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Protein chemistry

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https://www.readbyqxmd.com/read/28937222/variable-lysozyme-transport-dynamics-on-oxidatively-functionalized-polystyrene-films
#1
Nicholas Anthony Moringo, Hao Shen, Lawrence J Tauzin, Wenxiao Wang, Logan D C Bishop, Christy F Landes
Tuning protein adsorption dynamics at polymeric interfaces is of great interest to many biomedical and material applications. Functionalization of polymer surfaces is a common method to introduce application specific surface chemistries to a polymer interface. In this work single molecule fluorescence microscopy is utilized to determine the adsorption dynamics of lysozyme, a well-studied antibacterial protein, at the interface of polystyrene oxidized via UV exposure, oxygen plasma, and functionalized by ligand grafting to produce varying degrees of surface hydrophilicity, surface roughness, and induced oxygen content...
September 22, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28935952/application-of-bio-orthogonal-proteome-labeling-to-cell-transplantation-and-heterochronic-parabiosis
#2
Yan Liu, Michael J Conboy, Melod Mehdipour, Yutong Liu, Thanhtra P Tran, Aaron Blotnick, Prasanna Rajan, Thalie Cavalcante Santos, Irina M Conboy
Studies of heterochronic parabiosis demonstrated that with age, the composition of the circulatory milieu changes in ways that broadly inhibit tissue regenerative capacity. In addition, local tissue niches have age-specific influences on their resident stem cells. Here we use bio-orthogonal proteome labeling for detecting in vivo proteins present only in transplanted myoblasts, but not in host tissue, and proteins exclusive to one young mouse and transferred during parabiosis to its old partner. We use a transgenic mouse strain that ubiquitously expresses a modified tRNA methionine synthase, metRS, which preferentially incorporates the methionine surrogate azido-nor-leucine (ANL) into newly generated proteins...
September 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28935106/chemoenzymatic-glycan-remodeling-of-natural-and-recombinant-glycoproteins
#3
Qiang Yang, Lai-Xi Wang
N-glycosylation plays important roles in modulating the biological functions of glycoproteins, such as protein folding, stability, and immunogenicity. However, acquiring homogeneous glycoforms of glycoproteins has been a challenging task for functional studies and therapeutic applications. In this chapter, we describe an efficient chemoenzymatic glycan remodeling protocol for making homogeneous glycoproteins that involves enzymatic deglycosylation and subsequent reglycosylation procedures. Two therapeutic glycoproteins, Herceptin (trastuzumab, a therapeutic monoclonal antibody) and erythropoietin (EPO, a glycoprotein hormone), were chosen as the model systems...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28934470/monitoring-replication-protein-a-rpa-dynamics-in-homologous-recombination-through-site-specific-incorporation-of-non-canonical-amino-acids
#4
Nilisha Pokhrel, Sofia Origanti, Eric Parker Davenport, Disha Gandhi, Kyle Kaniecki, Ryan A Mehl, Eric C Greene, Chris Dockendorff, Edwin Antony
An essential coordinator of all DNA metabolic processes is Replication Protein A (RPA). RPA orchestrates these processes by binding to single-stranded DNA (ssDNA) and interacting with several other DNA binding proteins. Determining the real-time kinetics of single players such as RPA in the presence of multiple DNA processors to better understand the associated mechanistic events is technically challenging. To overcome this hurdle, we utilized non-canonical amino acids and bio-orthogonal chemistry to site-specifically incorporate a chemical fluorophore onto a single subunit of heterotrimeric RPA...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28933478/natural-product-modulators-of-human-sensations-and-mood-molecular-mechanisms-and-therapeutic-potential
#5
REVIEW
Tomáš Pluskal, Jing-Ke Weng
Humans perceive physical information about the surrounding environment through their senses. This physical information is registered by a collection of highly evolved and finely tuned molecular sensory receptors. A multitude of bioactive, structurally diverse ligands have evolved in nature that bind these molecular receptors. The complex, dynamic interactions between the ligands and the receptors lead to changes in our sensory perception or mood. Here, we review our current knowledge of natural products and their derived analogues that interact specifically with human G protein-coupled receptors, ion channels, and nuclear hormone receptors to modulate the sensations of taste, smell, temperature, pain, and itch, as well as mood and its associated behaviour...
