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Piotr Klukowski, Michal Augoff, Maciej Zieba, Maciej Drwal, Adam Gonczarek, Michal J Walczak
Motivation: Automated selection of signals in protein NMR spectra, known as peak picking, has been studied for over 20 years, nevertheless existing peak picking methods are still largely deficient. Accurate and precise automated peak picking would accelerate the structure calculation, and analysis of dynamics and interactions of macromolecules. Recent advancement in handling big data, together with an outburst of machine learning techniques, offer an opportunity to tackle the peak picking problem substantially faster than manual picking and on par with human accuracy...
March 14, 2018: Bioinformatics
Andrew R Tee
Mammalian target of rapamycin (mTOR, now referred to as mechanistic target of rapamycin) is considered as the master regulator of cell growth. A definition of cell growth is a build-up of cellular mass through the biosynthesis of macromolecules. mTOR regulation of cell growth and cell size is complex, involving tight regulation of both anabolic and catabolic processes. Upon a growth signal input, mTOR enhances a range of anabolic processes that coordinate the biosynthesis of macromolecules to build cellular biomass, while restricting catabolic processes such as autophagy...
March 16, 2018: International Journal of Molecular Sciences
Jejoong Yoo, Aleksei Aksimentiev
In contrast to ordinary polymers, the vast majority of biological macromolecules adopt highly ordered three-dimensional structures that define their functions. The key to folding of a biopolymer into a unique 3D structure or to an assembly of several biopolymers into a functional unit is a delicate balance between the attractive and repulsive forces that also makes such self-assembly reversible under physiological conditions. The all-atom molecular dynamics (MD) method has emerged as a powerful tool for studies of individual biomolecules and their functional assemblies, encompassing systems of ever increasing complexity...
March 16, 2018: Physical Chemistry Chemical Physics: PCCP
Milad Moloudizargari, Esmaeil Mortaz, Mohammad Hossein Asghari, Ian M Adcock, Frank A Redegeld, Johan Garssen
Omega-3 polyunsaturated fatty acids (PUFAs) have well established anti-cancer properties. Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) are among this biologically active family of macromolecules for which various anti-cancer effects have been explained. These PUFAs have a high safety profile and can induce apoptosis and inhibit growth of cancer cells both in vitro and in vivo , following a partially selective manner. They also increase the efficacy of chemotherapeutic agents by increasing the sensitivity of different cell lines to specific anti-neoplastic drugs...
February 20, 2018: Oncotarget
Karolina Pierzynowska, Lidia Gaffke, Zuzanna Cyske, Michał Puchalski, Estera Rintz, Michał Bartkowski, Marta Osiadły, Michał Pierzynowski, Jagoda Mantej, Ewa Piotrowska, Grzegorz Węgrzyn
Autophagy is a process of degradation of macromolecules in the cytoplasm, particularly proteins of a long half-life, as well as whole organelles, in eukaryotic cells. Lysosomes play crucial roles during this degradation. Autophagy is a phylogenetically old, and evolutionarily conserved phenomenon which occurs in all eukaryotic cells. It can be found in yeast Saccharomyces cerevisiae, insect Drosophila melanogaster, and mammals, including humans. Its high importance for cell physiology has been recognized, and in fact, dysfunctions causing impaired autophagy are associated with many severe disorders, including cancer and metabolic brain diseases...
March 14, 2018: Metabolic Brain Disease
Zackary M Herbst, Sayaka Shibata, Erkang Fan, Michael H Gelb
An inexpensive, in-house made microdialysis device is described that is suitable for measuring the binding of small molecules including drug candidates to serum proteins or other macromolecules. The device is based on the standard equilibrium dialysis method to measure the fraction of low molecular weight compound bound to proteins. It is constructed from a standard polypropylene 96-well plate, dialysis tubing, and low viscosity epoxy resin. The device can be readily prepared for a small fraction of the cost of a commercial, multichamber microdialysis device...
March 8, 2018: ACS Medicinal Chemistry Letters
Sara Silva Pereira, Andrew P Jackson
BACKGROUND: Trypanosomatid parasites such as Trypanosoma spp. and Leishmania spp. are a major source of infectious disease in humans and domestic animals worldwide. Fundamental to the host-parasite interactions of these potent pathogens are their cell surfaces, which are highly decorated with glycosylated proteins and other macromolecules. Trypanosomatid genomes contain large multi-copy gene families encoding UDP-dependent glycosyltransferases (UGTs), the primary role of which is cell-surface decoration...
