bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allosteric communication between ligand binding domains modulates substrate inhibition in adenylate kinase
Authors: Scheerer David , Adkar Bharat V. , Bhattacharyya Sanchari , Levy Dorit , Iljina Marija , Riven Inbal , Dym Orly , Haran Gilad , Shakhnovich Eugene I. 
Published: November 2022

AbstractEnzymes play a vital role in life processes; they control chemical reactions and allow functional cycles to be synchronized. Many enzymes harness large-scale motions of their domains to achieve tremendous catalytic prowess and high selectivity for specific substrates. One outstanding example is provided by the three-domain enzyme adenylate kinase (AK), which catalyzes phosphotransfer between ATP to AMP. Here we study the phenomenon of substrate inhibition by AMP and its correlation with domain motions. Using single-molecule FRET spectroscopy, we show that AMP does not block access to the ATP binding site, neither by competitive binding to the ATP cognate site nor by directly closing the LID domain. Instead, inhibitory concentrations of AMP lead to a faster and more cooperative domain closure by ATP, leading in turn to an increased population of the closed state. The effect of AMP binding can be modulated through mutations throughout the structure of the enzyme, as shown by the screening of an extensive AK mutant library. Mutation of multiple conserved residues leads to increased substrate inhibition, suggesting a positive selection during evolution. Combining these insights, we developed a model that explains the complex activity of AK, particularly substrate inhibition, based on the experimentally observed opening and closing rates. Notably, the model indicates that the catalytic power is affected by the microsecond balance between the open and closed states of the enzyme. Our findings highlight the crucial role of protein motions in enzymatic activity.Significance StatementHow conformational dynamics affect the catalytic activity of enzymes remains a topic of active debate. We focus here on the domain closure dynamics of adenylate kinase (AK) and how they are affected by substrate inhibition. By screening an extensive mutant library, we show that this feature of the enzyme is well conserved in evolution. Importantly, domain closure is required in order to bring AK’s substrates close together for their chemical reaction; single-molecule FRET studies directly measure the populations of the open and closed states. We find that overpopulation of the closed state can be detrimental to activity. The results allow us to develop a kinetic model that properly accounts for AK kinetics by combining conformational dynamics and biochemical steps.
Forward planning under uncertainty in a population-based alcohol use disorder sample
Authors: Fischbach Pascale C. , Gönner Lorenz , Steffen Johannes , Kiebel Stefan J. , Smolka Michael N. 
Published: November 2022

ABSTRACTAltered decision-making is a defining component of addiction, but there is little evidence whether these alterations affect multi-step planning in individuals with alcohol use disorder (AUD). We used a recently developed planning task in a cross-sectional approach to test the planning performance of 30 individuals diagnosed with AUD relative to 32 healthy control subjects, both sampled from the general population. To gain insight into the factors underlying behavioral performance, we inferred the parameters of a reinforcement learning agent performing rational planning, using a Bayesian inference scheme. This approach allowed us to differentiate between separate factors determining planning performance, e.g., planning depth, decision noise, and bias for certain action choices. Contrary to our hypothesis, we did not observe reduced planning depth in AUD subjects. Instead, our results show a small effect in the opposite direction: Healthy controls were slightly less efficient in the planning task. Importantly, subjects in the control group allocated less time for planning than AUD subjects, potentially indicative of motivational differences between groups. The group difference in planning depth persisted when controlling for both reaction times and general cognitive performance, albeit at a lesser magnitude. Altogether, our results do not favor the view that mild-to-moderate alcohol use disorder in general-population individuals generally involves impairments in cognitive tasks requiring forward planning across multiple steps.
Spherocytosis-related L1340P mutation in ankyrin affects its interactions with spectrin
Authors: Machnicka Beata , Czogalla Aleksander , M. Bogusławska Dżamila , Stasiak Piotr , Sikorski Aleksander F. 
Published: November 2022

