scholarly journals Substrates modulate charge-reorganization allosteric effects in protein-protein association

2021 ◽  
Author(s):  
Shirsendu Ghosh ◽  
Koyel Banerjee-Ghosh ◽  
Dorit Levy ◽  
Inbal Riven ◽  
Ron Naaman ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Protein Function ◽  
Phosphoglycerate Kinase ◽  
Target Antigen ◽  
Charge Redistribution ◽  
His Tag ◽  
Interaction Interface ◽  
Kinetics Of ◽  
Insight Into

ABSTRACTProtein function may be modulated by an event occurring far away from the functional site, a phenomenon termed allostery. While classically allostery involves conformational changes, we recently observed that charge redistribution within an antibody can also lead to an allosteric effect, modulating the kinetics of binding to target antigen. In the present study, we study the association of a poly-histidine tagged enzyme (phosphoglycerate kinase, PGK) to surface-immobilized anti-His antibodies, finding a significant Charge-Reorganization Allostery (CRA) effect. We further observe that PGK’s negatively charged nucleotide substrates modulate CRA substantially, even though they bind far away from the His-tag-antibody interaction interface. In particular, binding of ATP reduces CRA by more than 50%. The results indicate that CRA may be affected by charged substrates bound to a protein and provide further insight into the role of charge redistribution in protein function.TOC GRAPHIC

scholarly journals Dynamics of Tpm1.8 domains on actin filaments with single molecule resolution

2020 ◽  
Author(s):  
Ilina Bareja ◽  
Hugo Wioland ◽  
Miro Janco ◽  
Philip R. Nicovich ◽  
Antoine Jégou ◽  
...  
Keyword(s):  
Actin Filament ◽  
Single Molecule ◽  
Actin Filaments ◽  
High Probability ◽  
Actin Binding ◽  
Single Molecule Level ◽  
Filament Dynamics ◽  
Kinetics Of ◽  
Insight Into

ABSTRACTTropomyosins regulate dynamics and functions of the actin cytoskeleton by forming long chains along the two strands of actin filaments that act as gatekeepers for the binding of other actin-binding proteins. The fundamental molecular interactions underlying the binding of tropomyosin to actin are still poorly understood. Using microfluidics and fluorescence microscopy, we observed the binding of fluorescently labelled tropomyosin isoform Tpm1.8 to unlabelled actin filaments in real time. This approach in conjunction with mathematical modeling enabled us to quantify the nucleation, assembly and disassembly kinetics of Tpm1.8 on single filaments and at the single molecule level. Our analysis suggests that Tpm1.8 decorates the two strands of the actin filament independently. Nucleation of a growing tropomyosin domain proceeds with high probability as soon as the first Tpm1.8 molecule is stabilised by the addition of a second molecule, ultimately leading to full decoration of the actin filament. In addition, Tpm1.8 domains are asymmetrical, with enhanced dynamics at the edge oriented towards the barbed end of the actin filament. The complete description of Tpm1.8 kinetics on actin filaments presented here provides molecular insight into actin-tropomyosin filament formation and the role of tropomyosins in regulating actin filament dynamics.

Kinetics of Plasmon-Driven Hydrosilylation of Silicon Surfaces: Photogenerated Charges Drive Silicon- Carbon Bond Formation

2021 ◽  
Author(s):  
Chengcheng Rao ◽  
Brian Olsen ◽  
Erik Luber ◽  
Jillian Buriak
Keyword(s):  
Green Light ◽  
Kinetic Studies ◽  
Silicon Surfaces ◽  
Moderate Intensity ◽  
Carbon Bond ◽  
Silicon Carbon ◽  
Set Up ◽  
Kinetics Of ◽  
Insight Into

Optically transparent PDMS stamps coated with a layer of gold nanoparticles were employed as plasmonic stamps to drive surface chemistry on silicon surfaces. Illumination of a sandwich of plasmonic stamps, an alkene ink, and hydride-terminated silicon with green light of moderate intensity drives hydrosilylation on the surface. The key to the mechanism of the hydrosilylation is the presence of holes at the Si-H-terminated interface, which is followed by attack by a proximal alkene and formation of the silicon-carbon bond. In this work, detailed kinetic studies of the hydrosilylation on silicon with different doping levels, n++, p++, n, p, and intrinsic were carried out to provide further insight into the role of the metal-insulator-semiconductor (MIS) junction that is set up during the stamping.

scholarly journals Role of the cysteine residues in Arabidopsis thaliana cyclophilin CYP20-3 in peptidyl-prolyl cis–trans isomerase and redox-related functions

2006 ◽  
Vol 401 (1) ◽  
pp. 287-297 ◽  
Author(s):  
Miriam Laxa ◽  
Janine König ◽  
Karl-Josef Dietz ◽  
Andrea Kandlbinder
Keyword(s):  
Conformational Changes ◽  
Protein Function ◽  
Redox Regulation ◽  
Catalytic Efficiency ◽  
Structural Rearrangement ◽  
Disulfide Bridge ◽  
Cysteine Residues ◽  
Active Centre ◽  
Independent Functions

