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Protein chemistry

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https://www.readbyqxmd.com/read/28719022/engineering-the-surface-of-smart-nanocarriers-using-a-ph-thermal-gsh-responsive-polymer-zipper-for-precise-tumor-targeting-therapy-in-vivo
#1
Penghui Zhang, Yan Wang, Jing Lian, Qi Shen, Chen Wang, Bohan Ma, Yuchao Zhang, Tingting Xu, Jianxin Li, Yongping Shao, Feng Xu, Jun-Jie Zhu
Nanocarrier surface chemistry plays a vital role in mediating cell internalization and enhancing delivery efficiency during in vivo chemotherapy. Inspired by the ability of proteins to alter their conformation to mediate functions, a pH-/thermal-/glutathione-responsive polymer zipper consisting of cell-penetrating poly(disulfide)s and thermosensitive polymers bearing guanidinium/phosphate (Gu(+) /pY(-) ) motifs to spatiotemporally tune the surface composition of nanocarriers for precise tumor targeting and efficient drug delivery is developed...
July 18, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28717933/a-novel-ms-cleavable-azo-cross-linker-for-peptide-structure-analysis-by-free-radical-initiated-peptide-sequencing-frips
#2
Claudio Iacobucci, Christoph Hage, Mathias Schäfer, Andrea Sinz
The chemical cross-linking/mass spectrometry (MS) approach is a growing research field in structural proteomics that allows gaining insights into protein conformations. It relies on creating distance constraints between cross-linked amino acid side chains that can further be used to derive protein structures. Currently, the most urgent task for designing novel cross-linking principles is an unambiguous and automated assignment of the created cross-linked products. Here, we introduce the homobifunctional, amine-reactive, and water soluble cross-linker azobisimidoester (ABI) as a prototype of a novel class of cross-linkers...
July 17, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28717420/comprehensive-toxicity-and-immunogenicity-studies-reveal-minimal-effects-in-mice-following-sustained-dosing-of-extracellular-vesicles-derived-from-hek293t-cells
#3
Xiaohua Zhu, Mohamed Badawi, Steven Pomeroy, Dhruvitkumar S Sutaria, Zhiliang Xie, Alice Baek, Jinmai Jiang, Ola A Elgamal, Xiaokui Mo, Krista La Perle, Jeffrey Chalmers, Thomas D Schmittgen, Mitch A Phelps
Extracellular vesicles (EVs) are under evaluation as therapeutics or as vehicles for drug delivery. Preclinical studies of EVs often use mice or other animal models to assess efficacy and disposition. However, as most EVs under evaluation are derived from human cells, they may elicit immune responses which may contribute to toxicities or enhanced EV clearance. Furthermore, EVs from different cell sources or EVs comprising various cargo may differ with respect to immunogenicity or toxicity. To assess EV-induced immune response and toxicity, we dosed C57BL/6 mice with EVs intravenously and intraperitoneally for 3 weeks...
2017: Journal of Extracellular Vesicles
https://www.readbyqxmd.com/read/28717021/genetic-and-metabolic-engineering-in-diatoms
#4
REVIEW
Weichao Huang, Fayza Daboussi
Diatoms have attracted considerable attention due to their success in diverse environmental conditions, which probably is a consequence of their complex origins. Studies of their metabolism will provide insight into their adaptation capacity and are a prerequisite for metabolic engineering. Several years of investigation have led to the development of the genome engineering tools required for such studies, and a profusion of appropriate tools is now available for exploring and exploiting the metabolism of these organisms...
September 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28715203/a-bioinorganic-approach-to-fragment-based-drug-discovery-targeting-metalloenzymes
#5
Seth M Cohen
Metal-dependent enzymes (i.e., metalloenzymes) make up a large fraction of all enzymes and are critically important in a wide range of biological processes, including DNA modification, protein homeostasis, antibiotic resistance, and many others. Consequently, metalloenzymes represent a vast and largely untapped space for drug development. The discovery of effective therapeutics that target metalloenzymes lies squarely at the interface of bioinorganic and medicinal chemistry and requires expertise, methods, and strategies from both fields to mount an effective campaign...
