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Protein chemistry

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https://www.readbyqxmd.com/read/28646836/biochemical-parameters-as-monitoring-markers-of-the-inflammatory-reaction-by-patients-with-chronic-obstructive-pulmonary-disease-copd
#1
Petra Lenártová, Jana Kopčeková, Martina Gažarová, Jana Mrázová, Joanna Wyka
Background: Chronic obstructive pulmonary disease (COPD) is an airway inflammatory disease caused by inhalation of toxic particles, mainly cigarette smoking, and now is accepted as a disease associated with systemic characteristics. Objective: The aim of this work was to investigate and compare selected biochemical parameters in patients with and without COPD. Material and Methods: Observation group consisted of clinically stable patients with COPD (n = 60)...
2017: Roczniki Państwowego Zakładu Higieny
https://www.readbyqxmd.com/read/28645377/electrical-probes-of-dna-binding-proteins
#2
Jacqueline K Barton, Phillip L Bartels, Yingxin Deng, Elizabeth O'Brien
A DNA electrochemistry platform has been developed to probe proteins bound to DNA electrically. Here gold electrodes are modified with thiol-modified DNA, and DNA charge transport chemistry is used to probe DNA binding and enzymatic reaction both with redox-silent and redox-active proteins. For redox-active proteins, the electrochemistry permits the determination of redox potentials in the DNA-bound form, where comparisons to DNA-free potentials can be made using graphite electrodes without DNA modification...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28644760/expression-and-characterization-of-soybean-seed-coat-peroxidase-in-escherichia-coli-bl21-de3
#3
Changqing Liu, Kai Zheng, Ying Xu, Lacmata Tamekou Stephen, Jiming Wang, Hongwei Zhao, Tongqing Yue, Rui Nian, Haibo Zhang, Mo Xian, Huizhou Liu
Soybean seed coat peroxidase(SBP) is a valuable enzyme having a broad variety of applications in analytical chemistry, biochemistry and food processing. In the present study, the sscp gene (Gene ID: 548068) was optimized based on the preferred codon usage of Escherichia coli, synthesized, and expressed in E. coli BL21(DE3). SDS-PAGE and western blot analysis of this expressed protein revealed that its molecular weight is approximately 39 kDa. The effects of induction temperature, concentration of IPTG (isopropyl-β-D-thiogalactoside) and hemin, induction time, expression time were optimized to enhance SBP production with a maximum activity of 11...
June 23, 2017: Preparative Biochemistry & Biotechnology
https://www.readbyqxmd.com/read/28644476/enantioselective-intermolecular-benzylic-c-h-amination-catalysed-by-an-engineered-iron-haem-enzyme
#4
Christopher K Prier, Ruijie K Zhang, Andrew R Buller, Sabine Brinkmann-Chen, Frances H Arnold
C-H bonds are ubiquitous structural units of organic molecules. Although these bonds are generally considered to be chemically inert, the recent emergence of methods for C-H functionalization promises to transform the way synthetic chemistry is performed. The intermolecular amination of C-H bonds represents a particularly desirable and challenging transformation for which no efficient, highly selective, and renewable catalysts exist. Here we report the directed evolution of an iron-containing enzymatic catalyst-based on a cytochrome P450 monooxygenase-for the highly enantioselective intermolecular amination of benzylic C-H bonds...
July 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28644007/cyclotides-as-tools-in-chemical-biology
#5
Simon J de Veer, Joachim Weidmann, David J Craik
Among the various molecules that plants produce for defense against pests and pathogens, cyclotides stand out as exceptionally stable and structurally unique. These ribosomally synthesized peptides are around 30 amino acids in size, and are stabilized by a head-to-tail cyclic peptide backbone and three disulfide bonds that form a cystine knot. They occur in certain plants of the Rubiaceae, Violaceae, Cucurbitaceae, Fabaceae, and Solanaceae families, with an individual plant producing up to hundreds of different cyclotides...
