensin-peptides-as-at2-receptor-agonists
#6
Mathias Hallberg, Jonas Sävmarker, Anders Hallberg
In 2004, the first nonpeptide selective angiotensin II type 2 receptor (AT2R) agonist was reported. This nonpeptide (C21), which, exerts anti-inflammatory and antifibrotic actions in vivo, has been extensively explored and is currently in clinical trials. Subsequently, a large number of related drug-like AT2R agonists have been disclosed. Reviews that summarize known structure-activity relationships (SAR) of nonpeptide AT2R agonists have recently appeared in the literature; however, very few reviews discuss the role of angiotensin peptides as AT2R agonists...
February 3, 2017: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/28146347/highly-constrained-bicyclic-scaffolds-for-the-discovery-of-protease-stable-peptides-via-mrna-display
#7
David E Hacker, Jan Hoinka, Emil S Iqbal, Teresa M Przytycka, Matthew C T Hartman
Highly constrained peptides such as the knotted peptide natural products are promising medicinal agents because of their impressive biostability and potent activity. Yet, libraries of highly constrained peptides are challenging to prepare. Here, we present a method which utilizes two robust, orthogonal chemical steps to create highly constrained bicyclic peptide libraries. This technology was optimized to be compatible with in vitro selections by mRNA display. We performed side-by-side monocyclic and bicyclic selections against a model protein (streptavidin)...
February 1, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28137809/a-short-double-stapled-peptide-inhibits-respiratory-syncytial-virus-entry-and-spreading
#8
Vanessa Gaillard, Marie Galloux, Dominique Garcin, Jean-François Eléouët, Ronan Le Goffic, Thibaut Larcher, Marie-Anne Rameix-Welti, Abdelhak Boukadiri, Julien Héritier, Jean-Manuel Segura, Elodie Baechler, Miriam Arrell, Geneviève Mottet-Osman, Origène Nyanguile
Synthetic peptides derived from the heptad repeat (HR) of fusion (F) proteins can be used as dominant negative inhibitors to inhibit the fusion mechanism of class I viral F proteins. Here, we have performed a stapled peptide scan across the HR2 domain of the RSV F protein with the aim to identify a minimal domain capable of disrupting the formation of the post fusion six helix bundle required for viral cell entry. Constraining the peptides with a single staple was not sufficient to inhibit RSV infection. However, the insertion of double staples led to the identification of novel short stapled peptides, which display nanomolar potency in HEp-2 cells, and are exceptionally robust to proteolytic degradation...
January 30, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28135077/mechanistic-understanding-of-lanthipeptide-biosynthetic-enzymes
#9
Lindsay M Repka, Jonathan R Chekan, Satish K Nair, Wilfred A van der Donk
Lanthipeptides are ribosomally synthesized and post-translationally modified peptides (RiPPs) that display a wide variety of biological activities, from antimicrobial to antiallodynic. Lanthipeptides that display antimicrobial activity are called lantibiotics. The post-translational modification reactions of lanthipeptides include dehydration of Ser and Thr residues to dehydroalanine and dehydrobutyrine, a transformation that is carried out in three unique ways in different classes of lanthipeptides. In a cyclization process, Cys residues then attack the dehydrated residues to generate the lanthionine and methyllanthionine thioether cross-linked amino acids from which lanthipeptides derive their name...
January 30, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28107435/peptide-targeted-by-human-antibodies-associated-with-hiv-vaccine-associated-protection-assumes-a-dynamic-%C3%AE-helical-structure
#10
Mohammed S Aiyegbo, Evgeny Shmelkov, Lorenzo Dominguez, Michael Goger, Shibani Battacharya, Allan C deCamp, Peter B Gilbert, Phillip W Berman, Timothy Cardozo
The only evidence of vaccine-induced protection from HIV acquisition in humans was obtained in the RV144 HIV vaccine clinical trial. One immune correlate of risk in RV144 was observed to be higher titers of vaccine-induced antibodies (Abs) reacting with a 23-mer non-glycosylated peptide with the same amino acid sequence as a segment in the second variable (V2) loop of the MN strain of HIV. We used NMR to analyze the dynamic 3D structure of this peptide. Distance restraints between spatially proximate inter-residue protons were calculated from NOE cross peak intensities and used to constrain a thorough search of all possible conformations of the peptide...
