scholarly journals Molybdate pumping into the molybdenum storage protein via an ATP-powered piercing mechanism

2019 ◽  
Vol 116 (52) ◽  
pp. 26497-26504 ◽  
Author(s):  
Steffen Brünle ◽  
Martin L. Eisinger ◽  
Juliane Poppe ◽  
Deryck J. Mills ◽  
Julian D. Langer ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Storage Protein ◽  
Large Scale ◽  
Azotobacter Vinelandii ◽  
Current Data ◽  
Nucleophilic Attack ◽  
Valuable Insight ◽  
Similar Reaction ◽  
Α Subunit ◽  
Ump Kinase

The molybdenum storage protein (MoSto) deposits large amounts of molybdenum as polyoxomolybdate clusters in a heterohexameric (αβ)3cage-like protein complex under ATP consumption. Here, we suggest a unique mechanism for the ATP-powered molybdate pumping process based on X-ray crystallography, cryoelectron microscopy, hydrogen-deuterium exchange mass spectrometry, and mutational studies of MoSto fromAzotobacter vinelandii. First, we show that molybdate, ATP, and Mg2+consecutively bind into the open ATP-binding groove of the β-subunit, which thereafter becomes tightly locked by fixing the previously disordered N-terminal arm of the α-subunit over the β-ATP. Next, we propose a nucleophilic attack of molybdate onto the γ-phosphate of β-ATP, analogous to the similar reaction of the structurally related UMP kinase. The formed instable phosphoric-molybdic anhydride becomes immediately hydrolyzed and, according to the current data, the released and accelerated molybdate is pressed through the cage wall, presumably by turning aside the Metβ149 side chain. A structural comparison between MoSto and UMP kinase provides valuable insight into how an enzyme is converted into a molecular machine during evolution. The postulated direct conversion of chemical energy into kinetic energy via an activating molybdate kinase and an exothermic pyrophosphatase reaction to overcome a proteinous barrier represents a novelty in ATP-fueled biochemistry, because normally, ATP hydrolysis initiates large-scale conformational changes to drive a distant process.

scholarly journals Gut Microbiome in Psoriasis: An Updated Review

Pathogens ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 463
Author(s):  
Mariusz Sikora ◽  
Albert Stec ◽  
Magdalena Chrabaszcz ◽  
Aleksandra Knot ◽  
Anna Waskiel-Burnat ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Beta Diversity ◽  
Large Scale ◽  
Skin Diseases ◽  
Intestinal Barrier ◽  
Alpha Diversity ◽  
Current Data ◽  
Intestinal Microbiome ◽  
Microbial Composition ◽  
Alpha And Beta Diversity

(1) Background: A growing body of evidence highlights that intestinal dysbiosis is associated with the development of psoriasis. The gut–skin axis is the novel concept of the interaction between skin diseases and microbiome through inflammatory mediators, metabolites and the intestinal barrier. The objective of this study was to synthesize current data on the gut microbial composition in psoriasis. (2) Methods: We conducted a systematic review of studies investigating intestinal microbiome in psoriasis, using the PRISMA checklist. We searched MEDLINE, EMBASE, and Web of Science databases for relevant published articles (2000–2020). (3) Results: All of the 10 retrieved studies reported alterations in the gut microbiome in patients with psoriasis. Eight studies assessed alpha- and beta-diversity. Four of them reported a lack of change in alpha-diversity, but all confirmed significant changes in beta-diversity. At the phylum-level, at least two or more studies reported a lower relative abundance of Bacteroidetes, and higher Firmicutes in psoriasis patients versus healthy controls. (4) Conclusions: There is a significant association between alterations in gut microbial composition and psoriasis; however, there is high heterogeneity between studies. More unified methodological standards in large-scale studies are needed to understand microbiota’s contribution to psoriasis pathogenesis and its modulation as a potential therapeutic strategy.

scholarly journals Metastable Intermediates as Stepping Stones on the Maturation Pathways of Viral Capsids

mBio ◽  
2014 ◽  
Vol 5 (6) ◽  
Author(s):  
Giovanni Cardone ◽  
Robert L. Duda ◽  
Naiqian Cheng ◽  
Lili You ◽  
James F. Conway ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Large Scale ◽  
Structural Changes ◽  
Energy Landscape ◽  
Potential Hazard ◽  
Stepping Stones ◽  
Scanning Calorimetry ◽  
Conformational Effects ◽  
Capsid Maturation ◽  
Capsid Integrity

