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Amide protein transfer

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
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...
December 15, 2016: Oncotarget
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
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
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
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
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...
October 12, 2016: Journal of Antibiotics
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
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
Loren B Andreas, Kristaps Jaudzems, Jan Stanek, Daniela Lalli, Andrea Bertarello, Tanguy Le Marchand, Diane Cala-De Paepe, Svetlana Kotelovica, Inara Akopjana, Benno Knott, Sebastian Wegner, Frank Engelke, Anne Lesage, Lyndon Emsley, Kaspars Tars, Torsten Herrmann, Guido Pintacuda
Protein structure determination by proton-detected magic-angle spinning (MAS) NMR has focused on highly deuterated samples, in which only a small number of protons are introduced and observation of signals from side chains is extremely limited. Here, we show in two fully protonated proteins that, at 100-kHz MAS and above, spectral resolution is high enough to detect resolved correlations from amide and side-chain protons of all residue types, and to reliably measure a dense network of (1)H-(1)H proximities that define a protein structure...
August 16, 2016: Proceedings of the National Academy of Sciences of the United States of America
Cedric P Owens, Faith E H Katz, Cole H Carter, Victoria F Oswald, F Akif Tezcan
The P-cluster is a unique iron-sulfur center that likely functions as a dynamic electron (e(-)) relay site between the Fe-protein and the catalytic FeMo-cofactor in nitrogenase. The P-cluster has been shown to undergo large conformational changes upon 2-e(-) oxidation which entail the coordination of two of the Fe centers to a Ser side chain and a backbone amide N, respectively. Yet, how and if this 2-e(-) oxidized state (P(OX)) is involved in catalysis by nitrogenase is not well established. Here, we present the crystal structures of reduced and oxidized MoFe-protein (MoFeP) from Gluconacetobacter diazotrophicus (Gd), which natively possesses an Ala residue in the position of the Ser ligand to the P-cluster...
August 17, 2016: Journal of the American Chemical Society
Deng-Tai Wen, Lan Zheng, Liu Ni, Hui Wang, Yue Feng, Min Zhang
The CG9940 gene, which encodes the NAD(+) synthase protein in Drosophila, is conserved in human, zebra fish, and mosquito. NAD(+) synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD(+)) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). Both the CG9940 and exercise are closely relative to NAD(+) level, and NAD(+) plays important roles not only in energy metabolism and mitochondrial functions but also in aging...
October 2016: Experimental Gerontology
Parker E Deal, Rishikesh U Kulkarni, Sarah H Al-Abdullatif, Evan W Miller
We present the design, synthesis, and application of a new family of fluorescent voltage indicators based on isomerically pure tetramethylrhodamines. These new Rhodamine Voltage Reporters, or RhoVRs, use photoinduced electron transfer (PeT) as a trigger for voltage sensing, display excitation and emission profiles in the green to orange region of the visible spectrum, demonstrate high sensitivity to membrane potential changes (up to 47% ΔF/F per 100 mV), and employ a tertiary amide derived from sarcosine, which aids in membrane localization and simultaneously simplifies the synthetic route to the voltage sensors...
July 27, 2016: Journal of the American Chemical Society
Christoph Steininger, Ciril Reiner-Rozman, Andreas Schwaighofer, Wolfgang Knoll, Renate L C Naumann
Time-resolved surface-enhanced IR-absorption spectroscopy (tr-SEIRAS) has been performed on cytochrome c oxidase from Rhodobacter sphaeroides. The enzyme was converted electrochemically into the fully reduced state. Thereafter, in the presence of oxygen, the potential was switched to open circuit potential (OCP). Under these conditions, the enzyme is free to undergo enzymatic oxidation in the absence of an external electric field. Tr-SEIRAS was performed using the step-scan technique, triggered by periodic potential pulses switching between - 800mV and OCP...
December 2016: Bioelectrochemistry
James A Birrell, Christoph Laurich, Edward J Reijerse, Hideaki Ogata, Wolfgang Lubitz
Iron-sulfur clusters form one of the largest and most diverse classes of enzyme cofactors in nature. They may serve as structural factors, form electron transfer chains between active sites and external redox partners, or form components of enzyme active sites. Their specific role is a consequence of the cluster type and the surrounding protein environment. The relative effects of these factors are not completely understood, and it is not yet possible to predict the properties of iron-sulfur clusters based on amino acid sequences or rationally tune their properties to generate proteins with new desirable functions...