September 21, 2017: Chemical Society Reviews
https://www.readbyqxmd.com/read/28933286/ag-complexes-as-potential-therapeutic-agents-in-medicine-and-pharmacy
#6
Aleksandra Hecel, Paulina Kolkowska, Karolina Krzywoszynska, Agnieszka Szebesczyk, Magdalena Rowinska-Zyrek, Henryk Kozlowski
Silver is a non-essential element, with promising antimicrobial and anticancer properties. This work is a detailed summary of the newest findings on the bioinorganic chemistry of silver, with a special focus on the applications of Ag+ complexes and nanoparticles. The coordination chemistry of silver is given a reasonable amount of attention, summarizing the most common silver binding sites and giving examples of such binding motifs in biologically important proteins. Possible applications of this metal and its complexes in medicine, in particular as antibacterial and antifungal agents and in cancer therapy is discussed in detail...
September 20, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28932860/immobilized-enzymes-understanding-enzyme-surface-interactions-at-the-molecular-level
#7
REVIEW
Marie Hoarau, Somayesadat Badieyan, E Neil G Marsh
Enzymes immobilized on solid supports have important and industrial and medical applications. However, their uses are limited by the significant reductions in activity and stability that often accompany the immobilization process. Here we review recent advances in our understanding of the molecular level interactions between proteins and supporting surfaces that contribute to changes in stability and activity. This understanding has been facilitated by the application of various surface-sensitive spectroscopic techniques that allow the structure and orientation of enzymes at the solid/liquid interface to be probed, often with monolayer sensitivity...
September 21, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28928405/nanopore-extended-field-effect-transistor-for-selective-single-molecule-biosensing
#8
Ren Ren, Yanjun Zhang, Binoy Paulose Nadappuram, Bernice Akpinar, David Klenerman, Aleksandar P Ivanov, Joshua B Edel, Yuri Korchev
There has been a significant drive to deliver nanotechnological solutions to biosensing, yet there remains an unmet need in the development of biosensors that are affordable, integrated, fast, capable of multiplexed detection, and offer high selectivity for trace analyte detection in biological fluids. Herein, some of these challenges are addressed by designing a new class of nanoscale sensors dubbed nanopore extended field-effect transistor (nexFET) that combine the advantages of nanopore single-molecule sensing, field-effect transistors, and recognition chemistry...
September 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28926429/targeting-histone-acetylation-readers-and-writers-in-leukemia-and-cancer
#9
Christopher B Benton, Warren Fiskus, Kapil N Bhalla
Chromatin packaging of DNA provides a framework for transcriptional regulation. Modifications to DNA and histone proteins in nucleosomes lead to conformational changes, alterations in the recruitment of transcriptional complexes, and ultimately modulation of gene expression. We provide a focused review of control mechanisms that help modulate the activation and deactivation of gene transcription specifically through histone acetylation writers and readers in cancer. The chemistry of these modifications is subject to clinically actionable targeting, including state-of-the-art strategies to inhibit basic oncogenic mechanisms related to histone acetylation...
September 2017: Cancer Journal
https://www.readbyqxmd.com/read/28926241/supramolecular-chemistry-targeting-proteins
#10
Sam van Dun, Christian Ottmann, Lech-Gustav Milroy, Luc Brunsveld
The specific recognition of protein surface elements is a fundamental challenge in the life sciences. New developments in this field will form the basis of new therapeutic approaches and will lead to applications such as sensors, affinity-tags, immobilization techniques and protein-based materials. Synthetic supramolecular molecules and materials are creating new opportunities for protein recognition, which are orthogonal to classical small molecule and protein-based approaches. As outlined here, their unique molecular features enable the recognition of amino acids, peptides and even whole protein surfaces, which can be applied to the modulation and assembly of proteins...
