cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.27198744
title: Binding kinetics of quaternary ammonium ions in Kcv potassium channels

description: Kcv channels from plant viruses represent the autonomous pore module of potassium channels, devoid of any regulatory domains. These small proteins show very reproducible single-channel behavior in planar lipid bilayers. Thus, they are an optimum system for the study of the biophysics of ion transport and gating. Structural models based on homology modeling have been used successfully, but experimental structural data are currently not available. Here we determine the size of the cytosolic pore entrance by studying the blocker kinetics. Blocker binding and dissociation rate constants ranging from 0.01 to 1000 ms<sup>−1</sup> were determined for different quaternary ammonium ions. We found that the cytosolic pore entrance of Kcv<sub>NTS</sub> must be at least 11 Å wide. The results further indicate that the residues controlling a cytosolic gate in one of the Kcv isoforms influence blocker binding/dissociation as well as a second gate even when the cytosolic gate is in the open state. The voltage dependence of the rate constant of blocker release is used to test, which blockers bind to the same binding site.
DOI: 10.6084/m9.figshare.27198744.v1
title: Binding kinetics of quaternary ammonium ions in Kcv potassium channels

description: Kcv channels from plant viruses represent the autonomous pore module of potassium channels, devoid of any regulatory domains. These small proteins show very reproducible single-channel behavior in planar lipid bilayers. Thus, they are an optimum system for the study of the biophysics of ion transport and gating. Structural models based on homology modeling have been used successfully, but experimental structural data are currently not available. Here we determine the size of the cytosolic pore entrance by studying the blocker kinetics. Blocker binding and dissociation rate constants ranging from 0.01 to 1000 ms<sup>−1</sup> were determined for different quaternary ammonium ions. We found that the cytosolic pore entrance of Kcv<sub>NTS</sub> must be at least 11 Å wide. The results further indicate that the residues controlling a cytosolic gate in one of the Kcv isoforms influence blocker binding/dissociation as well as a second gate even when the cytosolic gate is in the open state. The voltage dependence of the rate constant of blocker release is used to test, which blockers bind to the same binding site.
DOI: 10.6084/m9.figshare.26806535.v1
title: The role of mechanosensitive ion channel Piezo1 in knee osteoarthritis inflammation

description: Mechanosensitive ion channel Piezo1 is known to mediate a variety of inflammatory pathways and is also involved in the occurrence and development of many orthopedic diseases. Although its role in the inflammatory mechanism of knee osteoarthritis (KOA) has been reported, a systematic explanation is yet to be seen. This article aims to summarize the role of inflammatory responses in the pathogenesis of KOA and elucidate the mechanism by which the Piezo1-mediated inflammatory response contributes to the pathogenesis of KOA, providing a theoretical basis for the prevention and treatment of knee osteoarthritis. The results indicate that in the mechanism leading to knee osteoarthritis, Piezo1 can mediate the inflammatory response through chondrocytes and synovial cells, participating in the pathological progression of KOA. Piezo1 has the potential to become a new target for the prevention and treatment of this disease. Additionally, as pain is one of the most severe manifestations in KOA patients, the inflammatory response mediated by Piezo1, which causes the release of inflammatory mediators and pro-inflammatory factors leading to pain, can be further explored.
DOI: 10.6084/m9.figshare.26889569.v1
title: Evaluation of four <i>KCNMA1</i> channelopathy variants on BK channel current under Ca<sub>V</sub>1.2 activation

