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https://www.readbyqxmd.com/read/28437077/peptide-and-protein-dynamics-and-low-temperature-dnp-magic-angle-spinning-nmr
#1
Qing Zhe Ni, Evgeny Markhasin, Thach V Can, Björn Corzilius, Kong O Tan, Alexander B Barnes, Eugenio Daviso, Yongchao Su, Judith Herzfeld, Robert G Griffin
In DNP MAS NMR experiments at ~80-110 K, the structurally important -13CH3 and -15NH3+ signals in MAS spectra of biological samples disappear due to the interference of the molecular motions with the 1H decoupling. Here we investigate the effect of these dynamic processes on the NMR lineshapes and signal intensities in several typical systems: (1) microcrystalline APG, (2) membrane protein bR, (3) amyloid fibrils PI3-SH3, (4) monomeric alanine-CD3 and (5) the pro-tonated and deuterated dipeptide N-Ac-VL over 78-300 K...
April 24, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28435985/elucidating-the-a%C3%AE-42-anti-aggregation-mechanism-of-action-of-tramiprosate-in-alzheimer-s-disease-integrating-molecular-analytical-methods-pharmacokinetic-and-clinical-data
#2
Petr Kocis, Martin Tolar, Jeremy Yu, William Sinko, Soumya Ray, Kaj Blennow, Howard Fillit, John A Hey
BACKGROUND: Amyloid beta (Aβ) oligomers play a critical role in the pathogenesis of Alzheimer's disease (AD) and represent a promising target for drug development. Tramiprosate is a small-molecule Aβ anti-aggregation agent that was evaluated in phase III clinical trials for AD but did not meet the primary efficacy endpoints; however, a pre-specified subgroup analysis revealed robust, sustained, and clinically meaningful cognitive and functional effects in patients with AD homozygous for the ε4 allele of apolipoprotein E4 (APOE4/4 homozygotes), who carry an increased risk for the disease...
April 24, 2017: CNS Drugs
https://www.readbyqxmd.com/read/28435872/unraveling-self-assembly-pathways-of-the-468-kda-proteolytic-machine-tet2
#3
Pavel Macek, Rime Kerfah, Elisabetta Boeri Erba, Elodie Crublet, Christine Moriscot, Guy Schoehn, Carlos Amero, Jerome Boisbouvier
The spontaneous formation of biological higher-order structures from smaller building blocks, called self-assembly, is a fundamental attribute of life. Although the protein self-assembly is a time-dependent process that occurs at the molecular level, its current understanding originates either from static structures of trapped intermediates or from modeling. Nuclear magnetic resonance (NMR) spectroscopy has the unique ability to monitor structural changes in real time; however, its size limitation and time-resolution constraints remain a challenge when studying the self-assembly of large biological particles...
April 2017: Science Advances
https://www.readbyqxmd.com/read/28433158/characterization-of-a-sulfated-galactoglucan-from-antrodia-cinnamomea-and-its-anticancer-mechanism-via-tgf%C3%AE-fak-slug-axis-suppression
#4
Mei-Kuang Lu, Tung-Yi Lin, Chun-Hao Hu, Chi-Hsein Chao, Chia-Chuan Chang, Hsien-Yeh Hsu
A sulfated 1,4-β-d-galactoglucan (B86-III) with 1,6-branches was isolated and identified from Antrodia cinnamomea. The repeating unit of B86-III was proposed based on one-dimensional 1D ((1)H, (13)C and DEPT-135) and 2D (DQF-COSY, TOCSY, HSQC and HMBC) NMR spectra. The conformation of the sugars was hypothesized to be a rare boat form instead of a (4)C1 chair form. The sulfate substitutions were suggested to be on the C-2 and C-3 positions, resulting in the following structure: B86-III inhibited the viability of H1975 lung cancer cells via cell apoptosis, including the activation of caspase 3 and PARP...
July 1, 2017: Carbohydrate Polymers
https://www.readbyqxmd.com/read/28433155/a-highly-regular-fucosylated-chondroitin-sulfate-from-the-sea-cucumber-massinium-magnum-structure-and-effects-on-coagulation
#5
Nadezhda E Ustyuzhanina, Maria I Bilan, Andrey S Dmitrenok, Elizaveta Yu Borodina, Valentin A Stonik, Nikolay E Nifantiev, Anatolii I Usov
A fucosylated chondroitin sulfate MM was isolated from the sea cucumber Massinium magnum. Structure of this polysaccharide was determined using chemical and NMR spectroscopic methods. The backbone of MM was shown to consist mainly of chondroitin sulfate E units with a small portion (about 10%) of chondroitin sulfate A fragments. Practically one type of branches Fuc3S4S attached to O-3 of GlcA residues was found in the polysaccharide molecules. The main repeating units of MM are →4)-[α-l-Fuc3S4S-(1→3)]-β-d-GlcA-(1→3)-β-d-GalNAc4S6S-(1→, whereas the minor repeating units are →4)-[α-l-Fuc3S4S-(1→3)]-β-d-GlcA-(1→3)-β-d-GalNAc4S-(1→...
