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https://www.readbyqxmd.com/read/29052959/peptide-ligands-for-targeting-the-extracellular-domain-of-egfr-comparison-between-linear-and-cyclic-peptides
#1
Tyrslai M Williams, Rushikesh Sable, Sitanshu Singh, M Graça H Vicente, Seetharama Jois
Colorectal cancer (CRC) is the third most common solid internal malignancy among cancers. Early detection of cancer is key to increasing the survival rate of colorectal cancer patients. Overexpression of the EGFR protein is associated with CRC. We have designed a series of peptides that are highly specific for the extracellular domain of EGFR, based on our earlier studies on linear peptides. The previously reported linear peptide LARLLT, known to bind to EGFR, was modified with the goals of increasing its stability and its specificity towards EGFR...
October 20, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/29052909/allosteric-control-of-a-bacterial-stress-response-system-by-an-anti-%C3%AF-factor
#2
Justin L Luebke, Daniel S Eaton, Joseph R Sachleben, Sean Crosson
Bacterial signal transduction systems commonly use receiver (REC) domains, which regulate adaptive responses to the environment as a function of their phosphorylation state. REC domains control cell physiology through diverse mechanisms, many of which remain understudied. We have defined structural features that underlie activation of the multi-domain REC protein, PhyR, which functions as an anti-anti-σ factor and regulates transcription of genes required for stress adaptation and host-microbe interactions in Alphaproteobacteria...
October 20, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/29050969/a-novel-selective-mao-b-inhibitor-with-neuroprotective-and-anti-parkinsonian-properties
#3
Hugh H Chan, Man Kit Tse, Saravana Kumar, Lang Zhuo
We previously reported that 1,3-bisbenzylimidazolium (DBZIM) bromide was neuroprotective for the dopaminergic system in Parkinson's disease (PD) models of rodent, however the underlying mechanism was unclear. We currently further confirmed that DBZIM ameliorated the Parkinsonian motor deficit and protected the nigrostriatal tract from the neurotoxicity of 1-methyl-4-(2'-methylphenyl)-1,2,3,6-tetrahydropyridine (2'-CH3-MPTP) in C57Bl/6 mice. The dopaminergic degeneration in the substantia nigra par compacta (SNc) and striatum was analyzed by immunohistochemistry while the monoamine oxidase B (MAO-B) inhibition effect of DBZIM was determined by enzyme kinetics...
October 16, 2017: European Journal of Pharmacology
https://www.readbyqxmd.com/read/29048831/-fabrication-of-acylsemicarbazide-based-porous-organic-polymer-for-selective-enrichment-of-glycopeptides
#4
Hongwei Wang, Zhongshan Liu, Xiaojun Peng, Junjie Ou, Mingliang Ye
An acylsemicarbazide-based porous organic polymer (POP) was facilely prepared by the polymerization of benzene-1,3,5-tricarbohydrazide (BTZ) and 1,4-phenylene diisocyanate (PDI). The physical properties of as-synthesized material were characterized by Fourier-transform infrared spectroscopy (FT-IR), solid-state cross polarisation magic angle spinning carbon-13 nuclear magnetic resonance (CP-MAS (13)C NMR), nitrogen adsorption/desorption measurement, water contact angle and so on. The specific surface area was 166 m(2)/g, and the water contact angle was 46...
July 8, 2017: Se Pu, Chinese Journal of Chromatography
https://www.readbyqxmd.com/read/29047011/comparing-pharmacophore-models-derived-from-crystallography-and-nmr-ensembles
#5
Phani Ghanakota, Heather A Carlson
NMR and X-ray crystallography are the two most widely used methods for determining protein structures. Our previous study examining NMR versus X-Ray sources of protein conformations showed improved performance with NMR structures when used in our Multiple Protein Structures (MPS) method for receptor-based pharmacophores (Damm, Carlson, J Am Chem Soc 129:8225-8235, 2007). However, that work was based on a single test case, HIV-1 protease, because of the rich data available for that system. New data for more systems are available now, which calls for further examination of the effect of different sources of protein conformations...
