scholarly journals The basic residues in the Orai1 channel inner pore promote opening of the outer hydrophobic gate

2019 ◽  
Vol 152 (1) ◽  
Author(s):  
Megumi Yamashita ◽  
Christopher E. Ing ◽  
Priscilla See-Wai Yeung ◽  
Mohammad M. Maneshi ◽  
Régis Pomès ◽  
...  
Keyword(s):  
Severe Combined Immunodeficiency ◽  
Range Effect ◽  
Cellular Functions ◽  
Ion Conduction ◽  
Basic Residue ◽  
Wide Range ◽  
Outer Pore ◽  
Dynamics Simulations ◽  
Positively Charged ◽  
Inner Pore

Store-operated Orai1 channels regulate a wide range of cellular functions from gene expression to cell proliferation. Previous studies have shown that gating of Orai1 channels is regulated by the outer pore residues V102 and F99, which together function as a hydrophobic gate to block ion conduction in resting channels. Opening of this gate occurs through a conformational change that moves F99 away from the permeation pathway, leading to pore hydration and ion conduction. In addition to this outer hydrophobic gate, several studies have postulated the presence of an inner gate formed by the basic residues R91, K87, and R83 in the inner pore. These positively charged residues were suggested to block ion conduction in closed channels via mechanisms involving either electrostatic repulsion or steric occlusion by a bound anion plug. However, in contrast to this model, here we find that neutralization of the basic residues dose-dependently abolishes both STIM1-mediated and STIM1-independent activation of Orai1 channels. Molecular dynamics simulations show that loss of the basic residues dehydrates the pore around the hydrophobic gate and stabilizes the pore in a closed configuration. Likewise, the severe combined immunodeficiency mutation, Orai1 R91W, closes the channel by dewetting the hydrophobic stretch of the pore and stabilizing F99 in a pore-facing configuration. Loss of STIM1-gating in R91W and in the other basic residue mutants is rescued by a V102A mutation, which restores pore hydration at the hydrophobic gate to repermit ion conduction. These results indicate that the inner pore basic residues facilitate opening of the principal outer hydrophobic gate through a long-range effect involving hydration of the outer pore.

General Trend of Negative Transference Number in Li Salt/Ionic Liquid Mixtures

2019 ◽  
Author(s):  
Nicola Molinari ◽  
Jonathan P. Mailoa ◽  
Boris Kozinsky
Keyword(s):  
Ionic Liquid ◽  
Transference Number ◽  
Liquid Mixtures ◽  
Single Linkage ◽  
Self Diffusion ◽  
Wide Range ◽  
Single Linkage Cluster ◽  
Concentrated Solution ◽  
The One ◽  
Dynamics Simulations

We show that strong cation-anion interactions in a wide range of lithium-salt/ionic liquid mixtures result in a negative lithium transference number, using molecular dynamics simulations and rigorous concentrated solution theory. This behavior fundamentally deviates from the one obtained using self-diffusion coefficient analysis and agrees well with experimental electrophoretic NMR measurements, which accounts for ion correlations. We extend these findings to several ionic liquid compositions. We investigate the degree of spatial ionic coordination employing single-linkage cluster analysis, unveiling asymmetrical anion-cation clusters. Additionally, we formulate a way to compute the effective lithium charge that corresponds to and agrees well with electrophoretic measurements and show that lithium effectively carries a negative charge in a remarkably wide range of chemistries and concentrations. The generality of our observation has significant implications for the energy storage community, emphasizing the need to reconsider the potential of these systems as next generation battery electrolytes.<br>

scholarly journals Thermodynamics of ion binding and occupancy in potassium channels

2021 ◽  
Author(s):  
Zhifeng Jing ◽  
Joshua A. Rackers ◽  
Lawrence Pratt ◽  
Chengwen Liu ◽  
Susan B. Rempe ◽  
...  
Keyword(s):  
Potassium Channels ◽  
Ion Binding ◽  
Cellular Functions ◽  
Ion Conduction

Potassium channels modulate various cellular functions through efficient and selective conduction of K+ ions. The mechanism of ion conduction in potassium channels has recently emerged as a topic of debate....

scholarly journals Polymer cyclization for the emergence of hierarchical nanostructures

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Chaojian Chen ◽  
Manjesh Kumar Singh ◽  
Katrin Wunderlich ◽  
Sean Harvey ◽  
Colette J. Whitfield ◽  
...  
Keyword(s):  
Self Assembly ◽  
Three Dimensional ◽  
Hierarchical Structures ◽  
Structural Similarity ◽  
Vital Role ◽  
Nanomaterial Synthesis ◽  
Wide Range ◽  
Linear Poly ◽  
Polymer Folding ◽  
Dynamics Simulations

