A study of pH-dependence of shrink and stretch of tetrahedral DNA nanostructures

Nanoscale ◽  
2015 ◽  
Vol 7 (15) ◽  
pp. 6467-6470 ◽  
Author(s):  
Ping Wang ◽  
Zhiwei Xia ◽  
Juan Yan ◽  
Xunwei Liu ◽  
Guangbao Yao ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Quartz Crystal ◽  
Ph Dependence ◽  
Dna Assembly ◽  
Dna Nanostructures ◽  
Ph Change ◽  
Assembly Layer

Conformational changes of the DNA assembly layer on the surface of a gold coated quartz crystal due to the pH change (pH 8.5–pH 4.5).

scholarly journals An equilibrium constant pH molecular dynamics method for accurate prediction of pH-dependence in protein systems: Theory and application

2020 ◽  
Author(s):  
Ekaterina Kots ◽  
Derek M. Shore ◽  
Harel Weinstein
Keyword(s):  
Molecular Dynamics ◽  
Equilibrium Constant ◽  
Conformational Changes ◽  
Ph Dependence ◽  
Md Simulations ◽  
Water Soluble ◽  
Conformational Sampling ◽  
Ph Change ◽  
Constant Ph ◽  
Dynamics Simulations

ABSTRACTComputational modeling and simulation of biomolecular systems at their functional pH ranges requires an accurate approach to exploring the pH dependence of conformations and interactions. Here we present a new approach – the Equilibrium Constant pH (ECpH) method – to perform conformational sampling of protein systems in the framework of molecular dynamics simulations in an N, P, T-thermodynamic ensemble. The performance of ECpH is illustrated for two proteins with experimentally determined conformational responses to pH change: the small globular water-soluble bovine b-lactoglobulin (BBL), and the dimer transmembrane antiporter CLC-ec1 Cl−/H+. We show that with computational speeds comparable to equivalent canonical MD simulations we performed, the ECpH trajectories reproduce accurately the pH-dependent conformational changes observed experimentally in these two protein systems, some of which were not seen in the corresponding canonical MD simulations.Abstract FigureTable of Contents artwork

Effect of Acute Exposure to Ammonia on Glutamate Transport in Glial Cells Isolated From the Salamander Retina

2001 ◽  
Vol 86 (2) ◽  
pp. 836-844 ◽  
Author(s):  
Dominic Mort ◽  
Païkan Marcaggi ◽  
James Grant ◽  
David Attwell
Keyword(s):  
Glial Cells ◽  
Glutamate Uptake ◽  
Ph Dependence ◽  
Glutamate Transporter ◽  
Ammonia Concentration ◽  
Ammonia Level ◽  
Glutamate Transport ◽  
Acute Exposure ◽  
Ph Change ◽  
Glutamine Synthesis

A rise of brain ammonia level, as occurs in liver failure, initially increases glutamate accumulation in neurons and glial cells. We investigated the effect of acute exposure to ammonia on glutamate transporter currents in whole cell clamped glial cells from the salamander retina. Ammonia potentiated the current evoked by a saturating concentration ofl-glutamate, and decreased the apparent affinity of the transporter for glutamate. The potentiation had a Michaelis-Menten dependence on ammonia concentration, with a K m of 1.4 mM and a maximum potentiation of 31%. Ammonia also potentiated the transporter current produced by d-aspartate. Potentiation of the glutamate transport current was seen even with glutamine synthetase inhibited, so ammonia does not act by speeding glutamine synthesis, contrary to a suggestion in the literature. The potentiation was unchanged in the absence of Cl− ions, showing that it is not an effect on the anion current gated by the glutamate transporter. Ammonium ions were unable to substitute for Na+in driving glutamate transport. Although they can partially substitute for K+ at the cation counter-transport site of the transporter, their occupancy of these sites would produce a potentiation of <1%. Ammonium, and the weak bases methylamine and trimethylamine, increased the intracellular pH by similar amounts, and intracellular alkalinization is known to increase glutamate uptake. Methylamine and trimethylamine potentiated the uptake current by the amount expected from the known pH dependence of uptake, but ammonia gave a potentiation that was larger than could be explained by the pH change, and some potentiation of uptake by ammonia was still seen when the internal pH was 8.8, at which pH further alkalinization does not increase uptake. These data suggest that ammonia speeds glutamate uptake both by increasing cytoplasmic pH and by a separate effect on the glutamate transporter. Approximately two-thirds of the speeding is due to the pH change.