description: Variants in <i>KCNMA1</i>, encoding the voltage- and calcium-activated K<sup>+</sup> (BK) channel, are associated with human neurological disease. The effects of gain-of-function (GOF) and loss-of-function (LOF) variants have been predominantly studied on BK channel currents evoked under steady-state voltage and Ca<sup>2+</sup> conditions. However, in their physiological context, BK channels exist in partnership with voltage-gated Ca<sup>2+</sup> channels and respond to dynamic changes in intracellular Ca<sup>2+</sup> (Ca<sup>2+</sup><sub>i</sub>). In this study, an L-type voltage-gated Ca<sup>2+</sup> channel present in the brain, Ca<sub>V</sub>1.2, was co-expressed with wild type and mutant BK channels containing GOF (D434G, N999S) and LOF (H444Q, D965V) patient-associated variants in HEK-293T cells. Whole-cell BK currents were recorded under Ca<sub>V</sub>1.2 activation using buffering conditions that restrict Ca<sup>2+</sup><sub>i</sub> to nano- or micro-domains. Both conditions permitted wild type BK current activation in response to Ca<sub>V</sub>1.2 Ca<sup>2+</sup> influx, but differences in behavior between wild type and mutant BK channels were reduced compared to prior studies in clamped Ca<sup>2+</sup><sub>i</sub>. Only the N999S mutation produced an increase in BK current in both micro- and nano-domains using square voltage commands and was also detectable in BK current evoked by a neuronal action potential within a microdomain. These data corroborate the GOF effect of N999S on BK channel activity under dynamic voltage and Ca<sup>2+</sup> stimuli, consistent with its pathogenicity in neurological disease. However, the patient-associated mutations D434G, H444Q, and D965V did not exhibit significant effects on BK current under Ca<sub>V</sub>1.2-mediated Ca<sup>2+</sup> influx, in contrast with prior steady-state protocols. These results demonstrate a differential potential for <i>KCNMA1</i> variant pathogenicity compared under diverse voltage and Ca<sup>2+</sup> conditions.
DOI: 10.6084/m9.figshare.25731144.v1
title: Role of the Ca<sub>V</sub>1.2 distal carboxy terminus in the regulation of L-type current

description: L-type calcium channels are essential for the excitation-contraction coupling in cardiac muscle. The Ca<sub>V</sub>1.2 channel is the most predominant isoform in the ventricle which consists of a multi-subunit membrane complex that includes the Ca<sub>V</sub>1.2 pore-forming subunit and auxiliary subunits like Ca<sub>V</sub>α<sub>2</sub>δ and Ca<sub>V</sub>β<sub>2b</sub>. The Ca<sub>V</sub>1.2 channel’s C-terminus undergoes proteolytic cleavage, and the distal C-terminal domain (DC<sub>term</sub>D) associates with the channel core through two domains known as proximal and distal C-terminal regulatory domain (PCRD and DCRD, respectively). The interaction between the DC<sub>term</sub>D and the remaining C-terminus reduces the channel activity and modifies voltage- and calcium-dependent inactivation mechanisms, leading to an autoinhibitory effect. In this study, we investigate how the interaction between DCRD and PCRD affects the inactivation processes and Ca<sub>V</sub>1.2 activity. We expressed a 14-amino acid peptide miming the DCRD-PCRD interaction sequence in both heterologous systems and cardiomyocytes. Our results show that overexpression of this small peptide can displace the DC<sub>term</sub>D and replicate the effects of the entire DC<sub>term</sub>D on voltage-dependent inactivation and channel inhibition. However, the effect on calcium-dependent inactivation requires the full DC<sub>term</sub>D and is prevented by overexpression of calmodulin. In conclusion, our results suggest that the interaction between DCRD and PCRD is sufficient to bring about the current inhibition and alter the voltage-dependent inactivation, possibly in an allosteric manner. Additionally, our data suggest that the DC<sub>term</sub>D competitively modifies the calcium-dependent mechanism. The identified peptide sequence provides a valuable tool for further dissecting the molecular mechanisms that regulate L-type calcium channels’ basal activity in cardiomyocytes.
DOI: 10.6084/m9.figshare.26806535
title: The role of mechanosensitive ion channel Piezo1 in knee osteoarthritis inflammation

description: Mechanosensitive ion channel Piezo1 is known to mediate a variety of inflammatory pathways and is also involved in the occurrence and development of many orthopedic diseases. Although its role in the inflammatory mechanism of knee osteoarthritis (KOA) has been reported, a systematic explanation is yet to be seen. This article aims to summarize the role of inflammatory responses in the pathogenesis of KOA and elucidate the mechanism by which the Piezo1-mediated inflammatory response contributes to the pathogenesis of KOA, providing a theoretical basis for the prevention and treatment of knee osteoarthritis. The results indicate that in the mechanism leading to knee osteoarthritis, Piezo1 can mediate the inflammatory response through chondrocytes and synovial cells, participating in the pathological progression of KOA. Piezo1 has the potential to become a new target for the prevention and treatment of this disease. Additionally, as pain is one of the most severe manifestations in KOA patients, the inflammatory response mediated by Piezo1, which causes the release of inflammatory mediators and pro-inflammatory factors leading to pain, can be further explored.
DOI: 10.6084/m9.figshare.26889569
title: Evaluation of four <i>KCNMA1</i> channelopathy variants on BK channel current under Ca<sub>V</sub>1.2 activation