June 23, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28641555/supervised-machine-learning-methods-applied-to-predict-ligand-binding-affinity
#6
Gabriela Sehnem Heck, Val Oliveira Pintro, Richard Rene Pereira, Mauricio Boff de Ávila, Nayara Maria Bernhardt Levin, Walter Filgueira de Azevedo
BACKGROUND: Calculation of ligand-binding affinity is an open problem in computational medicinal chemistry. The ability to computationally predict affinities has a beneficial impact in the early stages of drug development, since it allows a mathematical model to assess protein-ligand interactions. Due to the availability of structural and binding information, machine learning methods have been applied to generate scoring functions with good predictive power. OBJECTIVE: Our goal here is to review recent developments in the application of machine learning methods to predict ligand- binding affinity...
June 22, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28640526/development-and-characterisation-of-a-99m-tc-tricarbonyl-labelled-estradiol-derivative-obtained-by-click-chemistry-with-potential-application-in-estrogen-receptors-imaging
#7
María Emilia Tejería, Javier Giglio, Silvia Dematteis, Ana Rey
Assessment of the presence of estrogen receptors in breast cancer is crucial for treatment planning. With the objective to develop a potential agent for estrogen receptors imaging we present the development and characterization of a (99m) Tc tricarbonyl labelled estradiol derivative. Using ethinylestradiol as starting material, a estradiol derivative bearing a 1,4-disubstituted 1,2,3-triazole-containing tridentate ligand system was synthesized by "Click Chemistry" and fully characterized. Labelling with high yield and radiochemical purity was achieved through the formation of a (99m) Tc-tricarbonyl complex...
June 22, 2017: Journal of Labelled Compounds & Radiopharmaceuticals
https://www.readbyqxmd.com/read/28640297/preparation-of-tetrazine-containing-2-1-complexes-of-99m-tc-and-in-vivo-targeting-using-bioorthogonal-inverse-electron-demand-diels-alder-chemistry
#8
Abdolreza Yazdani, Nancy Janzen, Shannon Czorny, Robert G Ungard, Tanya Miladinovic, Gurmit Singh, John F Valliant
The aim of this work was to synthesize and evaluate [2 + 1] (99m)Tc(i) polypyridine complexes containing tetrazines, which along with the corresponding Re(i) complexes, represent a new class of isostructural nuclear and turn-on luminescent probes that can be derivatized and targeted using bioorthogonal chemistry. To this end, [2 + 1] complexes of (99m)Tc(i) of the type [(99m)Tc(CO)3(N^N)(L)] (N^N = bathophenanthroline disulfonate (BPS) or 2,2'-bipyridine (bipy)), where the monodentate ligand (L) was a tetrazine linked to the metal through an imidazole derivative, were prepared...
June 22, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28639657/exploring-the-catalytic-mechanism-of-dihydropteroate-synthase-elucidating-the-differences-between-the-substrate-and-inhibitor
#9
Warot Chotpatiwetchkul, Kanokthip Boonyarattanakalin, Duangkamol Gleeson, M Paul Gleeson
Dihydropteroate synthase (DHPS) catalyzes the condensation of 6-hydroxymethyl-7,8-dihydropterin pyrophosphate (DHPPP) with p-aminobenzoic acid (pABA) and is a well validated target for anti-malarial and anti-bacterial drugs. However, in recent years its utility as a therapeutic target has diminished considerably due to multiple mutations. As such, considerable structural biology and medicinal chemistry effort has been expended to understand and overcome this issue. To date no detailed computational analysis of the protein mechanism has been made despite the detailed crystal structures and multiple mechanistic proposals being made...
June 22, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28637399/biomineralized-recombinant-collagen-based-scaffold-mimicking-native-bone-enhances-mesenchymal-stem-cell-interaction-and-differentiation
#10
Gloria Belén Ramirez-Rodríguez, Monica Montesi, Silvia Panseri, Simone Sprio, Anna Tampieri, Monica Sandri
The need of synthetic bone grafts that recreate from macro to nanoscale level the biochemical and biophysical cues of bone extracellular matrix (ECM) has been a major driving force for the development of new generation of biomaterials. In this study, synthetic bone substitutes have been synthesized via biomimetic mineralization of a recombinant collagen type I derived peptide (RCP), enriched in tri-amino acid sequence arginine-glycine-aspartate (RGD). 3D isotropic porous scaffolds of three different compositions are developed by freeze-drying: non-mineralized (RCP, as a control), mineralized (Ap/RCP) and mineralized scaffolds in presence of magnesium (MgAp/RCP) that closely imitate bone composition...
