1,720,957 research outputs found
Structural Determinants of Kv7.2 Channel Function and Variant-Induced Dysfunction: Insights from Molecular Dynamics Simulations
No full textI canali del potassio voltaggio–dipendenti della famiglia Kv7 (KCNQ) sono sensibili a perturbazioni anche sottili a livello della porta di attivazione del poro (activation gate, AG) e del filtro di selettività (selectivity filter, SF). Questa tesi utilizza simulazioni di dinamica molecolare (MD) all-atomo per analizzare come quattro varianti clinicamente identificate di KCNQ2 rimodellano il gating e la permeazione: tre varianti gain-of-function (GoF) nella porzione distale dell’elica S6 (G313S, A317T, L318V) e una variante loss-of-function (LoF) nell’elica del poro (A265V). A partire da modelli di poro chiuso e aperto basati su strutture crio-EM, inseriti in membrane esplicitamente solvatate, combiniamo simulazioni di equilibrio e sotto voltaggio, insieme a un confronto tra diversi force field, per calcolare caratteristiche strutturali quali la geometria del poro, l’idratazione della cavità centrale (central cavity, CC), le microstati del filtro di selettività e l’accoppiamento tra porta e filtro, e per metterle in relazione con i fenotipi delle varianti. Per le varianti GoF in S6, le simulazioni di equilibrio mostrano un allentamento consistente della porta di attivazione nel modello chiuso, in particolare a livello delle caratteristiche costrizioni S314/L318, e una persistente idratazione della cavità centrale, mentre il modello aperto rimane sostanzialmente invariato. Questi cambiamenti razionalizzano i fenotipi sperimentali, caratterizzati da una maggiore probabilità di apertura a singolo canale e abbondanza di membrana conservate. I risultati risultano robusti rispetto alla scelta di diversi force field biomolecolari ampiamente utilizzati, sebbene l’entità dell’allargamento e dell’idratazione vari. Le simulazioni con differenza di potenziale transmembrana applicata mostrano che i canali mutati, in stato parzialmente aperto, supportano la permeazione ionica, mentre la struttura nativa rimane non conduttiva, in accordo con il fenotipo GoF. Il filtro di selettività visita occasionalmente conformazioni ristrette, “pinched”, associate al legame transiente di poche molecole d’acqua dietro il filtro. A differenza di quanto osservato in altri canali, tuttavia, questa disposizione non è duratura, verosimilmente a causa di caratteristiche di sequenza peculiari di Kv7.2, e il filtro preferisce conformazioni conduttive che ospitano file multi-ione senza acque intercalate. La variante A265V è stata dimostrata sperimentalmente indurre inattivazione in stato aperto nel canale Kv7.2, che in condizioni fisiologiche è considerato non inattivante. Coerentemente, le simulazioni del mutante inizializzate da una struttura con porta aperta mostrano un filtro di selettività leggermente dilatato ma più labile, che campiona in modo asimmetrico microstati non conduttivi, accompagnati da un modesto restringimento della porta distale in S6, una caratteristica di allosteria “inversa” rispetto alle varianti GoF. Complessivamente, questi risultati mettono in relazione ciascuna variante con un meccanismo supportato da caratteristiche strutturali coerenti: dilatazione della porta interna che stabilizza l’apertura per le sostituzioni GoF in S6, rispetto a una labilità centrata sul filtro di selettività con accoppiamento inverso per A265V. Questo lavoro definisce relazioni struttura–funzione a livello atomistico in Kv7.2 e offre un quadro sistematico per interpretare i fenotipi clinici e guidare strategie di modulazione mirata al poro.Voltage-gated potassium channels of the Kv7 (KCNQ) family are sensitive to subtle perturbations at the pore activation gate (AG) and the selectivity filter (SF). This dissertation uses all-atom molecular dynamics (MD) to dissect how four KCNQ2 clinical identified variant remodel gating and permeation: three gain-of-function (GoF) variants in the distal S6 helix (G313S, A317T, L318V) and one loss-of-function (LoF) variant in the pore helix (A265V). Starting from cryo-EM–based closed and open pore models embedded in explicitly solvated membranes, we leverage equilibrium and voltage-driven simulations, as well as force-field cross-checking, to calculate structural features like pore geometry, central-cavity (CC) hydration, SF microstate occupancies, and gate–filter coupling, and to correlate them with variant phenotypes. For the S6 GoF variants, equilibrium MD reveals a consistent loosening of the activation gate in the closed model, in particular at the level of S314/L318 