pH-mediated control of anti-aggregation activities of cyanobacterial and E. coli chaperonin GroELs

2020 ◽  
Author(s):  
Tahmina Akter ◽  
Hitoshi Nakamoto
Keyword(s):  
Escherichia Coli ◽  
Lactate Dehydrogenase ◽  
Malate Dehydrogenase ◽  
Citrate Synthase ◽  
Ph Dependence ◽  
Chaperone Activity ◽  
Ph Change ◽  
Aggregation Assay ◽  
E Coli ◽  
Aggregation Activity

Abstract In contrast to Escherichia coli, cyanobacteria have multiple GroELs, the bacterial homologues of chaperonin/Hsp60. We have shown that cyanobacterial GroELs are mutually distinct and different from E. coli GroEL with which the paradigm for chaperonin structure/function has been established. However, little is known about regulation of cyanobacterial GroELs. This study investigated effect of pH (varied from 7.0 to 8.5) on chaperone activity of GroEL1 and GroEL2 from the cyanobacterium Synechococcus elongatus PCC7942 and E. coli GroEL. GroEL1 and GroEL2 showed pH dependency in suppression of aggregation of heat-denatured malate dehydrogenase, lactate dehydrogenase and citrate synthase. They exhibited higher anti-aggregation activity at more alkaline pHs. Escherichia coli GroEL showed a similar pH-dependence in suppressing aggregation of heat-denatured lactate dehydrogenase. No pH dependence was observed in all the GroELs when urea-denatured lactate dehydrogenase was used for anti-aggregation assay, suggesting that the pH-dependence is related to some denatured structures. There was no significant influence of pH on the chaperone activity of all the GroELs to promote refolding of heat-denatured malate dehydrogenase. It is known that pH in cyanobacterial cytoplasm increases by one pH unit following a shift from darkness to light, suggesting that the pH-change modulates chaperone activity of cyanobacterial GroEL1 and GroEL2.

SURFACE PLASMON RESONANCE SPECTROSCOPY AND QUARTZ CRYSTAL MICROBALANCE STUDY OF PROTEIN-DNA INTERACTIONS IN HORMONE RECEPTOR BIOLOGY

COSMOS ◽  
2009 ◽  
Vol 05 (01) ◽  
pp. 79-95
Author(s):  
XIAODI SU
Keyword(s):  
Surface Plasmon Resonance ◽  
Surface Plasmon ◽  
Quartz Crystal Microbalance ◽  
Conformational Changes ◽  
Plasmon Resonance ◽  
Quartz Crystal ◽  
Resonance Spectroscopy ◽  
Dna Interactions ◽  
Protein Dna Interactions

Surface plasmon resonance (SPR) spectroscopy and quartz crystal microbalance (QCM) are surface sensitive analytical techniques capable of real-time monitoring of biomolecular interactions. In this article we review our past work on the use of these two techniques for studying protein–DNA interactions, exemplified with estrogen receptors (ER) and their response elements (ERE). Various assay schemes have been developed for a comprehensive characterization of ER–ERE interactions in terms of sequence specificity, binding affinity, stoichiometry, ligand effects on binding dynamics and conformational changes in the proteins and DNA. These are all important characteristics underlining the mechanism of ER-mediated gene transcription. With these studies we have made the following demonstrations to describe the advantages of these two techniques, namely (i) SPR technique is superior and more versatile than conventional (electrophoretic mobility shift assay) EMSA for studying protein-DNA interactions; (ii) QCM is an alternative tool for studying conformational changes in protein–DNA complexes and (iii) combinational SPR and QCM analysis provides additional characterization of biomolecular films, e.g. film thickness, water content, and conformation rigidity etc.

