scholarly journals Chemical-State-Dependent Free Energy Profile from Single-Molecule Trajectories of Biomolecular Motors: Application to Processive Chitinase

2021 ◽  
Vol 120 (3) ◽  
pp. 270a
Author(s):  
Kei-ichi Okazaki ◽  
Akihiko Nakamura ◽  
Ryota Iino
Keyword(s):  
Free Energy ◽  
Single Molecule ◽  
Chemical State ◽  
Energy Profile ◽  
Free Energy Profile ◽  
Biomolecular Motors ◽  
State Dependent

scholarly journals Chemical-state-dependent free energy profile from single-molecule trajectories of biomolecular motor: Application to processive chitinase

2019 ◽  
Author(s):  
Kei-ichi Okazaki ◽  
Akihiko Nakamura ◽  
Ryota Iino
Keyword(s):  
Free Energy ◽  
Single Molecule ◽  
Chemical State ◽  
Energy Profile ◽  
Free Energy Profile ◽  
Energy Profiles ◽  
Biomolecular Motors ◽  
State Dependent ◽  
Chitinase A ◽  
State Changes

ABSTRACTThe mechanism of biomolecular motors has been elucidated using single-molecule experiments for visualizing motor motion. However, it remains elusive that how changes in the chemical state during the catalytic cycle of motors lead to unidirectional motions. In this study, we use singlemolecule trajectories to estimate an underlying diffusion model with chemical-state-dependent free energy profile. To consider nonequilibrium trajectories driven by the chemical energy consumed by biomolecular motors, we develop a novel framework based on a hidden Markov model, wherein switching among multiple energy profiles occurs reflecting the chemical state changes in motors. The method is tested using simulation trajectories and applied to singlemolecule trajectories of processive chitinase, a linear motor that is driven by the hydrolysis energy of a single chitin chain. The chemical-state-dependent free energy profile underlying the burnt- bridge Brownian ratchet mechanism of processive chitinase is determined. The novel framework allows us to connect the chemical state changes to the unidirectional motion of biomolecular motors.

Probing Single Molecule Binding and Free Energy Profile with Plasmonic Imaging of Nanoparticles

2019 ◽  
Vol 141 (40) ◽  
pp. 16071-16078 ◽  
Author(s):  
Hui Wang ◽  
Zhuodong Tang ◽  
Yan Wang ◽  
Guangzhong Ma ◽  
Nongjian Tao
Keyword(s):  
Free Energy ◽  
Single Molecule ◽  
Energy Profile ◽  
Free Energy Profile ◽  
Plasmonic Imaging

Free energy profile analysis to identify factors activating the aggregation-induced emission of a cyanostilbene derivative

2021 ◽  
Author(s):  
Norifumi Yamamoto
Keyword(s):  
Free Energy ◽  
Profile Analysis ◽  
Energy Profile ◽  
Contributing Factors ◽  
Free Energy Profile ◽  
Aggregation Induced Emission ◽  
Energy Profiles ◽  
Free Energy Profiles

The contributing factors that cause the aggregation-induced emission (AIE) are determined by identifying characteristic differences in the free energy profiles of the AIE processes of the AIE-active E-form of CN-MBE and the inactive Z-form.

scholarly journals Nonequilibrium study of the intrinsic free-energy profile across a liquid-vapour interface

2016 ◽  
Vol 144 (4) ◽  
pp. 044703 ◽  
Author(s):  
Carlos Braga ◽  
Jordan Muscatello ◽  
Gabriel Lau ◽  
Erich A. Müller ◽  
George Jackson
Keyword(s):  
Free Energy ◽  
Energy Profile ◽  
Free Energy Profile

scholarly journals Free Energy Profile of APOBEC3G Protein Calculated by a Molecular Dynamics Simulation

Biology ◽  
2012 ◽  
Vol 1 (2) ◽  
pp. 245-259
Author(s):  
Yoshifumi Fukunishi ◽  
Saki Hongo ◽  
Masami Lintuluoto ◽  
Hiroshi Matsuo
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Energy Profile ◽  
Free Energy Profile
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