scholarly journals Dynamics of a Form-Fitting Protein in a Nanopore: Avidin in ClyA

2017 ◽  
Author(s):  
Bo Lu ◽  
Chris Stokes ◽  
Monifa Fahie ◽  
Min Chen ◽  
Jene A. Golovchenko ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Single Molecule ◽  
Electrical Conductance ◽  
Time Dependent ◽  
Sensitive Detection ◽  
Time Resolved ◽  
3D Printed ◽  
Biotin Molecule ◽  
General Studies

ABSTRACTWe probe the molecular dynamics of a protein, avidin, as it is captured and trapped in a nanopore, ClyA, with time-resolved single-molecule electrical conductance measurements, and we present a method for visualizing this process from the data. The case of avidin in ClyA has rich time-dependent conductance spectra of discrete levels that correlate with different configurations of the protein in the pore. One is very long-lasting, stable and noise-free, and portends the use of this system as a platform for more general studies of proteins and other molecules, where avidin acts as a shuttle that ferries analytes into the pore for probing. We demonstrate this by the sensitive detection of a biotin molecule attached to avidin captured by the pore. We also present an approach to determining the nanopore size based on a 3D printed model of the pore.

scholarly journals First-principles interpretation of electron transport though single-molecule junctions using molecular dynamics of electron attached states

2021 ◽  
Author(s):  
Dávid P. Jelenfi ◽  
Attila Tajti ◽  
Péter G. Szalay
Keyword(s):  
Molecular Dynamics ◽  
Electron Transport ◽  
Single Molecule ◽  
Transition Probabilities ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Bending Vibrations ◽  
Time Resolved ◽  
State Models

The electron transport through the single-molecule junction of 1,4-Diaminobenzene (BDA) is modeled using ab initio quantum-classical molecular dynamics of electron attached states. Observations on the nature of the process are made by time-resolved analysis of energy differences, non-adiabatic transition probabilities and the spatial distribution of the excess electron. The role of molecular vibrations that facilitate the transport by being responsible for the periodic behaviour of these quantities is shown using normal mode analysis. The results support a mechanism involving the electron's direct hopping between the electrodes, without its presence on the molecule, with the prime importance of the bending vibrations that periodically alter the molecule{electrode interactions. No relevant differences are found between results provided by the ADC(2) and SOS-ADC(2) excited state models. Our approach provides an alternative insight into the role of nuclear motions in the electron transport process, one which is more expressive from the chemical perspective.

Structural dynamics of P-type ATPase ion pumps

2019 ◽  
Vol 47 (5) ◽  
pp. 1247-1257 ◽  
Author(s):  
Mateusz Dyla ◽  
Sara Basse Hansen ◽  
Poul Nissen ◽  
Magnus Kjaergaard
Keyword(s):  
Structural Dynamics ◽  
Single Molecule ◽  
New Technologies ◽  
Atp Hydrolysis ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Time Resolved ◽  
Dynamics Simulations ◽  
Types Of Information ◽  
P Type

Abstract P-type ATPases transport ions across biological membranes against concentration gradients and are essential for all cells. They use the energy from ATP hydrolysis to propel large intramolecular movements, which drive vectorial transport of ions. Tight coordination of the motions of the pump is required to couple the two spatially distant processes of ion binding and ATP hydrolysis. Here, we review our current understanding of the structural dynamics of P-type ATPases, focusing primarily on Ca2+ pumps. We integrate different types of information that report on structural dynamics, primarily time-resolved fluorescence experiments including single-molecule Förster resonance energy transfer and molecular dynamics simulations, and interpret them in the framework provided by the numerous crystal structures of sarco/endoplasmic reticulum Ca2+-ATPase. We discuss the challenges in characterizing the dynamics of membrane pumps, and the likely impact of new technologies on the field.

Highly Sensitive Detection of Paraquat with Pillar[5]arene as an aptamer in α-Hemolysin Nanopore

2021 ◽  
Author(s):  
Xiaojia Jiang ◽  
Mingsong Zang ◽  
Fei Li ◽  
Chunxi Hou ◽  
Quan Luo ◽  
...  
Keyword(s):  
Real Time ◽  
High Throughput ◽  
Single Molecule ◽  
Single Molecule Detection ◽  
Sensitive Detection ◽  
High Throughput Analysis ◽  
Throughput Analysis ◽  
The Real ◽  
Highly Sensitive ◽  
Highly Sensitive Detection

Biological nanopore-based techniques have attracted more and more attention recently in the field of single-molecule detection, because they allow the real-time, sensitive, high-throughput analysis. Herein, we report an engineered biological...

Impact of vibronic coupling effects on light-driven charge transfer in pyrene-functionalized middle and large-sized Metalloid Gold Nanoclusters from Ehrenfest dynamics.

2021 ◽  
Author(s):  
Adrian Dominguez-Castro ◽  
Thomas Frauenheim
Keyword(s):  
Molecular Dynamics ◽  
Charge Transfer ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Gold Nanoclusters ◽  
Tight Binding ◽  
Time Dependent ◽  
Effective Strategy ◽  
Dynamics Simulations ◽  
Dependent Density

Theoretical calculations are an effective strategy to comple- ment and understand experimental results in atomistic detail. Ehrenfest molecular dynamics simulations based on the real-time time-dependent density functional tight-binding (RT-TDDFTB) approach...

scholarly journals Ground- and excited-state characteristics in photovoltaic polymer N2200

RSC Advances ◽  
2021 ◽  
Author(s):  
Guanzhao Wen ◽  
Xianshao Zou ◽  
Rong Hu ◽  
Jun Peng ◽  
Zhifeng Chen ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Excited State ◽  
Steady State ◽  
Excited States ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Time Dependent ◽  
Functional Theory ◽  
Time Resolved ◽  
Dependent Density

Ground- and excited-states properties of N2200 have been studied by steady-state and time-resolved spectroscopies as well as time-dependent density functional theory calculations.

Advances in the study of the mechanochemical coupling of kinesin

2018 ◽  
Vol 32 (18) ◽  
pp. 1840001 ◽  
Author(s):  
Ming Li ◽  
Zhong-Can Ou-Yang ◽  
Yao-Gen Shu
Keyword(s):  
Molecular Dynamics ◽  
Single Molecule ◽  
Intracellular Transport ◽  
Coordination Mechanism ◽  
Personal Perspective ◽  
Long Distance ◽  
Future Studies ◽  
Mechanochemical Coupling ◽  
Dynamics Simulations ◽  
Made In

Kinesin is a two-headed linear motor for intracellular transport. It can walk a long distance in a hand-over-hand manner along the track before detaching (i.e., high processivity), and it consumes one ATP molecule for each step (i.e., tight mechanochemical coupling). The mechanisms of the coordination of its two heads and the mechanochemical coupling are the central issues of numerous researches. A few advances have been made in recent decades, thanks to the development of single-molecule technologies and molecular dynamics simulations. In this paper, we review some progress of the studies on the kinematics, energetics, coordination mechanism, mechanochemical mechanism of kinesin. We also present a personal perspective on the future studies of kinesin.

scholarly journals Time-Resolved Fluorescence Anisotropy and Molecular Dynamics Analysis of a Novel GFP Homo-FRET Dimer

2020 ◽  
Author(s):  
Yurema Teijeiro-Gonzalez ◽  
Alessandro Crnjar ◽  
Andrew J. Beavil ◽  
Rebecca L. Beavil ◽  
Jakub Nedbal ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Fluorescence Anisotropy ◽  
Dynamics Analysis ◽  
Time Resolved Fluorescence ◽  
Time Resolved
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