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61.
Rafael Junqueira Borges Kathrin Meindl Josep Trivio Massimo Sammito Ana Medina Claudia Milln Martin Alcorlo Juan A. Hermoso Marcos Roberto de Mattos Fontes Isabel Usn 《Acta Crystallographica. Section D, Structural Biology》2020,76(3):221-237
Fragment‐based molecular‐replacement methods can solve a macromolecular structure quasi‐ab initio. ARCIMBOLDO, using a common secondary‐structure or tertiary‐structure template or a library of folds, locates these with Phaser and reveals the rest of the structure by density modification and autotracing in SHELXE. The latter stage is challenging when dealing with diffraction data at lower resolution, low solvent content, high β‐sheet composition or situations in which the initial fragments represent a low fraction of the total scattering or where their accuracy is low. SEQUENCE SLIDER aims to overcome these complications by extending the initial polyalanine fragment with side chains in a multisolution framework. Its use is illustrated on test cases and previously unknown structures. The selection and order of fragments to be extended follows the decrease in log‐likelihood gain (LLG) calculated with Phaser upon the omission of each single fragment. When the starting substructure is derived from a remote homolog, sequence assignment to fragments is restricted by the original alignment. Otherwise, the secondary‐structure prediction is matched to that found in fragments and traces. Sequence hypotheses are trialled in a brute‐force approach through side‐chain building and refinement. Scoring the refined models through their LLG in Phaser may allow discrimination of the correct sequence or filter the best partial structures for further density modification and autotracing. The default limits for the number of models to pursue are hardware dependent. In its most economic implementation, suitable for a single laptop, the main‐chain trace is extended as polyserine rather than trialling models with different sequence assignments, which requires a grid or multicore machine. SEQUENCE SLIDER has been instrumental in solving two novel structures: that of MltC from 2.7 Å resolution data and that of a pneumococcal lipoprotein with 638 residues and 35% solvent content. 相似文献
62.
Marina Plaza-Garrido M. Carmen Salinas-Garcia Daniel Alba-Elena Jose C. Martínez Ana Camara-Artigas 《Acta Crystallographica. Section D, Structural Biology》2020,76(9):845-856
Protein crystals can easily be coloured by adding dyes to their mother liquor, but most structures of these protein–dye complexes remain unsolved. Here, structures of lysozyme in complex with bromophenol blue obtained by soaking orthorhombic and tetragonal crystals in a saturated solution of the dye at different pH values from 5.0 to 7.5 are reported. Two different binding sites can be found in the lysozyme–bromophenol blue crystals: binding site I is located near the amino‐ and carboxyl‐termini, while binding site II is located adjacent to helices α1 (residues 4–15) and α3 (residues 88–100). In the orthorhombic crystals soaked at pH 7.0, binding of the dye takes place in both sites without significant changes in the unit cell. However, soaking tetragonal crystals with bromophenol blue results in two different complexes. Crystals soaked at pH 5.5 (HEWL‐T1) show a single dye molecule bound to site II, and the crystals belong to space group P43212 without significant changes in the unit cell (a = b = 78.50, c = 37.34 Å). On the other hand, crystals soaked at pH 6.5 in the presence of imidazole (HEWL‐T2) show up to eight molecules of the dye bound to site II, and display changes in space group (P212121) and unit cell (a = 38.00, b = 76.65, c = 84.86 Å). In all of the structures, the dye molecules are placed at the surface of the protein near to positively charged residues accessible through the main solvent channels of the crystal. Differences in the arrangement of the dye molecules at the surface of the protein suggest that the binding is not specific and is mainly driven by electrostatic interactions. 相似文献
63.