Cyps (cyclophilins) are ubiquitous proteins of the immunophilin superfamily with proposed functions in protein folding, protein degradation, stress response and signal transduction. Conserved cysteine residues further suggest a role in redox regulation. In order to get insight into the conformational change mechanism and functional properties of the chloroplast-located CYP20-3, site-directed mutagenized cysteine→serine variants were generated and analysed for enzymatic and conformational properties under reducing and oxidizing conditions. Compared with the wild-type form, elimination of three out of the four cysteine residues decreased the catalytic efficiency of PPI (peptidyl-prolyl cis–trans isomerase) activity of the reduced CYP20-3, indicating a regulatory role of dithiol–disulfide transitions in protein function. Oxidation was accompanied by conformational changes with a predominant role in the structural rearrangement of the disulfide bridge formed between Cys54 and Cys171. The rather negative Em (midpoint redox potential) of −319 mV places CYP20-3 into the redox hierarchy of the chloroplast, suggesting the activation of CYP20-3 in the light under conditions of limited acceptor availability for photosynthesis as realized under environmental stress. Chloroplast Prx (peroxiredoxins) were identified as interacting partners of CYP20-3 in a DNA-protection assay. A catalytic role in the reduction of 2-Cys PrxA and 2-Cys PrxB was assigned to Cys129 and Cys171. In addition, it was shown that the isomerization and disulfide-reduction activities are two independent functions of CYP20-3 that both are regulated by the redox state of its active centre.

scholarly journals Insight into the kinetics and the mode of the interaction between smooth muscle calponin and F-actin.

2002 ◽  
Vol 49 (2) ◽  
pp. 471-479
Author(s):  
Janusz Kołakowski ◽  
Renata Dabrowska
Keyword(s):  
Smooth Muscle ◽  
Light Scattering ◽  
Conformational Changes ◽  
Actin Filaments ◽  
Molar Ratio ◽  
Flow Measurements ◽  
Pyrene Fluorescence ◽  
Kinetics Of ◽  
Insight Into ◽  
Parallel Measurements

Kinetics of the smooth muscle calponin-F-actin interaction was studied by stopped-flow measurements of light scattering and fluorescence intensity of pyrene-labelled F-actin. The intensity and character of the changes in light scattering, and thus the mode of calponin binding to actin filaments leading to changes in their shape and bundling, depend on the molar ratio of the two proteins. Parallel measurements of pyrene-fluorescence quenching upon calponin binding revealed that intrinsic conformational changes in actin filaments are delayed relative to the binding process and are not markedly influenced by the mode of calponin binding. Bundling of actin filaments by calponin was not correlated with fluorescence changes and thus with alterations in the structure of actin filaments.

scholarly journals A Novel Insight into the Role of PLA2R and THSD7A in Membranous Nephropathy

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Pingna Zhang ◽  
Weijun Huang ◽  
Qiyan Zheng ◽  
Jingyi Tang ◽  
Zhaocheng Dong ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Membranous Nephropathy ◽  
Paradigm Shift ◽  
Molecular Mimicry ◽  
Autoantibody Production ◽  
Phospholipase A2 Receptor ◽  
Pathological Mechanism ◽  
Circulating Autoantibodies ◽  
Insight Into

Membranous nephropathy (MN) is an organ-restricted autoimmune disease mainly caused by circulating autoantibodies against podocyte antigens, including the M-type phospholipase A2 receptor (PLA2R) and thrombospondin domain-containing 7A (THSD7A). Antibodies against PLA2R are present in 70%–80% and against THSD7A in 2% of adult patients, which provides a paradigm shift in molecular diagnosis and management monitoring. Both antigens share some similar characteristics: they are expressed by podocytes and have wide tissue distributions; they are bound by autoantibodies only under nonreducing conditions, and the subtype of most autoantibodies is IgG4. However, the factors triggering autoantibody production as well as the association among air pollution, malignancy, and the pathogenesis of MN remain unclear. In this review, we discuss the similarity between the pathological mechanisms triggered by disparate antigens and their associated diseases. Furthermore, we demonstrated the possibility that PM2.5, malignancy, and gene expression specifically induce exposure of these antigens through conformational changes, molecular mimicry, or increased expression eliciting autoimmune responses. Thus, this review provides novel insights into the pathological mechanism of MN.

Insight into the role of piperazine in the thermodynamics and nucleation kinetics of the triethylenediamine–methyl tertiary butyl ether system

CrystEngComm ◽  
2019 ◽  
Vol 21 (6) ◽  
pp. 948-956 ◽  
Author(s):  
Yufeng Quan ◽  
Yang Yang ◽  
Shijie Xu ◽  
Peipei Zhu ◽  
Shiyuan Liu ◽  
...  
Keyword(s):  
Crystal Size ◽  
Methyl Tertiary Butyl Ether ◽  
Nucleation Kinetics ◽  
Butyl Ether ◽  
Tertiary Butyl ◽  
System P ◽  
Kinetics Of ◽  
Insight Into ◽  
Ether System

Considering the role of piperazine in the TEDA–MTBE system, we investigate how to control the crystal size distribution.