characteristic constrictions, and persistent CC wetting, while the open model remains essentially unchanged. These changes rationalize experimental phenotypes, characterized by a higher open probability with preserved single-channel conductance and membrane abundance. The results are robust against the choice of widely used biomolecular force fields, although the extent of widening and hydration varies. Simulations with applied transmembrane voltages show that the mutated, partially open channels support ion permeation, while the native structure remains nonconducting, consistent with the GoF phyenotype. The SF occasionaly visits narrow, “pinched” conformations, associated with the transient binding of few water molecules behind the SF. At variance with other channels, however, this arrangement is not long-lasting, likely because of unique Kv7.2 sequence features, and the filter prefers conductive conformations harboring multi-ion strings without intercalated waters. The A265V variant has been shown experimentally to induce open-state inactivation in the physiologically non-inactivating Kv7.2 channel. Consistently, simulations of the mutant initiated from an open-gate structure exhibit a slightly dilated and more labile SF that asymmetrically samples non-conductive microstates, accompanied by a modest tightening at the distal S6 gate, a reverse allosteric feature with respect to the GoF variants. Altogether, these results relate each variant to a mechanism supported by consistent structural features: inner-gate dilation that stabilizes opening for GoF S6 substitutions, versus SF-centric lability with reverse coupling for A265V. The work delineates atomistic structure–function relationships in Kv7.2 and offers a systematic framework for interpreting clinical phenotypes and informing pore-targeted modulation
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Unlocking the Potential of Field Effect Transistor (FET) Biosensors: A Perspective on Methodological Advances in Computational and Molecular Biology
Full text linkField-effect transistor (FET)-based sensors are increasingly gaining relevance in diagnostic, healthcare, and environmental monitoring applications. A FET operates by transducing chemical interactions between a surface-immobilized bioreceptor and the target analyte into a detectable electrical signal. FET biosensors can detect and monitor molecules (i.e., biomarkers, small molecules, viruses, bacterias) present in liquid samples, making a “liquid gate” configuration of FETs the most suitable approach. However, this FET architecture presents dimensional constraints that affect bioreceptors’ stability and immobilization in the liquid phase. To overcome these limitations, herein, a combination of computational and molecular biology techniques for improving bioreceptors' applicability in biosensing is proposed. This results in the optimized and problem-tailored protein receptors for specific FET biosensors applications, thus enhancing their overall performance. The interplay between the computational and experimental approaches will represent a ground-breaking solution for the development of next-generation biosensors
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
A physiologically-relevant intermediate state structure of a voltage-gated potassium channel
Full text linkVoltage-gated potassium ion (K+) channels perform critical roles in many physiological processes, while gain- or loss-of-function mutations lead to life-threatening pathologies. Here, we establish the high-resolution structure of a pivotal intermediate state of the Kv7.1 (KCNQ1) channel using cryogenic electron microscopy. The 3.53 Å resolution structure reveals straightened upper S1 and S2 voltage sensor helices, distancing them from the pore filter helix compared to fully activated channels. The outward translation of the S4 voltage sensor is essentially complete in this intermediate state, and the S4-S6 helices and the S4-S5 linker do not change position significantly between intermediate and activated states. The PIP2 ligand can bind in both states. Movement of S1 and S2 helices towards the filter helix from intermediate to activated states may explain smaller components of KCNQ1 voltage sensor fluorescence, differential Rb+/K+ selectivity, and pharmacological responses to activators and inhibitors. Single channel recordings and the location of long QT mutations suggest the potential physiological and disease importance of the intermediate state
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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