October 19, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/29045929/deciphering-the-complexation-process-of-a-fluoroquinolone-antibiotic-levofloxacin-with-bovine-serum-albumin-in-the-presence-of-additives
#6
Amandeep Kaur, Imran Ahmd Khan, Parampaul Kaur Banipal, Tarlok Singh Banipal
The current work aims to explore the thermodynamic and conformational aspects for the binding of fluoroquinolone antibacterial drug, levofloxacin (LFC), with bovine serum albumin (BSA) using calorimetric, spectroscopic (UV-visible, fluorescence, circular dichroism, and (1)H NMR), dynamic light scattering (DLS) and computational methods (molecular docking). The binding of LFC with BSA at two sequential sites with higher affinity (~10(3)M(-1)) at the first site has been explored by calorimetry whereas the binding at a single site with affinity of the order of ~10(4)M(-1) has been observed from fluorescence spectroscopy...
October 9, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/29045862/the-two-state-prehensile-tail-of-the-antibacterial-toxin-colicin-n
#7
Christopher L Johnson, Alexandra S Solovyova, Olli Hecht, Colin Macdonald, Helen Waller, J Günter Grossmann, Geoffrey R Moore, Jeremy H Lakey
Intrinsically disordered regions within proteins are critical elements in many biomolecular interactions and signaling pathways. Antibacterial toxins of the colicin family, which could provide new antibiotic functions against resistant bacteria, contain disordered N-terminal translocation domains (T-domains) that are essential for receptor binding and the penetration of the Escherichia coli outer membrane. Here we investigate the conformational behavior of the T-domain of colicin N (ColN-T) to understand why such domains are widespread in toxins that target Gram-negative bacteria...
October 17, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29045470/structural-and-functional-analysis-of-smo-1-the-sumo-homolog-in-caenorhabditis-elegans
#8
Parag Surana, Chandrakala M Gowda, Vasvi Tripathi, Limor Broday, Ranabir Das
SUMO proteins are important post-translational modifiers involved in multiple cellular pathways in eukaryotes, especially during the different developmental stages in multicellular organisms. The nematode C. elegans is a well known model system for studying metazoan development and has a single SUMO homolog, SMO-1. Interestingly, SMO-1 modification is linked to embryogenesis and development in the nematode. However, high-resolution information about SMO-1 and the mechanism of its conjugation is lacking. In this work, we report the high-resolution three dimensional structure of SMO-1 solved by NMR spectroscopy...
2017: PloS One
https://www.readbyqxmd.com/read/29045141/internal-motions-of-basic-side-chains-of-the-antennapedia-homeodomain-in-the-free-and-dna-bound-states
#9
Dan Nguyen, Zoe A Hoffpauir, Junji Iwahara
Basic side chains play crucial roles in protein-DNA interactions. In this study, using NMR spectroscopy, we investigated the dynamics of Arg and Lys side chains of the fruit fly Antennapedia homeodomain in the free state and in the complex with target DNA. We measured (15)N relaxation for Arg and Lys side chains at two magnetic fields, from which generalized order parameters for the cationic groups were determined. Mobility of the R5 side chain, which makes hydrogen bonds with a thymine base in the DNA minor groove, was greatly dampened...
October 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/29044868/effects-of-rubiadin-isolated-from-prismatomeris-connata-on-anti-hepatitis-b-virus-activity-in-vitro
#10
Zheng Peng, Gang Fang, Fenghui Peng, Zhiyu Pan, Zhengying Su, Wei Tian, Danrong Li, Huaxin Hou
Prismatomeris connata was a kind of Rubiaceae plant for treatment of hepatitis, hepatic fibrosis and silicosis. Whereas, the effective components of Prismatomeris connata remains unexplored. The aim of this study was to investigate the inhibitory effects and mechanisms of Rubiadin isolated from Prismatomeris connata against HBV using HepG2.2.15 cells. The levels of hepatitis B surface antigen (HBsAg), hepatitis B e antigen (HBeAg), and hepatitis B core antigen (HBcAg) in the supernatants or cytoplasm were examined using by enzyme-linked immunosorbent assay...