March 14, 2018: BMC Evolutionary Biology
Anthony Banks, Sanbo Qin, Kevin L Weiss, Christopher B Stanley, Huan-Xiang Zhou
Conformational malleability allows intrinsically disordered proteins (IDPs) to respond agilely to their environments, such as nonspecifically interacting with in vivo bystander macromolecules (or crowders). Previous studies have emphasized conformational compaction of IDPs due to steric repulsion by macromolecular crowders, but effects of soft attraction are largely unexplored. Here we studied the conformational ensembles of the IDP FlgM in both polymer and protein crowders by small-angle neutron scattering...
March 13, 2018: Biophysical Journal
Leila M Lopes-Bezerra, Hector M Mora-Montes, Yu Zhang, Gustavo Nino-Vega, Anderson Messias Rodrigues, Zoilo Pires de Camargo, Sybren de Hoog
The description of cryptic species with different pathogenic potentials has changed the perspectives on sporotrichosis. Sporothrix schenckii causes a benign chronic subcutaneous mycosis, Sporothrix brasiliensis is highly virulent, and Sporothrix globosa mainly causes fixed cutaneous lesions. Furthermore, S. brasiliensis is the prevalent species related to cat-transmitted sporotrichosis. Sources of infection, transmission, and distribution patterns also differ between species, and variability differs between species because of different degrees of clonality...
April 1, 2018: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
Sneha Munshi, Soundhararajan Gopi, Sandhyaa Subramanian, Luis A Campos, Athi N Naganathan
The amplitude of thermodynamic fluctuations in biological macromolecules determines their conformational behavior, dimensions, nature of phase transitions and effectively their specificity and affinity, thus contributing to fine-tuned molecular recognition. Unique among large-scale conformational changes in proteins are temperature-induced collapse transitions in intrinsically disordered proteins (IDPs). Here, we show that CytR DNA-binding domain, an IDP that folds on binding DNA, undergoes a coil-to-globule transition with temperature in the absence of DNA while exhibiting energetically decoupled local and global structural rearrangements, and maximal thermodynamic fluctuations at the optimal bacterial growth temperature...
March 10, 2018: Nucleic Acids Research
In-Yup Jeon, Hyuk-Jun Noh, Jong-Beom Baek
Hyperbranched macromolecules (HMs, also called hyperbranched polymers) are highly branched three-dimensional (3D) structures in which all bonds converge to a focal point or core, and which have a multiplicity of reactive chain-ends. This review summarizes major types of synthetic strategies exploited to produce HMs, including the step-growth polycondensation, the self-condensing vinyl polymerization and ring opening polymerization. Compared to linear analogues, the globular and dendritic architectures of HMs endow new characteristics, such as abundant functional groups, intramolecular cavities, low viscosity, and high solubility...
March 14, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Xiaoying Wang, Jiefu Peng, Jing Wang, Miao Li, Di Wu, Songyan Wu, Jipei Liao, Jun Dou
Background: Despite the breadth of understanding the noncoding RNAs' function in molecular biology, their functional roles in hepatocellular carcinoma (HCC) is poorly understood. In this study, we investigated the effect of hepatitis C virus (HCV) core upon the expression of noncoding RNAs. Methods: The lncRNAs, mRNAs, and circRNAs were employed for identification of HCV core protein gene expression in human Huh7 hepatoma (Huh7) cell line. In data analysis, we applied a threshold that eliminated all genes that were not increased or decreased by at least a 2-fold change in a comparison between transfected and control cells...
2018: OncoTargets and Therapy
A Mostek, M Slowinska, S Judycka, H Karol, A Ciereszko, M A Dietrich
During semen cryopreservation, spermatozoa are exposed to physical and chemical stressors that result in their functional and structural damage. Growing evidence suggests that most cryoinjuries result from oxidative stress accompanying sperm cryopreservation. Elevated amounts of reactive oxygen species (ROS) generated during cryopreservation can react with sperm macromolecules, including proteins. The goal of this study was to investigate the oxidative modifications (measured as carbonylation level changes) of carp spermatozoa proteins triggered by the cryopreservation process...
