scholarly journals Biased Brownian Motion of KIF1A and the Role of Tubulin’s C-Terminal Tail Studied by Molecular Dynamics Simulation

2021 ◽  
Vol 22 (4) ◽  
pp. 1547
Author(s):  
Yukinobu Mizuhara ◽  
Mitsunori Takano
Keyword(s):  
Molecular Dynamics ◽  
Brownian Motion ◽  
Energy Landscape ◽  
Dynamics Simulation ◽  
Long Distance ◽  
Post Translational Modifications ◽  
Family Protein ◽  
Dynamics Simulations ◽  
Kinesin Family

KIF1A is a kinesin family protein that moves over a long distance along the microtubule (MT) to transport synaptic vesicle precursors in neurons. A single KIF1A molecule can move toward the plus-end of MT in the monomeric form, exhibiting the characteristics of biased Brownian motion. However, how the bias is generated in the Brownian motion of KIF1A has not yet been firmly established. To elucidate this, we conducted a set of molecular dynamics simulations and observed the binding of KIF1A to MT. We found that KIF1A exhibits biased Brownian motion along MT as it binds to MT. Furthermore, we show that the bias toward the plus-end is generated by the ratchet-like energy landscape for the KIF1A-MT interaction, in which the electrostatic interaction and the negatively-charged C-terminal tail (CTT) of tubulin play an essential role. The relevance to the post-translational modifications of CTT is also discussed.

Carbon dioxide induced bubble formation in a CH4–CO2–H2O ternary system: a molecular dynamics simulation study

2016 ◽  
Vol 18 (5) ◽  
pp. 3746-3754 ◽  
Author(s):  
K. S. Sujith ◽  
C. N. Ramachandran
Keyword(s):  
Carbon Dioxide ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Ternary System ◽  
Simulation Study ◽  
Bubble Formation ◽  
Dynamics Simulation ◽  
System A ◽  
Dynamics Simulations

The role of carbon dioxide in the formation of gas bubbles in a CH4–CO2–H2O ternary system is studied using molecular dynamics simulations.

Solvent effect on xylose conversion under catalyst-free conditions: insights from molecular dynamics simulation and experiments

2020 ◽  
Vol 22 (2) ◽  
pp. 532-539 ◽  
Author(s):  
Qixuan Lin ◽  
Shouwei Liao ◽  
Libo Li ◽  
Weiying Li ◽  
Fengxia Yue ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Solvent Effect ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Catalyst Free ◽  
Dynamics Simulations ◽  
Role Of Solvent

In this study, experiments and molecular dynamics simulations were combined to get insights into the role of solvent during the process of xylose conversion under catalyst-free conditions.

scholarly journals Protein Interaction with Charged Macromolecules: From Model Polymers to Unfolded Proteins and Post-Translational Modifications

2019 ◽  
Vol 20 (5) ◽  
pp. 1252 ◽  
Author(s):  
Pavel Semenyuk ◽  
Vladimir Muronetz
Keyword(s):  
Molecular Dynamics ◽  
Electrostatic Interactions ◽  
Dynamics Simulation ◽  
Unfolded Proteins ◽  
Post Translational Modifications ◽  
Dna And Rna ◽  
Charged Polymers ◽  
Local Charge ◽  
Charged Macromolecules ◽  
Dynamics Simulations

Interaction of proteins with charged macromolecules is involved in many processes in cells. Firstly, there are many naturally occurred charged polymers such as DNA and RNA, polyphosphates, sulfated glycosaminoglycans, etc., as well as pronouncedly charged proteins such as histones or actin. Electrostatic interactions are also important for “generic” proteins, which are not generally considered as polyanions or polycations. Finally, protein behavior can be altered due to post-translational modifications such as phosphorylation, sulfation, and glycation, which change a local charge of the protein region. Herein we review molecular modeling for the investigation of such interactions, from model polyanions and polycations to unfolded proteins. We will show that electrostatic interactions are ubiquitous, and molecular dynamics simulations provide an outstanding opportunity to look inside binding and reveal the contribution of electrostatic interactions. Since a molecular dynamics simulation is only a model, we will comprehensively consider its relationship with the experimental data.

Multicanonical Molecular Dynamics Simulation Study of the Liquid-Solid and Solid-Solid Transitions in Lennard-Jones Clusters

2011 ◽  
Author(s):  
Toshihiro Kaneko ◽  
Kenji Yasuoka ◽  
Ayori Mitsutake ◽  
Xiao Cheng Zeng
Keyword(s):  
Molecular Dynamics ◽  
Heat Capacity ◽  
Transition Temperature ◽  
Peak Position ◽  
Temperature Curve ◽  
Dynamics Simulation ◽  
Lennard Jones ◽  
Dynamics Simulations ◽  
First Time ◽  
Good Agreement

Multicanonical molecular dynamics simulations are applied, for the first time, to study the liquid-solid and solid-solid transitions in Lennard-Jones (LJ) clusters. The transition temperatures are estimated based on the peak position in the heat capacity versus temperature curve. For LJ31, LJ58 and LJ98, our results on the solid-solid transition temperature are in good agreement with previous ones. For LJ309, the predicted liquid-solid transition temperature is also in agreement with previous result.

scholarly journals Reactive molecular dynamics simulation of the high-temperature pyrolysis of 2,2′,2′′,4,4′,4′′,6,6′,6′′-nonanitro-1,1′:3′,1′′-terphenyl (NONA)

RSC Advances ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 5507-5515
Author(s):  
Liang Song ◽  
Feng-Qi Zhao ◽  
Si-Yu Xu ◽  
Xue-Hai Ju
Keyword(s):  
Molecular Dynamics ◽  
High Temperature ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Reactive Molecular Dynamics ◽  
Ring Compounds ◽  
Fused Ring ◽  
Dynamics Simulations

The bimolecular and fused ring compounds are found in the high-temperature pyrolysis of NONA using ReaxFF molecular dynamics simulations.

Sign in / Sign up

Export Citation Format

Share Document