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Biological Chemistry

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https://www.readbyqxmd.com/read/28548838/synthesis-of-defined-and-functionalized-glycans-of-lipoteichoic-acid-a-cell-surface-polysaccharide-from-clostridium-difficile
#1
Kang Yu, Ningning Bi, Chenghe Xiong, Shuihong Cai, Zhongzhu Long, Zhongwu Guo, Guofeng Gu
Two structurally defined, functionalized glycans of lipoteichoic acid (LTA, also known as PS-III) from C. difficile, which have one or two repeating units of LTA linked to the core trisaccharide, were efficiently synthesized via a convergent [2 + 3] or [2 + 2 + 3] strategy. The α-linkage of both N-acetylglucosamine residues in the repeating unit were constructed with glycosyl imidates of azidosugars as donors, while the phosphodiester bridges between the oligosaccharides were fashioned using H-phosphonate chemistry...
May 26, 2017: Organic Letters
https://www.readbyqxmd.com/read/28548390/a-step-towards-removing-plasma-volume-variance-from-the-athlete-s-biological-passport-the-use-of-biomarkers-to-describe-vascular-volumes-from-a-simple-blood-test
#2
Louisa M Lobigs, Pierre-Edouard Sottas, Pitre C Bourdon, Zoran Nikolovski, Mohamed El-Gingo, Evdokia Varamenti, Peter Peeling, Brian Dawson, Yorck O Schumacher
The haematological module of the Athlete's Biological Passport (ABP) has significantly impacted the prevalence of blood manipulations in elite sports. However, the ABP relies on a number of concentration-based markers of erythropoiesis, such as haemoglobin concentration ([Hb]), which are influenced by shifts in plasma volume (PV). Fluctuations in PV contribute to the majority of biological variance associated with volumetric ABP markers. Our laboratory recently identified a panel of common chemistry markers (from a simple blood test) capable of describing ~67% of PV variance, presenting an applicable method to account for volume shifts within antidoping practices...
May 26, 2017: Drug Testing and Analysis
https://www.readbyqxmd.com/read/28548089/finding-multiple-reaction-pathways-via-global-optimization-of-action
#3
Juyong Lee, In-Ho Lee, InSuk Joung, Jooyoung Lee, Bernard R Brooks
Global searching for reaction pathways is a long-standing challenge in computational chemistry and biology. Most existing approaches perform only local searches due to computational complexity. Here we present a computational approach, Action-CSA, to find multiple diverse reaction pathways connecting fixed initial and final states through global optimization of the Onsager-Machlup action using the conformational space annealing (CSA) method. Action-CSA successfully overcomes large energy barriers via crossovers and mutations of pathways and finds all possible pathways of small systems without initial guesses on pathways...
May 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28546955/biofabrication-and-biomaterials-for-urinary-tract-reconstruction
#4
REVIEW
Moustafa M Elsawy, Achala de Mel
Reconstructive urologists are constantly facing diverse and complex pathologies that require structural and functional restoration of urinary organs. There is always a demand for a biocompatible material to repair or substitute the urinary tract instead of using patient's autologous tissues with its associated morbidity. Biomimetic approaches are tissue-engineering tactics aiming to tailor the material physical and biological properties to behave physiologically similar to the urinary system. This review highlights the different strategies to mimic urinary tissues including modifications in structure, surface chemistry, and cellular response of a range of biological and synthetic materials...
2017: Research and Reports in Urology
https://www.readbyqxmd.com/read/28545393/quantgenius-implementation-of-a-decision-support-system-for-qpcr-based-gene-quantification
#5
Špela Baebler, Miha Svalina, Marko Petek, Katja Stare, Ana Rotter, Maruša Pompe-Novak, Kristina Gruden
BACKGROUND: Quantitative molecular biology remains a challenge for researchers due to inconsistent approaches for control of errors in the final results. Due to several factors that can influence the final result, quantitative analysis and interpretation of qPCR data are still not trivial. Together with the development of high-throughput qPCR platforms, there is a need for a tool allowing for robust, reliable and fast nucleic acid quantification. RESULTS: We have developed "quantGenius" ( http://quantgenius...
May 25, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28544971/development-of-photostable-fluorophores-for-molecular-imaging
#6
REVIEW
Qinsi Zheng, Luke D Lavis
Advances in fluorescence microscopy promise to unlock details of biological systems with high spatiotemporal precision. These new techniques also place a heavy demand on the 'photon budget'-the number of photons one can extract from a sample. Improving the photostability of small molecule fluorophores using chemistry is a straightforward method for increasing the photon budget. Here, we review the (sometimes sparse) efforts to understand the mechanism of fluorophore photobleaching and recent advances to improve photostability through reducing the propensity for oxidation or through intramolecular triplet-state quenching...