July 1, 2017: Carbohydrate Polymers
https://www.readbyqxmd.com/read/28433147/mucopolysaccharide-from-cuttlefish-purification-chemical-characterization-and-bioactive-potential
#6
Palaniappan Seedevi, Meivelu Moovendhan, Shanmugam Vairamani, Annaian Shanmugam
The sulfated mucopolysaccharide (GAG) was isolated from S. pharonis and the carbohydrate and protein content was found to be 62.4% and 3.9%. The disaccharide profile of sulfated GAG composed glucuronic acid, N-acetyl glucosamine and sulfate content by contributing 50.11%, 38.00% and 27.69% respectively. The carbon, hydrogen and nitrogen content of the sulfated GAG showed 14.80%, 1.68% and 2.99% respectively. The molecular weight of sulfated GAG was calculated as 27kDa and the structural characterization was done by Fourier Transform Infrared (FT-IR) and NMR Spectroscopy...
July 1, 2017: Carbohydrate Polymers
https://www.readbyqxmd.com/read/28433015/probing-the-effects-of-surface-hydrophobicity-and-tether-orientation-on-antibody-antigen-binding
#7
Derek B Bush, Thomas A Knotts
Antibody microarrays have the potential to revolutionize molecular detection for many applications, but their current use is limited by poor reliability, and efforts to change this have not yielded fruitful results. One difficulty which limits the rational engineering of next-generation devices is that little is known, at the molecular level, about the antibody-antigen binding process near solid surfaces. Atomic-level structural information is scant because typical experimental techniques (X-ray crystallography and NMR) cannot be used to image proteins bound to surfaces...
April 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28432336/structure-function-analysis-of-the-dna-binding-domain-of-a-transmembrane-transcriptional-activator
#8
Andreas Schlundt, Sophie Buchner, Robert Janowski, Thomas Heydenreich, Ralf Heermann, Jürgen Lassak, Arie Geerlof, Ralf Stehle, Dierk Niessing, Kirsten Jung, Michael Sattler
The transmembrane DNA-binding protein CadC of E. coli, a representative of the ToxR-like receptor family, combines input and effector domains for signal sensing and transcriptional activation, respectively, in a single protein, thus representing one of the simplest signalling systems. At acidic pH in a lysine-rich environment, CadC activates the transcription of the cadBA operon through recruitment of the RNA polymerase (RNAP) to the two cadBA promoter sites, Cad1 and Cad2, which are directly bound by CadC...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28431929/effects-of-naturally-occurring-charged-mutations-on-the-structure-stability-and-binding-of-the-pin1-ww-domain
#9
Xiaoya Qiao, Ying Liu, Liting Luo, Lei Chen, Caixian Zhao, Xuanjun Ai
Pin1 is a peptidyl-prolyl cis-trans isomerase, whose WW domain specifically recognizes the pSer/Thr-Pro motif. Pin1 is involved in multiple phosphorylation events that regulate the activities of various substrates, and Pin1 deregulation has been reported in various diseases, including cancer and Alzheimer's disease. The WW domain of Pin1 has been used as a small model protein to investigate the folding mechanisms of the β-sheet structure by studying the effect of mutations or its naturally occurring variants...
April 19, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28430190/tuning-underwater-adhesion-with-cation-%C3%AF-interactions
#10
Matthew A Gebbie, Wei Wei, Alex M Schrader, Thomas R Cristiani, Howard A Dobbs, Matthew Idso, Bradley F Chmelka, J Herbert Waite, Jacob N Israelachvili
Cation-π interactions drive the self-assembly and cohesion of many biological molecules, including the adhesion proteins of several marine organisms. Although the origin of cation-π bonds in isolated pairs has been extensively studied, the energetics of cation-π-driven self-assembly in molecular films remains uncharted. Here we use nanoscale force measurements in combination with solid-state NMR spectroscopy to show that the cohesive properties of simple aromatic- and lysine-rich peptides rival those of the strong reversible intermolecular cohesion exhibited by adhesion proteins of marine mussel...