August 9, 2016: Biochemistry
Heather J Kulik, Natasha Seelam, Brendan D Mar, Todd J Martínez
Recent algorithmic and hardware advances have enabled the application of electronic structure methods to the study of large-scale systems such as proteins with O(10(3)) atoms. Most such methods benefit greatly from the use of reduced basis sets to further enhance their speed, but truly minimal basis sets are well-known to suffer from incompleteness error that gives rise to incorrect descriptions of chemical bonding, preventing minimal basis set use in production calculations. We present a strategy for improving these well-known shortcomings in minimal basis sets by selectively tuning the energetics and bonding of nitrogen and oxygen atoms within proteins and small molecules to reproduce polarized double-ζ basis set geometries at minimal basis set cost...
July 28, 2016: Journal of Physical Chemistry. A
Kwon Joo Yeo, Jin-Wan Park, Eun-Hee Kim, Young Ho Jeon, Kwang Yeon Hwang, Hae-Kap Cheong
In enterohemorrhagic Escherichia coli (EHEC), the QseEF two-component system causes attaching and effacing (AE) lesion on epithelial cells. QseE histidine kinase senses the host hormone epinephrine, sulfate, and phosphate; it also regulates QseF response regulator, which activates LEE gene that encodes AE lesion. In order to understand the recognition of ligand molecules and signal transfer mechanism in pathogenic bacteria, structural studies of the sensor domain of QseE of Escherichia coli should be conducted...
October 2016: Protein Expression and Purification
Mahdi Kadkhodazadeh, Ahmad Reza Ebadian, Reza Amid, Parisa Zarnegarnia, Fatemeh Mollaverdi, Nika Aghamohammadi
In inflammatory diseases such as peri-implantitis (PI) and chronic periodontitis (CP) both adaptive and innate immunity play a part. Natural resistance associated macrophage protein 1 (NRAMP1) has considerable effects on macrophage function (phagocytosis) and host innate immune response against infections. The present study was to investigate the relationship of NRAMP1 gene polymorphisms with PI and CP in an Iranian population. In this cross sectional study 79 patients with CP, 38 patients with PI and 84 healthy controls presenting to the Periodontology Department of Shahid Beheshti University of Medical Sciences were enrolled...
May 2016: Acta Medica Iranica
Yuet Wu, Ronald Wai Kung Wu, Kwan Wing Cheu, Ian D Williams, Sanjeev Krishna, Ksenija Slavic, Andrew M Gravett, Wai M Liu, Ho Ning Wong, Richard K Haynes
We sought to establish if methylene homologues of artemisone are biologically more active and more stable than artemisone. The analogy is drawn with the conversion of natural O- and N-glycosides into more stable C-glycosides that may possess enhanced biological activities and stabilities. Dihydroartemisinin was converted into 10β-cyano-10-deoxyartemisinin that was hydrolyzed to the α-primary amide. Reduction of the β-cyanide and the α-amide provided the respective methylamine epimers that upon treatment with divinyl sulfone gave the β- and α-methylene homologues, respectively, of artemisone...
July 5, 2016: ChemMedChem
Holger Schmidt, Nina F Schwenzer, Sergios Gatidis, Thomas Küstner, Konstantin Nikolaou, Fritz Schick, Petros Martirosian
OBJECTIVE: The goal of this work was to systematically evaluate the reproducibility of amide proton transfer chemical exchange saturation transfer (APT-CEST) at 3 T and its signal dependence on pH, protein concentration, and acquisition parameters. An in vitro system based on bovine serum albumin (BSA) was used, and its limitations were tested by comparing it to in vivo measurements. The contribution of small endogenous metabolites on the APT-CEST signal at 3 T was also investigated. In addition, the reliability of different z-spectrum interpolations as well as the use of only a few frequency offset data points instead of a whole z-spectrum were tested...
October 2016: Investigative Radiology
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