Biochemical physics modeling of biological nano-motors
Abstract
We present a biochemical physics model accounting for the dynamics and energetics of both translational and rotational protein motors. A modified version of the hand-over-hand mechanism considering competitive inhibition by ADP is presented. Transition state-like theory is used to reconstruct the time dependent free-energy landscape of the cycle catalyst process that allows to predicting the number of steps or rotations that a single motor can perform. In addition, following the usual approach of chemical kinetics, we calculate the average translational velocity and also the stopping time of processes involving a collectivity of motors, such as exocytosis and endocytosis processes. Finally, we formulate a stochastic model reproducing very well single realizations of kinesin and rotary ATPases.
- Authors:
-
- UMDI-Facultad de Ciencias, Universidad Nacional Autónoma de México, Campus Juriquilla, Boulevard Juriquilla 3001, 76230 Querétaro (Mexico)
- Publication Date:
- OSTI Identifier:
- 22264070
- Resource Type:
- Journal Article
- Journal Name:
- AIP Conference Proceedings
- Additional Journal Information:
- Journal Volume: 1579; Journal Issue: 1; Conference: 5. Leopoldo Garcia-Colin Mexican meeting on mathematical and experimental physics, Mexico City (Mexico), 9-13 Sep 2013; Other Information: (c) 2014 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA); Journal ID: ISSN 0094-243X
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; 77 NANOSCIENCE AND NANOTECHNOLOGY; CATALYSTS; FREE ENERGY; NANOSTRUCTURES; SIMULATION; STOCHASTIC PROCESSES; TIME DEPENDENCE
Citation Formats
Santamaría-Holek, I., and López-Alamilla, N. J. Biochemical physics modeling of biological nano-motors. United States: N. p., 2014.
Web. doi:10.1063/1.4862424.
Santamaría-Holek, I., & López-Alamilla, N. J. Biochemical physics modeling of biological nano-motors. United States. https://doi.org/10.1063/1.4862424
Santamaría-Holek, I., and López-Alamilla, N. J. 2014.
"Biochemical physics modeling of biological nano-motors". United States. https://doi.org/10.1063/1.4862424.
@article{osti_22264070,
title = {Biochemical physics modeling of biological nano-motors},
author = {Santamaría-Holek, I. and López-Alamilla, N. J.},
abstractNote = {We present a biochemical physics model accounting for the dynamics and energetics of both translational and rotational protein motors. A modified version of the hand-over-hand mechanism considering competitive inhibition by ADP is presented. Transition state-like theory is used to reconstruct the time dependent free-energy landscape of the cycle catalyst process that allows to predicting the number of steps or rotations that a single motor can perform. In addition, following the usual approach of chemical kinetics, we calculate the average translational velocity and also the stopping time of processes involving a collectivity of motors, such as exocytosis and endocytosis processes. Finally, we formulate a stochastic model reproducing very well single realizations of kinesin and rotary ATPases.},
doi = {10.1063/1.4862424},
url = {https://www.osti.gov/biblio/22264070},
journal = {AIP Conference Proceedings},
issn = {0094-243X},
number = 1,
volume = 1579,
place = {United States},
year = {Tue Jan 14 00:00:00 EST 2014},
month = {Tue Jan 14 00:00:00 EST 2014}
}