October 18, 2017: Phytotherapy Research: PTR
https://www.readbyqxmd.com/read/29044810/simultaneous-refinement-of-inaccurate-local-regions-and-overall-structure-in-the-casp12-protein-model-refinement-experiment
#11
Gyu Rie Lee, Lim Heo, Chaok Seok
Advances in protein model refinement techniques are required as diverse sources of protein structure information are available from low-resolution experiments or informatics-based computations such as cryo-EM, NMR, homology models, or predicted residue contacts. Given semi-reliable or incomplete structural information, structure quality of a protein model has to be improved by ab initio methods such as energy-based simulation. In this study, we describe a new automatic refinement server method designed to improve locally inaccurate regions and overall structure simultaneously...
October 16, 2017: Proteins
https://www.readbyqxmd.com/read/29044752/zn-ii-interrupts-r4-r3-association-leading-to-accelerated-aggregation-of-tau-protein
#12
Vinesh Vijayan
Direct binding of divalent metal ion, especially Zn2+ have been shown to increase the rate of tau aggregation and enhance tau toxicity in cells. Hence understanding the molecular basis of the Zn2+ accelerated tau aggregation can potentially determine the molecular interactions modulating tau aggregation. Here we show that Zn2+ coordinate through the cysteine in R3 repeat and significantly accelerate the aggregation rate of the three repeat tau construct (K19) but the coordination is incapable of increasing the aggregation rate of the 20 amino acid peptide derived from the R3 repeat (R3) of tau...
October 17, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29044728/comparison-of-nmr-and-crystal-structures-of-membrane-proteins-and-computational-refinement-to-improve-model-quality
#13
Julia Koehler Leman, Andrew R D'Avino, Yash Bhatnagar, Jeffrey J Gray
Membrane proteins are challenging to study and restraints for structure determination are typically sparse or of low resolution because the membrane environment that surrounds them leads to a variety of experimental challenges. When membrane protein structures are determined by different techniques in different environments, a natural question is "which structure is most biologically relevant?" Towards answering this question, we compiled a dataset of membrane proteins with known structures determined by both solution NMR and X-ray crystallography...
October 16, 2017: Proteins
https://www.readbyqxmd.com/read/29044220/structure-of-melanins-from-the-fungi-ochroconis-lascauxensis-and-ochroconis-anomala-contaminating-rock-art-in-the-lascaux-cave
#14
José Maria De la Rosa, Pedro M Martin-Sanchez, Santiago Sanchez-Cortes, Bernardo Hermosin, Heike Knicker, Cesareo Saiz-Jimenez
Two novel species of the fungal genus Ochroconis, O. lascauxensis and O. anomala have been isolated from the walls of the Lascaux Cave, France. The interest in these fungi and their melanins lies in the formation of black stains on the walls and rock art which threatens the integrity of the paintings. Here we report solid-state cross polarization magic-angle spinning (13)C and (15)N nuclear magnetic resonance (NMR) spectroscopy and surface-enhanced Raman spectroscopy (SERS) of the melanins extracted from the mycelia of O...
October 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29043470/comprehensive-analysis-of-nmr-data-using-advanced-line-shape-fitting
#15
Markus Niklasson, Renee Otten, Alexandra Ahlner, Cecilia Andresen, Judith Schlagnitweit, Katja Petzold, Patrik Lundström
NMR spectroscopy is uniquely suited for atomic resolution studies of biomolecules such as proteins, nucleic acids and metabolites, since detailed information on structure and dynamics are encoded in positions and line shapes of peaks in NMR spectra. Unfortunately, accurate determination of these parameters is often complicated and time consuming, in part due to the need for different software at the various analysis steps and for validating the results. Here, we present an integrated, cross-platform and open-source software that is significantly more versatile than the typical line shape fitting application...
October 17, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29042280/biochemical-and-biophysical-characterization-of-a-mycoredoxin-protein-glutaredoxin-a1-from-corynebacterium-pseudotuberculosis
#16
Raphael J Eberle, Liege A Kawai, Fabio R de Moraes, Ljubica Tasic, Raghuvir K Arni, Monika A Coronado
Glutaredoxin A1 from Corynebacterium pseudotuberculosis was shown to be a mycoredoxin protein. In this study, we established a process to overexpress and purify glutaredoxin A1. The aim of this study was the investigation of the Glutaredoxin A1 from C. pseudotuberculosis behavior under different redox environments and the identification of lead molecules, which can be used for specific inhibitor development for this protein family. A quantitative assay was performed measuring the rate of insulin reduction spectrophotometrically at 640nm through turbidity formation from the precipitation of the free insulin...
