scholarly journals Structural evidence for a proline-specific glycopeptide recognition domain in an O-glycopeptidase

Glycobiology ◽  
2020 ◽  
Author(s):  
Ilit Noach ◽  
Alisdair B Boraston
Keyword(s):  
Active Sites ◽  
Substrate Recognition ◽  
Peptide Bond ◽  
Multidomain Protein ◽  
Threonine Residue ◽  
Tyrosine Residues ◽  
Host Pathogen Interaction ◽  
A Site ◽  
Insight Into

Abstract The glycosylation of proteins is typically considered as a stabilizing modification, including resistance to proteolysis. A class of peptidases, referred to as glycopeptidases or O-glycopeptidases, circumvent the protective effect of glycans against proteolysis by accommodating the glycans in their active sites as specific features of substrate recognition. IMPa from Pseudomonas aeruginosa is such an O-glycopeptidase that cleaves the peptide bond immediately preceding a site of O-glycosylation, and through this glycoprotein-degrading function contributes to the host-pathogen interaction. IMPa, however, is a relatively large multidomain protein and how its additional domains may contribute to its function remains unknown. Here, through the determination of a crystal structure of IMPa in complex with an O-glycopeptide, we reveal that the N-terminal domain of IMPa, which is classified in Pfam as IMPa_N_2, is a proline recognition domain that also shows the properties of recognizing an O-linked glycan on the serine/threonine residue following the proline. The proline is bound in the center of a bowl formed by four functionally conserved aromatic amino acid side chains while the glycan wraps around one of the tyrosine residues in the bowl to make classic aromatic ring-carbohydrate CH-π interactions. This structural evidence provides unprecedented insight into how the ancillary domains in glycoprotein-specific peptidases can noncatalytically recognize specific glycosylated motifs that are common in mucin and mucin-like molecules.

scholarly journals Orthoformimycin inhibits translation elongation by displacing the A-site tRNA and preventing peptide bond formation

2021 ◽  
Author(s):  
Andreas Schedlbauer ◽  
Tatsuya Kaminishi ◽  
Attilio Fabbretti ◽  
Pohl Milon ◽  
Xu Han ◽  
...  
Keyword(s):  
Ribosomal Subunit ◽  
Peptide Bond ◽  
Resistance Mechanisms ◽  
Peptide Bond Formation ◽  
Translation Elongation ◽  
X Ray Crystallography ◽  
Steady State Kinetics ◽  
A Site ◽  
Insight Into ◽  
Major Target

The ribosome is a major target for antibiotics owing to its essential cellular role in protein synthesis. Structural analysis of ribosome-antibiotic complexes provides insight into the molecular basis for their inhibitory action and highlights possible avenues to improve their potential or overcome existing resistance mechanisms. Here we use X-ray crystallography and pre-steady state kinetics to detail the inhibitory mechanism of the antimicrobial on the large ribosomal subunit.

scholarly journals Development of Fragility Curves for Piping and Slope Stability of River Levees

Water ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 738
Author(s):  
Nicola Rossi ◽  
Mario Bačić ◽  
Meho Saša Kovačević ◽  
Lovorka Librić
Keyword(s):  
Slope Stability ◽  
Fragility Curves ◽  
Safety Margin ◽  
Water Levels ◽  
Flood Event ◽  
Soil Parameters ◽  
Design Code ◽  
A Site ◽  
Insight Into

The design code Eurocode 7 relies on semi-probabilistic calculation procedures, through utilization of the soil parameters obtained by in situ and laboratory tests, or by the means of transformation models. To reach a prescribed safety margin, the inherent soil parameter variability is accounted for through the application of partial factors to either soil parameters directly or to the resistance. However, considering several sources of geotechnical uncertainty, including the inherent soil variability, measurement error and transformation uncertainty, full probabilistic analyses should be implemented to directly consider the site-specific variability. This paper presents the procedure of developing fragility curves for levee slope stability and piping as failure mechanisms that lead to larger breaches, where a direct influence of the flood event intensity on the probability of failure is calculated. A range of fragility curve sets is presented, considering the variability of levee material properties and varying durations of the flood event, thus providing crucial insight into the vulnerability of the levee exposed to rising water levels. The procedure is applied to the River Drava levee, a site which has shown a continuous trend of increased water levels in recent years.

