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Amide protein transfer

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https://www.readbyqxmd.com/read/28823107/fluorescent-labeling-of-protein-using-blue-emitting-8-amino-bodipy-derivatives
#1
Dokyoung Kim, Donghee Ma, Muwoong Kim, Yuna Jung, Na Hee Kim, Chiho Lee, Seo Won Cho, Sungnam Park, Youngbuhm Huh, Junyang Jung, Kyo Han Ahn
8-Amino-BODIPY (boron-dipyrromethane) dyes show bright blue fluorescence. Disclosed here are synthesis and characterization of the photophysical properties of a series of functionalized 8-Amino-BODIPY (BP1-4) for protein labeling. The compact structure and solvent-insensitive absorption property of the dye are desirable features for protein labeling. For the model protein, bovine serum albumin (BSA), the labeling proceeds under mild condition via amide bond formation or thiol-ene conjugation with maintaining the bright blue fluorescence...
August 19, 2017: Journal of Fluorescence
https://www.readbyqxmd.com/read/28792111/solid-state-nmr-h-n-c-h-and-h-n-c-c-3d-4d-correlation-experiments-for-resonance-assignment-of-large-proteins
#2
Hugo Fraga, Charles-Adrien Arnaud, Diego F Gauto, Maxime J C Audin, Vilius Kurauskas, Pavel Macek, Carsten Krichel, Jia-Ying Guan, Jérôme Boisbouvier, Remco Sprangers, Cécile Breyton, Paul Schanda
Solid-state NMR can provide insight into protein structure and dynamics at the atomic level without inherent protein size limitations. However, a major hurdle to studying large proteins by solid-state NMR spectroscopy is related to spectral complexity and resonance overlap, which increase with molecular weight and severely hamper the assignment process. Here we show the use of two sets of experiments that expand the tool kit of 1H-detected assignment approaches, and which correlate a given amide pair either to the two adjacent CO-CA pairs (4D hCOCANH/hCOCAcoNH), or to the amide 1H of the neighboring residue (3D HcocaNH/HcacoNH, which can be extended to up to 5D)...
August 9, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28763201/tracking-reactive-water-and-hydrogen-bonding-networks-in-photosynthetic-oxygen-evolution
#3
Bridgette A Barry, Udita Brahmachari, Zhanjun Guo
In oxygenic photosynthesis, photosystem II (PSII) converts water to molecular oxygen through four photodriven oxidation events at a Mn4CaO5 cluster. A tyrosine, YZ (Y161 in the D1 polypeptide), transfers oxidizing equivalents from an oxidized, primary chlorophyll donor to the metal center. Calcium or its analogue, strontium, is required for activity. The Mn4CaO5 cluster and YZ are predicted to be hydrogen bonded in a water-containing network, which involves amide carbonyl groups, amino acid side chains, and water...
August 1, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28722742/characterization-of-hydrogen-bonding-motifs-in-proteins-hydrogen-elimination-monitoring-by-ultraviolet-photodissociation-mass-spectrometry
#4
Lindsay J Morrison, Wenrui Chai, Jake A Rosenberg, Graeme Henkelman, Jennifer S Brodbelt
Determination of structure and folding of certain classes of proteins remains intractable by conventional structural characterization strategies and has spurred the development of alternative methodologies. Mass spectrometry-based approaches have a unique capacity to differentiate protein heterogeneity due to the ability to discriminate populations, whether minor or major, featuring modifications or complexation with non-covalent ligands on the basis of m/z. Cleavage of the peptide backbone can be further utilized to obtain residue-specific structural information...
