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Amide protein transfer

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https://www.readbyqxmd.com/read/28516297/subcritical-water-hydrolysis-of-peptides-amino-acid-side-chain-modifications
#1
Thomas Powell, Steve Bowra, Helen J Cooper
Previously we have shown that subcritical water may be used as an alternative to enzymatic digestion in the proteolysis of proteins for bottom-up proteomics. Subcritical water hydrolysis of proteins was shown to result in protein sequence coverages greater than or equal to that obtained following digestion with trypsin; however, the percentage of peptide spectral matches for the samples treated with trypsin were consistently greater than for those treated with subcritical water. This observation suggests that in addition to cleavage of the peptide bond, subcritical water treatment results in other hydrolysis products, possibly due to modifications of amino acid side chains...
May 17, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28474409/amide-proton-transfer-cest-of-the-cervical-spinal-cord-in-multiple-sclerosis-patients-at-3t
#2
Samantha By, Robert L Barry, Alex K Smith, Bailey D Lyttle, Bailey A Box, Francesca R Bagnato, Siddharama Pawate, Seth A Smith
PURPOSE: The ability to evaluate pathological changes in the spinal cord in multiple sclerosis (MS) is limited because T1 - and T2 -w MRI imaging are not sensitive to biochemical changes in vivo. Amide proton transfer (APT) chemical exchange saturation transfer (CEST) can indirectly detect amide protons associated with proteins and peptides, potentially providing more pathological specificity. Here, we implement APT CEST in the cervical spinal cord of healthy and MS cohorts at 3T. METHODS: APT CEST of the cervical spinal cord was obtained in a cohort of 10 controls and 10 MS patients using a novel respiratory correction methodology...
May 5, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28383498/quef-like-a-non-homologous-archaeosine-synthase-from-the-crenarchaeota
#3
Adriana Bon Ramos, Lide Bao, Ben Turner, Valérie de Crécy-Lagard, Dirk Iwata-Reuyl
Archaeosine (G⁺) is a structurally complex modified nucleoside ubiquitous to the Archaea, where it is found in the D-loop of virtually all archaeal transfer RNA (tRNA). Its unique structure, which includes a formamidine group that carries a formal positive charge, and location in the tRNA, led to the proposal that it serves a key role in stabilizing tRNA structure. Although G⁺ is limited to the Archaea, it is structurally related to the bacterial modified nucleoside queuosine, and the two share homologous enzymes for the early steps of their biosynthesis...
April 6, 2017: Biomolecules
https://www.readbyqxmd.com/read/28374993/removable-backbone-modification-method-for-the-chemical-synthesis-of-membrane-proteins
#4
Jia-Bin Li, Shan Tang, Ji-Shen Zheng, Chang-Lin Tian, Lei Liu
Chemical synthesis can produce water-soluble globular proteins bearing specifically designed modifications. These synthetic molecules have been used to study the biological functions of proteins and to improve the pharmacological properties of protein drugs. However, the above advances notwithstanding, membrane proteins (MPs), which comprise 20-30% of all proteins in the proteomes of most eukaryotic cells, remain elusive with regard to chemical synthesis. This difficulty stems from the strong hydrophobic character of MPs, which can cause considerable handling issues during ligation, purification, and characterization steps...
April 4, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28357518/longitudinal-relaxation-optimized-amide-1-h-cest-experiments-for-studying-slow-chemical-exchange-processes-in-fully-protonated-proteins
#5
Tairan Yuwen, Lewis E Kay
Chemical Exchange Saturation Transfer (CEST) experiments are increasingly used to study slow timescale exchange processes in biomolecules. Although (15)N- and (13)C-CEST have been the approaches of choice, the development of spin state selective (1)H-CEST pulse sequences that separate the effects of chemical and dipolar exchange [T. Yuwen, A. Sekhar and L. E. Kay, Angew Chem Int Ed Engl 2016 doi: 10.1002/anie.201610759 (Yuwen et al. 2017)] significantly increases the utility of (1)H-based experiments. Pulse schemes have been described previously for studies of highly deuterated proteins...