AbstractPreviously, we reported a new missense mutation in theANK1gene correlated with the HS phenotype. This mutation, resulting in L1340P substitution (HGMD CM149731), likely leads to the changes in the conformation of the ankyrin ZZUD domain important for ankyrin binding to spectrin. In this report, we have shown the molecular and physiological effects of this mutation. First, we assessed the binding activity of human β-spectrin to the mutated ZZUDL1340P domain of ankyrin using two different experimental approaches – the study of association and dissociation responses of spectrin ankyrin binding domain and sedimentation assay. In addition, we demonstrated changes in morphology caused by the overexpressed ankyrin ZZUD domain in human cell models. Our results prove the key role of L1340 aa residue in the UPA domain for the correct alignment of the ZZUD domain of ankyrin, which results in binding the latter with spectrin within the erythrocyte membrane. Replacing the L1340 with a proline residue disrupts the spectrin binding activity of ankyrin.
Divisome core complex in bacterial cell division revealed by cryo-EM
Authors: Käshammer Lisa , van den Ent Fusinita , Jeffery Magnus , Jean Nicolas L. , Hale Victoria L. , Löwe Jan 
Published: November 2022

Cell division, or cytokinesis is a fundamental process of life and, in most bacteria, is driven by peptidoglycan synthesis at the septum1. It is catalysed by the divisome, a multi-protein complex with more than 20 components that spans the cell envelope in bacteria harbouring a cell wall2. Central to the divisome is the peptidoglycan-synthesising protein complex FtsWI, with the transglycosylase (TG) FtsW polymerising glycan strands from its substrate Lipid II3,4, and the transpeptidase (TP) FtsI crosslinking peptide stems, thus forming a covalent mesh between glycan strands5,6(Fig. 1a). Septal peptidoglycan synthesis occurs after activation of the divisome glycosyltransferase-transpeptidase pair FtsWI3, in particular through an interaction with the heterotrimer FtsQBL7.Here, we present the cryo-EM structure of the catalytic divisome core complex FtsWIQBL fromPseudomonas aeruginosaat 3.7 Å resolution. The structure reveals the intricate details of the periplasmic interfaces within FtsWIQBL, including the positioning of FtsI by the coiled coil of FtsBL, as well as a transmembrane domain containing FtsWIBL but not FtsQ. With our structure we are able to provide molecular mechanisms of a multitude of known mutations that interfere with divisome activation and regulation. Finally, we reveal a large conformational switch between presumably inactive and active states of the FtsWI core enzymes.Our work is foundational for further structural, biochemical and genetic studies elucidating the molecular mechanisms of bacterial cell division. Since the divisome peptidoglycan synthase is essential for cell division in most bacteria, and is absent in eukaryotic cells entirely, it is a key target of important antibiotics and antibiotic development8, and we suggest that our structure will help to accelerate these efforts.
De novo identification of CD4+ T cell epitopes
Authors: Zdinak Paul , Grebinoski Stephanie , Torrey Jessica , Zarate-Martinez Eduardo , Hicks Louise , Ranjan Rashi , Trivedi Nishtha , Arshad Sanya , Anderson Mark , Vignali Dario AA , Joglekar Alok V. 
Published: November 2022

ABSTRACTCD4+ T cells recognize peptide antigens presented on class II Major Histocompatibility Complex (MHC-II) molecules to carry out their function. The remarkable diversity of T cell receptor (TCR) sequences and lack of antigen discovery approaches for MHC-II make profiling the specificities of CD4+ T cells challenging. We have expanded our platform of Signaling and Antigen-presenting Bifunctional Receptors to encode MHC-II molecules presenting covalently linked peptides (SABR-IIs) for CD4+ cell antigen discovery. SABR-IIs can present epitopes to CD4+ T cells and induce signaling upon their recognition, allowing a readable output. Here, we demonstrate that SABR-IIs libraries presenting endogenous and post-translationally modified epitopes can be used for antigen discovery. Using SABR-II libraries in conjunction with single cell RNA sequencing, we de-convoluted multiple highly expanded TCRs from pancreatic islets of Non-Obese Diabetic (NOD) mice. We compounded antigen discovery by incorporating computational TCR similarity prediction metrics followed by experimental validation. Finally, we showed SABR-IIs presenting epitopes in class II HLA alleles can be used for antigen discovery for human CD4+ T cells. Taken together, we have developed a rapid, flexible, scalable, and versatile approach for the de novo identification of CD4+ T cell ligands from single cell RNA sequencing data using experimental and computational approaches.
Host response of Syrian hamster to SARS-CoV-2 infection, including differences with humans and between sexes
Authors: Castellan Martina , Zamperin Gianpiero , Franzoni Giulia , Foiani Greta , Zorzan Maira , Drzewnioková Petra , Mancin Marzia , Brian Irene , Bortolami Alessio , Pagliari Matteo , Oggiano Annalisa , Vascellari Marta , Panzarin Valentina , Crovella Sergio , Monne Isabella , Terregino Calogero , De Benedictis Paola , Leopardi Stefania 
Published: November 2022