May 22, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28544574/reversing-polarity-carbonyl-%C3%AE-aminations-with-nitrogen-nucleophiles
#7
Aurelien de la Torre, Veronica Tona, Nuno Maulide
The synthesis of alpha-amino carbonyl compounds is an important challenge in synthesis en route to biologically essential structures. While classical approaches involve the use of enol or enolate chemistries in combination with an electrophilic source of nitrogen, those strategies usually necessitate further transformations in order to reach the desired targets. In recent years, a new approach arose involving the direct use of nucleophilic sources of nitrogen along with an oxidant. This advantageously leads in one-pot to the biologically relevant alpha-amino compounds, without further transformation required...
May 20, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28544442/sensitization-initiated-electron-transfer-for-photoredox-catalysis
#8
Indrajit Ghosh, Rizwan S Shaikh, Burkhard König
Photosynthetic organisms exploit antenna chromophores to absorb light and transfer excitation energy to the reaction center where redox reactions occur. In contrast, in visible-light chemical photoredox catalysis, a single species (i.e., the photoredox catalyst) absorbs light and performs the redox chemistry. Mimicking the energy flow of the biological model, we report a two-center photoredox catalytic approach in which the tasks of light energy collection and electron transfer (i.e., redox reactions) are assigned to two different molecules...
May 24, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28540940/modelling-charge-transfer-processes-in-c-2-tetrahydrofuran-collision-for-ion-induced-radiation-damage-in-dna-building-blocks
#9
Ewa Erdmann, Marie-Christine Bacchus-Montabonel, Marta Łabuda
Investigations of collision-induced processes involving carbon ions and molecules of biological interest, in particular DNA building blocks, are crucial to model the effect of radiation on cells in order to improve medical treatments for cancer therapy. Using carbon ions appears to be one of the most efficient ways to increase biological effectiveness to damage cancerous cells by irradiating deep-seated tumors. Therefore, interest in accurate calculations to understand fundamental processes occurring in ion-molecule collision systems has been growing recently...
May 25, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28538697/mammalian-metallothionein-3-new-functional-and-structural-insights
#10
REVIEW
Milan Vašák, Gabriele Meloni
Metallothionein-3 (MT-3), a member of the mammalian metallothionein (MT) family, is mainly expressed in the central nervous system (CNS). MT-3 possesses a unique neuronal growth inhibitory activity, and the levels of this intra- and extracellularly occurring metalloprotein are markedly diminished in the brain of patients affected by a number of metal-linked neurodegenerative disorders, including Alzheimer's disease (AD). In these pathologies, the redox cycling of copper, accompanied by the production of reactive oxygen species (ROS), plays a key role in the neuronal toxicity...
May 24, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28538101/chemical-endgroup-modified-diblock-copolymers-elucidate-anchor-and-chain-mechanism-of-membrane-stabilization
#11
Evelyne M Houang, Karen J Haman, Mihee Kim, Wenjia Zhang, Dawn A Lowe, Yuk Yin Sham, Timothy P Lodge, Benjamin J Hackel, Frank S Bates, Joseph M Metzger
Block copolymers can be synthesized in an array of architectures and compositions to yield diverse chemical properties. The triblock copolymer Poloxamer 188 (P188), the family archetype, consisting of a hydrophobic polypropylene oxide core flanked by hydrophilic polyethylene oxide chains, can stabilize cellular membranes during stress. However, little is known regarding the molecular basis of membrane interaction by copolymers in living organisms. By leveraging diblock architectural design, discrete end-group chemistry modifications can be tested...
May 24, 2017: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/28538099/iodide-selective-synthetic-ion-channels-based-on-shape-persistent-organic-cages
#12
Bahiru Punja Benke, Pulakesh Aich, Younghoon Kim, Kyung Lock Kim, Md Rumum Rohman, Soonsang Hong, In-Chul Hwang, Eun Hui Lee, Joon Ho Roh, Kimoon Kim
We report here a synthetic ion channel developed from a shape-persistent porphyrin-based covalent organic cage. The cage was synthesized by employing a synthetically economical dynamic covalent chemistry (DCC) approach. The organic cage selectively transports biologically relevant iodide ions over other inorganic anions by a dehydration-driven, channel mechanism as evidenced by vesicle-based fluorescence assays and planar lipid bilayer-based single channel recordings. Furthermore, the organic cage appears to facilitate iodide transport across the membrane of a living cell, suggesting that the cage could be useful as a biological tool that may replace defective iodide channels in living systems...
May 26, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28537746/classical-dynamics-simulations-of-dissociation-of-protonated-tryptophan-in-the-gas-phase
#13
Yogeshwaran Krishnan, Nishant Sharma, Upakarasamy Lourderaj, Manikandan Paranjothy
Gas phase decomposition of protonated amino acids are of great interest due to their role in understanding protein and peptide chemistry. Several experimental and theoretical studies have been reported in the literature on this subject. In the present work, decomposition of the aromatic amino acid protonated tryptophan was studied by on-the-fly classical chemical dynamics simulations using density functional theory. Mass spectrometry and electronic structure theory studies have shown multiple dissociation pathways for this biologically relevant molecule...