March 29, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28345879/vibrational-probes-from-small-molecule-solvatochromism-theory-and-experiments-to-applications-in-complex-systems
#6
Bartosz Błasiak, Casey H Londergan, Lauren J Webb, Minhaeng Cho
The vibrational frequency of a chosen normal mode is one of the most accurately measurable spectroscopic properties of molecules in condensed phases. Accordingly, infrared absorption and Raman scattering spectroscopy have provided valuable information on both distributions and ensemble-average values of molecular vibrational frequencies, and these frequencies are now routinely used to investigate structure, conformation, and even absolute configuration of chemical and biological molecules of interest. Recent advancements in coherent time-domain nonlinear vibrational spectroscopy have allowed the study of heterogeneous distributions of local structures and thermally driven ultrafast fluctuations of vibrational frequencies...
March 27, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28299727/metal-fluorides-tools-for-structural-and-computational-analysis-of-phosphoryl-transfer-enzymes
#7
REVIEW
Yi Jin, Robert W Molt, G Michael Blackburn
The phosphoryl group, PO3(-), is the dynamic structural unit in the biological chemistry of phosphorus. Its transfer from a donor to an acceptor atom, with oxygen much more prevalent than nitrogen, carbon, or sulfur, is at the core of a great majority of enzyme-catalyzed reactions involving phosphate esters, anhydrides, amidates, and phosphorothioates. The serendipitous discovery that the phosphoryl group could be labeled by "nuclear mutation," by substitution of PO3(-) by MgF3(-) or AlF4(-), has underpinned the application of metal fluoride (MF x ) complexes to mimic transition states for enzymatic phosphoryl transfer reactions, with sufficient stability for experimental analysis...
April 2017: Topics in Current Chemistry (Journal)
https://www.readbyqxmd.com/read/28195376/irreversible-cysteine-selective-protein-labeling-employing-modular-electrophilic-tetrafluoroethylation-reagents
#8
Jiří Václavík, Reinhard Zschoche, Iveta Klimánková, Václav Matoušek, Petr Beier, Donald Hilvert, Antonio Togni
Fluoroalkylation reagents based on hypervalent iodine are widely used to transfer fluoroalkyl moieties to various nucleophiles. However, the transferred groups have so far been limited to simple structural motifs. We herein report a reagent featuring a secondary amine that can be converted to amide, sulfonamide, and tertiary amine derivatives in one step. The resulting reagents bear manifold functional groups, many of which would not be compatible with the original synthetic pathway. Exploiting this structural versatility and the known high reactivity toward thiols, the new-generation reagents were used in bioconjugation with an artificial retro-aldolase, containing an exposed cysteine and a reactive catalytic lysine...
May 11, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28194737/regio-selective-intramolecular-hydrogen-deuterium-exchange-in-gas-phase-electron-transfer-dissociation
#9
Yoshitomo Hamuro
Protein backbone amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) typically utilizes enzymatic digestion after the exchange reaction and before MS analysis to improve data resolution. Gas-phase fragmentation of a peptic fragment prior to MS analysis is a promising technique to further increase the resolution. The biggest technical challenge for this method is elimination of intramolecular hydrogen/deuterium exchange (scrambling) in the gas phase. The scrambling obscures the location of deuterium...
February 13, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28154122/measurement-of-lactate-content-and-amide-proton-transfer-values-in-the-basal-ganglia-of-a-neonatal-piglet-hypoxic-ischemic-brain-injury-model-using-mri
#10
Y Zheng, X-M Wang
BACKGROUND AND PURPOSE: As amide proton transfer imaging is sensitive to protein content and intracellular pH, it has been widely used in the nervous system, including brain tumors and stroke. This work aimed to measure the lactate content and amide proton transfer values in the basal ganglia of a neonatal piglet hypoxic-ischemic brain injury model by using MR spectroscopy and amide proton transfer imaging. MATERIALS AND METHODS: From 58 healthy neonatal piglets (3-5 days after birth; weight, 1-1...