AbstractThe emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the importance of having proper tools and models to study the pathophysiology of emerging infectious diseases to test therapeutic protocols, assess changes in viral phenotype and evaluate the effect of viral evolution. This study provides a comprehensive characterization of the Syrian hamster (Mesocricetus auratus) as an animal model for SARS-CoV-2 infection, using different approaches (description of clinical signs, viral load, receptor profiling and host immune response) and targeting four different organs (lungs, intestine, brain and PBMCs). Our data showed that both male and female hamsters are susceptible to the infection and develop a disease similar to the one observed in patients with COVID-19, including moderate to severe pulmonary lesions, inflammation and recruitment of the immune system in lungs and at systemic level. However, all animals recovered within 14 days without developing the severe pathology seen in humans, and none of them died. We found faint evidence for intestinal and neurological tropism associated with the absence of lesions and a minimal host response in intestines and brains, highlighting another crucial difference with the multi-organ impairment of severe COVID-19. When comparing male and female hamsters, it was observed that males sustained higher viral RNA shedding and replication in the lungs, suffered from more severe symptoms and histopathological lesions and triggered higher pulmonary inflammation. Overall, these data confirm the Syrian hamster as a suitable model for mildmoderate COVID-19 and reflect sex-related differences in the response against the virus observed in humans.
Ion permeation pathway within the internal pore of P2X receptor channels
Authors: Tam Stephanie W. , Huffer Kate , Li Mufeng , Swartz Kenton J. 
Published: November 2022

AbstractP2X receptor channels are trimeric ATP-activated ion channels expressed in neuronal and non-neuronal cells that are attractive therapeutic targets for human disorders. Seven subtypes of P2X receptor channels have been identified in mammals that can form both homomeric and heteromeric channels. P2X1-4 and P2X7 receptor channels are cation selective, whereas P2X5 has been reported to have both cation and anion permeability. P2X receptor channel structures reveal that each subunit is comprised of two transmembrane helices, with both N-and C-termini on the intracellular side of the membrane, and a large extracellular domain that contains the ATP binding sites at subunit interfaces. Recent structures of ATP-bound P2X receptors with the activation gate open reveal the unanticipated presence of a cytoplasmic cap over the central ion permeation pathway, leaving lateral fenestrations that may be largely buried within the membrane as potential pathways for ions to permeate the intracellular end of the pore. In the present study we identify a critical residue within the intracellular lateral fenestrations that is readily accessible to thiol reactive compounds from both sides of the membrane and where substitutions influence the relative permeability of the channel to cations and anions. Taken together, our results demonstrate that ions can enter or exit the internal pore through lateral fenestrations that play a critical role in determining the ion selectivity of P2X receptor channels. (223)
The Lamin A/C Ig-fold undergoes cell density-dependent changes that alter epitope binding
Authors: Wallace Melanie , Fedorchak Gregory R. , Agrawal Richa , Gilbert Rachel M. , Patel Jineet , Park Sangwoo , Paszek Matthew , Lammerding Jan 
Published: November 2022

