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Amide protein transfer

Daniel L Dunkelmann, Yuki Hirata, Kyle A Totaro, Daniel T Cohen, Chi Zhang, Zachary P Gates, Bradley L Pentelute
The facile rearrangement of " S -acyl isopeptides" to native peptide bonds via S , N -acyl shift is central to the success of native chemical ligation, the widely used approach for protein total synthesis. Proximity-driven amide bond formation via acyl transfer reactions in other contexts has proven generally less effective. Here, we show that under neutral aqueous conditions, " O -acyl isopeptides" derived from hydroxy-asparagine [aspartic acid-β-hydroxamic acid; Asp(β-HA)] rearrange to form native peptide bonds via an O , N -acyl shift...
March 26, 2018: Proceedings of the National Academy of Sciences of the United States of America
Or Szekely, Gregory Lars Olsen, Isabella Caterina Felli, Lucio Frydman
This study demonstrates the usefulness derived from relying on hyperpolarized water obtained by dissolution DNP, for site-resolved biophysical NMR studies of intrinsically disordered proteins. Thanks to the facile amide-solvent exchange experienced by protons in these proteins, 2D NMR experiments that like HMQC rely on the polarization of the amide protons, can be enhanced using hyperpolarized water by several orders of magnitude over their conventional counterparts. Optimizations of the DNP procedure and of the subsequent injection into the protein sample are necessary to achieve these gains while preserving state-of-the-art resolution; procedures enabling this transfer of the hyperpolarized water and the achievement of foamless hyperpolarized protein solutions, are here demonstrated...
March 12, 2018: Analytical Chemistry
James Tolchard, Manoj Kumar Pandey, Mélanie Berbon, Abdelmajid Noubhani, Sven J Saupe, Yusuke Nishiyama, Birgit Habenstein, Antoine Loquet
We present a new solid-state NMR proton-detected three-dimensional experiment dedicated to the observation of protein proton side chain resonances in nano-liter volumes. The experiment takes advantage of very fast magic angle spinning and double quantum 13C-13C transfer to establish efficient (H)CCH correlations detected on side chain protons. Our approach is demonstrated on the HET-s prion domain in its functional amyloid fibrillar form, fully protonated, with a sample amount of less than 500 µg using a MAS frequency of 70 kHz...
March 3, 2018: Journal of Biomolecular NMR
Leo E Wong, Joachim Maier, Jürgen Wienands, Stefan Becker, Christian Griesinger
Proline is prevalent in intrinsically disordered proteins (IDPs). NMR assignment of proline-rich IDPs is a challenge due to low dispersion of chemical shifts. We propose here new sensitivity-enhanced 4D NMR experiments that correlate two pairs of amide resonances that are either consecutive (NHi-1 , NHi ) or flanking a proline at position i-1 (NHi-2 , NHi ). The maximum two-fold enhancement of sensitivity is achieved by employing two coherence order-selective (COS) transfers incorporated unconventionally into the pulse sequence...
February 28, 2018: Journal of the American Chemical Society
Ji Eun Park, Ji Ye Lee, Ho Sung Kim, Joo-Young Oh, Seung Chai Jung, Sang Joon Kim, Jochen Keupp, Minyoung Oh, Jae Seung Kim
OBJECTIVES: To compare the diagnostic performance of amide proton transfer (APT) imaging and 11-C methionine positron emission tomography (MET-PET) for in vivo molecular imaging of protein metabolism in post-treatment gliomas. MATERIALS AND METHODS: This study included 43 patients (12 low and 31 high grade) with post-treatment gliomas who underwent both APT and MET-PET imaging within 3 weeks. APT-weighted voxel values and semi-quantitative tumour-to-normal ratios (TNR) were obtained from tumour portions...
February 27, 2018: European Radiology
Uta Wille, Joses Nathanael, Luke Gamon, Meike Cordes, Paul Rablen, Thomas Bally, Katharina Fromm, Bernd Giese
Nature uses proteins as medium for long-distance electron transfer (ET) to carry out redox reactions in distant compartments. This ET occurs either by a single-step superexchange or through a multi-step charge hopping process, which uses side chains of amino acids as stepping stones. In this study we demonstrate that Phe can act as a relay amino acid for long-distance electron hole transfer through peptides. The considerably increased susceptibility of the aromatic ring to oxidation is caused by the lone pairs of neighbouring amide carbonyl groups, which stabilize the Phe radical cation...
February 19, 2018: Chembiochem: a European Journal of Chemical Biology
Peter P Knox, Vladimir V Gorokhov, Boris N Korvatovskiy, Eugene P Lukashev, Sergey N Goryachev, Vladimir Z Paschenko, Andrew B Rubin
The temperature dependencies of the rate of dark recombination of separated charges between the photoactive bacteriochlorophyll and the primary quinone acceptor (QA) in photosynthetic reaction centers (RCs) of the purple bacteria Rhodobacter sphaeroides (Rb. sphaeroides) were investigated. Measurements were performed in water-glycerol and trehalose environments after freezing to -180 °C in the dark and under actinic light with subsequent heating. Simultaneously, the RC tryptophanyl fluorescence lifetime in the spectral range between 323 and 348 nm was measured under these conditions...
