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Amide proton transfer

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https://www.readbyqxmd.com/read/28808429/fast-reliable-3d-amide-proton-transfer-imaging-of-brain-tumors-at-3t-with-variably-accelerated-sensitivity-encoding-vsense
#1
Yi Zhang, Hye-Young Heo, Shanshan Jiang, Paul A Bottomley, Jinyuan Zhou
The clinical use of amide proton transfer (APT) imaging is hindered by long scan times. Accuracy generally limits the use of conventional sensitivity encoding (SENSE) methods in APT, to an acceleration factor of 2. A novel variably-accelerated sensitivity encoding (vSENSE) method can provide more accurate results and therefore substantially higher overall acceleration factors than conventional SENSE. Here, vSENSE is further developed to eliminate the requirement that one fully-sampled APT frame be acquired, and extended to three dimensions (3D)...
April 2017: Proceedings of the International Society for Magnetic Resonance in Medicine ... Scientific Meeting and Exhibition
https://www.readbyqxmd.com/read/28799280/amide-proton-transfer-weighted-imaging-to-differentiate-malignant-from-benign-pulmonary-lesions-comparison-with-diffusion-weighted-imaging-and-fdg-pet-ct
#2
Yoshiharu Ohno, Yuji Kishida, Shinichiro Seki, Masao Yui, Mitsue Miyazaki, Hisanobu Koyama, Takeshi Yoshikawa
PURPOSE: To compare the capability of amide proton transfer-weighted (APTw) imaging, diffusion-weighted imaging (DWI), and FDG-PET/CT for the differentiation of malignant from benign pulmonary nodules. MATERIALS AND METHODS: In all, 82 consecutive patients with pulmonary nodules underwent APTw imaging and DWI with a 3T system, and FDG-PET/CT. All nodules were divided as either malignant (n = 49) or benign (n = 39) groups based on pathological and follow-up examinations...
August 11, 2017: Journal of Magnetic Resonance Imaging: JMRI
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
#3
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
#4
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/28750319/theoretically-obtained-insight-into-the-mechanism-and-dioxetanone-species-responsible-for-the-singlet-chemiexcitation-of-coelenterazine
#5
Chun-Gang Min, Paulo J O Ferreira, Luís Pinto da Silva
Coelenterazine is a widespread bioluminescent substrate for a diverse set of marine species. Moreover, its imidazopyrazinone core is present in eight phyla of bioluminescent organisms. Given their very attractive intrinsic properties, these bioluminescent systems have been used in bioimaging, photodynamic therapy of cancer, as gene reporter and in sensing applications, among others. While it is known that bioluminescence results from the thermolysis of high-energy dioxetanones, the mechanism and dioxetanone species responsible for the singlet chemiexcitation of Coelenterazine are not fully understood...
July 20, 2017: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/28745750/asymmetric-alkylation-of-remote-c-sp-3-h-bonds-by-combining-proton-coupled-electron-transfer-with-chiral-lewis-acid-catalysis
#6
Wei Yuan, Zijun Zhou, Lei Gong, Eric Meggers
The catalytic asymmetric alkylation of the remote, unactivated δ-position of N-alkyl amides was enabled by the combination of visible-light-induced proton-coupled electron transfer, 1,5-hydrogen atom transfer, and chiral Lewis acid catalysis in up to 82% yield and up to 97% ee.
August 8, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28739967/reactions-of-biologically-inspired-hydride-sources-with-b-c6f5-3
#7
Lewis C Wilkins, Nicolò Santi, Louis Y P Luk, Rebecca L Melen
The combination of 1-benzyl-1,4-dihydropyridines with the strong Lewis acid, B(C6F5)3, generates a stable pyridinium borohydride species in high yields (94%) in as little as 10 min. This use of biologically inspired hydride sources further builds on the recent work of new hydride donors in the formation of borohydrides. When functionalizing the dihydropyridine with an amide or carboxylic acid moiety, a disproportionation reaction composed of a series of protonation/reduction steps is observed upon the addition of B(C6F5)3 As a result, one equivalent of dihydropyridine undergoes net hydrogenation, whereas the other is dehydrogenated yielding the pyridinium counterpart in a transfer hydrogenation-type mechanism...
August 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28733991/ph-sensitive-amide-proton-transfer-effect-dominates-the-magnetization-transfer-asymmetry-contrast-during-acute-ischemia-quantification-of-multipool-contribution-to-in-vivo-cest-mri
#8
Yin Wu, Iris Yuwen Zhou, Dongshuang Lu, Emiri Manderville, Eng H Lo, Hairong Zheng, Phillip Zhe Sun
PURPOSE: To determine the origins of in vivo magnetization transfer asymmetry contrast during acute ischemic stroke, particularly in the diffusion lesion, perfusion lesion, and their mismatch using a middle cerebral artery occlusion rat model of acute stroke. METHODS: Adult male Wistar rats underwent multiparametric MRI of diffusion, perfusion, T1 , and amide proton transfer (APT) imaging at 4.7 T following a middle cerebral artery occlusion procedure. A multipool Lorentzian model, including the nuclear Overhauser effect, magnetization transfer, direct water saturation, amine and amide chemical exchange saturation transfer effects, was applied for Z-spectrum fitting to determine the sources of in vivo magnetization transfer asymmetry following acute stroke...