2017: PloS One
https://www.readbyqxmd.com/read/28105269/electrophilic-helical-peptides-that-bond-covalently-irreversibly-and-selectively-in-a-protein-protein-interaction-site
#11
Aline Dantas de Araujo, Junxian Lim, Andrew C Good, Renato T Skerlj, David P Fairlie
Protein-protein interactions mediate most physiological and disease processes. Helix-constrained peptides potently mimic or inhibit these interactions by making multiple contacts over large surface areas. However, despite high affinities, they typically have short lifetimes bound to the protein. Here we insert both a helix-inducing constraint and an adjacent electrophile into the native peptide ligand BIM to target the oncogenic protein Bcl2A1. The modified BIM peptide bonds covalently and irreversibly to one cysteine within the helix-binding groove of Bcl2A1, but not to two other exposed cysteines on its surface, and shows no covalent bonding to other Bcl2 proteins...
January 12, 2017: ACS Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28059508/non-classical-size-dependence-of-permeation-defines-bounds-for-passive-adsorption-of-large-drug-molecules
#12
Cameron R Pye, William M Hewitt, Joshua A Schwochert, Terra D Haddad, Chad E Townsend, Lyns Etienne, Yongtong Lao, Chris Limberakis, Akihiro Furukawa, Alan M Mathiowetz, David A Price, Spiros Liras, R Scott Lokey
There is a growing number of intracellular protein-protein interactions (PPI's) with potential therapeutic importance that demand larger ligands than those that neatly fit into most common criteria for "drug-likeness". Macrocyclic peptides pro-vide the large surface area required to inhibit PPIs and, in principle, avoid many of the pitfalls associated with peptides, including low stability and membrane permeability. However, the design of passively cell-permeable molecules in this space remains a great challenge due to the poorly understood roles of molecular size and lipophilicity in determining pas-sive membrane permeability above MW ~500...
January 6, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28054413/the-importance-of-being-aib-aggregation-and-self-assembly-studies-on-conformationally-constrained-oligopeptides
#13
Mariano Venanzi, Emanuela Gatto, Fernando Formaggio, Claudio Toniolo
The role of the conformationally constrained α-aminoisobutyric acid (Aib) residue in the aggregation and self-assembly properties of oligopeptides is discussed, critically reviewing our recent work in the field. In this connection, three significant case studies are presented: (i) aggregation propensity of Aib homo-oligopeptides of different length; (ii) perturbation of the conformational and aggregation properties of Ala-based pentapeptides by a single Aib versus Ala substitution; and (iii) build up of self-assembled monolayers formed by Aib homo-hexapeptide building blocks...
January 5, 2017: Journal of Peptide Science: An Official Publication of the European Peptide Society
https://www.readbyqxmd.com/read/28035784/enhancing-the-cell-permeability-and-metabolic-stability-of-peptidyl-drugs-by-reversible-bicyclization
#14
Ziqing Qian, Curran A Rhodes, Lucas C McCroskey, Jin Wen, George Appiah-Kubi, David J Wang, Denis C Guttridge, Dehua Pei
Therapeutic applications of peptides are currently limited by their proteolytic instability and impermeability to the cell membrane. A general, reversible bicyclization strategy is now reported to increase both the proteolytic stability and cell permeability of peptidyl drugs. A peptide drug is fused with a short cell-penetrating motif and converted into a conformationally constrained bicyclic structure through the formation of a pair of disulfide bonds. The resulting bicyclic peptide has greatly enhanced proteolytic stability as well as cell-permeability...
February 1, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28004737/investigating-the-neuroprotective-effects-of-turmeric-extract-structural-interactions-of-%C3%AE-amyloid-peptide-with-single-curcuminoids
#15
Rosario Randino, Manuela Grimaldi, Marco Persico, Augusta De Santis, Elena Cini, Walter Cabri, Antonella Riva, Gerardino D'Errico, Caterina Fattorusso, Anna Maria D'Ursi, Manuela Rodriquez
A broad biophysical analysis was performed to investigate the molecular basis of the neuroprotective action of Curcuma longa extracts in Alzheimer's disease. By combining circular dichroism and electron paramagnetic resonance experiments with molecular modeling calculations, the minor components of Curcuma longa extracts, such as demethoxycurcumin (2, DMC), bisdemethoxycurcumin (3, BDMC) and cyclocurcumin (4, CYC), were analyzed in a membrane environment mimicking the phospholipid bilayer. Our study provides the first evidence on the relative role of single curcuminoids interacting with Aβ-peptide...