A pH-dependent conformational transition of Aβ peptide and physicochemical properties of the conformers in the glial cell

2002 ◽  
Vol 361 (3) ◽  
pp. 547-556 ◽  
Author(s):  
Yoichi MATSUNAGA ◽  
Nobuhiro SAITO ◽  
Akihiro FUJII ◽  
Junichi YOKOTANI ◽  
Tadakazu TAKAKURA ◽  
...  
Keyword(s):  
Glial Cell ◽  
Conformational Changes ◽  
Conformational Transition ◽  
Early Stage ◽  
Ph Dependence ◽  
Amyloid Β ◽  
Proteinase K ◽  
Aβ Peptide ◽  
Ph Dependent ◽  
Insight Into

In the present study we identified the epitopes of antibodies against amyloid β-(1–42)-peptide (Aβ1–42): 4G8 reacted with peptides corresponding to residues 17–21, 6F/3D reacted with peptides corresponding to residues 9–14, and anti 5-10 reacted with peptides corresponding to residues 5–10. The study also yielded some insight into the Aβ1–42 structures resulting from differences in pH. An ELISA study using monoclonal antibodies showed that pH-dependent conformational changes occur in the 6F/3D and 4G8 epitopes modified at pH 4.6, but not in the sequences recognized by anti 1-7 and anti 5-10. This was unique to Aβ1–40 and Aβ1–42 and did not occur with Aβ1–16 or Aβ17–42. The reactivity profile of 4G8 was not affected by blockage of histidine residues of pH-modified Aβ1–40 and Aβ1–42 with diethyl pyrocarbonate; however, the mutant [Gln11]Aβ1–40 abrogated the unique pH-dependence towards 4G8 observed with Aβ1–40. These findings suggest that these epitopes are cryptic at pH4.6, and that Glu11 is responsible for the changes. We suggest that the abnormal folding of 6F/3D epitope affected by pH masked the 4G8 epitope. A study of the binding of metal ions to Aβ1–42 suggested that Cu2+ and Zn2+ induced a conformational transition around the 6F/3D region at pH7.4, but did not affect the region when it was modified at pH4.6. However, Fe2+ had no effect, irrespective of pH. Aβ modified at pH 4.6 appeared to be relatively resistant to proteinase K compared with Aβs modified at pH7.4, and the former might be preferentially internalized and accumulated in a human glial cell. Our findings suggest the importance of microenvironmental changes, such as pH, in the early stage of formation of Aβ aggregates in the glial cell.

scholarly journals Conformational heterogeneity in closed and open states of the KcsA potassium channel in lipid bicelles

2016 ◽  
Vol 148 (2) ◽  
pp. 119-132 ◽  
Author(s):  
Dorothy M. Kim ◽  
Igor Dikiy ◽  
Vikrant Upadhyay ◽  
David J. Posson ◽  
David Eliezer ◽  
...  
Keyword(s):  
Ion Channel ◽  
Potassium Channel ◽  
Conformational Changes ◽  
Ph Dependence ◽  
Channel Gating ◽  
Conformational Heterogeneity ◽  
Ion Channel Gating ◽  
Potassium Channel Kcsa ◽  
Functional States ◽  
Open States

