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Amide protein transfer

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https://www.readbyqxmd.com/read/28942555/the-applicability-of-amide-proton-transfer-imaging-in-the-nervous-system-focus-on-hypoxic-ischemic-encephalopathy-in-the-neonate
#1
REVIEW
Yang Zheng, Xiaoming Wang
In recent years, magnetic resonance imaging (MRI) has become more widely used in neonatal hypoxic-ischemic encephalopathy (HIE), involving, for example, evaluation of cerebral edema, white matter fiber bundle tracking, cerebral perfusion status, and assessment of brain metabolites. MRI has many imaging modalities. However, its application for assessing changes in the internal environment at the tissue and cellular level after hypoxia-ischemia remains a challenge and is currently the focus of intense research...
September 23, 2017: Cellular and Molecular Neurobiology
https://www.readbyqxmd.com/read/28940131/nitrogen-nutrition-in-cotton-and-control-strategies-for-greenhouse-gas-emissions-a-review
#2
Aziz Khan, Daniel Kean Yuen Tan, Fazal Munsif, Muhammad Zahir Afridi, Farooq Shah, Fan Wei, Shah Fahad, Ruiyang Zhou
Cotton (Gossypium hirustum L.) is grown globally as a major source of natural fiber. Nitrogen (N) management is cumbersome in cotton production systems; it has more impacts on yield, maturity, and lint quality of a cotton crop than other primary plant nutrient. Application and production of N fertilizers consume large amounts of energy, and excess application can cause environmental concerns, i.e., nitrate in ground water, and the production of nitrous oxide a highly potent greenhouse gas (GHG) to the atmosphere, which is a global concern...
October 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28885830/oligoprolines-as-molecular-entities-for-controlling-distance-in-biological-and-material-sciences
#3
Stefanie Dobitz, Matthew R Aronoff, Helma Wennemers
Nature utilizes large biomolecules to fulfill tasks that require spatially well-defined arrangements at the molecular level such as electron transfer, ligand-receptor interactions, or catalysis. The creation of synthetic molecules that enable precise control over spacing and functionalization provides opportunities across diverse disciplines. Key requirements of functionalizable oligomeric scaffolds include the specific control of their molecular properties where the correct balance of flexibility and rigidity must be maintained in addition to the prerequisite of defined length...
October 17, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28869714/ultrafast-vibrational-dynamics-of-membrane-bound-peptides-at-the-lipid-bilayer-water-interface
#4
Junjun Tan, Baixiong Zhang, Yi Luo, Shuji Ye
Vibrational energy transfer (VET) of proteins at cell membrane plays critical roles in controlling the protein functionalities, but its detection is very challenging. By using a surface-sensitive femtosecond time-resolved sum-frequency generation vibrational spectroscopy with infrared pump, the detection of the ultrafast VET in proteins at cell membrane has finally become possible. The vibrational relaxation time of the N-H groups is determined to be 1.70(±0.05) ps for the α-helix located in the hydrophobic core of the lipid bilayer and 0...
September 4, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28823107/fluorescent-labeling-of-protein-using-blue-emitting-8-amino-bodipy-derivatives
#5
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
#6
Hugo Fraga, Charles-Adrien Arnaud, Diego F Gauto, Maxime Audin, Vilius Kurauskas, Pavel Macek, Carsten Krichel, Jia-Ying Guan, Jerome Boisbouvier, Remco Sprangers, Cécile Breyton, Paul Schanda
Solid-state NMR spectroscopy 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 the use of two sets of experiments is shown to expand the tool kit of (1) H-detected assignment approaches, which correlate a given amide pair either to the two adjacent CO-CA pairs (4D hCOCANH/hCOCAcoNH), or to the amide (1) H of the neighboring residue (3D HcocaNH/HcacoNH, which can be extended to 5D)...
October 6, 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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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)
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