December 22, 2016: Scientific Reports
https://www.readbyqxmd.com/read/28004569/strategies-for-the-activation-and-release-of-the-membranolytic-peptide-melittin-from-liposomes-using-endosomal-ph-as-a-trigger
#16
E Oude Blenke, M Sleszynska, M J W Evers, G Storm, N I Martin, E Mastrobattista
Endosomolytic peptides are often coupled to drug delivery systems to enhance endosomal escape, which is crucial for the delivery of macromolecular drugs that are vulnerable to degradation in the endolysosomal pathway. Melittin is a 26 amino acid peptide derived from bee venom that has a very high membranolytic activity. However, such lytic peptides also impose a significant safety risk when applied in vivo as they often have similar activity against red blood cells and other nontarget cell membranes. Our aim is to control the membrane-disrupting capacity of these peptides in time and space by physically constraining them to a nanocarrier surface in such a way that they only become activated when delivered inside acidic endosomes...
January 13, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28000361/cyclopropane-based-peptidomimetics-mimicking-wide-ranging-secondary-structures-of-peptides-conformational-analysis-and-their-use-in-rational-ligand-optimization
#17
Akira Mizuno, Tomoshi Kameda, Tomoki Kuwahara, Hideyuki Endoh, Yoshihiko Ito, Shizuo Yamada, Kimiko Hasegawa, Akihito Yamano, Mizuki Watanabe, Mitsuhiro Arisawa, Satoshi Shuto
Detailed conformational analyses of our previously reported cyclopropane-based peptidomimetics and conformational analysis-driven ligand optimization are described. Computational calculations and X-ray crystallography showed that the characteristic features of cyclopropane function effectively to constrain the molecular conformation in a three-dimensionally diverse manner. Subsequent principal component analysis revealed that the diversity covers the broad chemical space filled by peptide secondary structures in terms of both main-chain and side-chain conformations...
December 21, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27995801/molecular-dynamics-study-of-nitrogen-pyramidalized-bicyclic-%C3%AE-proline-oligomers-length-dependent-convergence-to-organized-structures
#18
Yuko Otani, Satoshi Watanabe, Tomohiko Ohwada, Akio Kitao
In this study, the solution structures of the homooligomers of a conformationally constrained bicyclic proline-type β-amino acid were studied by means of molecular dynamics (MD) calculations in explicit methanol and water using the umbrella sampling method. The ratio of trans-amide and cis-amide was estimated by NMR and the rotational barrier of the amide of acetylated bicyclic amino acid monomer was estimated by two-dimensional (2D) exchange spectroscopy (EXSY) or line-shape analysis. A bias potential was introduced with respect to the amide torsion angle ω to enhance conformational exchange including isomerization of amide bonds by lowering the rotation energy barrier...
December 20, 2016: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/27974608/rapid-synthesis-of-cyclic-oligomeric-depsipeptides-with-positional-stereochemical-and-macrocycle-size-distribution-control
#19
Suzanne M Batiste, Jeffrey N Johnston
Macrocyclic small molecules are attractive tools in the development of sensors, new materials, and therapeutics. Within early-stage drug discovery, they are increasingly sought for their potential to interact with broad surfaces of peptidic receptors rather than within their narrow folds and pockets. Cyclization of linear small molecule precursors is a straightforward strategy to constrain conformationally mobile motifs, but forging a macrocycle bond typically becomes more difficult at larger ring sizes. We report the development of a general approach to discrete collections of oligomeric macrocyclic depsipeptides using an oligomerization/macrocyclization process governed by a series of Mitsunobu reactions of hydroxy acid monomers...
December 27, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27964762/new-tools-to-analyze-overlapping-coding-regions
#20
Amir H Bayegan, Juan Antonio Garcia-Martin, Peter Clote
BACKGROUND: Retroviruses transcribe messenger RNA for the overlapping Gag and Gag-Pol polyproteins, by using a programmed -1 ribosomal frameshift which requires a slippery sequence and an immediate downstream stem-loop secondary structure, together called frameshift stimulating signal (FSS). It follows that the molecular evolution of this genomic region of HIV-1 is highly constrained, since the retroviral genome must contain a slippery sequence (sequence constraint), code appropriate peptides in reading frames 0 and 1 (coding requirements), and form a thermodynamically stable stem-loop secondary structure (structure requirement)...
December 13, 2016: BMC Bioinformatics
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