September 19, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28924661/correlative-sim-storm-microscopy
#11
O Burri, T Laroche, R Guiet, A Seitz
The ability to specifically label subcellular structures or even proteins of interest in combination with the ability to look at live specimens turned fluorescence light microscopy into an invaluable tool. However, conventional light microscopy is diffraction limited, which restricts the lateral resolution to around 200 nm laterally and 600-800 nm axially. In 2014, the Nobel Prize in Chemistry was awarded to Eric Betzig, Stefan W. Hell, and William E. Moerner for the development of super-resolved fluorescent microscopy techniques...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28922574/super-resolution-microscopy-unveils-dynamic-heterogeneities-in-nanoparticle-protein-corona
#12
Natalia Feiner-Gracia, Michaela Beck, Sílvia Pujals, Sébastien Tosi, Tamoghna Mandal, Christian Buske, Mika Linden, Lorenzo Albertazzi
The adsorption of serum proteins, leading to the formation of a biomolecular corona, is a key determinant of the biological identity of nanoparticles in vivo. Therefore, gaining knowledge on the formation, composition, and temporal evolution of the corona is of utmost importance for the development of nanoparticle-based therapies. Here, it is shown that the use of super-resolution optical microscopy enables the imaging of the protein corona on mesoporous silica nanoparticles with single protein sensitivity...
September 18, 2017: Small
https://www.readbyqxmd.com/read/28921971/paper-sensor-coated-with-a-poly-carboxybetaine-multiple-dopa-conjugate-via-dip-coating-for-biosensing-in-complex-media
#13
Fang Sun, Kan Wu, Hsiang-Chieh Hung, Peng Zhang, Xinran Che, Joshua Kenyon Smith, Xiaojie Lin, Bowen Li, Priyesh Jain, Qiuming Yu, Shaoyi Jiang
Cellulose paper is an ideal diagnostic platform for low-cost, easily disposable and lightweight implementation, but requires surface modification to achieve detection with high sensitivity and specificity in complex media. In this work, a polymer-catechol conjugate containing a super-hydrophilic nonfouling poly(carboxylbetaine) (pCB) and four surface-binding L-3,4-dihydroxyphenylalanine (DOPA) groups, pCB-(DOPA)4, were applied onto a paper-based sensor surface via a simple "graft-to" immersion process to render the surface with both nonfouling and protein functionalizable properties...
September 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28921867/polymer-cancerostatics-targeted-with-an-antibody-fragment-bound-via-a-coiled-coil-motif-in-vivo-therapeutic-efficacy-against-murine-bcl1-leukemia
#14
Michal Pechar, Robert Pola, Olga Janoušková, Irena Sieglová, Vlastimil Král, Milan Fábry, Barbora Tomalová, Marek Kovář
A BCL1 leukemia-cell-targeted polymer-drug conjugate with a narrow molecular weight distribution consisting of an N-(2-hydroxypropyl)methacrylamide copolymer carrier and the anticancer drug pirarubicin is prepared by controlled radical copolymerization followed by metal-free click chemistry. A targeting recombinant single chain antibody fragment (scFv) derived from a B1 monoclonal antibody is attached noncovalently to the polymer carrier via a coiled coil interaction between two complementary peptides. Two pairs of coiled coil forming peptides (abbreviated KEK/EKE and KSK/ESE) are used as linkers between the polymer-pirarubicin conjugate and the targeting protein...
September 15, 2017: Macromolecular Bioscience
https://www.readbyqxmd.com/read/28921842/anchorquery-rapid-online-virtual-screening-for-small-molecule-protein-protein-interaction-inhibitors
#15
David R Koes, Alexander Dömling, Carlos J Camacho
AnchorQuery ( http://anchorquery.csb.pitt.edu) is a web application for rational structure-based design of protein-protein interaction (PPI) inhibitors. A specialized variant of pharmacophore search is used to rapidly screen libraries consisting of more than 31 million synthesizable compounds biased by design to preferentially target PPIs. Every library compound is accessible through one-step multi-component reaction (MCR) chemistry and contains an anchor motif that is bioisosteric to an amino acid residue...
