scholarly journals Computer simulation of knotted proteins unfold and translocation through nano-pores

2018 ◽  
Author(s):  
M. A. Shahzad
Keyword(s):  
Computer Simulation ◽  
Computational Model ◽  
Coarse Grained ◽  
Kinetic Properties ◽  
Constant Force ◽  
Translocation Mechanism ◽  
Translocation Time ◽  
Knotted Protein ◽  
Knotted Proteins ◽  
Pulling Force

We study the unfold and translocation of knotted protein, YibK and YbeA, through α-hemolysin nano-pore via a coarse grained computational model. We observe that knot of protein unfold in advance before the translocation take place. We also characterized the translocation mechanism by studying the thermodynamical and kinetic properties of the process. In particular, we study the average of translocation time, and the translocation probability as a function of pulling force F acting in the channel. In limit of low pulling inward constant force acting along the axis of the pore, the YibK knotted protein takes longer average translocation time as compare to YbeA knotted protein.

scholarly journals Translocation process of structured polypeptides across nanopores

2010 ◽  
Vol 24 (3-4) ◽  
pp. 421-426 ◽  
Author(s):  
Fabio Cecconi ◽  
Umberto Marini Bettolo Marconi ◽  
Angelo Vulpiani
Keyword(s):  
Statistical Physics ◽  
Coarse Grained ◽  
Free Energy Barrier ◽  
Transport Dynamics ◽  
Alpha Hemolysin ◽  
Translocation Mechanism ◽  
Smoluchowski Equations ◽  
Pulling Force ◽  
Molecular Manipulation ◽  
Polypeptide Chains

The progress of molecular manipulation technology has made it possible to conduct controlled experiments on translocation of polynucleotide and polypeptide chains across alpha-Hemolysin channels and solid-state nanopores. To study the translocation process we combined Molecular Dynamics at coarse-grained level and appropriate drift-diffusion Smoluchowski equations as an integrated statistical physics approach. In particular, we performed simulations of the passage across a cylindrical nanopore of Ubiquitin described by a coarse-grained native-centric model to investigate the influence of protein structural properties on translocation mechanism. The kinetic characterization of the process is achieved by studying the statistics of blockage times, the mobility and translocation probability as a function of the pulling forceFacting in the pore. We find that the transport dynamics displays a thresholdFcdepending on a free-energy barrier that Ubiquitin overcomes to translocate. Our simulations show this barrier to be the result from competition of the unfolding energy and the entropy associated to the confinement effects of the pore.

The structure of polymer brushes near the transition from dilute to dense systems. A computer simulation study

Soft Matter ◽  
2021 ◽  
Author(s):  
Piotr Polanowski ◽  
Andrzej Sikorski
Keyword(s):  
Computer Simulation ◽  
Monte Carlo ◽  
Monte Carlo Simulations ◽  
Simulation Study ◽  
Polymer Brushes ◽  
Polymer Brush ◽  
Coarse Grained ◽  
Computer Simulation Study ◽  
Coarse Grained Model ◽  
Cooperative Motion

Monodisperse polymer brushes were studied by means of Monte Carlo simulations. A coarse-grained model of a polymer brush was designed in order and the Cooperative Motion Algorithm was employed to...

scholarly journals Translocation through a narrow pore under a pulling force

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Mohammadreza Niknam Hamidabad ◽  
Rouhollah Haji Abdolvahab
Keyword(s):  
Interaction Energy ◽  
External Force ◽  
Center Of Mass ◽  
Three Dimensional ◽  
Major Effect ◽  
Translocation Time ◽  
Polymer Translocation ◽  
Pulling Force ◽  
External Forces ◽  
Polymer Shape

AbstractWe employ a three-dimensional molecular dynamics to simulate a driven polymer translocation through a nanopore by applying an external force, for four pore diameters and two external forces. To see the polymer and pore interaction effects on translocation time, we studied nine interaction energies. Moreover, to better understand the simulation results, we investigate polymer center of mass, shape factor and the monomer spatial distribution through the translocation process. Our results reveal that increasing the polymer-pore interaction energy is accompanied by an increase in the translocation time and decrease in the process rate. Furthermore, for pores with greater diameter, the translocation becomes faster. The shape analysis of the polymer indicates that the polymer shape is highly sensitive to the interaction energy. In great interactions, the monomers come close to the pore from both sides. As a result, the translocation becomes fast at first and slows down at last. Overall, it can be concluded that the external force does not play a major role in the shape and distribution of translocated monomers. However, the interaction energy between monomer and nanopore has a major effect especially on the distribution of translocated monomers on the trans side.

scholarly journals Prion Protein Translocation Mechanism Revealed by Pulling Force Studies

2020 ◽  
Vol 432 (16) ◽  
pp. 4447-4465 ◽  
Author(s):  
Theresa Kriegler ◽  
Sven Lang ◽  
Luigi Notari ◽  
Tara Hessa
Keyword(s):  
Prion Protein ◽  
Protein Translocation ◽  
Translocation Mechanism ◽  
Pulling Force

Coarse-Grained Computer Simulation of Nanoconfined Polyamide-6,6

2011 ◽  
Vol 44 (8) ◽  
pp. 3117-3128 ◽  
Author(s):  
Hossein Eslami ◽  
Hossein Ali Karimi-Varzaneh ◽  
Florian Müller-Plathe
Keyword(s):  
Computer Simulation ◽  
Coarse Grained

