scholarly journals Effects of Gold Nanoparticles on the Stepping Trajectories of Kinesin

2020 ◽  
Author(s):  
Sabeeha Hasnain ◽  
Mauro Lorenzo Mugnai ◽  
Dave Thirumalai
Keyword(s):  
Gold Nanoparticles ◽  
Gold Nanoparticle ◽  
Coiled Coil ◽  
Time Dependent ◽  
Coarse Grained ◽  
Dependent Position ◽  
Coarse Grained Simulations ◽  
Conventional Kinesin ◽  
The Right ◽  
Residue Position

Substantial increase in the temporal resolution of the stepping of dimeric molec- ular motors is possible by tracking the position of a large gold nanoparticle (GNP) attached to a labeled site on one of the heads. This technique was used to measure the stepping trajectories of conventional kinesin (Kin1) using the time dependent position of the GNP as a proxy. The trajectories revealed that the detached head always passes to the right of the head that is tightly bound to the microtubule (MT) during a step. In interpreting the results of such experiments, it is implicitly assumed that the GNP does not significantly alter the diffusive motion of the detached head. We used coarse-grained simulations of a system consisting of the MT-Kin1 complex with and without attached GNP to investigate how the stepping trajectories are affected. The two significant findings are: (1) The GNP does not faithfully track the position of the stepping head. (2) The rightward bias is typically exaggerated by the GNP. Both these findings depend on the precise residue position to which the GNP is attached. Surprisingly, we predict that the stepping trajectories of kinesin are not significantly affected if, in addition to the GNP, a 1 μm diameter cargo is attached to the coiled coil. Our simulations suggest the effects of the large probe have to be considered when inferring the stepping mechanisms using GNP tracking experiments.

Protein Corona on Gold Nanoparticles Studied with Coarse-Grained Simulations

Langmuir ◽  
2020 ◽  
Vol 36 (44) ◽  
pp. 13356-13363
Author(s):  
Md Symon Jahan Sajib ◽  
Pranab Sarker ◽  
Yong Wei ◽  
Xiuping Tao ◽  
Tao Wei
Keyword(s):  
Gold Nanoparticles ◽  
Protein Corona ◽  
Coarse Grained ◽  
Coarse Grained Simulations

Protein Corona on Gold Nanoparticles Studied with Coarse-Grained Simulations

2020 ◽  
Author(s):  
Md Symon Jahan Sajib ◽  
Pranab Sarker ◽  
Yong Wei ◽  
Xiuping Tao ◽  
Tao Wei
Keyword(s):  
Gold Nanoparticles ◽  
Protein Corona ◽  
Coarse Grained ◽  
Coarse Grained Simulations

scholarly journals On the Importance of Hydrodynamic Interactions in the Stepping Kinetics of Kinesin

2016 ◽  
Author(s):  
Dave Thirumalai ◽  
Yonathan Goldtzvik ◽  
Zhechun Zhang
Keyword(s):  
Coiled Coil ◽  
Quantitative Agreement ◽  
Single Step ◽  
Hydrodynamic Interactions ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Target Binding ◽  
Conventional Kinesin ◽  
Kinetics Of ◽  
Target Binding Site

Conventional kinesin walks by a hand-over-hand mechanism on the microtubule (MT) by taking ∼ 8nmdiscrete steps, and consumes one ATP molecule per step. The time needed to complete a single step is on the order of twenty microseconds. We show, using simulations of a coarse-grained model of the complex containing the two motor heads, the MT, and the coiled coil that in order to obtain quantitative agreement with experiments for the stepping kinetics hydrodynamic interactions (HI) have to be included. In simulations without hydrodynamic interactions spanning nearly twenty microseconds not a single step was completed in hundred trajectories. In sharp contrast, nearly 14% of the steps reached the target binding site within 6 microseconds when HI were included. Somewhat surprisingly, there are qualitative differences in the diffusion pathways in simulations with and without HI. The extent of movement of the trailing head of kinesin on the MT during the diffusion stage of stepping is considerably greater in simulations with HI than in those without HI. Our results suggest that inclusion of HI is crucial in the accurate description of motility of other motors as well.

Structural properties of polymer-brush-grafted gold nanoparticles at the oil–water interface: insights from coarse-grained simulations

Soft Matter ◽  
2016 ◽  
Vol 12 (14) ◽  
pp. 3352-3359 ◽  
Author(s):  
Xuebo Quan ◽  
ChunWang Peng ◽  
Jiaqi Dong ◽  
Jian Zhou
Keyword(s):  
Gold Nanoparticles ◽  
Structural Properties ◽  
Phase Transfer ◽  
Polymer Brush ◽  
Coarse Grained ◽  
Water Interface ◽  
Oil Water ◽  
Coarse Grained Simulations

Phase transfer of polymer brush-grafted gold nanoparticles across the oil–water interface.

Symmetrizable Difference Dchemes

2005 ◽  
Vol 5 (1) ◽  
pp. 3-50 ◽  
Author(s):  
Alexei A. Gulin
Keyword(s):  
Initial Data ◽  
Difference Scheme ◽  
Difference Schemes ◽  
Time Dependent ◽  
Stability Boundaries ◽  
Typical Representative ◽  
Variable Weight ◽  
The Stability ◽  
Conditions Of Stability ◽  
The Right

AbstractA review of the stability theory of symmetrizable time-dependent difference schemes is represented. The notion of the operator-difference scheme is introduced and general ideas about stability in the sense of the initial data and in the sense of the right hand side are formulated. Further, the so-called symmetrizable difference schemes are considered in detail for which we manage to formulate the unimprovable necessary and su±cient conditions of stability in the sense of the initial data. The schemes with variable weight multipliers are a typical representative of symmetrizable difference schemes. For such schemes a numerical algorithm is proposed and realized for constructing stability boundaries.