AbstractLamins A/C are nuclear intermediate filament proteins that are involved in diverse cellular mechanical and biochemical functions. Here, we report that recognition of Lamins A/C by a commonly used antibody (JOL-2) that binds the Lamin A/C Ig-fold and other antibodies targeting similar epitopes is highly dependent on cell density, even though Lamin A/C protein levels do not change with cell density. The density-dependent Lamin A/C labeling was distinct from previously reported differential apico-basal labeling, which was independent of cell density. Comparison of the density-dependent labeling effects of antibodies recognizing different Lamin A/C epitopes suggests that the effect is caused by partial unfolding or masking of the C’E and/or EF loops of the Ig-fold in response to cell spreading. Seeding cells on micropatterned surfaces with different areas confirmed that increased cell spreading resulted in reduced Lamin A/C labeling with the JOL-2 antibody. Surprisingly, JOL-2 antibody labeling was insensitive to depolymerization of cytoskeletal filaments or disruption of the Linker of Nucleoskeleton and Cytoskeleton (LINC) complex. Although the density-dependent changes of the Ig-fold did not alter nuclear stiffness or nucleo-cytoskeletal force transmission, they may nonetheless modulate interaction with lamin binding partners and thereby affect cellular functions. Taken together, our results point to a previously unrecognized change in the Lamin A/C Ig-fold that affects recognition by the JOL-2 antibody. These findings are not only important for the interpretation of immunofluorescence data for Lamin A/C, but also raise the intriguing prospect that the conformational changes may play a role in Lamin A/C mediated cellular function.
The binding sites of E2F transcription factor inDrosophilametabolic genes are functionally distinct
Authors: Zappia Maria Paula , Kwon Yong-Jae , Westacott Anton , Liseth Isabel , Lee Hyun Min , Islam Abul B.M.M.K. , Kim Jiyeon , Frolov Maxim V. 
Published: November 2022

ABSTRACTThe canonical role of the transcription factor E2F is to control the expression of cell cycle genes by binding to the E2F sites in their promoters. However, the list of putative E2F target genes is extensive and includes many metabolic genes, yet the significance of E2F in controlling expression of these genes remains largely unknown. Here, we used the CRISPR/Cas9 technology to introduce point mutations in the E2F sites upstream of five endogenous metabolic genes inDrosophila. We found that the impact of these mutations on both the recruitment of E2F and the expression of the target genes varied, with the glycolytic gene,Phosphoglycerate kinase(Pgk), being mostly affected. The loss of E2F regulation onPgkgene led to a decrease in glycolytic flux, TCA cycle intermediates levels, ATP content and an abnormal mitochondrial morphology. Remarkably, chromatin accessibility was significantly reduced at multiple genomic regions inPgkΔE2Fmutants. These regions contained hundreds of genes, including metabolic genes that were downregulated inPgkΔE2Fmutants. Moreover,PgkΔE2Fanimals had shortened life span and exhibited defects in high-energy consuming organs, such as ovaries and muscles. Collectively, our results illustrate how the pleiotropic effects on metabolism, gene expression and development in thePgkΔE2Fanimals underscore the importance of E2F regulation on a single E2F target,Pgk.
Analysis of factors affecting the purchase of private label products by different age consumers
Authors: Musso Fabio , Colamatteo Annarita , Bravi Laura , Pagnanelli Maria Anna , Murmura Federica , Sansone Marcello 
Published: November 2022

PurposeThe aim of this study is to determine how the different age of consumers impacts on some factors that drive consumers to the purchasing of private label products, considering differences and similarities of behaviors.Design/methodology/approachThe research was conducted through the administration of a questionnaire to evaluate consumers' perceptions about private label food products. To collect data, the convenience sampling method has been used. The valid answers collected and analyzed are 358.FindingsThe results of this study highlight that the response of different age groups to the Private Label Brands (PLBs) must be considered in the light of the positioning adopted by the individual retailers. Value for money and satisfaction on previous consumption are relevant for purchasing decisions regardless of the retailer's strategy and the age of consumers. A third factor, price, is important for the whole sample. Focusing on the specific age clusters, the younger respondents seem to be attentive to factors such as healthy and in-store promotion, while the more experienced consumer are attentive to the origin and traceability of products.Originality/valueAn analysis of the main literature on Private Labels showed that the results of research about the role of consumer age in PLB choices are contrasting. This study aims at integrating the literature, measuring how the factors influencing the purchase of PLB products vary for different age groups of consumers.
Incentivisation of digital technology takers in the construction industry
Authors: Ebekozien Andrew , Samsurijan Mohamad Shaharudin 
Published: November 2022