AbstractThe creation of synthetic polymer nanoobjects with well-defined hierarchical structures is important for a wide range of applications such as nanomaterial synthesis, catalysis, and therapeutics. Inspired by the programmability and precise three-dimensional architectures of biomolecules, here we demonstrate the strategy of fabricating controlled hierarchical structures through self-assembly of folded synthetic polymers. Linear poly(2-hydroxyethyl methacrylate) of different lengths are folded into cyclic polymers and their self-assembly into hierarchical structures is elucidated by various experimental techniques and molecular dynamics simulations. Based on their structural similarity, macrocyclic brush polymers with amphiphilic block side chains are synthesized, which can self-assemble into wormlike and higher-ordered structures. Our work points out the vital role of polymer folding in macromolecular self-assembly and establishes a versatile approach for constructing biomimetic hierarchical assemblies.

scholarly journals Antimicrobial Nodule-Specific Cysteine-Rich Peptides Induce Membrane Depolarization-Associated Changes in the Transcriptome of Sinorhizobium meliloti

2013 ◽  
Vol 79 (21) ◽  
pp. 6737-6746 ◽  
Author(s):  
Hilda Tiricz ◽  
Attila Szűcs ◽  
Attila Farkas ◽  
Bernadett Pap ◽  
Rui M. Lima ◽  
...  
Keyword(s):  
Stress Responses ◽  
Sinorhizobium Meliloti ◽  
Antimicrobial Agents ◽  
Cellular Functions ◽  
Gram Positive ◽  
Content Type ◽  
Gram Positive Bacteria ◽  
Peptide Family ◽  
Wide Range ◽  
Natural Target

ABSTRACTLeguminous plants establish symbiosis with nitrogen-fixing alpha- and betaproteobacteria, collectively called rhizobia, which provide combined nitrogen to support plant growth. Members of the inverted repeat-lacking clade of legumes impose terminal differentiation on their endosymbiotic bacterium partners with the help of the nodule-specific cysteine-rich (NCR) peptide family composed of close to 600 members. Among the few tested NCR peptides, cationic ones had antirhizobial activity measured by reduction or elimination of the CFU and uptake of the membrane-impermeable dye propidium iodide. Here, the antimicrobial spectrum of two of these peptides, NCR247 and NCR335, was investigated, and their effect on the transcriptome of the natural targetSinorhizobium melilotiwas characterized. Both peptides were able to kill quickly a wide range of Gram-negative and Gram-positive bacteria; however, their spectra were only partially overlapping, and differences were found also in their efficacy on given strains, indicating that the actions of NCR247 and NCR335 might be similar though not identical. Treatment ofS. meliloticultures with either peptide resulted in a quick downregulation of genes involved in basic cellular functions, such as transcription-translation and energy production, as well as upregulation of genes involved in stress and oxidative stress responses and membrane transport. Similar changes provoked mainly in Gram-positive bacteria by antimicrobial agents were coupled with the destruction of membrane potential, indicating that it might also be a common step in the bactericidal actions of NCR247 and NCR335.

scholarly journals The AAA+ ATPase p97, a cellular multitool

2017 ◽  
Vol 474 (17) ◽  
pp. 2953-2976 ◽  
Author(s):  
Lasse Stach ◽  
Paul S. Freemont
Keyword(s):  
Atp Hydrolysis ◽  
Current Status ◽  
Cellular Functions ◽  
Aaa Atpase ◽  
Cellular Processes ◽  
Proteotoxic Stress ◽  
Binding Domains ◽  
Wide Range ◽  
Aaa Atpases ◽  
Substrate Proteins

The AAA+ (ATPases associated with diverse cellular activities) ATPase p97 is essential to a wide range of cellular functions, including endoplasmic reticulum-associated degradation, membrane fusion, NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) activation and chromatin-associated processes, which are regulated by ubiquitination. p97 acts downstream from ubiquitin signaling events and utilizes the energy from ATP hydrolysis to extract its substrate proteins from cellular structures or multiprotein complexes. A multitude of p97 cofactors have evolved which are essential to p97 function. Ubiquitin-interacting domains and p97-binding domains combine to form bi-functional cofactors, whose complexes with p97 enable the enzyme to interact with a wide range of ubiquitinated substrates. A set of mutations in p97 have been shown to cause the multisystem proteinopathy inclusion body myopathy associated with Paget's disease of bone and frontotemporal dementia. In addition, p97 inhibition has been identified as a promising approach to provoke proteotoxic stress in tumors. In this review, we will describe the cellular processes governed by p97, how the cofactors interact with both p97 and its ubiquitinated substrates, p97 enzymology and the current status in developing p97 inhibitors for cancer therapy.

scholarly journals In Silico Electrophysiology of Inner-Ear Mechanotransduction Channel TMC1 Models