March 9, 2018: Journal of Animal Science
Pavol Skubák
Thus far, the application of phase-retrieval methods in crystallography has mainly been aimed at variants of charge flipping or structure-factor flipping. In this work, the relaxed averaged alternating reflections (RAAR) algorithm is applied to determine anomalously scattering substructures from single-wavelength anomalous diffraction (SAD) data of macromolecules. The algorithm has been implemented in a new program, PRASA, and has been shown to significantly outperform charge flipping in determining anomalously scattering substructures on a test sample of 169 SAD data sets with resolutions up to 3...
February 1, 2018: Acta Crystallographica. Section D, Structural Biology
Isabel Usón, George M Sheldrick
For the purpose of this article, experimental phasing is understood to mean the determination of macromolecular structures by exploiting small intensity differences of Friedel opposites and possibly of reflections measured at different wavelengths or for heavy-atom derivatives, without the use of specific structural models. The SHELX programs provide a robust and efficient route for routine structure solution by the SAD, MAD and related methods, but involve a number of simplifying assumptions that may limit their applicability in borderline cases...
February 1, 2018: Acta Crystallographica. Section D, Structural Biology
Oliver S Smart, Vladimír Horský, Swanand Gore, Radka Svobodová Vařeková, Veronika Bendová, Gerard J Kleywegt, Sameer Velankar
Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) play a crucial role in structure-guided drug discovery and design, and also provide atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. The quality with which small-molecule ligands have been modelled in Protein Data Bank (PDB) entries has been, and continues to be, a matter of concern for many investigators. Correctly interpreting whether electron density found in a binding site is compatible with the soaked or co-crystallized ligand or represents water or buffer molecules is often far from trivial...
March 1, 2018: Acta Crystallographica. Section D, Structural Biology
Steffen Jeschke, Patrik Johansson, Piotr Jankowski, Adam Best
Cyclodextrins (CDs) are pyranoside-based macromolecules with a hydrophobic cavity to encapsulate small molecules. They are used as molecular vehicles, for instance in pharmaceutical drug delivery or as solubility enhancer of monomers for their polymerization in aqueous solution. In this context, it was discovered about 10 years ago that the bis(trifluoromethylsulonyl)imide (TFSI) anion forms host-guest complexes with βCD in aqueous media. The rising interest in using the TFSI anion in lithium-based battery electrolytes open for its encapsulation by βCD as an attractive approach to increase the contribution of the cation to the total ion conductivity...
March 12, 2018: ChemSusChem
Massimiliano Magro, Mattia Zaccarin, Giovanni Miotto, Laura Da Dalt, Davide Baratella, Piero Fariselli, Gianfranco Gabai, Fabio Vianello
Surface active maghemite nanoparticles (SAMNs) are able to recognize and bind selected proteins in complex biological systems, forming a hard protein corona. Upon a 5-min incubation in bovine whey from mastitis-affected cows, a significant enrichment of a single peptide characterized by a molecular weight at 4338 Da originated from the proteolysis of aS1 -casein was observed. Notably, among the large number of macromolecules in bovine milk, the detection of this specific peptide can hardly be accomplished by conventional analytical techniques...
March 12, 2018: Analytical and Bioanalytical Chemistry
G Zhou, K P Wang, H W Liu, L Wang, X F Xiao, D D Dou, Y B Fan
Owing to low bearing capacity and efficiency, traditional filters or adsorbents for removal of contaminants like crystal violet (CV) dye required frequent replacement. Besides, the combination of three-dimensional (3D) printing and bionics could break the constraints of traditional configuration. In this study, a novel depth-type hybrid polylactic acid (PLA)@graphene oxide (GO)/chitosan (CS) sponge filter with bionic fish-mouth structure was prepared and fabricated, assisted by 3D printing and double freeze-drying technology, according to the theories of vertical cross-step filtration and swirling flow...
March 9, 2018: International Journal of Biological Macromolecules
Liora Werber, Yitzhak Mastai
One of the most powerful techniques that are currently available to measure thermodynamic parameters such as enthalpy (ΔH), Gibbs free energy (ΔG), entropy changes (ΔS), and binding affinity in chemical reactions is isothermal titration calorimetry (ITC). Recent advances in instrumentation have facilitated the development of ITC as a very essential analytical tool in biology and chemistry. In this article, we will focus on a review of the literature on the application of ITC for the study of chiral systems and chiral interactions...
March 12, 2018: Chirality
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