description: Variants in <i>KCNMA1</i>, encoding the voltage- and calcium-activated K<sup>+</sup> (BK) channel, are associated with human neurological disease. The effects of gain-of-function (GOF) and loss-of-function (LOF) variants have been predominantly studied on BK channel currents evoked under steady-state voltage and Ca<sup>2+</sup> conditions. However, in their physiological context, BK channels exist in partnership with voltage-gated Ca<sup>2+</sup> channels and respond to dynamic changes in intracellular Ca<sup>2+</sup> (Ca<sup>2+</sup><sub>i</sub>). In this study, an L-type voltage-gated Ca<sup>2+</sup> channel present in the brain, Ca<sub>V</sub>1.2, was co-expressed with wild type and mutant BK channels containing GOF (D434G, N999S) and LOF (H444Q, D965V) patient-associated variants in HEK-293T cells. Whole-cell BK currents were recorded under Ca<sub>V</sub>1.2 activation using buffering conditions that restrict Ca<sup>2+</sup><sub>i</sub> to nano- or micro-domains. Both conditions permitted wild type BK current activation in response to Ca<sub>V</sub>1.2 Ca<sup>2+</sup> influx, but differences in behavior between wild type and mutant BK channels were reduced compared to prior studies in clamped Ca<sup>2+</sup><sub>i</sub>. Only the N999S mutation produced an increase in BK current in both micro- and nano-domains using square voltage commands and was also detectable in BK current evoked by a neuronal action potential within a microdomain. These data corroborate the GOF effect of N999S on BK channel activity under dynamic voltage and Ca<sup>2+</sup> stimuli, consistent with its pathogenicity in neurological disease. However, the patient-associated mutations D434G, H444Q, and D965V did not exhibit significant effects on BK current under Ca<sub>V</sub>1.2-mediated Ca<sup>2+</sup> influx, in contrast with prior steady-state protocols. These results demonstrate a differential potential for <i>KCNMA1</i> variant pathogenicity compared under diverse voltage and Ca<sup>2+</sup> conditions.
DOI: 10.6084/m9.figshare.25731144
title: Role of the Ca<sub>V</sub>1.2 distal carboxy terminus in the regulation of L-type current

description: L-type calcium channels are essential for the excitation-contraction coupling in cardiac muscle. The Ca<sub>V</sub>1.2 channel is the most predominant isoform in the ventricle which consists of a multi-subunit membrane complex that includes the Ca<sub>V</sub>1.2 pore-forming subunit and auxiliary subunits like Ca<sub>V</sub>α<sub>2</sub>δ and Ca<sub>V</sub>β<sub>2b</sub>. The Ca<sub>V</sub>1.2 channel’s C-terminus undergoes proteolytic cleavage, and the distal C-terminal domain (DC<sub>term</sub>D) associates with the channel core through two domains known as proximal and distal C-terminal regulatory domain (PCRD and DCRD, respectively). The interaction between the DC<sub>term</sub>D and the remaining C-terminus reduces the channel activity and modifies voltage- and calcium-dependent inactivation mechanisms, leading to an autoinhibitory effect. In this study, we investigate how the interaction between DCRD and PCRD affects the inactivation processes and Ca<sub>V</sub>1.2 activity. We expressed a 14-amino acid peptide miming the DCRD-PCRD interaction sequence in both heterologous systems and cardiomyocytes. Our results show that overexpression of this small peptide can displace the DC<sub>term</sub>D and replicate the effects of the entire DC<sub>term</sub>D on voltage-dependent inactivation and channel inhibition. However, the effect on calcium-dependent inactivation requires the full DC<sub>term</sub>D and is prevented by overexpression of calmodulin. In conclusion, our results suggest that the interaction between DCRD and PCRD is sufficient to bring about the current inhibition and alter the voltage-dependent inactivation, possibly in an allosteric manner. Additionally, our data suggest that the DC<sub>term</sub>D competitively modifies the calcium-dependent mechanism. The identified peptide sequence provides a valuable tool for further dissecting the molecular mechanisms that regulate L-type calcium channels’ basal activity in cardiomyocytes.
DOI: 10.15468/dl.xzuc68
title: Occurrence Download

