scholarly journals Coupled dynamics of charged macromolecules and counterions mediated by binding enzymes

2021 ◽  
Author(s):  
Murugappan Muthukumar ◽  
Tapas Singha ◽  
Siao-Fong Li

We investigate the role of active coupling on the transport properties of the macromolecules. The active coupling comes due to bound enzymes with a segment of the macromolecule wherein the enzyme exerts an electrostatic force on the segment of the macromolecule, and eventually, it gets unbound due to the thermal fluctuations. This binding and unbinding process generates active fluctuations in the dynamics of the macromolecule. Starting with segment dynamics and correlations for three dynamical models with active coupling, we obtain the cooperative diffusivity for the realistic charged macromolecules with hydrodynamics. First, we construct the three models by incorporating the features of a real polymer systematically, starting from simple Rouse dynamics with active coupling. We further include segment-segment interactions and in addition, hydrodynamic interactions with active coupling. Our obtained scaling form for segment-segment correlations for the models in terms of the size exponent of the polymer indicating that hydrodynamic and segment-segment interactions along with the active coupling lead to new scaling regimes. We finally study the dynamics of a homogeneously charged flexible polymer in an infinitely dilute solution where enzymes and counterions affect the dynamics of the polymers. We analytically investigate how these active fluctuations affect the coupled dynamics of the polymer and counterions. It turns out that these active fluctuations enhance the effective diffusivity of the polymer. The derived closed-form expression for diffusivity is pertinent to accurate interpretation of light scattering data on multi-component systems with binding-unbinding equilibria.

2011 ◽  
Vol 25 (28) ◽  
pp. 2209-2217 ◽  
Author(s):  
KHABAT GHAMARI ◽  
ALI NAJAFI

In this article, we address the problem of Euler's buckling instability in a charged semi-flexible polymer that is under the action of a compressive force. We consider this instability as a phase transition and investigate the role of thermal fluctuations in the buckling critical force. By performing molecular dynamic simulations, we show that the critical force decreases when the temperature increases. Repulsive electrostatic interaction in the finite temperature is in competition with thermal fluctuations to increase the buckling threshold.


2021 ◽  
Vol 103 (3) ◽  
Author(s):  
Moupriya Das ◽  
Holger Kantz
Keyword(s):  

2007 ◽  
Author(s):  
David P. Wilson ◽  
Todd Lillian ◽  
Sachin Goyal ◽  
Alexei V. Tkachenko ◽  
Noel C. Perkins ◽  
...  

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1527
Author(s):  
Miki Kawada-Matsuo ◽  
Mi Nguyen-Tra Le ◽  
Hitoshi Komatsuzawa

Staphylococcus aureus is a bacterium that mainly colonizes the nasal cavity and skin. To colonize the host, it is necessary for S. aureus to resist many antibacterial factors derived from human and commensal bacteria. Among them are the bacteria-derived antimicrobial peptides (AMPs) called bacteriocins. It was reported that some two-component systems (TCSs), which are signal transduction systems specific to bacteria, are involved in the resistance to several bacteriocins in S. aureus. However, the TCS-mediated resistance is limited to relatively low concentrations of bacteriocins, while high concentrations of bacteriocins still exhibit antibacterial activity against S. aureus. To determine whether we could obtain highly bacteriocin-resistant mutants, we tried to isolate highly nisin A-resistant mutants by exposing the cells to sub-minimum inhibitory concentrations (MICs) of nisin A. Nisin A is one of the bacteriocins produced by Lactococcus lactis and is utilized as a food preservative worldwide. Finally, we obtained highly nisin A-resistant mutants with mutations in one TCS, BraRS, and in PmtR, which is involved in the expression of pmtABCD. Notably, some highly resistant strains also showed increased pathogenicity. Based on our findings, this review provides up-to-date information on the role of TCSs in the susceptibility to antibacterial peptides. Additionally, the mechanism for high antimicrobial peptides resistance and its association with pathogenicity in S. aureus is elucidated.


2016 ◽  
Vol 7 ◽  
pp. 328-350 ◽  
Author(s):  
Igor Goychuk

The main physical features and operating principles of isothermal nanomachines in the microworld, common to both classical and quantum machines, are reviewed. Special attention is paid to the dual, constructive role of dissipation and thermal fluctuations, the fluctuation–dissipation theorem, heat losses and free energy transduction, thermodynamic efficiency, and thermodynamic efficiency at maximum power. Several basic models are considered and discussed to highlight generic physical features. This work examines some common fallacies that continue to plague the literature. In particular, the erroneous beliefs that one should minimize friction and lower the temperature for high performance of Brownian machines, and that the thermodynamic efficiency at maximum power cannot exceed one-half are discussed. The emerging topic of anomalous molecular motors operating subdiffusively but very efficiently in the viscoelastic environment of living cells is also discussed.


Author(s):  
Tewfik Souier

In this chapter, the main scanning probe microscopy-based methods to measure the transport properties in advanced polymer-Carbon Nanotubes (CNT) nanocomposites are presented. The two major approaches to investigate the electrical and charge transport (i.e., Electrostatic Force Microscopy [EFM] and Current-Sensing Atomic Force Microscopy [CS-AFM]) are illustrated, starting from their basic principles. First, the authors show how the EFM-related techniques can be used to provide, at high spatial resolution, a three-dimensional representation CNT networks underneath the surface. This allows the studying of the role of nanoscopic features such as CNTs, CNT-CNT direct contact, and polymer-CNT junctions in determining the overall composite properties. Complementary, CS-AFM can bring insight into the transport mechanism by imaging the spatial distribution of currents percolation paths within the nanocomposite. Finally, the authors show how the CS-AFM can be used to quantify the surface/bulk percolation probability and the nanoscopic electrical conductivity, which allows one to predict the macroscopic percolation model.


2020 ◽  
Vol 846 ◽  
pp. 156368
Author(s):  
Mohammad Shahnawaze Ansari ◽  
Mohd Hafiz Dzarfan Othman ◽  
Mohammad Omaish Ansari ◽  
Sana Ansari ◽  
Huda Abdullah ◽  
...  

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