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Structural biology

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https://www.readbyqxmd.com/read/29166561/structural-characterization-of-native-and-modified-encapsulins-as-nanoplatforms-for-in-vitro-catalysis-and-cellular-uptake
#1
Rindia M Putri, Carolina Allende-Ballestero, Daniel Luque, Robin Klem, Katerina-Asteria Rousou, Aijie Liu, Christoph H-H Traulsen, W Frederik Rurup, Melissa S T Koay, Jose R Castón, Jeroen J L M Cornelissen
Recent years have witnessed the emergence of bacterial semi-organelle encapsulins as promising platforms for bio-nanotechnology. To advance the development of encapsulins as nanoplatforms, a functional and structural basis of these assemblies is required. Encapsulin from Brevibacterium linens is known to be a protein-based vessel for an enzyme cargo in its cavity, which could be replaced with a foreign cargo resulting in a modified encapsulin. Here, we characterize the native structure of B. linens encapsulins with both native and foreign cargo using cryo-electron microscopy (cryo-EM)...
November 22, 2017: ACS Nano
https://www.readbyqxmd.com/read/29166560/analytical-challenges-and-recent-advances-in-mass-spectrometry-based-lipidomics
#2
Yepy Hardi Rustam, Gavin Edmund Reid
Although no internationally accepted consensus definition exists, lipids can be broadly defined as "fatty acids and their derivatives, and substances related biosynthetically or functionally to these compounds". Lipids play critical roles as (i) the major structural components of biological membranes, and as functional and regulatory components of membrane protein signaling, (ii) bioactive intra- and inter-cellular signaling molecules, and (iii) energy storage molecules for the maintenance of energy homeostasis...
November 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29166154/predator-persistence-through-variability-of-resource-productivity-in-tritrophic-systems
#3
Floor H Soudijn, André M de Roos
The trophic structure of species communities depends on the energy transfer between trophic levels. Primary productivity varies strongly through time, challenging the persistence of species at higher trophic levels. Yet resource variability has mostly been studied in systems with only one or two trophic levels. We test the effect of variability in resource productivity in a tritrophic model system including a resource, a size-structured consumer, and a size-specific predator. The model complies with fundamental principles of mass conservation and the body-size dependence of individual-level energetics and predator-prey interactions...
December 2017: American Naturalist
https://www.readbyqxmd.com/read/29166086/focused-conformational-sampling-in-proteins
#4
Marco Bacci, Cassiano Langini, Jiří Vymětal, Amedeo Caflisch, Andreas Vitalis
A detailed understanding of the conformational dynamics of biological molecules is difficult to obtain by experimental techniques due to resolution limitations in both time and space. Computer simulations avoid these in theory but are often too short to sample rare events reliably. Here we show that the progress index-guided sampling (PIGS) protocol can be used to enhance the sampling of rare events in selected parts of biomolecules without perturbing the remainder of the system. The method is very easy to use as it only requires as essential input a set of several features representing the parts of interest sufficiently...
November 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29165993/hybrid-structured-illumination-expansion-microscopy-reveals-microbial-cytoskeleton-organization
#5
Aaron R Halpern, Germain C M Alas, Tyler J Chozinski, Alexander R Paredez, Joshua C Vaughan
Recently developed tissue-hydrogel methods for specimen expansion now enable researchers to perform super-resolution microscopy with ~65 nm lateral resolution using ordinary microscopes, standard fluores-cent probes, and inexpensive reagents. Here we use the combination of specimen expansion and the optical super-resolution microscopy technique structured illumination microscopy (SIM) to extend the spatial reso-lution to ~30 nm. We apply this hybrid method, which we call ExSIM, to study the cytoskeleton of the im-portant human pathogen Giardia lamblia including the adhesive disc and flagellar axonemes...