description: A dataset containing 438 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thamnaconus modestus (Günther, 1877)",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 438 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025784-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.25592233
title: A lineage-specific protein network at the trypanosome nuclear envelope

description: The nuclear envelope (NE) separates translation and transcription and is the location of multiple functions, including chromatin organization and nucleocytoplasmic transport. The molecular basis for many of these functions have diverged between eukaryotic lineages. <i>Trypanosoma brucei</i>, a member of the early branching eukaryotic lineage Discoba, highlights many of these, including a distinct lamina and kinetochore composition. Here, we describe a cohort of proteins interacting with both the lamina and NPC, which we term lamina-associated proteins (LAPs). LAPs represent a diverse group of proteins, including two candidate NPC-anchoring pore membrane proteins (POMs) with architecture conserved with <i>S. cerevisiae</i> and <i>H. sapiens</i>, and additional peripheral components of the NPC. While many of the LAPs are Kinetoplastid specific, we also identified broadly conserved proteins, indicating an amalgam of divergence and conservation within the trypanosome NE proteome, highlighting the diversity of nuclear biology across the eukaryotes, increasing our understanding of eukaryotic and NPC evolution.
DOI: 10.6084/m9.figshare.25592233.v2
title: A lineage-specific protein network at the trypanosome nuclear envelope

description: The nuclear envelope (NE) separates translation and transcription and is the location of multiple functions, including chromatin organization and nucleocytoplasmic transport. The molecular basis for many of these functions have diverged between eukaryotic lineages. <i>Trypanosoma brucei</i>, a member of the early branching eukaryotic lineage Discoba, highlights many of these, including a distinct lamina and kinetochore composition. Here, we describe a cohort of proteins interacting with both the lamina and NPC, which we term lamina-associated proteins (LAPs). LAPs represent a diverse group of proteins, including two candidate NPC-anchoring pore membrane proteins (POMs) with architecture conserved with <i>S. cerevisiae</i> and <i>H. sapiens</i>, and additional peripheral components of the NPC. While many of the LAPs are Kinetoplastid specific, we also identified broadly conserved proteins, indicating an amalgam of divergence and conservation within the trypanosome NE proteome, highlighting the diversity of nuclear biology across the eukaryotes, increasing our understanding of eukaryotic and NPC evolution.
DOI: 10.6084/m9.figshare.25592233.v1
title: A lineage-specific protein network at the trypanosome nuclear envelope

description: The nuclear envelope (NE) separates translation and transcription and is the location of multiple functions, including chromatin organization and nucleocytoplasmic transport. The molecular basis for many of these functions have diverged between eukaryotic lineages. <i>Trypanosoma brucei</i>, a member of the early branching eukaryotic lineage Discoba, highlights many of these, including a distinct lamina and kinetochore composition. Here, we describe a cohort of proteins interacting with both the lamina and NPC, which we term lamina-associated proteins (LAPs). LAPs represent a diverse group of proteins, including two candidate NPC-anchoring pore membrane proteins (POMs) with architecture conserved with <i>S. cerevisiae</i> and <i>H. sapiens</i>, and additional peripheral components of the NPC. While many of the LAPs are Kinetoplastid specific, we also identified broadly conserved proteins, indicating an amalgam of divergence and conservation within the trypanosome NE proteome, highlighting the diversity of nuclear biology across the eukaryotes, increasing our understanding of eukaryotic and NPC evolution.
DOI: 10.6084/m9.figshare.27187116
title: Cytogenetic bands and sharp peaks of Alu underlie large-scale segmental regulation of nuclear genome architecture