RNA secondary structure dependence in METTL3–METTL14 mRNA methylation is modulated by the N-terminal domain of METTL3

2020 ◽  
Vol 402 (1) ◽  
pp. 89-98
Author(s):  
Nathalie Meiser ◽  
Nicole Mench ◽  
Martin Hengesbach
Keyword(s):  
Secondary Structure ◽  
Rna Binding ◽  
Specific Protein ◽  
Structure Dependence ◽  
Terminal Domain ◽  
Methylation Assay ◽  
A Site ◽  
Methylation Activity

AbstractN6-methyladenosine (m6A) is the most abundant modification in mRNA. The core of the human N6-methyltransferase complex (MTC) is formed by a heterodimer consisting of METTL3 and METTL14, which specifically catalyzes m6A formation within an RRACH sequence context. Using recombinant proteins in a site-specific methylation assay that allows determination of quantitative methylation yields, our results show that this complex methylates its target RNAs not only sequence but also secondary structure dependent. Furthermore, we demonstrate the role of specific protein domains on both RNA binding and substrate turnover, focusing on postulated RNA binding elements. Our results show that one zinc finger motif within the complex is sufficient to bind RNA, however, both zinc fingers are required for methylation activity. We show that the N-terminal domain of METTL3 alters the secondary structure dependence of methylation yields. Our results demonstrate that a cooperative effect of all RNA-binding elements in the METTL3–METTL14 complex is required for efficient catalysis, and that binding of further proteins affecting the NTD of METTL3 may regulate substrate specificity.

An insight into the determination of size and number concentration of silver nanoparticles in blood using single particle ICP-MS (spICP-MS): Feasibility of application to samples relevant to in vivo toxicology studies

2021 ◽  
Author(s):  
Isabel Abad-Álvaro ◽  
Diego Leite ◽  
Dorota Bartczak ◽  
Susana Cuello ◽  
Beatriz Gomez-Gomez ◽  
...  
Keyword(s):  
Silver Nanoparticles ◽  
Single Particle ◽  
Number Concentration ◽  
Biological Matrices ◽  
Icp Ms ◽  
Toxicological Studies ◽  
Insight Into

Toxicological studies concerning nanomaterials in complex biological matrices usually require a carefully designed workflow that involves handling, transportation and preparation of a large number of samples without affecting the nanoparticle...

scholarly journals The RelA hydrolase domain acts as a molecular switch for (p)ppGpp synthesis

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Anurag Kumar Sinha ◽  
Kristoffer Skovbo Winther
Keyword(s):  
Active Sites ◽  
Molecular Switch ◽  
Cell Physiology ◽  
Synthetase Activity ◽  
Wild Type ◽  
Functional Studies ◽  
Loop Region ◽  
A Site ◽  
Trna Binding

AbstractBacteria synthesize guanosine tetra- and penta phosphate (commonly referred to as (p)ppGpp) in response to environmental stresses. (p)ppGpp reprograms cell physiology and is essential for stress survival, virulence and antibiotic tolerance. Proteins of the RSH superfamily (RelA/SpoT Homologues) are ubiquitously distributed and hydrolyze or synthesize (p)ppGpp. Structural studies have suggested that the shift between hydrolysis and synthesis is governed by conformational antagonism between the two active sites in RSHs. RelA proteins of γ-proteobacteria exclusively synthesize (p)ppGpp and encode an inactive pseudo-hydrolase domain. Escherichia coli RelA synthesizes (p)ppGpp in response to amino acid starvation with cognate uncharged tRNA at the ribosomal A-site, however, mechanistic details to the regulation of the enzymatic activity remain elusive. Here, we show a role of the enzymatically inactive hydrolase domain in modulating the activity of the synthetase domain of RelA. Using mutagenesis screening and functional studies, we identify a loop region (residues 114–130) in the hydrolase domain, which controls the synthetase activity. We show that a synthetase-inactive loop mutant of RelA is not affected for tRNA binding, but binds the ribosome less efficiently than wild type RelA. Our data support the model that the hydrolase domain acts as a molecular switch to regulate the synthetase activity.