May 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28429411/nanodiscs-for-inpharma-nmr-characterization-of-gpcrs-ligand-binding-to-the-human-a2a-adenosine-receptor
#11
Kai Fredriksson, Philip Lottmann, Sonja Hinz, Iounut Onila, Aliaksei Shymanets, Christian Harteneck, Christa E Müller, Christian Griesinger, Thomas E Exner
G-protein-coupled-receptors (GPCRs) are of fundamental importance for signal transduction through cell membranes. This makes them important drug targets, but structure-based drug design (SBDD) is still hampered by the limitations for structure determination of unmodified GPCRs. We show that the interligand NOEs for pharmacophore mapping (INPHARMA) method can provide valuable information on ligand poses inside the binding site of the unmodified human A2A adenosine receptor reconstituted in nanodiscs. By comparing experimental INPHARMA spectra with back-calculated spectra based on ligand poses obtained from molecular dynamics simulations, a complex structure for A2A R with the low-affinity ligand 3-pyrrolidin-1-ylquinoxalin-2-amine was determined based on the X-ray structure of ligand ZM-241,358 in complex with a modified A2A R...
April 21, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28428246/key-features-of-an-hsp70-chaperone-allosteric-landscape-revealed-by-ion-mobility-native-mass-spectrometry-and-double-electron-electron-resonance
#12
Alex L Lai, Eugenia M Clerico, Mandy E Blackburn, Nisha A Patel, Carol V Robinson, Peter P Borbat, Jack H Freed, Lila M Gierasch
Proteins are dynamic entities that populate conformational ensembles, and most functions of proteins depend on their dynamic character. Allostery, in particular, relies on ligand-modulated shifts in these conformational ensembles. Hsp70s are allosteric molecular chaperones with conformational landscapes that involve large rearrangements of their two domains (viz, the nucleotide-binding domain and substrate-binding domain) in response to adenine nucleotides and substrates. However, it remains unclear how the Hsp70 conformational ensemble is populated at each point of the allosteric cycle and how ligands control these populations...
April 20, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28428126/interactions-of-tetracyclines-with-ovalbumin-the-main-allergen-protein-from-egg-white-spectroscopic-and-electrophoretic-studies
#13
Maria Dayanne de A Dantas, Humberto de Araújo Tenório, Thiago Inácio B Lopes, Hugo Juarez V Pereira, Anita J Marsaioli, Isis M Figueiredo, Josué Carinhanha Caldas Santos
The interactions of tetracycline (TC), oxytetracycline (OTC) and chlortetracycline (CTC) with ovalbumin (OVA), the main allergen protein of egg white, were investigated by molecular spectroscopy and electrophoresis at three pH conditions (1.5, 4.6 and 7.4). Molecular and synchronous fluorescence, UV-vis spectroscopy, electrophoresis and (1)H NMR were used to study the interaction process. Tetracyclines interact with ovalbumin fluorescence by a static quenching mechanism with non-fluorescent complex formation changing the native protein structure...
April 17, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28428022/cloning-and-identification-of-a-novel-steroid-11%C3%AE-hydroxylase-gene-from-absidia-coerulea
#14
Ruijie Wang, Pengcheng Sui, Xiangjiang Hou, Tong Cao, Longgang Jia, Fuping Lu, Suren Singh, Zhengxiang Wang, Xiaoguang Liu
Steroid 11-hydroxylation by filamentous fungi is a major route for industrial scale production of key intermediates in the synthesis of steroid drugs. Although it is well established that enzymes involved in fungal hydroxylation of steroids are cytochrome P450s (CYP), few fungal steroid hydroxylase genes have been identified. In this study, we identified a novel 11α-hydroxylase gene CYP5311B1 from Absidia coerulea AS3.65 by a combination of transcriptome sequencing, Real-Time qRT-PCR and heterologous expression in Pichia pastoris...
April 17, 2017: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28426169/microsecond-dynamics-in-ubiquitin-probed-by-solid-state-nmr-15n-r1rho-relaxation-experiments-under-fast-mas-60-110-khz
#15
Nils-Alexander Lakomek, Susanne Penzel, Alons Lends, Riccardo Cadalbert, Matthias Ernst, Beat H Meier
15N R1ρ relaxation experiments in solid-state NMR are sensitive to timescales and amplitudes of internal protein motions in the hundreds of ns to µs time window, difficult to probe with solution-state NMR. Using 15N R1ρ relaxation experiments with variable MAS frequency (60-110 kHz) and a model-free analysis, we describe an approach to detect hundreds of ns to low µs protein dynamics and determine residue-specific correlation times from the ratio of 15N R1ρ rate constants at different MAS frequencies. We find that microcrystalline ubiquitin exhibits small-amplitude dynamics on a timescale of about 1 µs across the entire protein, and larger amplitude motions, also on the 1 µs timescale, for several sites, including the β1-β2 turn and the N-terminus of the α-helix...