description: Cytogenetic bands reflect genomic organization in large blocks of DNA with similar properties. Because banding patterns are invariant, this organization may often be assumed unimportant for genome regulation. Results here challenge that view. Findings here suggest cytogenetic bands reflect a visible framework upon which regulated genome architecture is built. Given Alu and L1 densities differ in cytogenetic bands, we examined their distribution after X-chromosome inactivation or formation of senescent-associated heterochromatin foci (SAHFs). Alu-rich regions remain outside both SAHFs and the Barr Body (BB), affirming that the BB is not the whole chromosome but a condensed, L1-rich core. Hi-C analysis of senescent cells demonstrates large (~10 Mb) G-bands remodel as a contiguous unit, gaining distal intrachromosomal interactions as syntenic G-bands coalesce into SAHFs. Striking peaks of Alu within R-bands strongly resist condensation. Thus, large-scale segmental genome architectur relates to dark versus light cytogenetic bands and Alu-peaks, implicating both in chromatin regulation.
DOI: 10.6084/m9.figshare.27187116.v1
title: Cytogenetic bands and sharp peaks of Alu underlie large-scale segmental regulation of nuclear genome architecture

description: Cytogenetic bands reflect genomic organization in large blocks of DNA with similar properties. Because banding patterns are invariant, this organization may often be assumed unimportant for genome regulation. Results here challenge that view. Findings here suggest cytogenetic bands reflect a visible framework upon which regulated genome architecture is built. Given Alu and L1 densities differ in cytogenetic bands, we examined their distribution after X-chromosome inactivation or formation of senescent-associated heterochromatin foci (SAHFs). Alu-rich regions remain outside both SAHFs and the Barr Body (BB), affirming that the BB is not the whole chromosome but a condensed, L1-rich core. Hi-C analysis of senescent cells demonstrates large (~10 Mb) G-bands remodel as a contiguous unit, gaining distal intrachromosomal interactions as syntenic G-bands coalesce into SAHFs. Striking peaks of Alu within R-bands strongly resist condensation. Thus, large-scale segmental genome architectur relates to dark versus light cytogenetic bands and Alu-peaks, implicating both in chromatin regulation.
DOI: 10.6084/m9.figshare.27231712
title: Apoptosis-induced translocation of nesprin-2 from the nuclear envelope to mitochondria is associated with mitochondrial dysfunction

description: Accumulating evidence suggests that the nuclear envelope (NE) is not just a target, but also a mediator of apoptosis. We showed recently that the NE protein nesprin-2 has pro-apoptotic activity, which involves its subcellular redistribution and Bcl-2 proteins. Here we further characterize the pro-apoptotic activity of nesprin-2 focusing on its redistribution. We assessed the redistribution kinetics of endogenous nesprin-2 tagged with GFP relative to apoptosis-associated mitochondrial dysfunction. The results show apoptosis-induced GFP-nesprin-2G redistribution occurred by two different modes – complete and partial, both lead to appearance of nesprin-2G near the mitochondria. Moreover, GFP-nesprin-2 redistribution is associated with reduction in mitochondrial membrane potential and mitochondrial outer membrane permeabilization and precedes the appearance of morphological features of apoptosis. Our results show that nesprin-2G redistribution and translocation near mitochondria is an early apoptotic effect associated with mitochondrial dysfunction, which may be responsible for the pro-apoptotic function of nesprin-2.
DOI: 10.6084/m9.figshare.27231712.v1
title: Apoptosis-induced translocation of nesprin-2 from the nuclear envelope to mitochondria is associated with mitochondrial dysfunction

description: Accumulating evidence suggests that the nuclear envelope (NE) is not just a target, but also a mediator of apoptosis. We showed recently that the NE protein nesprin-2 has pro-apoptotic activity, which involves its subcellular redistribution and Bcl-2 proteins. Here we further characterize the pro-apoptotic activity of nesprin-2 focusing on its redistribution. We assessed the redistribution kinetics of endogenous nesprin-2 tagged with GFP relative to apoptosis-associated mitochondrial dysfunction. The results show apoptosis-induced GFP-nesprin-2G redistribution occurred by two different modes – complete and partial, both lead to appearance of nesprin-2G near the mitochondria. Moreover, GFP-nesprin-2 redistribution is associated with reduction in mitochondrial membrane potential and mitochondrial outer membrane permeabilization and precedes the appearance of morphological features of apoptosis. Our results show that nesprin-2G redistribution and translocation near mitochondria is an early apoptotic effect associated with mitochondrial dysfunction, which may be responsible for the pro-apoptotic function of nesprin-2.