February 2, 2017: AJNR. American Journal of Neuroradiology
https://www.readbyqxmd.com/read/28145121/redox-driven-conformational-dynamics-in-a-photosystem-ii-inspired-%C3%AE-hairpin-maquette-determined-through-spectroscopy-and-simulation
#11
Hyea Hwang, Tyler G McCaslin, Anthony Hazel, Cynthia V Pagba, Christina M Nevin, Anna Pavlova, Bridgette A Barry, James C Gumbart
Tyrosine-based radical transfer plays an important role in photosynthesis, respiration, and DNA synthesis. Radical transfer can occur either by electron transfer (ET) or proton coupled electron transfer (PCET), depending on the pH. Reversible conformational changes in the surrounding protein matrix may control reactivity of radical intermediates. De novo designed Peptide A is a synthetic 18 amino-acid β-hairpin, which contains a single tyrosine (Y5) and carries out a kinetically significant PCET reaction between Y5 and a cross-strand histidine (H14)...
April 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28035783/separating-dipolar-and-chemical-exchange-magnetization-transfer-processes-in-1-h-cest
#12
Tairan Yuwen, Ashok Sekhar, Lewis E Kay
An amide (1) H-Chemical Exchange Saturation Transfer (CEST) experiment is presented for studies of conformational exchange in proteins. The approach, exploiting spin-state-selective magnetization transfer, completely suppresses undesired NOE-based dips in CEST profiles so that chemical exchange processes can be studied. The methodology is demonstrated with applications involving proteins that interconvert on the millisecond timescale between major and invisible minor states, and accurate amide (1) H chemical shifts of the minor conformer are obtained in each case...
December 30, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27992380/noninvasive-amide-proton-transfer-magnetic-resonance-imaging-in-evaluating-the-grading-and-cellularity-of-gliomas
#13
Yan Bai, Yusong Lin, Wei Zhang, Lingfei Kong, Lifu Wang, Panli Zuo, Ignacio Vallines, Benjamin Schmitt, Jie Tian, Xiaolei Song, Jinyuan Zhou, Meiyun Wang
Using noninvasive magnetic resonance imaging techniques to accurately evaluate the grading and cellularity of gliomas is beneficial for improving the patient outcomes. Amide proton transfer imaging is a noninvasive molecular magnetic resonance imaging technique based on chemical exchange saturation transfer mechanism that detects endogenous mobile proteins and peptides in biological tissues. Between August 2012 and November 2015, a total number of 44 patients with pathologically proven gliomas were included in this study...
January 24, 2017: Oncotarget
https://www.readbyqxmd.com/read/27912065/phosphoribosylation-of-ubiquitin-promotes-serine-ubiquitination-and-impairs-conventional-ubiquitination
#14
Sagar Bhogaraju, Sissy Kalayil, Yaobin Liu, Florian Bonn, Thomas Colby, Ivan Matic, Ivan Dikic
Conventional ubiquitination involves the ATP-dependent formation of amide bonds between the ubiquitin C terminus and primary amines in substrate proteins. Recently, SdeA, an effector protein of pathogenic Legionella pneumophila, was shown to mediate NAD-dependent and ATP-independent ubiquitin transfer to host proteins. Here, we identify a phosphodiesterase domain in SdeA that efficiently catalyzes phosphoribosylation of ubiquitin on a specific arginine via an ADP-ribose-ubiquitin intermediate. SdeA also catalyzes a chemically and structurally distinct type of substrate ubiquitination by conjugating phosphoribosylated ubiquitin to serine residues of protein substrates via a phosphodiester bond...
December 1, 2016: Cell
https://www.readbyqxmd.com/read/27802648/effective-representation-of-amide-iii-ii-i-and-a-modes-on-local-vibrational-modes-analysis-of-ab-initio-quantum-calculation-results
#15
Seungsoo Hahn
The Hamiltonian matrix for the first excited vibrational states of a protein can be effectively represented by local vibrational modes constituting amide III, II, I, and A modes to simulate various vibrational spectra. Methods for obtaining the Hamiltonian matrix from ab initio quantum calculation results are discussed, where the methods consist of three steps: selection of local vibrational mode coordinates, calculation of a reduced Hessian matrix, and extraction of the Hamiltonian matrix from the Hessian matrix...