PurposeStudies showed that digital technology applications in the construction industry are low, especially in many developing nations. Construction incentivisation (CI) is one of the long-standing principles adopted to enhance project performance. There is a paucity of studies concerning CI to improve digital technology applications. Thus, this research investigated the relevance and perceived hindrances that may hinder the implementation of CI from promoting digital technologies and proffer ways to improve digital technology applications in the construction sector.Design/methodology/approachIn Nigeria’s context, this research is exploratory. Twenty-four semi-structured virtual interviews were conducted in Lagos and Abuja, Nigeria, with knowledgeable participants that indicated interest and were interviewed. The engaged interviewees were drawn from government agencies, academicians in construction consultancy, Internet and communication technology experts, construction contracting firms and construction consulting firms. The collected data were coded and analysed through a thematic method.FindingsDigitalisation of the industry via CI may face some hindrances. The perceived issues that may hinder CI implementation were classified into most severe, severe and fairly severe in Nigeria’s construction industry context. Findings proffer feasible policy solutions that can mitigate these issues and improve digital technology applications in the industry via the CI.Research limitations/implicationsThis study covered the relevance and perceived issues that may hinder the implementation of the CI to improve digital technology applications in the industry. Also, the study proffers policy solutions to enhance digital technology applications in the industry via the CI concept.Practical implicationsFindings from this research will support and offer a valuable understanding of the relevance of the “incentivisation concept” to improve digital technology applications in the Nigerian-built environment. Other developing countries with low applications of digital technology in construction may consider the suggested policy solutions from this research. Also, this study will stir policymakers and construction practitioners to support policies tailored towards improving digital technology applications in construction.Originality/valueThis research contributes by exploring the effectiveness of the CI concept and informing construction practitioners and policymakers on how to improve digital technology applications in the Nigerian construction industry.
Future of healthcare start-ups in the era of digitalization: bibliometric analysis
Authors: Sreenivasan Aswathy , Suresh M. 
Published: November 2022

PurposeIt is the responsibility of the national governments to deliver healthcare services that are both effective and affordable to everyone. There are still gaps in this supply, which is extremely demanding. In this sense, companies are attempting to reach neglected markets and disrupt the marketplace with novel solutions. Although there are still anecdotal examples, a thorough literature evaluation is lacking. This study aims to provide a synthesis of the future of healthcare start-ups.Design/methodology/approachPapers that included the term “healthcare start-ups,” “health-tech start-ups,” “start-up,” “Artificial intelligence in healthcare,” and “Health tech start-ups in India” were considered for the analysis. The Biblioshiny package under the R programming tool was considered for a detailed analysis of the papers.FindingsA total of 854 documents were related to healthcare start-ups, from which only 14 papers are related to health-tech start-ups and four papers are related to artificial intelligence in healthcare start-ups. It has been found from the past works of literature that the effectiveness of technology for information and communication in healthcare has significantly increased in recent years. Technology has already begun to permeate the healthcare market from other fields and industries. One way that the internet will help the industry evolve is by integrating digital health into daily life.Research limitations/implicationsThe study is not using other databases but is limited to Google Scholar and Scopus. A significant constraint of this study is the paucity of relevant literature in reputable publications on health and information systems. Another restriction was that gray literature, such as any journal or newspaper written by members of the health community about health-tech start-ups, was not taken into account.Practical implicationsHealthcare players should exhibit a fundamental openness to novel solutions to facilitate the digitalization of the healthcare system. Developing technology is widely used, and from an innovation perspective, a start-up should focus on innovation by employing technology and offering revolutionary healthcare solutions.Originality/valueThe novelty of this research is based on its presentation of an organized and thorough literature evaluation, which defines the current state of the art concerning green start-ups. To create a sustainable start-up, a thorough study of the information gained in respect of its healthcare start-up is presented.