November 22, 2017: ACS Nano
https://www.readbyqxmd.com/read/29165987/hierarchical-self-assembly-of-a-porphyrin-into-chiral-macroscopic-flowers-with-superhydrophobic-and-enantioselective-property
#6
Hejin Jiang, Li Zhang, Jie Chen, Minghua Liu
Supramolecular self-assembly provides an efficient way to fabricate simple units into various hierarchical nano/microstructures, which could mimic the bio-self-assembly and develop functional materials. Since chiral molecules and chiral nanostructures are widely adopted by biological systems, an introduction of the chiral factor into the self-assembly process will provide better understanding of the biological systems. Here, using a chiral amphiphilic histidine to assist the self-assembly of a porphyrin with four carboxylic acids, we obtained hierarchical chiral nano to micro structures...
November 22, 2017: ACS Nano
https://www.readbyqxmd.com/read/29165985/nanoscale-dynamics-of-amyloid-beta-42-oligomers-as-revealed-by-high-speed-atomic-force-microscopy
#7
Siddhartha Banerjee, Zhiqiang Sun, Eric Y Hayden, David B Teplow, Yuri L Lyubchenko
Amyloid β-protein (Aβ) oligomers are emerging as potent neurotoxic species in Alzheimer's disease pathogenesis. Detailed characterization of oligomer structure and dynamics are necessary to develop oligomer-specific therapeutic agents. However, oligomers exist transiently, which complicates their structural analysis. One approach to mitigate these problems has been photochemical cross-linking of native oligomers. In these states, the oligomers can be isolated and purified for physical and chemical studies...
November 22, 2017: ACS Nano
https://www.readbyqxmd.com/read/29165906/noninvasive-high-speed-near-infrared-imaging-of-the-biomolecular-distribution-and-molecular-mechanism-of-embryonic-development-in-fertilized-fish-eggs
#8
Mika Ishigaki, Takashi Nishii, Paralee Puangchit, Yui Yasui, Christian W Huck, Yukihiro Ozaki
In the present study, the distribution of biomaterials and its molecular mechanism of embryonic development in Japanese medaka fish were analyzed nondestructively and noninvasively without staining using near-infrared (NIR) imaging. The microscope NIR imaging system used in this research was a device capable of ultra-high-speed imaging; using this system, one can acquire microscopic imaging data in a few seconds. Therefore, the medaka eggs remained alive throughout measurements and were successfully monitored in vivo...
November 22, 2017: Journal of Biophotonics
https://www.readbyqxmd.com/read/29165806/host-preference-and-network-properties-in-biotrophic-plant-fungal-associations
#9
Sergei Põlme, Mohammad Bahram, Hans Jacquemyn, Peter Kennedy, Petr Kohout, Mari Moora, Jane Oja, Maarja Öpik, Lorenzo Pecoraro, Leho Tedersoo
Analytical methods can offer insights into the structure of biological networks, but mechanisms that determine the structure of these networks remain unclear. We conducted a synthesis based on 111 previously published datasets to assess a range of ecological and evolutionary mechanisms that may influence the plant-associated fungal interaction networks. We calculated the relative host effect on fungal community composition and compared nestedness and modularity among different mycorrhizal types and endophytic fungal guilds...
November 22, 2017: New Phytologist
https://www.readbyqxmd.com/read/29165495/electronic-structure-and-dynamics-of-torsion-locked-photoactive-yellow-protein-chromophores
#10
Alice Henley, Matus E Diveky, Anand M Patel, Michael A Parkes, James C Anderson, Helen H Fielding
The photocycle of photoactive yellow protein (PYP) begins with small-scale torsional motions of the chromophore leading to large-scale movements of the protein scaffold triggering a biological response. The role of single-bond torsional molecular motions of the chromophore in the initial steps of the PYP photocycle are not fully understood. Here, we employ anion photoelectron spectroscopy measurements and quantum chemistry calculations to investigate the electronic relaxation dynamics following photoexcitation of four model chromophores, para-coumaric acid, its methyl ester, and two analogues with aliphatic bridges hindering torsional motions around the single bonds adjacent to the alkene group...