scholarly journals Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Taolan Zhao ◽  
Yan-Ming Chen ◽  
Yu Li ◽  
Jia Wang ◽  
Siyu Chen ◽  
...  
Keyword(s):  
Protein Quality ◽  
Peptide Bond ◽  
Peptide Bond Formation ◽  
Translation Elongation ◽  
Cryo Electron Microscopy ◽  
Cotranslational Folding ◽  
A Cell ◽  
Exit Tunnel ◽  
Hidden Layer ◽  
A Site

Abstract Background The folding of proteins is challenging in the highly crowded and sticky environment of a cell. Regulation of translation elongation may play a crucial role in ensuring the correct folding of proteins. Much of our knowledge regarding translation elongation comes from the sequencing of mRNA fragments protected by single ribosomes by ribo-seq. However, larger protected mRNA fragments have been observed, suggesting the existence of an alternative and previously hidden layer of regulation. Results In this study, we performed disome-seq to sequence mRNA fragments protected by two stacked ribosomes, a product of translational pauses during which the 5′-elongating ribosome collides with the 3′-paused one. We detected widespread ribosome collisions that are related to slow ribosome release when stop codons are at the A-site, slow peptide bond formation from proline, glycine, asparagine, and cysteine when they are at the P-site, and slow leaving of polylysine from the exit tunnel of ribosomes. The structure of disomes obtained by cryo-electron microscopy suggests a different conformation from the substrate of the ribosome-associated protein quality control pathway. Collisions occurred more frequently in the gap regions between α-helices, where a translational pause can prevent the folding interference from the downstream peptides. Paused or collided ribosomes are associated with specific chaperones, which can aid in the cotranslational folding of the nascent peptides. Conclusions Therefore, cells use regulated ribosome collisions to ensure protein homeostasis.

scholarly journals “IF YOU DON’T KNOW ME BY NOW…”

2021 ◽  
pp. 1-28
Author(s):  
Ellen M. Whitehead ◽  
Allan Farrell ◽  
Jenifer L. Bratter
Keyword(s):  
Race And Ethnicity ◽  
Mate Selection ◽  
Racial Identities ◽  
Hispanic Origin ◽  
Socially Constructed ◽  
Attitudinal Factors ◽  
A Site ◽  
Intimate Partnerships ◽  
College Educated ◽  
Insight Into

ABSTRACT The racial composition of couples is a salient indicator of race’s impact on mate selection, but how well do those in intimate partnerships know the racial identities of their partners? While prior research has revealed that an individual’s race may be perceived differently than how they identify, most of what is known comes from brief interactions, with less information on established relationships. This study examines whether discrepancies in the reports of a person’s race or ethnicity can be identified even within intimate relationships, as well as which relational, social, and attitudinal factors are predictive of divergent or concordant reports. We draw on the Fragile Families and Child Wellbeing Study (n=3467), a U.S.-based dataset that uniquely provides both the father’s self-reported race and Hispanic origin and the mother’s report of the father’s race and ethnicity. We compare reports of the father’s race/Hispanic origin from both parents to assess the extent of mismatch, and we distinguish between whether mothers view the father’s race as similar to or different from her own. We find roughly 14% of mothers provide a race and Hispanic origin that is inconsistent with the father’s report, with a large share reflecting differences in the self-identified and perceived race of fathers who are reported as Hispanic. Among mismatched reports, mothers are more likely to report a race/ethnicity for the father that matches her own, depressing the number reporting interracial unions. Perceptions of racial homogamy are especially likely when mothers view racial sameness as important to marriage. Further, mismatches are more common in the midst of weak relational ties (i.e. non-marital relationships) and are less common when both parents are college-educated. These findings reveal that intimate unions are a site where race is socially constructed and provide insight into how norms of endogamy manifest within formed relationships.