June 22, 2017: Tissue Engineering. Part A
https://www.readbyqxmd.com/read/28636761/molecular-tools-for-facilitative-carbohydrate-transporters
#11
Marina Tanasova, Joseph R Fedie
Facilitative carbohydrate transporters - Gluts - have received a wide attention over decades due to their essential role in the nutrient uptake and links with various metabolic disorders, including diabetes, obesity, and cancer. Endeavors into understanding mechanisms of Glut-mediated nutrient uptake have resulted in the multidisciplinary research field, branching protein chemistry, chemical biology, organic synthesis, crystallography, and biomolecular modeling. Gluts became attractive targets for cancer research and medicinal chemistry, leading to the development of new approaches to cancer diagnostics and providing avenues for cancer-targeting therapeutics...
June 21, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28636680/unifying-the-microscopic-picture-of-his-containing-turns-from-gas-phase-model-peptides-to-crystallized-proteins
#12
Woon Yong Sohn, Sana Habka, Eric Gloaguen, Michel Mons
The presence in crystallized proteins of a local anchoring between the side chain of a His residue, located in the central position of a γ- or β-turn, and its local main chain environment, was assessed by the comparison of protein structures with relevant isolated model peptides. Gas phase laser spectroscopy, combined with relevant quantum chemistry methods, was used to characterize the γ- and β-turn structures in these model peptides. A conformer-selective NH stretch infrared study provided evidence for the formation in vacuo of two types of short-range H-bonded motifs, labelled ε-6(δ) and δ-(δ)7/π(H), bridging the His side chain (in its gauche+ rotamer) to the neighbouring NH(i) and CO(i) sites of the backbone; each side chain-backbone motif was found to be specific of the tautomer (ε or δ) adopted by the His side chain in its neutral form...
June 21, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28636382/development-of-efficient-chemistry-to-generate-site-specific-disulfide-linked-protein-and-peptide-payload-conjugates-application-to-thiomab%C3%A2-antibody-drug-conjugates
#13
Jack David Sadowsky, Thomas H Pillow, Jinhua Chen, Fang Fan, Changrong He, Yanli Wang, Gang Yan, Hui Yao, Zijin Xu, Shanique Martin, Donglu Zhang, Phillip Chu, Josefa Dela Cruz-Chuh, Aimee O'Donohue, Guangmin Li, Geoffrey Del Rosario, Jintang He, Luna Liu, Carl K Ng, Dian Su, Gail D Lewis Phillips, Katherine Ruth Kozak, Shang-Fan Yu, Keyang Xu, Douglas Leipold, John S Wai
Conjugation of small molecule payloads to specific cysteine residues on proteins via a disulfide bond represents an attractive strategy to generate redox-sensitive bioconjugates, which have value as potential diagnostic reagents or therapeutics. Advancement of such "direct-disulfide" bioconjugates to the clinic necessitates chemical methods to form disulfide connections efficiently, without byproducts. The disulfide connection must also be resistant to premature cleavage by thiols prior to arrival at the targeted tissue...
June 21, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28636358/transferable-atom-centered-potentials-for-the-correction-of-basis-set-incompleteness-errors-in-density-functional-theory
#14
Alberto Otero-de-la-Roza, Gino A DiLabio
Recent progress in the accurate calculation of non-covalent interactions has enabled density-functional theory (DFT) to model systems relevant in biological and supramolecular chemistry. The application of DFT methods using atom-centered Gaussian basis sets to large systems is limited by the number of basis functions required to accurately model thermochemistry and, in particular, weak intermolecular interactions. Basis-set incompleteness error (BSIE) arising from the use of incomplete basis sets leads to erroneous intermolecular energies, bond dissociation energies, and structures...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28636349/water-dynamics-from-the-surface-to-the-interior-of-a-supramolecular-nanostructure
#15
Julia H Ortony, Baofu Qiao, Christina J Newcomb, Timothy J Keller, Liam C Palmer, Elad Deiss-Yehiely, Monica Olvera de la Cruz, Songi Han, Samuel I Stupp
Water within and surrounding the structure of a biological system adopts context-specific dynamics that mediate virtually all of the events involved in the inner workings of a cell. These events range from protein folding and molecular recognition to the formation of hierarchical structures. Water dynamics are mediated by the chemistry and geometry of interfaces where water and biomolecules meet. Here we investigate experimentally and computationally the translational dynamics of vicinal water molecules within the volume of a supramolecular peptide nanofiber measuring 6...