April 20, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28425852/discovery-of-novel-2-amino-5-substituted-1-3-4-thiadiazole-derivatives-new-utilities-for-colon-cancer-treatment
#16
Vinit Raj, Amit Rai, Ashok K Singh, Amit K Keshari, Prakruti Harshvardhanbhai Trivedi, Balaram Ghosh, Umesh Kumar, Dinesh Kumar, Sudipta Saha
In this study, we designed and synthesized (VR1 to VR35) a novel series of 1,3,4-thiadiazole derivatives from 2-amino-5-(substituted)-1,3,4-thiadiazole condensed with substituted aldehyde or ketone in the presence of glacial acetic acid via Wolff-Kishner reduction. Further, synthesized compounds were characterized by FTIR, NMR (1H and 13C), MS and elemental analyses. Before the synthesis, docking studies were performed using various molecular targets of colon cancer like IL-2, IL-6, COX-2, caspase-3, and caspase-8...
April 19, 2017: Anti-cancer Agents in Medicinal Chemistry
https://www.readbyqxmd.com/read/28425709/beyond-structural-biology-to-functional-biology-solid-state-nmr-experiments-and-strategies-for-understanding-the-m2-proton-channel-conductance
#17
Huajun Qin, Yimin Miao, Timothy A Cross, Riqiang Fu
In terms of structural biology, solid-state NMR experiments and strategies have been well established for resonance assignments leading to the determination of three-dimensional structures of insoluble membrane proteins in their native-like environment. It is also known that NMR has the unique capabilities to characterize structure-function relationships of membrane-bound biological systems beyond structural biology. Here, we report on solid-state NMR experiments and strategies for extracting functional activities on a sub-msec time scale...
April 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28425707/development-of-a-potent-wound-healing-agent-based-on-the-liver-fluke-granulin-structural-fold
#18
Paramjit S Bansal, Michael J Smout, David Wilson, Claudia Cobos Caceres, Mohadeseh Dastpeyman, Javier Sotillo, Julia Seifert, Paul J Brindley, Alex Loukas, Norelle L Daly
Granulins are a family of protein growth factors that are involved in cell proliferation. An orthologue of granulin from the human parasitic liver fluke Opisthorchis viverrini, known as Ov-GRN-1, induces angiogenesis and accelerates wound repair. Recombinant Ov-GRN-1 production is complex, and poses an obstacle for clinical development. To identify the bioactive region(s) of Ov-GRN-1, four truncated N-terminal analogues were synthesized and characterized structurally using NMR spectroscopy. Peptides that contained only two native disulfide bonds lack the characteristic granulin -hairpin structure...
April 20, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28420127/glycosaminoglycan-binding-and-non-endocytic-membrane-translocation-of-cell-permeable-octaarginine-monitored-by-real-time-in-cell-nmr-spectroscopy
#19
Yuki Takechi-Haraya, Kenzo Aki, Yumi Tohyama, Yuichi Harano, Toru Kawakami, Hiroyuki Saito, Emiko Okamura
Glycosaminoglycans (GAGs), which are covalently-linked membrane proteins at the cell surface have recently been suggested to involve in not only endocytic cellular uptake but also non-endocytic direct cell membrane translocation of arginine-rich cell-penetrating peptides (CPPs). However, in-situ comprehensive observation and the quantitative analysis of the direct membrane translocation processes are challenging, and the mechanism therefore remains still unresolved. In this work, real-time in-cell NMR spectroscopy was applied to investigate the direct membrane translocation of octaarginine (R8) into living cells...
April 15, 2017: Pharmaceuticals
https://www.readbyqxmd.com/read/28420092/analysis-of-sub-lethal-toxicity-of-perfluorooctane-sulfonate-pfos-to-daphnia-magna-using-%C3%A2-h-nuclear-magnetic-resonance-based-metabolomics
#20
Martha N Kariuki, Edward G Nagato, Brian P Lankadurai, André J Simpson, Myrna J Simpson
¹H nuclear magnetic resonance (NMR)-based metabolomics was used to characterize the response of Daphnia magna after sub-lethal exposure to perfluorooctane sulfonate (PFOS), a commonly found environmental pollutant in freshwater ecosystems. Principal component analysis (PCA) scores plots showed significant separation in the exposed samples relative to the controls. Partial least squares (PLS) regression analysis revealed a strong linear correlation between the overall metabolic response and PFOS exposure concentration...
April 14, 2017: Metabolites
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