November 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29165453/structural-and-electronic-properties-of-barbituric-acid-and-melamine-containing-ribonucleosides-as-plausible-components-of-prebiotic-rna-implications-for-prebiotic-self-assembly
#11
Sarabjeet Kaur, Purshotam Sharma, Stacey D Wetmore
The RNA world hypothesis assumes that RNA was the first informational polymer that originated from prebiotic chemical soup. However, since the reaction of d-ribose with canonical nucleobases (A, C, G and U) fails to yield ribonucleosides (rNs) in substantial amounts, the spontaneous origin of rNs and the subsequent synthesis of RNA remains an unsolved mystery. To this end, it has been suggested that RNA may have evolved from primitive genetic material (preRNA) composed of simpler prebiotic heterocycles that spontaneously form glycosidic bonds with ribose...
November 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29165324/in-vivo-evaluation-of-modified-silk-fibroin-scaffolds-with-a-mimicked-microenvironment-of-fibronectin-decellularized-pulp-tissue-for-maxillofacial-surgery
#12
Thanh H Thai, Thongchai Nuntanaranont, Suttatip Kamolmatyakul, Jirut Meesane
This study aimed to carry out in vivo testing of the formation of new bone by modified silk fibroin scaffolds with a mimicked microenvironment of fibronectin/decellularized pulp in bone defects. Silk fibroin scaffolds were fabricated into three-dimensional scaffolds before being coated with fibronectin/decellularized pulp. The coated scaffolds were implanted into rabbits. Twenty-four bicortical calvarial defects in 12 rabbits were divided randomly into two groups: non-coated and coated silk fibroin scaffolds...
November 22, 2017: Biomedical Materials
https://www.readbyqxmd.com/read/29165235/synthesis-of-n-acetyl-d-quinovosamine-in-rhizobium-etli-ce3-is-completed-after-its-4-keto-precursor-is-linked-to-a-carrier-lipid
#13
Tiezheng Li, K Dale Noel
Bacterial O-antigens are synthesized on lipid carriers before being transferred to lipopolysaccharide core structures. Rhizobium etli CE3 lipopolysaccharide is a model for understanding O-antigen biological function. CE3 O-antigen structure and genetics are known. However, proposed enzymology for CE3 O-antigen synthesis has been examined very little in vitro, and even the sugar added to begin the synthesis is uncertain. A model based on mutagenesis studies predicts that 2-acetamido-2,6-dideoxy-d-glucose (QuiNAc) is the first O-antigen sugar and that genes wreV, wreQ and wreU direct QuiNAc synthesis and O-antigen initiation...
November 22, 2017: Microbiology
https://www.readbyqxmd.com/read/29165051/a-structure-function-analysis-in-patients-with-prekallikrein-deficiency
#14
Antonio Girolami, Silvia Ferrari, Elisabetta Cosi, Anna Maria Lombardi
OBJECTIVE: To investigate the structure-function relation in prekallikrein (PK) deficiency. PK is one of the proteins of the contact phase of blood coagulation which at the present time is the object of a revival of interest. METHODS: All patients with PK deficiency who had been investigated by molecular biology techniques are the object of the present investigation. Details of patients were obtained from personal files and a time-unlimited PubMed search. Only cases with a molecular-biology-based diagnosis were included...
November 22, 2017: Hematology (Amsterdam, Netherlands)
https://www.readbyqxmd.com/read/29164858/circular-dichroism-of-cdse-nanocrystals-bound-by-chiral-carboxylic-acids
#15
Mayank Puri, Vivian E Ferry
Chiral semiconductor nanocrystals, or quantum dots (QDs), are promising materials for applications in biological sensing, photonics, and spin-polarized devices. Many of these applications rely on large dissymmetry, or g-factors, the difference in absorbance between left- and right-handed circularly polarized light compared to the unpolarized absorbance. The majority of chiral QDs, specifically CdSe, reported to date have used thiolated amino acid ligands to introduce chirality onto the nanoparticles, but these systems have ultimately reported small g-factors of ∼2 × 10(-4)...