August 2, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28639301/improving-the-detection-sensitivity-of-ph-weighted-amide-proton-transfer-mri-in-acute-stroke-patients-using-extrapolated-semisolid-magnetization-transfer-reference-signals
#5
Hye-Young Heo, Yi Zhang, Tina M Burton, Shanshan Jiang, Yansong Zhao, Peter C M van Zijl, Richard Leigh, Jinyuan Zhou
PURPOSE: To quantify amide protein transfer (APT) effects in acidic ischemic lesions and assess the spatial-temporal relationship among diffusion, perfusion, and pH deficits in acute stroke patients. METHODS: Thirty acute stroke patients were scanned at 3 T. Quantitative APT (APT(#) ) effects in acidic ischemic lesions were measured using an extrapolated semisolid magnetization transfer reference signal technique and compared with commonly used MTRasym (3.5ppm) or APT-weighted parameters...
September 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28613875/modeling-of-polarization-transfer-kinetics-in-protein-hydration-using-hyperpolarized-water
#6
Jihyun Kim, Mengxiao Liu, Christian Hilty
Water-protein interactions play a central role in protein structure, dynamics, and function. These interactions, traditionally, have been studied using nuclear magnetic resonance (NMR) by measuring chemical exchange and nuclear Overhauser effect (NOE). Polarization transferred from hyperpolarized water can result in substantial transient signal enhancements of protein resonances due to these processes. Here, we use dissolution dynamic nuclear polarization and flow-NMR for measuring the pH dependence of transferred signals to the protein trypsin...
June 29, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28589218/h-n-n-c-%C3%AE-and-c-%C3%AE-assignments-of-the-two-periplasmic-domains-of-neisseria-meningitidis-dsbd
#7
Roxanne P Smith, Biswaranjan Mohanty, Martin L Williams, Martin J Scanlon, Begoña Heras
DsbD is a disulfide bond reductase present in the inner membrane of many Gamma-Proteobacteria. In the human pathogen Neisseria meningitidis, DsbD is required for viability and represents a potential target for the development of antibiotics. Here we report the chemical shift assignments (H(N), N, C(α) and C(β)) for the reduced and oxidized forms of the two periplasmic domains of N. meningitidis DsbD, n-NmDsbD and c-NmDsbD. The backbone amide resonances in all four forms were completely assigned, and the secondary structures for the core regions of the proteins were calculated using (13)C(αβ) shifts...
June 6, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28542634/crystallographic-characterization-of-the-high-potential-iron-sulfur-protein-in-the-oxidized-state-at-0-8-%C3%A3-resolution
#8
Hiraku Ohno, Kazuki Takeda, Satomi Niwa, Tomotaka Tsujinaka, Yuya Hanazono, Yu Hirano, Kunio Miki
High-potential iron-sulfur protein (HiPIP) is a soluble electron carrier protein of photosynthetic bacteria with an Fe4S4 cluster. Although structural changes accompanying the electron transfer are important for understanding of the functional mechanism, the changes have not been clarified in sufficient detail. We previously reported the high-resolution crystal structures of HiPIP from a thermophilic purple bacterium Thermochromatium tepidum in the reduced state. In order to perform a detailed comparison between the structures in different redox states, the oxidized structure should also be revealed at high resolution...
2017: PloS One
https://www.readbyqxmd.com/read/28534162/applying-protein-based-amide-proton-transfer-mr-imaging-to-distinguish-solitary-brain-metastases-from-glioblastoma
#9
Hao Yu, Huiling Lou, Tianyu Zou, Xianlong Wang, Shanshan Jiang, Zhongqing Huang, Yongxing Du, Chunxiu Jiang, Ling Ma, Jianbin Zhu, Wen He, Qihong Rui, Jianyuan Zhou, Zhibo Wen
OBJECTIVES: To determine the utility of amide proton transfer-weighted (APTw) MR imaging in distinguishing solitary brain metastases (SBMs) from glioblastomas (GBMs). METHODS: Forty-five patients with SBMs and 43 patients with GBMs underwent conventional and APT-weighted sequences before clinical intervention. The APTw parameters and relative APTw (rAPTw) parameters in the tumour core and the peritumoral brain zone (PBZ) were obtained and compared between SBMs and GBMs...
May 22, 2017: European Radiology
https://www.readbyqxmd.com/read/28516297/subcritical-water-hydrolysis-of-peptides-amino-acid-side-chain-modifications
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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