July 17, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28715190/chemical-topic-modeling-exploring-molecular-datasets-using-a-common-text-mining-approach
#6
Nadine Schneider, Nikolas Fechner, Gregory A Landrum, Nikolaus Stiefl
Big data is one of the key transformative factors which are increasingly influencing all aspects of modern life. Although this transformation brings vast opportunities it also generates novel challenges, not the least of which is organizing and searching this data deluge. The field of medicinal chemistry is not different: more and more data are being generated, for instance by technologies such as DNA encoded libraries, peptide libraries, text mining of large literature corpora, and new in silico enumeration methods...
July 17, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28714902/fluorescence-modulation-of-green-fluorescent-protein-using-fluorinated-unnatural-amino-acids
#7
Jordan K Villa, Hong-Anh Tran, Megha Vipani, Stephanie Gianturco, Konark Bhasin, Brent L Russell, Elizabeth J Harbron, Douglas D Young
The ability to modulate protein function through minimal perturbations to amino acid structure represents an ideal mechanism to engineer optimized proteins. Due to the novel spectroscopic properties of green fluorescent protein, it has found widespread application as a reporter protein throughout the fields of biology and chemistry. Using site-specific amino acid mutagenesis, we have incorporated various fluorotyrosine residues directly into the fluorophore of the protein, altering the fluorescence and shifting the pKa of the phenolic proton associated with the fluorophore...
July 16, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28714536/the-evaluation-of-acute-toxicity-antimicrobial-activity-of-1-phenyl-5-p-tolyl-1h-1-2-3-triazole-and-binding-to-human-serum-albumin
#8
Hong-Ye Duan, Jian-Ling Li, Lu-Yong Wu, Huo-Ming Shu, Yu-Xue Chen, Guo-Hua Ding, Run-Cong Dong, Hong-Zong Si, Xia Zhong, Wen-Ying He
1-Phenyl-5-p-tolyl-1H-1, 2, 3-triazole (PPTA) was a synthesized compound. The result of acute toxicities to mice of PPTA by intragastric administration indicated that PPTA did not produce any significant acute toxic effect on Kunming strain mice. It exhibited the various potent inhibitory activities against two kinds of bananas pathogenic bacteria, black sigatoka and freckle, when compared with that of control drugs and the inhibitory rates were up to 64.14% and 43.46%, respectively, with the same concentration of 7...
July 17, 2017: Journal of Biochemical and Molecular Toxicology
https://www.readbyqxmd.com/read/28712284/mn-ii-oxidation-by-the-multicopper-oxidase-complex-mnx-a-binuclear-activation-mechanism
#9
Alexandra V Soldatova, Lizhi Tao, Christine A Romano, Troy A Stich, William H Casey, R David Britt, Bradley M Tebo, Thomas G Spiro
The bacterial protein complex Mnx contains a multicopper oxidase (MCO) MnxG that, unusually, catalyzes the two-electron oxidation of Mn(II) to MnO2 biomineral, via a Mn(III) intermediate. Although Mn(III)/Mn(II) and Mn(IV)/Mn(III) reduction potentials are expected to be high, we find a low reduction potential, 0.38V (pH 7.8), for the MnxG type 1 Cu(2+), the electron acceptor. Indeed the type 1 Cu(2+) is not reduced by Mn(II) in the absence of molecular oxygen, indicating that substrate oxidation requires an activation step...
July 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28711855/exploiting-and-engineering-hemoproteins-for-abiological-carbene-and-nitrene-transfer-reactions
#10
REVIEW
Oliver F Brandenberg, Rudi Fasan, Frances H Arnold
The surge in reports of heme-dependent proteins as catalysts for abiotic, synthetically valuable carbene and nitrene transfer reactions dramatically illustrates the evolvability of the protein world and our nascent ability to exploit that for new enzyme chemistry. We highlight the latest additions to the hemoprotein-catalyzed reaction repertoire (including carbene Si-H and C-H insertions, Doyle-Kirmse reactions, aldehyde olefinations, azide-to-aldehyde conversions, and intermolecular nitrene C-H insertion) and show how different hemoprotein scaffolds offer varied reactivity and selectivity...