Kinetics of Plasmon-Driven Hydrosilylation of Silicon Surfaces: Photogenerated Charges Drive Silicon- Carbon Bond Formation

2021 ◽  
Author(s):  
Chengcheng Rao ◽  
Brian Olsen ◽  
Erik Luber ◽  
Jillian Buriak
Keyword(s):  
Green Light ◽  
Kinetic Studies ◽  
Silicon Surfaces ◽  
Moderate Intensity ◽  
Carbon Bond ◽  
Silicon Carbon ◽  
Set Up ◽  
Kinetics Of ◽  
Insight Into

Optically transparent PDMS stamps coated with a layer of gold nanoparticles were employed as plasmonic stamps to drive surface chemistry on silicon surfaces. Illumination of a sandwich of plasmonic stamps, an alkene ink, and hydride-terminated silicon with green light of moderate intensity drives hydrosilylation on the surface. The key to the mechanism of the hydrosilylation is the presence of holes at the Si-H-terminated interface, which is followed by attack by a proximal alkene and formation of the silicon-carbon bond. In this work, detailed kinetic studies of the hydrosilylation on silicon with different doping levels, n++, p++, n, p, and intrinsic were carried out to provide further insight into the role of the metal-insulator-semiconductor (MIS) junction that is set up during the stamping.

Chloride-dependent conformational changes in the GlyT1 glycine transporter

2020 ◽  
Author(s):  
Yuan-Wei Zhang ◽  
Stacy Uchendu ◽  
Vanessa Leone ◽  
Richard T. Bradshaw ◽  
Ntumba Sangwa ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Ion Pair ◽  
Cysteine Residues ◽  
Glycine Transporter ◽  
Open Conformation ◽  
Transporter Family ◽  
Transport Cycle ◽  
Dynamics Simulations ◽  
Insight Into

AbstractThe human GlyT1 glycine transporter requires chloride for its function. However, the mechanism by which Cl- exerts its influence is unknown. To examine the role that Cl- plays in the transport cycle, we measured the effect of Cl- on both glycine binding and conformational changes. The ability of glycine to displace the high-affinity radioligand [3H]CHIBA-3007 required Na+ and was potentiated over 1000-fold by Cl-. We generated GlyT1b mutants containing reactive cysteine residues in either the extracellular or cytoplasmic permeation pathways and measured changes in the reactivity of those cysteine residues as indicators of conformational changes in response to ions and substrate. Na+ increased accessibility in the extracellular pathway and decreased it in the cytoplasmic pathway, consistent with stabilizing an outward-open conformation as observed in other members of this transporter family. In the presence of Na+, both glycine and Cl- independently shifted the conformation of GlyT1b toward an outward-closed conformation. Together, Na+, glycine and Cl- stabilized an inward-open conformation of GlyT1b. We then examined whether Cl- acts by interacting with a conserved glutamine to allow formation of an ion pair that stabilizes the closed state of the extracellular pathway. Molecular dynamics simulations of a GlyT1 homologue indicated that this ion pair is formed more frequently as that pathway closes. Mutation of the glutamine blocked the effect of Cl-, and substituting it with glutamate or lysine resulted in outward- or inward-facing transporter conformations, respectively. These results provide novel and unexpected insight into the role of Cl- in this family of transporters.

scholarly journals Decoding the Kinetic Limitations of Plasmon Catalysis: The Case of 4-Nitrothiophenol Dimerization

2020 ◽  
Author(s):  
Wouter Koopman ◽  
Radwan M. Sarhan ◽  
Felix Stete ◽  
Clemens N. Z. Schmitt ◽  
Matias Bargheer
Keyword(s):  
Thermal Effects ◽  
Dominant Role ◽  
Relative Importance ◽  
New Approach ◽  
Multistep Reaction ◽  
Kinetics Of ◽  
Complex Organic ◽  
Insight Into ◽  
Unique Ability

Plasmon-mediated chemistry presents an intriguing new approach to photocatalysis. However, the reaction enhancement<br>mechanism is not well understood. In particular, the relative importance of plasmon-generated hot charges and<br>photoheating are strongly debated. In this article, we evaluate the influence of microscopic photoheating on the kinetics of<br>a model plasmon-catalyzed reaction: the light-induced 4-nitrothiophenol (4NTP) to 4,4’-dimercaptoazobenzene (DMAB)<br>dimerization. Direct measurement of the reaction temperature by nanoparticle Raman-thermometry demonstrated that<br>the thermal effect plays a dominant role in the kinetic limitations of this multistep reaction. On the same time, no reaction<br>is possible by dark heating to the same temperature. This shows that plasmon nanoparticles have the unique ability to<br>enhance several steps of complex tandem reactions simultaneously. These results provide insight into the role of hot<br>electron and thermal effects in plasmonic catalysis of complex organic reactions, which highly important for the ongoing<br>development of plasmon based photosynthesis. <br>

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