February 6, 2018: Journal of Photochemistry and Photobiology. B, Biology
Karolina Bossak, Simon C Drew, Ewelina Stefaniak, Dawid Płonka, Arkadiusz Bonna, Wojciech Bal
Copper Transporter 1 (CTR1) is a homotrimeric membrane protein providing the main route of copper transport into eukaryotic cells from the extracellular milieu. Its N-terminal extracellular domain, rich in His and Met residues, is considered responsible for directing copper into the transmembrane channel. Most of vertebrate CTR1 proteins contain the His residue in position three from N-terminus, creating a well-known Amino Terminal Cu(II)- and Ni(II)-Binding (ATCUN) site. CTR1 from humans, primates and many other species contains the Met-Asp-His (MDH) sequence, while some rodents including mouse have the Met-Asn-His (MNH) N-terminal sequence...
February 2, 2018: Journal of Inorganic Biochemistry
Jiří Kessler, Valery Andrushchenko, Josef Kapitán, Petr Bouř
Vibrational circular dichroism (VCD) spectroscopy is an excellent method to determine the secondary structure of proteins in solution. Comparison of experimental spectra with quantum-chemical simulations represents a convenient and objective way to extract information on the structure. This has been difficult for such large molecules where approximate theoretical models have to be used. In the present study we applied the Cartesian-coordinate based tensor transfer (CCT) making it possible to extend the density functional theory (DFT) and model spectral intensities of large globular proteins nearly at quantum-chemical precision...
January 31, 2018: Physical Chemistry Chemical Physics: PCCP
Ramonita Díaz-Ayala, Lisa Torres-González, Ruth Pietri, Carlos R Cabrera, Juan López-Garriga
The recombinant HbI was fused with a poly-Lys tag ((Lys)6 -tagged rHbI) for specific-site covalent immobilization on two carbon nanotube transducer surfaces, i.e., powder and vertically aligned carbon nanotubes. The immobilization was achieved by following two steps: (1) generation of amine-reactive ester from the carboxylic acid groups of the surfaces and (2) coupling these groups with the amine groups of the Lys-tag. We analyzed the immobilization process using different conditions and techniques to differentiate protein covalent attachment from physical adsorption...
December 31, 2017: ACS Omega
Xiao-Yong Zhang, Feng Wang, Junzhong Xu, Daniel F Gochberg, John C Gore, Zhongliang Zu
Chemical exchange saturation transfer (CEST) imaging of amides at 3.5 ppm and fast-exchanging amines at 3 ppm provides a unique means to enhance the sensitivity of detection of, for example, proteins/peptides and neurotransmitters, respectively, and hence can provide important information on molecular composition. However, despite the high sensitivity relative to conventional magnetic resonance spectroscopy (MRS), in practice, CEST often has relatively poor specificity. For example, CEST signals are typically influenced by several confounding effects, including direct water saturation (DS), semi-solid non-specific magnetization transfer (MT), the influence of water relaxation times (T1w ) and nearby overlapping CEST signals...
February 2018: NMR in Biomedicine
Fengyu Yang, Yonglan Liu, Yanxian Zhang, Baiping Ren, Jianxiong Xu, Jie Zheng
The rational design of biomaterials with antifouling properties still remains a challenge, although this is important for many bench-to-bedside applications for biomedical implants, drug delivery carriers, and marine coatings. Herein, we synthesized and characterized poly(N-acryloylglycinamide) (polyNAGA) and then grafted poly(NAGA) onto Au substrate to form polymer brushes with well-controlled film stability, wettability, and thickness using surface-initiated atom transfer radical polymerization (SI-ATRP)...
December 12, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Xinran Wang, Xuehua Lin, Xuanqi Xu, Wei Li, Lijuan Hao, Chunchi Liu, Dongmei Zhao, Maosheng Cheng
Cholesteryl ester transfer protein (CETP) has been identified as a potential target for cardiovascular disease (CVD) for its important role in the reverse cholesteryl transfer (RCT) process. In our previous work, compound 5 was discovered as a moderate CETP inhibitor. The replacement of the amide linker by heterocyclic aromatics and then a series of N,N-substituted-4-arylthiazole-2-methylamine derivatives were designed by utilizing a conformational restriction strategy. Thirty-six compounds were synthesized and evaluated for their CETP inhibitory activities...
November 7, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Jing Zhao, Yinsheng Chen, Yiying Zhao, Shasha Yang, Zhongping Chen, Yin Wu
Magnetic resonance amide proton transfer (APT) imaging has proved its potential for detecting tumors and evaluating treatment response by depicting chemical exchange saturation transfer effect between the endogenous protein/peptide amide proton and bulk water. However, conventional asymmetry analysis for APT effect measurement is susceptible to concomitant contributions, particular semisolid magnetic transfer (MT) and nuclear overhauser effect. In this study, dominant saturation transfer (ST) effects, including direct water saturation and MT, were estimated from a sum of two Lorentzian functions...
July 2017: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
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
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
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
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
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...
November 2017: Journal of Fluorescence
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 of1 H-detected assignment approaches, which correlate a given amide pair either to the two adjacent CO-CA pairs (4D hCOCANH/hCOCAcoNH), or to the amide1 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
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