2021 ◽  
Author(s):  
Sanket Walujkar ◽  
Jeffrey M Lotthammer ◽  
Collin R Nisler ◽  
Joseph C Sudar ◽  
Angela Ballesteros ◽  
...  
Keyword(s):  
Inner Ear ◽  
Conformational Changes ◽  
Hair Cells ◽  
Head Movements ◽  
Mechanical Stimuli ◽  
Ion Conduction ◽  
Sensory Hair Cells ◽  
Activation Mechanisms ◽  
Dynamics Simulations ◽  
Molecular Components

Inner-ear sensory hair cells convert mechanical stimuli from sound and head movements into electrical signals during mechanotransduction. Identification of all molecular components of the inner-ear mechanotransduction apparatus is ongoing; however, there is strong evidence that TMC1 and TMC2 are pore-forming subunits of the complex. We present molecular dynamics simulations that probe ion conduction of TMC1 models built based on two different structures of related TMEM16 proteins. Unlike most channels, the TMC1 models do not show a central pore. Instead, simulations of these models in a membrane environment at various voltages reveal a peripheral permeation pathway that is exposed to lipids and that shows cation permeation at rates comparable to those measured in hair cells. Furthermore, our analyses suggest that TMC1 gating mechanisms involve protein conformational changes and tension-induced lipid-mediated pore widening. These results provide insights into ion conduction and activation mechanisms of hair-cell mechanotransduction channels essential for hearing and balance.

Influence of the size and charge of gold nanoclusters on complexation with siRNA: a molecular dynamics simulation study

2015 ◽  
Vol 17 (45) ◽  
pp. 30307-30317 ◽  
Author(s):  
Sathish Kumar Mudedla ◽  
Ettayapuram Ramaprasad Azhagiya Singam ◽  
Kanagasabai Balamurugan ◽  
Venkatesan Subramanian
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Simulation Study ◽  
Gold Nanoclusters ◽  
Dynamics Simulation ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations ◽  
Positively Charged

The complexation of siRNA with positively charged gold nanoclusters has been studied using classical molecular dynamics simulations.

A Review on Application of Novel Solid Nanostructures in Drug Delivery

2018 ◽  
Vol 53 ◽  
pp. 22-36 ◽  
Author(s):  
Habibollah Faraji ◽  
Reza Nedaeinia ◽  
Esmaeil Nourmohammadi ◽  
Bizan Malaekeh-Nikouei ◽  
Hamid Reza Sadeghnia ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Drug Therapy ◽  
Biomedical Applications ◽  
Imaging Biomarkers ◽  
Cellular Functions ◽  
Scientific Innovation ◽  
Wide Range ◽  
Targeted Drug

Nanotechnology as a multidisciplinary and scientific innovation plays an important role in numerous biomedical applications, such as molecular imaging, biomarkers and biosensors and also drug delivery. A wide range of studies have been conducted on using of nanoparticles for early diagnosis and targeted drug therapy of various diseases. In fact, the small size, customized surface, upgraded solubility, or multi-functionality of nanoparticles enabled them to interact with complex cellular functions in new ways which opened many doors and created new biomedical applications. These studies demonstrated that nanotechnology vehicles can formulate biological products effectively, and this nano-formulated products with a potent ability against different diseases, were represented to have better biocompatibility, bioaccessibility and efficacy, under in vitro and in vivo conditions.

A flow-dependent estimation of constriction size distribution in gap-graded soils: an integrated statistical approach

2022 ◽  
Vol 12 (1) ◽  
pp. 1-25
Author(s):  
S.M. Dassanayake ◽  
A. Mousa
Keyword(s):  
Fluid Dynamics ◽  
Size Distribution ◽  
Statistical Approach ◽  
One Dimensional ◽  
Loading Pattern ◽  
Wide Range ◽  
Hydraulic Gradients ◽  
Computational Fluid Dynamics Simulations ◽  
Dynamics Simulations ◽  
Estimate Flow

The clogging-unclogging process in gap-graded soils is a result of the migration of seepage-driven fines, which subsequently induces measurable changes in the local hydraulic gradients. This process can be temporally observed in the variations of Darcy's hydraulic conductivity (K). The current study proposes an integrated statistical Monte Carlo approach combining the discrete element method and 2D computational fluid dynamics simulations to estimate the flow-dependent constriction size distribution (CSD) for a gap-graded soil. The computational inferences were supported with experimental results using an internally stable soil, which was subjected to one-dimensional flow stimulating desired hydraulic loadings: a hydraulic gradient lower than the critical gradient applied as a multi-staged loading pattern. The 35th percentile size of the flow-dependent CSD (Dc35) for both internally stable and unstable gap-graded soils becomes approximately equal to Dc35 at steady-state. However, a greater variation of larger constrictions persists for the unstable soils. This pilot study has shown the applicability of the proposed method to estimate flow-dependent CSD for a wide range of experimentally observed K values.

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