November 22, 2017: ACS Nano
https://www.readbyqxmd.com/read/29164819/decellularized-bovine-cotyledons-may-serve-as-biological-scaffolds-with-preserved-vascular-arrangement
#16
Rodrigo da Silva Nunes Barreto, Patricia Romagnolli, Andrea Maria Mess, Maria Angelica Miglino
Technically produced scaffolds are common to establish transplantable tissues for Regenerative Medicine, but also biological ones that are closer to the natural condition become of interest. Placentas are promising, because they represented available, complete organs with rich extracellular matrix (ECM) and well developed vasculature that easily could build anastomoses to a host´s organ. Only placentas from larger animal models such as the bovine meet the dimensions large enough for most organs, but are not adequately described yet...
November 21, 2017: Journal of Tissue Engineering and Regenerative Medicine
https://www.readbyqxmd.com/read/29164812/inter-and-intraspecific-variability-of-nitrogenated-compounds-in-gorgonian-corals-via-application-of-a-fast-one-step-analytical-protocol
#17
Chiara Samorì, Federica Costantini, Paola Galletti, Emilio Tagliavini, Marco Abbiati
Gorgonian corals play a structural role in temperate and tropical biogenic reefs, forming animal forests and creating biodiversity hot spots. In the Mediterranean Sea, slow-growing and long-lived gorgonian species are threatened by human disturbances and global environmental changes and concern about their conservation is rising. Alkaloid metabolites have proven to be essential in protecting these species from environmental stressors.. Traditional profiling methodologies to detect these metabolites require a large quantity of living tissue...
November 21, 2017: Chemistry & Biodiversity
https://www.readbyqxmd.com/read/29164646/b-factor-profile-prediction-for-rna-flexibility-using-support-vector-machines
#18
Ivantha Guruge, Ghazaleh Taherzadeh, Jian Zhan, Yaoqi Zhou, Yuedong Yang
Determining the flexibility of structured biomolecules is important for understanding their biological functions. One quantitative measurement of flexibility is the atomic Debye-Waller factor or temperature B-factor. Most existing studies are limited to temperature B-factors of proteins and their prediction. Only one method attempted to predict temperature B-factors of ribosomal RNA. Here, we developed and compared machine-learning techniques in prediction of temperature B-factors of RNAs. The best model based on Support Vector Machines yields Pearson's correction coefficient at 0...
November 21, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29164638/the-piwi-interacting-rna-molecular-pathway-insights-from-cultured-silkworm-germline-cells
#19
Kazuhiro Sakakibara, Mikiko C Siomi
The PIWI-interacting RNA (piRNA) pathway, one of the major eukaryotic small RNA silencing pathways, is a genome surveillance system that silences selfish genes in animal gonads. piRNAs guide PIWI protein to target genes through Watson-Crick RNA-RNA base-parings. Loss of piRNA function causes genome instability, inducing failure in gametogenesis and infertility. Studies using fruit flies and mice as key experimental models have resulted in tremendous progress in understanding the mechanism underlying the piRNA pathway...
November 22, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29164617/differential-perturbation-of-the-protrotropic-equilibrium-of-a-biological-photosensitizer-within-bile-salt-aggregates-of-varying-hydrophobicity-a-fluorimetric-investigation
#20
Riya Sett, Nikhil Guchhait
The present work reveals the binding interactions of a credible cancer cell photosensitizer, harmane (HM) with some selected bile salt aggregates of dissimilar hydrophobicity viz. sodium deoxycholate (NaDC), sodium cholate (NaC) and sodium taurocholate (NaTC). The explicit variation of the prototropic equilibrium of the photosensitizer both in the ground and excited state has been utilized to scrutinize the interaction phenomena. Differential modulation in the prototropic equilibrium of HM in the aforesaid aggregates has been explained on the basis of the structural dissimilarities of the bile-salt monomers...
November 22, 2017: Photochemistry and Photobiology
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