July 13, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28708394/human-viperin-causes-radical-sam-dependent-elongation-of-escherichia-coli-hinting-at-its-physiological-role
#11
Micah T Nelp, Anthony P Young, Branden M Stepanski, Vahe Bandarian
Viperin (virus inhibitory protein, endoplasmic reticulum-associated, interferon-inducible) is a widely distributed protein that is expressed in response to infection and causes antiviral effects against a broad spectrum of viruses. Viperin is a member of the radical S-adenosyl-l-methionine (SAM) superfamily of enzymes, which typically employ a 4Fe-4S cluster to reductively cleave SAM to initiate chemistry. Though the specific reaction catalyzed by viperin remains unknown, it has been shown that expression of viperin causes an increase in the fluidity of lipid membranes, which impedes the budding of nascent viral particles from the membrane inhibiting propagation of the infection...
July 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28707880/pinpoint-chemical-modification-of-the-quinone-access-channel-of-mitochondrial-complex-i-via-a-two-step-conjugation-reaction
#12
Takahiro Masuya, Masatoshi Murai, Takeshi Ito, Shunsuke Aburaya, Wataru Aoki, Hideto Miyoshi
We previously showed that a bulky ring-strained cycloalkyne possessing a rhodamine fluorophore directly reacts (via strain-promoted click chemistry) with the azido group incorporated (via ligand-directed tosyl chemistry) into Asp160 in the 49 kDa subunit of complex I in bovine heart submitochondrial particles [Masuya et al. (2014) Biochemistry 53, 7816-7823]. This two-step conjugation may be a promising technique for specific chemical modifications of the quinone-access channel in complex I by various molecular probes, which would lead to new methodologies for studying the enzyme...
July 14, 2017: Biochemistry
https://www.readbyqxmd.com/read/28706325/axsis-exploring-the-frontiers-in-attosecond-x-ray-science-imaging-and-spectroscopy
#13
F X Kärtner, F Ahr, A-L Calendron, H Çankaya, S Carbajo, G Chang, G Cirmi, K Dörner, U Dorda, A Fallahi, A Hartin, M Hemmer, R Hobbs, Y Hua, W R Huang, R Letrun, N Matlis, V Mazalova, O D Mücke, E Nanni, W Putnam, K Ravi, F Reichert, I Sarrou, X Wu, A Yahaghi, H Ye, L Zapata, D Zhang, C Zhou, R J D Miller, K K Berggren, H Graafsma, A Meents, R W Assmann, H N Chapman, P Fromme
X-ray crystallography is one of the main methods to determine atomic-resolution 3D images of the whole spectrum of molecules ranging from small inorganic clusters to large protein complexes consisting of hundred-thousands of atoms that constitute the macromolecular machinery of life. Life is not static, and unravelling the structure and dynamics of the most important reactions in chemistry and biology is essential to uncover their mechanism. Many of these reactions, including photosynthesis which drives our biosphere, are light induced and occur on ultrafast timescales...
September 1, 2016: Nuclear Instruments & Methods in Physics Research. Section A, Accelerators, Spectrometers, Detectors and Associated Equipment
https://www.readbyqxmd.com/read/28704989/in-vitro-study-of-the-influence-of-octocrylene-on-a-selected-metastatic-melanoma-cell-line
#14
Tanja Prunk Zdravković, Bogdan Zdravković, Marko Zdravković, Barbara Dariš, Mojca Lunder, Polonca Ferk
BACKGROUND: Octocrylene (OCT) is one of the most widespread chemical UV filters used in sunscreens and cosmetic products. Despite the use of sunscreens and personal care products over decades, melanoma as the most serious and aggressive form of skin cancer is still a cause of concern. Hence the aim of this study was to investigate any potential influence of OCT on metabolic activity, cytotoxicity and ABCB5 mRNA expression in melanoma cells. The ABCB5 transmembrane protein was tested due to its well-known role in the initiation, invasion and metastatic spread of various cancers, including melanoma...
July 11, 2017: Giornale Italiano di Dermatologia e Venereologia: Organo Ufficiale, Società Italiana di Dermatologia e Sifilografia
https://www.readbyqxmd.com/read/28704605/protein-adsorption-to-charged-gold-nanospheres-as-a-function-of-protein-deformability
#15
Jordan M Dennison, Jennifer M Zupancic, Wayne Lin, Jonathan H Dwyer, Catherine J Murphy
The corona that forms as protein adsorbs to gold nanospheres (AuNSs) is directly influenced by the surface chemistry of the AuNS. Tools to predict adsorption outcomes are needed for intelligent design of nanomaterials for biological applications. We hypothesized that the denaturation behavior of a protein might be a useful predictor of adsorption behavior to AuNSs, and used this idea to study protein adsorption to anionic citrate capped AuNSs and to cationic poly(allylamine hydrochloride) (PAH) wrapped AuNSs...