ABSTRACT As they mature, many capsids undergo massive conformational changes that transform their stability, reactivity, and capacity for DNA. In some cases, maturation proceeds via one or more intermediate states. These structures represent local minima in a rich energy landscape that combines contributions from subunit folding, association of subunits into capsomers, and intercapsomer interactions. We have used scanning calorimetry and cryo-electron microscopy to explore the range of capsid conformations accessible to bacteriophage HK97. To separate conformational effects from those associated with covalent cross-linking (a stabilization mechanism of HK97), a cross-link-incompetent mutant was used. The mature capsid Head I undergoes an endothermic phase transition at 60°C in which it shrinks by 7%, primarily through changes in its hexamer conformation. The transition is reversible, with a half-life of ~3 min; however, >50% of reverted capsids are severely distorted or ruptured. This observation implies that such damage is a potential hazard of large-scale structural changes such as those involved in maturation. Assuming that the risk is lower for smaller changes, this suggests a rationalization for the existence of metastable intermediates: that they serve as stepping stones that preserve capsid integrity as it switches between the radically different conformations of its precursor and mature states. IMPORTANCE Large-scale conformational changes are widespread in virus maturation and infection processes. These changes are accompanied by the release of conformational free energy as the virion (or fusogenic glycoprotein) switches from a precursor state to its mature state. Each state corresponds to a local minimum in an energy landscape. The conformational changes in capsid maturation are so radical that the question arises of how maturing capsids avoid being torn apart. Offering proof of principle, severe damage is inflicted when a bacteriophage HK97 capsid reverts from the (nonphysiological) state that it enters when heated past 60°C. We suggest that capsid proteins have been selected in part by the criterion of being able to avoid sustaining collateral damage as they mature. One way of achieving this—as with the HK97 capsid—involves breaking the overall transition down into several smaller steps in which the risk of damage is reduced.

scholarly journals Understanding Student Engagement in Large-Scale Open Online Courses: A Machine Learning Facilitated Analysis of Student’s Reflections in 18 Highly Rated MOOCs

2018 ◽  
Vol 19 (3) ◽  
Author(s):  
Khe Foon Hew ◽  
Chen Qiao ◽  
Ying Tang
Keyword(s):  
Machine Learning ◽  
Large Scale ◽  
Online Courses ◽  
Subject Area ◽  
Online Course ◽  
Valuable Insight ◽  
Course Quality ◽  
Learning Classifier ◽  
Quality Rating ◽  
Open Courses

Although massive open online courses (MOOCs) have attracted much worldwide attention, scholars still understand little about the specific elements that students find engaging in these large open courses. This study offers a new original contribution by using a machine learning classifier to analyze 24,612 reflective sentences posted by 5,884 students, who participated in one or more of 18 highly rated MOOCs. Highly rated MOOCs were sampled because they exemplify good practices or teaching strategies. We selected highly rated MOOCs from Coursetalk, an open user-driven aggregator and discovery website that allows students to search and review various MOOCs. We defined a highly rated MOOC as a free online course that received an overall five-star course quality rating, and received at least 50 reviews from different learners within a specific subject area. We described six specific themes found across the entire data corpus: (a) structure and pace, (b) video, (c) instructor, (d) content and resources, (e) interaction and support, and (f) assignment and assessment. The findings of this study provide valuable insight into factors that students find engaging in large-scale open online courses.

scholarly journals The history of settlement and agrarian land use in a boreal forest in Värmland, Sweden, new evidence from pollen analysis

2021 ◽  
Author(s):  
Sigrún Dögg Eddudóttir ◽  
Eva Svensson ◽  
Stefan Nilsson ◽  
Anneli Ekblom ◽  
Karl-Johan Lindholm ◽  
...  
Keyword(s):  
Land Use ◽  
Pollen Analysis ◽  
Large Scale ◽  
Pollen Grains ◽  
Ice Age ◽  
Valuable Insight ◽  
Archaeological Survey ◽  
History Of ◽  
New Evidence ◽  
Insight Into