September 16, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28920818/biochemistry-panel-reference-intervals-for-juvenile-goldfish-carassius-auratus
#16
Laura A Adamovicz, Macy R Trosclair, Gregory A Lewbart
Reference intervals for diagnostic tests are vitally important for clinical decision making. Despite the popularity of pet goldfish (Carassius auratus), reference intervals have not been generated for routine biochemistry panel analytes in this species. This study establishes de novo reference intervals for packed cell volume and total solids, using 47 apparently healthy immature goldfish, and for 11 common chemistry panel analytes (albumin, aspartate aminotransferase, calcium, creatine kinase, globulin, blood glucose, sodium, potassium, phosphorous, total protein, and uric acid) using 39 immature goldfish...
September 2017: Journal of Zoo and Wildlife Medicine: Official Publication of the American Association of Zoo Veterinarians
https://www.readbyqxmd.com/read/28920010/exploring-step-by-step-assembly-of-nanoparticle-cytochrome-biohybrid-photoanodes
#17
Ee Taek Hwang, Katherine L Orchard, Daisuke Hojo, Joseph Beton, Colin W J Lockwood, Tadafumi Adschiri, Julea N Butt, Erwin Reisner, Lars J C Jeuken
Coupling light-harvesting semiconducting nanoparticles (NPs) with redox enzymes has been shown to create artificial photosynthetic systems that hold promise for the synthesis of solar fuels. High quantum yields require efficient electron transfer from the nanoparticle to the redox protein, a property that can be difficult to control. Here, we have compared binding and electron transfer between dye-sensitized TiO2 nanocrystals or CdS quantum dots and two decaheme cytochromes on photoanodes. The effect of NP surface chemistry was assessed by preparing NPs capped with amine or carboxylic acid functionalities...
August 2017: ChemElectroChem
https://www.readbyqxmd.com/read/28919707/quantum-mechanics-implementation-in-drug-design-workflows-does-it-really-help
#18
REVIEW
Olayide A Arodola, Mahmoud Es Soliman
The pharmaceutical industry is progressively operating in an era where development costs are constantly under pressure, higher percentages of drugs are demanded, and the drug-discovery process is a trial-and-error run. The profit that flows in with the discovery of new drugs has always been the motivation for the industry to keep up the pace and keep abreast with the endless demand for medicines. The process of finding a molecule that binds to the target protein using in silico tools has made computational chemistry a valuable tool in drug discovery in both academic research and pharmaceutical industry...
2017: Drug Design, Development and Therapy
https://www.readbyqxmd.com/read/28918628/breaking-benzene-aromaticity-computational-insights-into-the-mechanism-of-the-tungsten-containing-benzoyl-coa-reductase
#19
Martin Culka, Simona G Huwiler, Matthias Boll, G Matthias Ullmann
Aromatic compounds are environmental pollutants with toxic and carcinogenic properties. Despite the stability of aromatic rings, bacteria are able to degrade the aromatic compounds into simple metabolites and use them as growth substrates under oxic or even under anoxic conditions. In anaerobic microorganisms, most monocyclic aromatic growth substrates are converted to the central intermediate benzoyl-coenzyme A, which is enzymatically reduced to cyclohexa-1,5-dienoyl-CoA. The strcitly anaerobic bacterium \textit{Geobacter metallireducens} uses the class II benzoyl-CoA reductase complex for this reaction...
September 18, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28917797/a-rapid-and-specific-colorimetric-method-for-free-tryptophan-quantification
#20
Yinan Wu, Tianmin Wang, Chong Zhang, Xin-Hui Xing
Tryptophan is one of the eight essential amino acids and plays an important role in many biological processes. For its interaction with human health, environment and relevant commercial interest in biotechnology-based production, rapid and specific quantification method for this molecule accessible to common laboratories is badly needed. We herein reported a simple colorimetric method for free tryptophan quantification with 96-well-plate-level throughput. Our protocol firstly converted tryptophan to indole enzymatically by purified tryptophanases and then used reactivity of indole with hydroxylamine to form pink product with absorption peak at 530nm, enabling the quantification of tryptophan with simple spectrometry in just two hours...
January 1, 2018: Talanta
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