scholarly journals Insight into Glutamatergic Involvement in Rewarding Effects of Mephedrone in Rats: In Vivo and Ex Vivo Study

2021 ◽  
Author(s):  
Olga Wronikowska ◽  
Maria Zykubek ◽  
Agnieszka Michalak ◽  
Anna Pankowska ◽  
Paulina Kozioł ◽  
...  
Keyword(s):  
Ex Vivo ◽  
Interdisciplinary Approach ◽  
Nmda Antagonist ◽  
Exchange Chromatography ◽  
Resonance Spectroscopy ◽  
Monoamine Transporters ◽  
Ex Vivo Study ◽  
Insight Into

AbstractMephedrone is a widely used drug of abuse, exerting its effects by interacting with monoamine transporters. Although this mechanism has been widely studied heretofore, little is known about the involvement of glutamatergic transmission in mephedrone effects. In this study, we comprehensively evaluated glutamatergic involvement in rewarding effects of mephedrone using an interdisciplinary approach including (1) behavioural study on effects of memantine (non-selective NMDA antagonist) on expression of mephedrone-induced conditioned place preference (CPP) in rats; (2) evaluation of glutamate concentrations in the hippocampus of rats following 6 days of mephedrone administration, using in vivo magnetic resonance spectroscopy (MRS); and (3) determination of glutamate levels in the hippocampus of rats treated with mephedrone and subjected to MRS, using ion-exchange chromatography. In the presented research, we confirmed priorly reported mephedrone-induced rewarding effects in the CPP paradigm and showed that memantine (5 mg/kg) was able to reverse the expression of this effect. MRS study showed that subchronic mephedrone administration increased glutamate level in the hippocampus when measured in vivo 24 h (5 mg/kg, 10 mg/kg and 20 mg/kg) and 2 weeks (5 mg/kg and 20 mg/kg) after last injection. Ex vivo chromatographic analysis did not show significant changes in hippocampal glutamate concentrations; however, it showed similar results as obtained in the MRS study proving its validity. Taken together, the presented study provides new insight into glutamatergic involvement in rewarding properties of mephedrone.

scholarly journals Prediction of Dead Oil Viscosity: Machine Learning vs. Classical Correlations

Energies ◽  
2021 ◽  
Vol 14 (4) ◽  
pp. 930
Author(s):  
Fahimeh Hadavimoghaddam ◽  
Mehdi Ostadhassan ◽  
Ehsan Heidaryan ◽  
Mohammad Ali Sadri ◽  
Inna Chapanova ◽  
...  
Keyword(s):  
Machine Learning ◽  
Viscosity Data ◽  
Oil Viscosity ◽  
Pvt Data ◽  
Proposed Model ◽  
Wide Range ◽  
Engineering Problems ◽  
Functional Forms ◽  
Insight Into

Dead oil viscosity is a critical parameter to solve numerous reservoir engineering problems and one of the most unreliable properties to predict with classical black oil correlations. Determination of dead oil viscosity by experiments is expensive and time-consuming, which means developing an accurate and quick prediction model is required. This paper implements six machine learning models: random forest (RF), lightgbm, XGBoost, multilayer perceptron (MLP) neural network, stochastic real-valued (SRV) and SuperLearner to predict dead oil viscosity. More than 2000 pressure–volume–temperature (PVT) data were used for developing and testing these models. A huge range of viscosity data were used, from light intermediate to heavy oil. In this study, we give insight into the performance of different functional forms that have been used in the literature to formulate dead oil viscosity. The results show that the functional form f(γAPI,T), has the best performance, and additional correlating parameters might be unnecessary. Furthermore, SuperLearner outperformed other machine learning (ML) algorithms as well as common correlations that are based on the metric analysis. The SuperLearner model can potentially replace the empirical models for viscosity predictions on a wide range of viscosities (any oil type). Ultimately, the proposed model is capable of simulating the true physical trend of the dead oil viscosity with variations of oil API gravity, temperature and shear rate.

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