June 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28636311/insights-into-integrated-lead-generation-and-target-identification-in-malaria-and-tuberculosis-drug-discovery
#16
John Okombo, Kelly Chibale
New, safe and effective drugs are urgently needed to treat and control malaria and tuberculosis, which affect millions of people annually. However, financial return on investment in the poor settings where these diseases are mostly prevalent is very minimal to support market-driven drug discovery and development. Moreover, the imminent loss of therapeutic lifespan of existing therapies due to evolution and spread of drug resistance further compounds the urgency to identify novel effective drugs. However, the advent of new public-private partnerships focused on tropical diseases and the recent release of large data sets by pharmaceutical companies on antimalarial and antituberculosis compounds derived from phenotypic whole cell high throughput screening have spurred renewed interest and opened new frontiers in malaria and tuberculosis drug discovery...
June 21, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28636310/sensing-mechanisms-in-the-redox-regulated-2fe-2s-cluster-containing-bacterial-transcriptional-factor-soxr
#17
Kazuo Kobayashi
Bacteria possess molecular biosensors that enable responses to a variety of stressful conditions, including oxidative stress, toxic compounds, and interactions with other organisms, through elaborately coordinated regulation of gene expression. In Escherichia coli and related bacteria, the transcription factor SoxR functions as a sensor of oxidative stress and nitric oxide (NO). SoxR protein contains a [2Fe-2S] cluster essential for its transcription-enhancing activity, which is regulated by redox changes in the [2Fe-2S] cluster...
June 21, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28636028/supramolecular-functional-assemblies-dynamic-membrane-transporters-and-peptide-nanotubular-composites
#18
Alberto Fuertes, Marisa Juanes, Juan R Granja, Javier Montenegro
The fabrication of functional molecular devices constitutes one of the most important current challenges for chemical sciences. The complex processes accomplished by living systems continuously demand the assistance of non-covalent interactions between molecular building blocks. Additionally, these building blocks (proteins, membranes, nucleotides) are also constituted by self-assembled structures. Therefore, supramolecular chemistry is the discipline required to understand the properties of the minimal self-assembled building blocks of living systems and to develop new functional smart materials...
June 21, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28635627/molecular-quantum-similarity-chemical-reactivity-and-database-screening-of-3d-pharmacophores-of-the-protein-kinases-a-b-and-g-from-mycobacterium-tuberculosis
#19
Alejandro Morales-Bayuelo
Mycobacterium tuberculosis remains one of the world's most devastating pathogens. For this reason, we developed a study involving 3D pharmacophore searching, selectivity analysis and database screening for a series of anti-tuberculosis compounds, associated with the protein kinases A, B, and G. This theoretical study is expected to shed some light onto some molecular aspects that could contribute to the knowledge of the molecular mechanics behind interactions of these compounds, with anti-tuberculosis activity...
June 21, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28634286/conjugate-vaccine-immunotherapy-for-substance-use-disorder
#20
REVIEW
Paul T Bremer, Kim D Janda
Substance use disorder, especially in relation to opioids such as heroin and fentanyl, is a significant public health issue and has intensified in recent years. As a result, substantial interest exists in developing therapeutics to counteract the effects of abused drugs. A promising universal strategy for antagonizing the pharmacology of virtually any drug involves the development of a conjugate vaccine, wherein a hapten structurally similar to the target drug is conjugated to an immunogenic carrier protein...
July 2017: Pharmacological Reviews
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