May 24, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28537738/a-peptoid-square-helix-via-synergistic-control-of-backbone-dihedral-angles
#14
Benjamin Craig Gorske, Emily M Mumford, Charles G Gerrity, Imelda Ko
The continued expansion of the fields of macromolecular chemistry and nanoscience has motivated the development of new secondary structures that can serve as architectural elements of innovative materials, molecular machines, biological probes, and even commercial medicines. Synthetic foldamers are particularly attractive systems for developing such elements because they are specifically designed to facilitate synthetic manipulation and functional diversity. However, relatively few predictive design principles exist that permit both rational and modular control of foldamer secondary structure, while maintaining the capacity for facile diversification of displayed functionality...
May 24, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28537720/chromone-as-a-privileged-scaffold-in-drug-discovery-recent-advances
#15
Joana Reis, Alexandra Gaspar, Nuno Milhazes, Fernanda M Borges
The use of privileged structures in drug discovery has proven to be an effective strategy allowing the generation of innovative hits/leads and successful optimization processes. Chromone is actually recognized as a privileged structure and a valid template for the design of novel compounds with potential pharmacological interest, particularly in the field of neurodegenerative, inflammatory and infectious diseases as well as diabetes and cancer. Within this framework, this review provides the reader with a literature update following the preceding article entitled Chromone: a valid scaffold in Medicinal Chemistry...
May 24, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28537383/emerging-droplet-microfluidics
#16
Luoran Shang, Yao Cheng, Yuanjin Zhao
Droplet microfluidics generates and manipulates discrete droplets through immiscible multiphase flows inside microchannels. Due to its remarkable advantages, droplet microfluidics bears significant value in an extremely wide range of area. In this review, we provide a comprehensive and in-depth insight into droplet microfluidics, covering fundamental research from microfluidic chip fabrication and droplet generation to the applications of droplets in bio(chemical) analysis and materials generation. The purpose of this review is to convey the fundamentals of droplet microfluidics, a critical analysis on its current status and challenges, and opinions on its future development...
May 24, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28535807/identification-of-putative-olfactory-g-protein-coupled-receptors-in-crown-of-thorns-starfish-acanthaster-planci
#17
Rebecca E Roberts, Cherie A Motti, Kenneth W Baughman, Noriyuki Satoh, Michael R Hall, Scott F Cummins
BACKGROUND: In marine organisms, and in particular for benthic invertebrates including echinoderms, olfaction is a dominant sense with chemosensation being a critical signalling process. Until recently natural product chemistry was the primary investigative approach to elucidate the nature of chemical signals but advances in genomics and transcriptomics over the last decade have facilitated breakthroughs in understanding not only the chemistry but also the molecular mechanisms underpinning chemosensation in aquatic environments...
May 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28535052/programming-ionic-pore-accessibility-in-zwitterionic-polymer-modified-nanopores
#18
Laura Silies, Annette Andrieu-Brunsen
Creating switchable and gradually tunable pores or channels that display transport control similar to biological pores remains a major challenge in nanotechnology. It requires the generation and manipulation of complex charge situations at the nanoscale and the understanding of how confinement influences chemistry and transport. Here, two different pore sizes, ∼100 nm and less than 10 nm, functionalized with varying amounts of responsive zwitterionic polycarboxybetaine methyl acrylate (PCBMA) give fascinating insight into the confinement controlled ionic transport of pores functionalized with pH-dependent zwitterionic polymers...
May 23, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28534784/incorporation-of-solvent-effect-into-multi-objective-evolutionary-algorithm-for-improved-protein-structure-prediction
#19
Shangce Gao, Jiujun Cheng, Yuki Todo, Mengchu Zhou
The problem of predicting the three-dimensional structure of a protein from its one-dimensional sequence has been called the "holy grail of molecular biology", and it has become an important part of structural genomics projects. Despite the rapid developments in computer technology and computational intelligence, it remains challenging and fascinating. In this paper, to solve it we propose a multi-objective evolutionary algorithm. We decompose the protein energy function Chemistry at HARvard Macromolecular Mechanics force fields into bond and non-bond energies as the first and second objectives...
May 17, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28534494/airborne-observations-reveal-elevational-gradient-in-tropical-forest-isoprene-emissions
#20
Dasa Gu, Alex B Guenther, John E Shilling, Haofei Yu, Maoyi Huang, Chun Zhao, Qing Yang, Scot T Martin, Paulo Artaxo, Saewung Kim, Roger Seco, Trissevgeni Stavrakou, Karla M Longo, Julio Tóta, Rodrigo Augusto Ferreira de Souza, Oscar Vega, Ying Liu, Manish Shrivastava, Eliane G Alves, Fernando C Santos, Guoyong Leng, Zhiyuan Hu
Isoprene dominates global non-methane volatile organic compound emissions, and impacts tropospheric chemistry by influencing oxidants and aerosols. Isoprene emission rates vary over several orders of magnitude for different plants, and characterizing this immense biological chemodiversity is a challenge for estimating isoprene emission from tropical forests. Here we present the isoprene emission estimates from aircraft eddy covariance measurements over the Amazonian forest. We report isoprene emission rates that are three times higher than satellite top-down estimates and 35% higher than model predictions...
May 23, 2017: Nature Communications
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