July 13, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28704030/chemistry-is-dead-long-live-chemistry
#16
Luke D Lavis
Chemistry, once king of fluorescence microscopy, was usurped by the field of fluorescent proteins. The increased demands of modern microscopy techniques on the "photon budget" requires better and brighter fluorophores. Here, we review the recent advances in biochemistry, protein engineering, and organic synthesis that have allowed a triumphant return of chemical dyes to modern biological imaging.
July 13, 2017: Biochemistry
https://www.readbyqxmd.com/read/28703877/biochemical-and-hematological-evaluations-of-black-howler-monkeys-alouatta-pigra-in-highly-degraded-landscapes-in-mexico
#17
Luis M García-Feria, Colin A Chapman, Rosalía Pastor-Nieto, Juan Carlos Serio-Silva
BACKGROUND: Loss and fragmentation of Neotropical primates' habitat can alter the health and individual adaptation. Physiological parameters reflect health status and individuals responses to the habitat conditions. METHODS: We captured six wild adult females and six adult males of Alouatta pigra to evaluate their physical condition (body mass, respiratory and heart rate, and rectal temperature), hematology and blood chemistry on fragmentation habitat condition at southeastern Mexico...
July 13, 2017: Journal of Medical Primatology
https://www.readbyqxmd.com/read/28703007/a-chaperonin-nanocaged-hemin-as-an-artificial-metalloenzyme-for-oxidation-catalysis
#18
Xiaoqiang Wang, Chao Wang, Meihong Pan, Junting Wei, Fuping Jiang, Rongsheng Lu, Xuan Liu, Yihui Huang, Fang Huang
Taking inspiration from biology's effectiveness in functionalizing protein-based nanocages for chemical processes, we describe here a rational design of an artificial metalloenzyme for oxidations with the bacterial chaperonin GroEL, a nanocage for protein folding in nature, by supramolecular anchoring of catalytically active hemin in its hydrophobic central cavity. The promiscuity of the chaperonin cavity is an essential element of this design, which can mimic the hydrophobic binding pocket in natural metalloenzymes to accept cofactor and substrate without requiring specific ligand-protein interactions...
July 13, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28702661/clinically-approved-pegylated-nanoparticles-are-covered-by-a-protein-corona-that-boosts-the-uptake-by-cancer-cells
#19
M Papi, D Caputo, V Palmieri, R Coppola, S Palchetti, F Bugli, C Martini, L Digiacomo, D Pozzi, G Caracciolo
Today, liposomes are an advanced technology of drug carriers with a dozen drugs in clinical practice and many more in clinical trials. A bottleneck associated with the clinical translation of liposomes has long been 'opsonization', i.e. the adsorption of plasma proteins at the liposome surface resulting in their rapid clearance from circulation. For decades, the most popular way to avoid opsonization has been grafting polyethylene glycol (PEG) onto the liposome surface. Recent studies have clarified that grafting PEG onto the liposome surface reduces, but does not completely prevent protein binding...
July 12, 2017: Nanoscale
https://www.readbyqxmd.com/read/28702564/ru-based-co-releasing-molecules-with-azole-ligands-interaction-with-proteins-and-the-co-release-mechanism-disclosed-by-x-ray-crystallography
#20
Nicola Pontillo, Giarita Ferraro, Luigi Messori, Gabriella Tamasi, Antonello Merlino
fac-[Ru(II)(CO)3Cl2(N(3)-Imidazole)] (Ru(II)IM), fac-[Ru(II)(CO)3Cl2(N(3)-methyl-imidazole)] (Ru(II)MIM) and fac-[Ru(II)(CO)3Cl2(N(3)-methyl-benzimidazole)] (Ru(II)MBI) are three ruthenium based CO releasing molecules (Ru-CORMs) that are cytotoxic towards ovarian and colon carcinoma cell lines. Detailed structural information on the adducts formed upon reaction of Ru(II)IM and Ru(II)MIM with hen egg white lysozyme and of the three Ru-CORMs with bovine pancreatic ribonuclease is provided here by X-ray crystallography...
July 13, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
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