The process of ion channel gating—opening and closing—involves local and global structural changes in the channel in response to external stimuli. Conformational changes depend on the energetic landscape that underlies the transition between closed and open states, which plays a key role in ion channel gating. For the prokaryotic, pH-gated potassium channel KcsA, closed and open states have been extensively studied using structural and functional methods, but the dynamics within each of these functional states as well as the transition between them is not as well understood. In this study, we used solution nuclear magnetic resonance (NMR) spectroscopy to investigate the conformational transitions within specific functional states of KcsA. We incorporated KcsA channels into lipid bicelles and stabilized them into a closed state by using either phosphatidylcholine lipids, known to favor the closed channel, or mutations designed to trap the channel shut by disulfide cross-linking. A distinct state, consistent with an open channel, was uncovered by the addition of cardiolipin lipids. Using selective amino acid labeling at locations within the channel that are known to move during gating, we observed at least two different slowly interconverting conformational states for both closed and open channels. The pH dependence of these conformations and the predictable disruptions to this dependence observed in mutant channels with altered pH sensing highlight the importance of conformational heterogeneity for KcsA gating.

scholarly journals Chloride Fluxes in Isolated Dialyzed Barnacle Muscle Fibers

1972 ◽  
Vol 60 (4) ◽  
pp. 471-497 ◽  
Author(s):  
R. DiPolo
Keyword(s):  
Ph Dependence ◽  
Muscle Fibers ◽  
Membrane Conductance ◽  
Chloride Ions ◽  
Resting Potential ◽  
Constant Field ◽  
Ph Change ◽  
Decreasing Ph ◽  
Barnacle Muscle Fibers ◽  
External Ph

Chloride outflux and influx has been studied in single isolated muscle fibers from the giant barnacle under constant internal composition by means of a dialysis perfusion technique. Membrane potential was continually recorded. The chloride outfluxes and influxes were 143 and 144 pmoles/cm2-sec (mean resting potential: 58 mv, temperature: 22°–24°C) with internal and external chloride concentrations of 30 and 541 mM, respectively. The chloride conductance calculated from tracer measurements using constant field assumptions is about fourfold greater than that calculated from published electrical data. Replacing 97% of the external chloride ions by propionate reduces the chloride efflux by 51%. Nitrate ions applied either to the internal or external surface of the membrane slows the chloride efflux. The external pH dependence of the chloride efflux follows the external pH dependence of the membrane conductance, in the range pH 3.9–4.7, increasing with decreasing pH. In the range pH 5–9, the chloride efflux increased with increasing pH, in a manner similar to that observed in frog muscle fibers. The titration curve for internal pH changes in the range 4.0–7.0 was quantitatively much different from that for external pH change, indicating significant asymmetry in the internal and external pH dependence of the chloride efflux.

scholarly journals Preparation of Nafion/Polycation Layer-by-Layer Films for Adsorption and Release of Insulin

Polymers ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 812 ◽  
Author(s):  
Kentaro Yoshida ◽  
Katsuhiko Sato ◽  
Tetsuya Ono ◽  
Takenori Dairaku ◽  
Yoshitomo Kashiwagi
Keyword(s):  
Quartz Crystal ◽  
Fluorescence Emission ◽  
Layer By Layer ◽  
Ph Change ◽  
Mild Conditions ◽  
Atomic Force ◽  
Insulin Solution ◽  
Lbl Films ◽  
Uv Visible ◽  
Allylamine Hydrochloride

Thin films were prepared using layer-by-layer (LbL) deposition of Nafion (NAF) and polycations such as poly(allylamine hydrochloride) (PAH), poly(ethyleneimine) (PEI), and poly(diallydimethylammonium chloride) (PDDA). Insulin was then adsorbed on the NAF-polycation LbL films by immersion in an insulin solution. The NAF-polycation LbL films were characterized using a quartz crystal microbalance and an atomic force microscope. The release of insulin from the LbL films was characterized using UV-visible adsorption spectroscopy and fluorescence emission spectroscopy. The greatest amount of insulin was adsorbed on the NAF-PAH LbL film. The amount of insulin adsorbed on the (NAF/PAH)5NAF LbL films by immersion in a 1 mg mL−1 insulin solution at pH 7.4 was 61.8 µg cm−2. The amount of insulin released from the LbL films was higher when immersed in insulin solutions at pH 2.0 and pH 9.0 than at pH 7.4. Therefore, NAF-polycations could be employed as insulin delivery LbL films under mild conditions and as an insulin release control system according to pH change.

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