AbstractShielings are the historically known form of transhumance in Scandinavia, where livestock were moved from the farmstead to sites in the outlands for summer grazing. Pollen analysis has provided a valuable insight into the history of shielings. This paper presents a vegetation reconstruction and archaeological survey from the shieling Kårebolssätern in northern Värmland, western Sweden, a renovated shieling that is still operating today. The first evidence of human activities in the area near Kårebolssätern are Hordeum- and Cannabis-type pollen grains occurring from ca. 100 bc. Further signs of human impact are charcoal and sporadic occurrences of apophyte pollen from ca. ad 250 and pollen indicating opening of the canopy ca. ad 570, probably a result of modification of the forest for grazing. A decrease in land use is seen between ad 1000 and 1250, possibly in response to a shift in emphasis towards large scale commodity production in the outlands. Emphasis on bloomery iron production and pitfall hunting may have caused a shift from agrarian shieling activity. The clearest changes in the pollen assemblage indicating grazing and cultivation occur from the mid-thirteenth century, coinciding with wetter climate at the beginning of the Little Ice Age. The earliest occurrences of anthropochores in the record predate those of other shieling sites in Sweden. The pollen analysis reveals evidence of land use that predates the results of the archaeological survey. The study highlights how pollen analysis can reveal vegetation changes where early archaeological remains are obscure.

scholarly journals Minimal mechanistic component of proteasome activation and prevention of impairment by pathological oligomers

2021 ◽  
Author(s):  
Janelle Chuah ◽  
Tifffany Thibaudeau ◽  
David Smith
Keyword(s):  
Small Molecules ◽  
Conformational Changes ◽  
Bound State ◽  
Proof Of Concept ◽  
Α Subunit ◽  
Gate Opening ◽  
Allosteric Mechanism ◽  
Dependent Mechanism ◽  
Degradation Of Peptides

Abstract Impairment of proteasomal function has been implicated in neurodegenerative diseases, justifying the need to understand how the proteasome is activated for protein degradation. Here, using biochemical and structural (cryo-EM) strategies in both archaeal and mammalian proteasomes, we further determine the HbYX(-motif)-dependent mechanism of proteasomal activation used by multiple proteasome-activating complexes including the 19S Particle. We identify multiple proteasome α subunit residues involved in HbYX-dependent activation, a point mutation that activates the proteasome by partially mimicking a HbYX-bound state, and conformational changes involved in gate-opening with a 2.0A structure. Through an iterative process of peptide synthesis, we successfully design a HbYX-like dipeptide mimetic as a robust tool to elucidate how the motif autonomously activates the proteasome. The mimetic induces near complete gate-opening at saturating concentration, activating mammalian proteasomal degradation of peptides and proteins. Findings using our peptide mimetic suggest the HbYX-dependent mechanism requires cooperative binding in at least two intersubunit pockets of the α ring. Collectively, the results presented here unambiguously demonstrate the lone role of the HbYX tyrosine in the allosteric mechanism of proteasome activation and offer proof of concept for the robust potential of HbYX-like small molecules to activate the proteasome.

scholarly journals Nuclear pores constrict upon energy depletion

2020 ◽  
Author(s):  
Christian E Zimmerli ◽  
Matteo Allegretti ◽  
Vasileios Rantos ◽  
Sara K Goetz ◽  
Agnieszka Obarska-Kosinska ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Large Scale ◽  
Electron Tomography ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Energy Status ◽  
Energy Depletion ◽  
Time Variations ◽  
Subtomogram Averaging ◽  
Pore Complexes

Nuclear pore complexes (NPCs) fuse the inner and outer nuclear membranes and mediate nucleocytoplasmic exchange. They are made of 30 different nucleoporins that form an intricate cylindrical architecture around an aqueous central channel. This architecture is highly dynamic in space and time. Variations in NPC diameter were reported, but the physiological circumstances and the molecular details remain unknown. Here we combined cryo-electron tomography and subtomogram averaging with integrative structural modeling to capture a molecular movie of the respective large-scale conformational changes in cellulo. While actively transporting NPCs adopt a dilated conformation, they strongly constrict upon cellular energy depletion. Fluorescence recovery after photo bleaching experiments show that NPC constriction is concomitant with reduced diffusion and active transport across the nuclear envelope. Our data point to a model where the energy status of cells is linked to the conformation of NPC architecture.

scholarly journals Plants as alternative platforms for monoclonal antibodies productions.