Grand-Reaction Method for Simulations of Ionization Equilibria and Ion Partitioning in a Broad Range of pH and Ionic Strength

2019 ◽  
Author(s):  
Jonas Landsgesell ◽  
Oleg Rud ◽  
Pascal Hebbeker ◽  
Raju Lunkad ◽  
Peter Košovan ◽  
...  
Keyword(s):  
Mean Field ◽  
Coarse Grained ◽  
Reactive System ◽  
Acid Base ◽  
Buffer Solution ◽  
Reaction Method ◽  
Ionization Equilibria ◽  
Coarse Grained Simulations ◽  
Ph Range ◽  
Weak Polyelectrolytes

We introduce the grand-reaction method for coarse-grained simulations of acid-base equilibria in a system coupled to a reservoir at a given pH and concentration of added salt. It can be viewed as an extension of the constant-pH method and the reaction ensemble, combining explicit simulations of reactions within the system, and grand-canonical exchange of particles with the reservoir. Unlike the previously introduced methods, the grand-reaction method is applicable to acid-base equilibria in the whole pH range because it avoids known artifacts. However, the method is more general, and can be used for simulations of any reactive system coupled to a reservoir of a known composition. To demonstrate the advantages of the grand-reaction method, we simulated a model system: A solution of weak polyelectrolytes in equilibrium with a buffer solution. By carefully accounting for the exchange of all constituents, the method ensures that all chemical potentials are equal in the system and in the multi-component reservoir. Thus, the grand-reaction method is able to predict non-monotonic swelling of weak polyelectrolytes as a function of pH, that has been known from mean-field predictions and from experiments but has never been observed in coarse-grained simulations. Finally, we outline possible extensions and further generalizations of the method, and provide a set of guidelines to enable safe usage of the method by a broad community of users.<br><br>

Interference of Gold Nanoparticles with In vitro Endotoxin Detection Assays

2020 ◽  
Vol 16 (2) ◽  
pp. 204-213 ◽  
Author(s):  
Melissa A. Vetten ◽  
Mary Gulumian
Keyword(s):  
Gold Nanoparticles ◽  
Gold Nanoparticle ◽  
Surface Reactivity ◽  
In Vitro Assays ◽  
Limulus Amebocyte Lysate ◽  
Chromogenic Assay ◽  
Nanoparticle Suspensions ◽  
Endotoxin Contamination ◽  
Factor C

Background: Endotoxin-free engineered nanoparticle suspensions are imperative for their successful applications in the field of nanomedicine as well as in the investigations in their toxicity. Gold nanoparticles are known to interfere with various in vitro assays due to their optical properties and potential for surface reactivity. In vitro endotoxin testing assays are known to be susceptible to interference caused by the sample being tested. Objective: This study aimed to identify a preferred assay for the testing of endotoxin contamination in gold nanoparticle suspensions. Methods: The interference by gold nanoparticles on three assays namely, the commonly used limulus amebocyte lysate chromogenic assay, the limulus amebocyte lysate gel-clot method, and the less common recombinant Factor C (rFC) assay, was tested. Results: Possible interference could be observed with all three assays. The interference with the absorbance- based chromogenic assay could not be overcome by dilution; whilst the qualitative nature of the gel-clot assay excluded the possibility of distinguishing between a false positive result due to enhancement of the sensitivity of the assay, and genuine endotoxin contamination. However, interference with the rFC assay was easily overcome through dilution. Conclusion: The rFC assay is recommended as an option for endotoxin contamination detection in gold nanoparticle suspensions.

scholarly journals CRISPR/Cas12a-mediated gold nanoparticle aggregation for colorimetric detection of SARS-CoV-2

2021 ◽  
Author(s):  
Yiren Cao ◽  
Jinjun Wu ◽  
Bo Pang ◽  
Hongquan Zhang ◽  
X. Chris Le
Keyword(s):  
Gold Nanoparticles ◽  
Gold Nanoparticle ◽  
Colorimetric Detection ◽  
Isothermal Amplification ◽  
Nanoparticle Aggregation ◽  
Cleavage Activity ◽  
Gold Nanoparticle Aggregation

The trans-cleavage activity of the target-activated CRISPR-Cas12a liberated an RNA crosslinker from a molecular transducer, which facilitated assembly of gold nanoparticles. Integration of the molecular transducer with isothermal amplification and...

Fluorescence biosensor for Salmonella typhimurium detection in food based on nano-self-assembly of alendronic acid modified upconversion and gold nanoparticles

2021 ◽  
Author(s):  
Min Chen ◽  
Leiqing Pan ◽  
K. Tu
Keyword(s):  
Gold Nanoparticles ◽  
Salmonella Typhimurium ◽  
Gold Nanoparticle ◽  
Alendronic Acid ◽  
Self Assembly ◽  
Upconversion Nanoparticles ◽  
Fluorescent Biosensor ◽  
Fluorescence Biosensor

A simple and quick responsive fluorescent biosensor for Salmonella typhimurium detection based on the recognition of aptamer coupled with alendronic acid (ADA)@upconversion nanoparticles (UCNPs) and gold nanoparticle (AuNPs) has been...

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