Csar Paz‐y‐Mio Vernica Yumiceba Germania Moreta Rosario Paredes Mnica Ruiz Ligia Ocampo Arianne Llamos Paneque Catalina Ochoa Prez Juan Carlos Ruiz‐Cabezas Jenny lvarez Vidal Idarmis Jimnez Torres Ramn Vargas‐Vera Fernando Cruz Víctor Hugo Guapi N Martha Montalvn Sara Meneses lvarez Maribel Garzn Castro Elizabeth Lamar Segura María Augusta Recalde Bez María Elena Naranjo Nina Tambaco Jijn María Sinche Pedro Licuy Ramiro Burgos Fabin Porras‐Borja Gabriela Echeverría‐Garcs Andy Prez‐Villa Isaac Armendriz‐Castillo Jennyfer M. García‐Crdenas Santiago Guerrero Patricia Guevara‐Ramírez Andrs Lpez‐Corts Ana Karina Zambrano Paola E. Leone 《Molecular Genetics & Genomic Medicine》2020,8(2)
64.
Emanuela Saracino Luca Maiolo Davide Polese M. Semprini Ana Isabel Borrachero‐Conejo Jacopo Gasparetto Stefano Murtagh Margherita Sola Lorenzo Tomasi Francesco Valle Luca Pazzini Francesco Formaggio Michela Chiappalone Saber Hussain Marco Caprini Michele Muccini Luigi Ambrosio Guglielmo Fortunato Roberto Zamboni Annalisa Convertino Valentina Benfenati 《Advanced Biosystems》2020,4(4)
The correct human brain function is dependent on the activity of non‐neuronal cells called astrocytes. The bioelectrical properties of astrocytes in vitro do not closely resemble those displayed in vivo and the former are incapable of generating action potential; thus, reliable approaches in vitro for noninvasive electrophysiological recording of astrocytes remain challenging for biomedical engineering. Here it is found that primary astrocytes grown on a device formed by a forest of randomly oriented gold coated‐silicon nanowires, resembling the complex structural and functional phenotype expressed by astrocytes in vivo. The device enables noninvasive extracellular recording of the slow‐frequency oscillations generated by differentiated astrocytes, while flat electrodes failed on recording signals from undifferentiated cells. Pathophysiological concentrations of extracellular potassium, occurring during epilepsy and spreading depression, modulate the power of slow oscillations generated by astrocytes. A reliable approach to study the role of astrocytes function in brain physiology and pathologies is presented. 相似文献
65.
66.
We carried out an ecosystem service (ES) assessment at Soto de Pajares, a 400 ha active gravel quarry site located close to protected areas in the southeast of the Community of Madrid, Spain. The currently approved restoration plan is for quarry‐made excavations to be restored back to agricultural land. However, the site has been identified as being important for nature, so different restoration strategies should be considered. To better understand how these compare in terms of ES provision, which had not previously been done at mineral extraction sites in Spain, we used an established toolkit: the Toolkit for Ecosystem Service Site‐based Assessments (TESSA). We compared the agriculture‐focused restoration plan and two nature‐focused alternative scenarios, one without public access (conservation scenario) and the other with public access (compromise scenario). Monetary estimations of the value of agricultural production, climate change mitigation, and recreation were calculated in three scenarios. Results indicated that the compromise scenario provided the greatest annual value (€91,409), mainly due to its potential visitors, surpassing both agricultural (€68,504) and conservation (€48,556) scenarios. Considering the higher costs associated with restoring sites to agricultural production, nature conservation may be an attractive option for extraction companies. The use of TESSA at this site has provided valuable information to quarry managers to help guide their decision‐making. 相似文献
67.
68.
Aingeru Martínez Juliana Barros Ana Lúcia Gonçalves Cristina Canhoto 《Freshwater Biology》2020,65(8):1475-1483
- Salinisation (i.e. increased ion concentrations) in fresh waters is a growing threat worldwide that impacts freshwater communities. However, less is known about how increased salt concentrations affect key ecosystem processes such as leaf decomposition.