Computer Simulation of Polymer Chains in Confinement

2008 ◽  
Vol 138 ◽  
pp. 451-475 ◽  
Author(s):  
Andrzej Sikorski
Keyword(s):  
Computer Simulation ◽  
Brownian Dynamics ◽  
Dynamic Properties ◽  
Practical Importance ◽  
Polymer Chains ◽  
Coarse Grained ◽  
Theoretical Treatment ◽  
Narrow Slit ◽  
Exchange Method ◽  
Confined Polymers

Properties of macromolecules confined in a narrow slit, pore or capillary are important due to of their practical importance. Theoretical treatment of such systems is also interesting because the introduction of confinement has an impact on most properties of polymer chains and it gained a longstanding attention. In order to determine the properties of such systems coarse-grained models of confined polymers were designed where macromolecules were represented by united atoms. Lattice approximation was also often introduced. Different macromolecular architectures were studied: linear, cyclic and star-branched chains. Computer simulation techniques (the variants of the Monet Carlo method like the Metropolis algorithm and the Replica Exchange method as well as Molecular Dynamics and Brownian Dynamics methods) applied for studies of such models were reviewed and evaluated. The structure of the polymer film and the dynamic properties were mainly presented and discussed. The influence of the width of the slit, the temperature and the force field on the dimension and the structure of chains were studied. It was shown that a moderate confinement stabilizes folded chains while a strong confinement does not.

scholarly journals Structural-Kinetic-Thermodynamic Relationships Identified from Physics-based Molecular Simulation Models

2017 ◽  
Author(s):  
Joseph F. Rudzinski ◽  
Tristan Bereau
Keyword(s):  
Thermodynamic Properties ◽  
Force Field ◽  
Molecular Simulation ◽  
Simulation Models ◽  
Coarse Grained ◽  
Kinetic Properties ◽  
Coarse Grained Model ◽  
Forbidden Configurations ◽  
Force Field Parameters ◽  
Representative System

Coarse-grained molecular simulation models have provided immense, often general, insight into the complex behavior of condensed-phase systems, but suffer from a lost connection to the true dynamical properties of the underlying system. In general, the physics that is built into a model shapes the free-energy landscape, restricting the attainable static and kinetic properties. In this work, we perform a detailed investigation into the property interrelationships resulting from these restrictions, for a representative system of the helix-coil transition. Inspired by high-throughput studies, we systematically vary force-field parameters and monitor their structural, kinetic, and thermodynamic properties. The focus of our investigation is a simple coarse-grained model, which accurately represents the underlying structural ensemble, i.e., effectively avoids sterically-forbidden configurations. As a result of this built-in physics, we observe a rather large restriction in the topology of the networks characterizing the simulation kinetics. When screening across force-field parameters, we find that structurally-accurate models also best reproduce the kinetics, suggesting structural-kinetic relationships for these models. Additionally, an investigation into thermodynamic properties reveals a link between the cooperativity of the transition and the network topology at a single reference temperature.

Gelation of patchy ligand shell nanoparticles decorated by liquid-crystalline ligands: computer simulation study

Soft Matter ◽  
2018 ◽  
Vol 14 (19) ◽  
pp. 3799-3810 ◽  
Author(s):  
Jaroslav M. Ilnytskyi ◽  
Arsen Slyusarchuk ◽  
Stefan Sokołowski
Keyword(s):  
Computer Simulation ◽  
Simulation Study ◽  
Liquid Crystalline ◽  
Coarse Grained ◽  
Computer Simulation Study ◽  
Shell Nanoparticles ◽  
Ligand Shell

We consider the coarse-grained modelling of patchy ligand shell nanoparticles with liquid crystalline ligands.

scholarly journals The role of conformational entropy in the determination of structural-kinetic relationships for helix-coil transitions

2017 ◽  
Author(s):  
Joseph F. Rudzinski ◽  
Tristan Bereau
Keyword(s):  
Simulation Models ◽  
Structural Features ◽  
Coarse Grained ◽  
Kinetic Properties ◽  
Conformational Entropy ◽  
Peptide Backbone ◽  
The Relationship ◽  
Insight Into

Coarse-grained molecular simulation models can provide significant insight into the complex behavior of protein systems, but suffer from an inherently distorted description of dynamical properties. We recently demonstrated that, for a heptapeptide of alanine residues, the structural and kinetic properties of a simulation model are linked in a rather simple way, given a certain level of physics present in the model. In this work, we extend these findings to a longer peptide, for which the representation of configuration space in terms of a full enumeration of sequences of helical/coil states along the peptide backbone is impractical. We verify the structural-kinetic relationships by scanning the parameter space of a simple native-biased model and then employ a distinct transferable model to validate and generalize the conclusions. Our results further demonstrate the validity of the previous findings, while clarifying the role of conformational entropy in the determination of the structural-kinetic relationships. More specifically, while the global, long timescale kinetic properties of a particular class of models with varying energetic parameters but approximately fixed conformational entropy are determined by the overarching structural features of the ensemble, a shift in these kinetic observables occurs for models with a distinct representation of steric interactions. At the same time, the relationship between structure and more local, faster kinetic properties is not affected by varying the conformational entropy of the model.

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