October 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27802572/crystal-structure-of-the-archaeosine-synthase-quef-like-insights-into-amidino-transfer-and-trna-recognition-by-the-tunnel-fold
#16
Xianghan Mei, Jonathan Alvarez, Adriana Bon Ramos, Uttamkumar Samanta, Dirk Iwata-Reuyl, Manal A Swairjo
The tunneling-fold (T-fold) structural superfamily has emerged as a versatile protein scaffold of diverse catalytic activities. This is especially evident in the pathways to the 7-deazaguanosine modified nucleosides of tRNA queuosine and archaeosine. Four members of the T-fold superfamily have been confirmed in these pathways and here we report the crystal structure of a fifth enzyme; the recently discovered amidinotransferase QueF-Like (QueF-L), responsible for the final step in the biosynthesis of archaeosine in the D-loop of tRNA in a subset of Crenarchaeota...
January 2017: Proteins
https://www.readbyqxmd.com/read/27762418/local-nh-%C3%AF-interactions-involving-aromatic-residues-of-proteins-influence-of-backbone-conformation-and-%C3%AF-%C3%AF-excitation-on-the-%C3%AF-h-bond-strength-as-revealed-from-studies-of-isolated-model-peptides
#17
Woon Yong Sohn, Valérie Brenner, Eric Gloaguen, Michel Mons
Conformer-selective IR gas phase spectroscopy and high level quantum chemistry methods have been used to characterise the diversity of local NH-π interactions between the π ring of a phenylalanine aromatic residue and the nearby main chain amide groups. The study of model systems shows how the amide NH stretch vibrational features, in the 3410-3460 cm(-1) frequency range, can be used to monitor the strength of these local π H-bonds, which is found to depend on both the backbone conformation and the aromatic side chain orientation...
October 20, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27731335/amide-compound-synthesis-by-adenylation-domain-of-bacillibactin-synthetase
#18
Tomoko Abe, Yoshiteru Hashimoto, Sayaka Sugimoto, Kenta Kobayashi, Takuto Kumano, Michihiko Kobayashi
The adenylation domain of nonribosomal peptide synthetase (NRPS) is responsible for the selective substrate recognition and its activation (as an acyl-O-AMP intermediate) during ATP consumption. DhbE, a stand-alone adenylation domain, acts on an aromatic acid, 2,3-dihydroxybenzoic acid (DHB). This activation is the initial step of the synthesis of bacillibactin that is a high-affinity small-molecule iron chelator also termed siderophore. Subsequently, the activated DHB is transferred and attached covalently to a peptidyl carrier protein domain via a thioester bond...
April 2017: Journal of Antibiotics
https://www.readbyqxmd.com/read/27628768/core-shell-protein-reactive-nanogels-via-a-combination-of-raft-polymerization-and-vinyl-sulfone-postmodification
#19
Nane Vanparijs, Lutz Nuhn, Samantha J Paluck, Maria Kokkinopoulou, Ingo Lieberwirth, Heather D Maynard, Bruno G De Geest
AIM: A promising nanogel vaccine platform was expanded toward antigen conjugation. MATERIALS & METHODS: Block copolymers containing a reactive ester solvophobic block and a PEG-like solvophilic block were synthesized via reversible addition-fragmentation chain-transfer polymerization. Following self-assembly in DMSO, the esters allow for core-crosslinking and hydrophilization by amide bond formation with primary amines. Free thiols were accessed at the polymer chain ends through aminolysis of the reversible addition-fragmentation chain-transfer groups, and into the nanogel core by reactive ester conversion with cysteamine...
October 2016: Nanomedicine
https://www.readbyqxmd.com/read/27616165/fucoidan-mimetic-glycopolymers-as-tools-for-studying-molecular-and-cellular-responses-in-human-blood-platelets
#20
Mattias Tengdelius, Caroline Kardeby, Knut Fälker, May Griffith, Peter Påhlsson, Peter Konradsson, Magnus Grenegård
The marine sulfated polysaccharide fucoidan displays superior ability to induce platelet aggregation compared to other sulfated polysaccharides. As such, it is an attractive tool for studying molecular and cellular responses in activated platelets. The heterogeneous structure, however, poses a problem in such applications. This study describes the synthesis of sulfated α-l-fucoside-pendant poly(methacryl amides) with homogeneous structures. By using both thiol-mediated chain transfer and reversible addition-fragmentation chain transfer polymerization techniques, glycopolymers with different chain lengths are obtained...
September 12, 2016: Macromolecular Bioscience
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