- We designed a laboratory experiment to assess the effects of a concentration gradient (1, 3, and 6 g/L) of three different salts (NaCl, CaCl2 and CH3CO2K), on leaf litter decomposition mediated by microbial decomposers and the larvae of a cased caddis fly (Schizopelex festiva, Trichoptera). Leaf discs of Quercus robur inoculated with microbial decomposers (a mixture of 5 fungal species) were incubated in microcosms under every possible salt × concentration combination and without salt addition (control), with a single individual of the cased caddis fly. Half of the leaf disks were not available for consumption by the trichopteran and represent a microbial only treatment when leaf mass loss was measured.
- Leaf decomposition driven by microbial decomposers was not affected by salinity despite the fact that all salt treatments depressed fungal biomass and microbial respiration compared to the control. However, the caddis flies were strongly affected by the high salt concentrations and consumed less leaf material at 6 g/L salt concentrations compared to control microcosms. The feeding activity of the trichopteran further depended on the salt type: CaCl2 had the most deleterious effects.
- Salinisation of fresh waters depresses leaf litter decomposition, mainly through deleterious effects on detritivores, the magnitude of the response being dependent on the ionic composition. Our results reiterate the need to reduce terrestrial run-off of salts into fresh waters because salinisation (especially increased levels of CaCl2) affects invertebrates and the key ecosystem processes they drive.
69.
Carolina Gomes Diana Ferreira João P. F. Carvalho Carlos A. V. Barreto Joana Fernandes Marisol Gouveia Fernando Ribeiro Ana S. Duque Sandra I. Vieira 《Biotechnology and bioengineering》2020,117(8):2610-2628
Hypertension is a major and highly prevalent risk factor for various diseases. Among the most frequently prescribed antihypertensive first-line drugs are synthetic angiotensin I-converting enzyme inhibitors (ACEI). However, since their use in hypertension therapy has been linked to various side effects, interest in the application of food-derived ACEI peptides (ACEIp) as antihypertensive agents is rapidly growing. Although promising, the industrial production of ACEIp through conventional methods such as chemical synthesis or enzymatic hydrolysis of food proteins has been proven troublesome. We here provide an overview of current antihypertensive therapeutics, focusing on ACEI, and illustrate how biotechnology and bioengineering can overcome the limitations of ACEIp large-scale production. Latest advances in ACEIp research and current genetic engineering-based strategies for heterologous production of ACEIp (and precursors) are also presented. Cloning approaches include tandem repeats of single ACEIp, ACEIp fusion to proteins/polypeptides, joining multivariate ACEIp into bioactive polypeptides, and producing ACEIp-containing modified plant storage proteins. Although bacteria have been privileged ACEIp heterologous hosts, particularly when testing for new genetic engineering strategies, plants and microalgae-based platforms are now emerging. Besides being generally safer, cost-effective and scalable, these “pharming” platforms can perform therelevant posttranslational modifications and produce (and eventually deliver) biologically active protein/peptide-based antihypertensive medicines. 相似文献
70.
Anete P. Lourenço Ana Paula M. Santos Hélio H. Checon Mayra R. Costa Sebastião L. Assis Júnior 《Studies on Neotropical Fauna and Environment》2020,55(2):116-128
ABSTRACT The reasons for the decline of bee diversity and abundance include the destruction and loss of natural habitats. Protected areas are created for biodiversity conservation, but these areas vary strongly in their level of vegetation disturbance. Using trap-nests, we assessed changes in solitary bee abundance, richness, and composition in areas ranging from naturally conserved to degraded. Solitary bees were sampled during an 18-month period in three areas of southeastern Brazil: a preserved area in Rio Preto State Park – PERP; a restored/altered area with exotic plants at the Federal University of the Jequitinhonha and Mucuri Valleys – JK Campus; and a degraded area in Biribiri State Park – PEBi. A total of seven species of bees built 115 nests. In the degraded area, only two nests were built. Abundance of built nests was higher in the preserved area (PERP), but diversity was higher in the restored area (JK Campus). Our results show that the solitary bee population responds positively to habitat complexity (local scale). The presence of a diverse solitary bee fauna in the restored area indicates that altered areas should also be protected as suitable areas for re-colonization of cavity-nesting bees. 相似文献