October 14, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29040952/design-synthesis-kinetic-mechanism-and-molecular-docking-studies-of-novel-1-pentanoyl-3-arylthioureas-as-inhibitors-of-mushroom-tyrosinase-and-free-radical-scavengers
#17
Fayaz Ali Larik, Aamer Saeed, Pervaiz Ali Channar, Urooj Muqadar, Qamar Abbas, Mubashir Hassan, Sung-Yum Seo, Michael Bolte
A series of novel 1-pentanoyl-3-arylthioureas was designed as new mushroom tyrosinase inhibitors and free radical scavengers. The title compounds were obtained in excellent yield and characterized by FTIR, (1)H NMR, (13)C NMR and X-ray crystallography in case of compound (4a). The inhibitory effects on mushroom tyrosinase and DPPH were evaluated and it was observed that 1-Pentanoyl-3-(4-methoxyphenyl) thiourea (4f) showed tyrosinase inhibitory activity (IC50 1.568 ± 0.01 mM) comparable to Kojic acid (IC50 16...
September 29, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29040928/calorimetric-and-spectroscopic-studies-of-the-interaction-between-zidovudine-and-human-serum-albumin
#18
Adrian Pîrnău, Mihaela Mic, Silvia Neamţu, Călin G Floare, Mircea Bogdan
A quantitative analysis of the interaction between zidovudine (AZT) and human serum albumin (HSA) was achieved using Isothermal titration calorimetry (ITC) in combination with fluorescence and (1)H NMR spectroscopy. ITC directly measure the heat during a biomolecular binding event and gave us thermodynamic parameters and the characteristic association constant. By fluorescence quenching, the binding parameters of AZT-HSA interaction was determined and location to binding site I of HSA was confirmed. Via T1 NMR selective relaxation time measurements the drug-protein binding extent was evaluated as dissociation constants Kd and the involvement of azido moiety of zidovudine in molecular complex formation was put in evidence...
October 10, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/29040648/molecular-basis-for-asymmetry-sensing-of-sirnas-by-the-drosophila-loqs-pd-dcr-2-complex-in-rna-interference
#19
Jan-Niklas Tants, Stephanie Fesser, Thomas Kern, Ralf Stehle, Arie Geerlof, Christoph Wunderlich, Michael Juen, Christoph Hartlmüller, Romy Böttcher, Stefan Kunzelmann, Oliver Lange, Christoph Kreutz, Klaus Förstemann, Michael Sattler
RNA interference defends against RNA viruses and retro-elements within an organism's genome. It is triggered by duplex siRNAs, of which one strand is selected to confer sequence-specificity to the RNA induced silencing complex (RISC). In Drosophila, Dicer-2 (Dcr-2) and the double-stranded RNA binding domain (dsRBD) protein R2D2 form the RISC loading complex (RLC) and select one strand of exogenous siRNAs according to the relative thermodynamic stability of base-pairing at either end. Through genome editing we demonstrate that Loqs-PD, the Drosophila homolog of human TAR RNA binding protein (TRBP) and a paralog of R2D2, forms an alternative RLC with Dcr-2 that is required for strand choice of endogenous siRNAs in S2 cells...
October 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29040295/hydrophobic-residues-are-critical-for-the-helix-forming-hemolytic-and-bactericidal-activities-of-amphipathic-antimicrobial-peptide-tp4
#20
Ting-Wei Chang, Shu-Yi Wei, Shih-Han Wang, Hung-Mu Wei, Yu-June Wang, Chiu-Feng Wang, Chinpan Chen, You-Di Liao
Antimicrobial peptides are important components of the host innate defense mechanism against invading pathogens, especially for drug-resistant bacteria. In addition to bactericidal activity, the 25 residue peptide TP4 isolated from Nile tilapia also stimulates cell proliferation and regulates the innate immune system in mice. In this report, TP4 hyperpolarized and depolarized the membrane potential of Pseudomonas aeruginosa at sub-lethal and lethal concentrations. It also inhibited and eradicated biofilm formation...
2017: PloS One
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