July 21, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28729292/amide-proton-transfer-imaging-allows-detection-of-glioma-grades-and-tumor-proliferation-comparison-with-ki-67-expression-and-proton-mr-spectroscopy-imaging
#9
C Su, C Liu, L Zhao, J Jiang, J Zhang, S Li, W Zhu, J Wang
BACKGROUND AND PURPOSE: Prognosis in glioma depends strongly on tumor grade and proliferation. In this prospective study of patients with untreated primary cerebral gliomas, we investigated whether amide proton transfer-weighted imaging could reveal tumor proliferation and reliably distinguish low-grade from high-grade gliomas compared with Ki-67 expression and proton MR spectroscopy imaging. MATERIALS AND METHODS: This study included 42 patients with low-grade (n = 28) or high-grade (n = 14) glioma, all of whom underwent conventional MR imaging, proton MR spectroscopy imaging, and amide proton transfer-weighted imaging on the same 3T scanner within 2 weeks before surgery...
July 20, 2017: AJNR. American Journal of Neuroradiology
https://www.readbyqxmd.com/read/28717802/a-computational-study-on-the-mechanism-of-ynamide-mediated-amide-bond-formation-from-carboxylic-acids-and-amines
#10
Song-Lin Zhang, Hai-Xing Wan, Zhu-Qin Deng
This paper reports a computational study elucidating the reaction mechanism for ynamide-mediated amide bond formation from carboxylic acids and amines. The mechanisms have been studied in detail for ynamide hydrocarboxylation and the subsequent aminolysis of the resulting adduct by an amine. Ynamide hydrocarboxylation is kinetically favorable and thermodynamically irreversible, resulting in the formation of a key low-lying intermediate CP1 featuring geminal vinylic acyloxy and sulfonamide groups. The aminolysis of CP1 by the amine is proposed to be catalyzed by the carboxylic acid itself that imparts favourable bifunctional effects...
August 2, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28714279/predicting-idh-mutation-status-in-grade-ii-gliomas-using-amide-proton-transfer-weighted-aptw-mri
#11
Shanshan Jiang, Tianyu Zou, Charles G Eberhart, Maria A V Villalobos, Hye-Young Heo, Yi Zhang, Yu Wang, Xianlong Wang, Hao Yu, Yongxing Du, Peter C M van Zijl, Zhibo Wen, Jinyuan Zhou
PURPOSE: To assess the amide proton transfer-weighted (APTw) MRI features of isocitrate dehydrogenase (IDH)-wildtype and IDH-mutant grade II gliomas and to test the hypothesis that the APTw signal is a surrogate imaging marker for identifying IDH mutation status preoperatively. METHODS: Twenty-seven patients with pathologically confirmed low-grade glioma, who were previously scanned at 3T, were retrospectively analyzed. The Mann-Whitney test was used to evaluate relationships between APTw intensities for IDH-mutant and IDH-wildtype groups, and receiver operator characteristic (ROC) analysis was used to assess the diagnostic performance of APTw...
September 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28708326/loss-of-benzaldehyde-in-the-fragmentation-of-protonated-benzoylamines-benzoyl-cation-as-a-hydride-acceptor-in-the-gas-phase
#12
Yunfeng Chai, Yunlong Shao, Lu Wang, Lin Wang
In electrospray ionization tandem mass spectrometry of protonated 1-benzoylamines (1-benzoylpiperadine, 1-benzoylmorpholine, and 1-benzoyl-4-methylpiperazine), the dominant fragmentation pathway was amide bond cleavage to form benzoyl cation and neutral amine. Meanwhile, in their fragmentations, an interesting loss of benzaldehyde (106 Da) was observed and identified to derive from hydride transfer reaction between the benzoyl cation and amine. A stepwise mechanism for loss of 106 Da (benzene and CO) could be excluded with the aid of deuterium labeling experiment...
July 14, 2017: Journal of Mass Spectrometry: JMS
https://www.readbyqxmd.com/read/28707688/probing-the-excited-state-chemical-shifts-and-exchange-parameters-by-nitrogen-decoupled-amide-proton-chemical-exchange-saturation-transfer-hn-dec-cest
#13
Qinglin Wu, Benjamin A Fenton, Jessica L Wojtaszek, Pei Zhou
CEST-NMR spectroscopy is a powerful tool for probing the conformational dynamics of macromolecules. We present a HN(dec)-CEST experiment that simplifies the relaxation matrix, reduces fitting parameters, and enhances signal resolution. Importantly, fitting of HN(dec)-CEST profiles enables robust extraction of exchange rates as well as excited-state chemical shifts and populations.