2021 ◽  
Author(s):  
Natalia Glumińska ◽  
Magdalena Krzesłowska
Keyword(s):  
Monoclonal Antibodies ◽  
Capital Investment ◽  
Protein Modification ◽  
Large Scale ◽  
Current Data ◽  
Production Costs ◽  
Future Market ◽  
Market Demand ◽  
Mammalian Expression ◽  
Animal Pathogens

Monoclonal antibodies (mAbs) are widely used in medical therapy and diagnostics, veterinary therapy, and research. The demand for mAbs reaches several dozen tons per year and is constantly growing, approaching the limits of current production possibilities. Mammalian expression systems, which currently dominate the bioproduction industry, have limited production capacity and require high capital investment and production costs. Plants are becoming promising expression platforms due to their scalability, speed, low cost of production, low risk of contamination from animal pathogens and eukaryotic mechanisms of post-translational protein modification. The transgenic plants used for the production of mAbs can be obtained by stable transformation of plant cells as well as transient expression of foreign proteins. In this review, we extract a broad overview of articles, many of them from recent years, concerning modern approaches to producing monoclonal antibodies in plants, methods for modifying the carbohydrate profile of mAbs, and purifying the resulting product. We also present current data on the practical use of mAbs in medical therapies and potential methods of producing antibodies on a very large scale, able to meet the future market demand.

scholarly journals Structural insights into the activation of human calcium-sensing receptor

2021 ◽  
Author(s):  
Xiaochen Chen ◽  
Lu Wang ◽  
Zhanyu Ding ◽  
Qianqian Cui ◽  
Li Han ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Large Scale ◽  
Transmembrane Domains ◽  
Structural Basis ◽  
Calcium Sensing Receptor ◽  
Calcium Sensing ◽  
Cryo Electron Microscopy ◽  
Activation Mechanisms ◽  
G Protein Coupled ◽  
Structural Insights

AbstractHuman calcium-sensing receptor (CaSR) is a G-protein-coupled receptor that maintains Ca2+ homeostasis in serum. Here, we present the cryo-electron microscopy structures of the CaSR in the inactive and active states. Complemented with previously reported crystal structures of CaSR extracellular domains, it suggests that there are three distinct conformations: inactive, intermediate and active state during the activation. We used a negative allosteric nanobody to stabilize the CaSR in the fully inactive state and found a new binding site for Ca2+ ion that acts as a composite agonist with L-amino acid to stabilize the closure of active Venus flytraps. Our data shows that the agonist binding leads to the compaction of the dimer, the proximity of the cysteine-rich domains, the large-scale transitions of 7-transmembrane domains, and the inter-and intrasubunit conformational changes of 7-transmembrane domains to accommodate the downstream transducers. Our results reveal the structural basis for activation mechanisms of the CaSR.

scholarly journals SOIL MANAGEMENT IN THE URBAN ENVIRONMENT: TODAY AND FUTURE

2019 ◽  
Vol 1 (1) ◽  
pp. 66-71
Author(s):  
Bogdan Stanescu ◽  
Adriana Cuciureanu
Keyword(s):  
Performance Management ◽  
Urban Environment ◽  
Urban Areas ◽  
Large Scale ◽  
Current Data ◽  
Soil Protection ◽  
The European Union ◽  
Residential Areas

The present article presents the expertise realized by the Department of Environmental Monitoring Pollution Evaluation within the INCD ECOIND, in the evaluation of the quality of urban soils in the municipality of Bucharest and the main big cities in Romania. The current data available at the level of the 27 member states of the European Union show that annually over 100,000 hectares of land are introduced into the urban environment, a direct consequence of the development of cities. There are a number of legislative obstacles to strategic soil protection measures. Moreover, at the level of the local authorities there is a conflict regarding the measures of soil protection in the long term, on the one hand, and, the accelerated economic development in the short term, on the other. European environmental experts consider that the urban development, absolutely necessary for the economic growth, requires an adequate management of the natural resources in order for the development to be done on a sustainable basis, respectively to follow a series of strategic objectives. In our country, at least in the last decade, we find on a large scale the conversion of industrial areas into commercial or residential areas. The footprint of industrial activities can be found even after long periods of time present by identifying the remnant of soil pollution or in those areas known as historically polluted (for example the town of Copsa Mica). The conclusions stemming from the assessment of pollution in urban areas over large areas, in correlation with the potential sources of pollution, underline the need to monitor the quality of soils in the urban environment, but also to apply a performance management in order to protect this natural resource in the long term.

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