July 27, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28704644/amide-proton-transfer-weighted-magnetic-resonance-image-guided-stereotactic-biopsy-in-patients-with-newly-diagnosed-gliomas
#14
Shanshan Jiang, Charles G Eberhart, Yi Zhang, Hye-Young Heo, Zhibo Wen, Lindsay Blair, Huamin Qin, Michael Lim, Alfredo Quinones-Hinojosa, Jon D Weingart, Peter B Barker, Martin G Pomper, John Laterra, Peter C M van Zijl, Jaishri O Blakeley, Jinyuan Zhou
PURPOSE: Pathological assessment using World Health Organization (WHO) criteria is the gold standard for diagnosis of gliomas. However, the accuracy of diagnosis is limited by tissue sampling, particularly for infiltrating, heterogeneous tumours. We assessed the accuracy of amide proton transfer-weighted (APTw) magnetic resonance imaging (MRI)-guided tissue sampling to identify regions of high-grade glioma via radiographic-histopathologic correlation in patients with newly suspected glioma...
July 10, 2017: European Journal of Cancer
https://www.readbyqxmd.com/read/28687916/amide-proton-transfer-imaging-for-differentiation-of-benign-and-atypical-meningiomas
#15
Bio Joo, Kyunghwa Han, Yoon Seong Choi, Seung-Koo Lee, Sung Soo Ahn, Jong Hee Chang, Seok-Gu Kang, Se Hoon Kim, Jinyuan Zhou
PURPOSE: To investigate the difference in amide proton transfer (APT)-weighted signals between benign and atypical meningiomas and determine the value of APT imaging for differentiating the two. METHODS: Fifty-seven patients with pathologically diagnosed meningiomas (benign, 44; atypical, 13), who underwent preoperative MRI with APT imaging between December 2014 and August 2016 were included. We compared normalised magnetisation transfer ratio asymmetry (nMTR asym ) values between benign and atypical meningiomas on APT-weighted images...
July 7, 2017: European Radiology
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
#16
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
#17
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/28602944/enhancing-sensitivity-of-ph-weighted-mri-with-combination-of-amide-and-guanidyl-cest
#18
Tao Jin, Ping Wang, T Kevin Hitchens, Seong-Gi Kim
Amide-proton-transfer weighted (APTw) MRI has emerged as a non-invasive pH-weighted imaging technique for studies of several diseases such as ischemic stroke. However, its pH-sensitivity is relatively low, limiting its capability to detect small pH changes. In this work, computer simulations, protamine phantom experiments, and in vivo gas challenge and experimental stroke in rats showed that, with judicious selection of the saturation pulse power, the amide-CEST at 3.6ppm and guanidyl-CEST signals at 2.0ppm changed in opposite directions with decreased pH...
June 7, 2017: NeuroImage
https://www.readbyqxmd.com/read/28582725/investigations-of-vibrational-spectra-and-bioactivity-of-novel-anticancer-drug-n-6-ferrocenyl-2-naphthoyl-gamma-amino-butyric-acid-ethyl-ester
#19
Geethu Sudhi, S R Rajina, S G Praveen, T S Xavier, Peter T M Kenny, D Jaiswal-Nagar, J Binoy
The bioactivity of compounds is mainly dependent on molecular structure and the present work aims to explore the bonding features responsible for biological activity of novel anticancer drug N-(6-ferrocenyl-2-naphthoyl)-gamma-amino butyric acid ethyl ester (FNGABEE). In the present study, we investigate the molecular structural properties of newly synthesized title compound through experimental and quantum chemical studies. The detailed vibrational analysis has been performed using FT IR and FT Raman spectrum, aided by DFT computed geometry, vibrational spectrum, Eigen vector distribution and PED, at B3LYP/6-311++G(d,p) level...
May 28, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28578873/mechanism-informed-refinement-reveals-altered-substrate-binding-mode-for-catalytically-competent-nitroreductase
#20
Warintra Pitsawong, Chad A Haynes, Ronald L Koder, David W Rodgers, Anne-Frances Miller
Nitroreductase (NR) from Enterobacter cloacae reduces diverse nitroaromatics including herbicides, explosives, and prodrugs, and holds promise for bioremediation, prodrug activation, and enzyme-assisted synthesis. We solved crystal structures of NR complexes with bound substrate or analog for each of its two half-reactions. We complemented these with kinetic isotope effect (KIE) measurements elucidating H-transfer steps essential to each half-reaction. KIEs indicate hydride transfer from NADH to the flavin consistent with our structure of NR with the NADH analog nicotinic acid adenine dinucleotide (NAAD)...
July 5, 2017: Structure
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