Simulating the role of microtubules in depolymerization-driven transport: A Monte Carlo approach

Yong Chuan Tao, Charles Peskin

Research output: Contribution to journalArticle

Abstract

In this paper we present a model that simulates the role of microtubules in depolymerization-driven transport. The model simulates a system that consists of a 13-protofilament microtubule with 'five-start' helical structure and a motor protein-coated bead that moves along one of the protofilaments of the microtubule, as in in vitro experiments. The microtubule is simulated using the lateral cap model, with substantial generalizations. For the new terminal configurations in the presence of the bead, rate constants for association and dissociation events of tubulin molecules are calculated by exploring the geometric similarities between different patterns of terminal configurations and by decomposing complex patterns into simpler patterns whose corresponding rate constants are known. In comparison with a previous model, in which simplifications are made about the structure of the microtubule and in which the microtubule can only depolymerize, the detailed structure of the microtubule is taken into account in the present model. Furthermore, the microtubule can be either polymerizing or depolymerizing. Force-velocity curves are obtained for both zero and non- zero tubulin guanosine 5'-triphosphate (GTP) concentrations. By analyzing the trajectory of the bead under different parameters, the condition for 'run and pause' is analyzed, and the time scale of 'run' and 'pause' is found to be different for different motor proteins. We also suggest experiments that can be used to examine the results predicted by the model.

Original languageEnglish (US)
Pages (from-to)1529-1540
Number of pages12
JournalBiophysical Journal
Volume75
Issue number3
StatePublished - Sep 1998

Fingerprint

Microtubules
Tubulin
Guanosine Triphosphate
Proteins

ASJC Scopus subject areas

  • Biophysics

Cite this

Simulating the role of microtubules in depolymerization-driven transport : A Monte Carlo approach. / Tao, Yong Chuan; Peskin, Charles.

In: Biophysical Journal, Vol. 75, No. 3, 09.1998, p. 1529-1540.

Research output: Contribution to journalArticle

Tao, Yong Chuan ; Peskin, Charles. / Simulating the role of microtubules in depolymerization-driven transport : A Monte Carlo approach. In: Biophysical Journal. 1998 ; Vol. 75, No. 3. pp. 1529-1540.
@article{37d368dbed4c4605a49bd134e23cc7e8,
title = "Simulating the role of microtubules in depolymerization-driven transport: A Monte Carlo approach",
abstract = "In this paper we present a model that simulates the role of microtubules in depolymerization-driven transport. The model simulates a system that consists of a 13-protofilament microtubule with 'five-start' helical structure and a motor protein-coated bead that moves along one of the protofilaments of the microtubule, as in in vitro experiments. The microtubule is simulated using the lateral cap model, with substantial generalizations. For the new terminal configurations in the presence of the bead, rate constants for association and dissociation events of tubulin molecules are calculated by exploring the geometric similarities between different patterns of terminal configurations and by decomposing complex patterns into simpler patterns whose corresponding rate constants are known. In comparison with a previous model, in which simplifications are made about the structure of the microtubule and in which the microtubule can only depolymerize, the detailed structure of the microtubule is taken into account in the present model. Furthermore, the microtubule can be either polymerizing or depolymerizing. Force-velocity curves are obtained for both zero and non- zero tubulin guanosine 5'-triphosphate (GTP) concentrations. By analyzing the trajectory of the bead under different parameters, the condition for 'run and pause' is analyzed, and the time scale of 'run' and 'pause' is found to be different for different motor proteins. We also suggest experiments that can be used to examine the results predicted by the model.",
author = "Tao, {Yong Chuan} and Charles Peskin",
year = "1998",
month = "9",
language = "English (US)",
volume = "75",
pages = "1529--1540",
journal = "Biophysical Journal",
issn = "0006-3495",
publisher = "Biophysical Society",
number = "3",

}

TY - JOUR

T1 - Simulating the role of microtubules in depolymerization-driven transport

T2 - A Monte Carlo approach

AU - Tao, Yong Chuan

AU - Peskin, Charles

PY - 1998/9

Y1 - 1998/9

N2 - In this paper we present a model that simulates the role of microtubules in depolymerization-driven transport. The model simulates a system that consists of a 13-protofilament microtubule with 'five-start' helical structure and a motor protein-coated bead that moves along one of the protofilaments of the microtubule, as in in vitro experiments. The microtubule is simulated using the lateral cap model, with substantial generalizations. For the new terminal configurations in the presence of the bead, rate constants for association and dissociation events of tubulin molecules are calculated by exploring the geometric similarities between different patterns of terminal configurations and by decomposing complex patterns into simpler patterns whose corresponding rate constants are known. In comparison with a previous model, in which simplifications are made about the structure of the microtubule and in which the microtubule can only depolymerize, the detailed structure of the microtubule is taken into account in the present model. Furthermore, the microtubule can be either polymerizing or depolymerizing. Force-velocity curves are obtained for both zero and non- zero tubulin guanosine 5'-triphosphate (GTP) concentrations. By analyzing the trajectory of the bead under different parameters, the condition for 'run and pause' is analyzed, and the time scale of 'run' and 'pause' is found to be different for different motor proteins. We also suggest experiments that can be used to examine the results predicted by the model.

AB - In this paper we present a model that simulates the role of microtubules in depolymerization-driven transport. The model simulates a system that consists of a 13-protofilament microtubule with 'five-start' helical structure and a motor protein-coated bead that moves along one of the protofilaments of the microtubule, as in in vitro experiments. The microtubule is simulated using the lateral cap model, with substantial generalizations. For the new terminal configurations in the presence of the bead, rate constants for association and dissociation events of tubulin molecules are calculated by exploring the geometric similarities between different patterns of terminal configurations and by decomposing complex patterns into simpler patterns whose corresponding rate constants are known. In comparison with a previous model, in which simplifications are made about the structure of the microtubule and in which the microtubule can only depolymerize, the detailed structure of the microtubule is taken into account in the present model. Furthermore, the microtubule can be either polymerizing or depolymerizing. Force-velocity curves are obtained for both zero and non- zero tubulin guanosine 5'-triphosphate (GTP) concentrations. By analyzing the trajectory of the bead under different parameters, the condition for 'run and pause' is analyzed, and the time scale of 'run' and 'pause' is found to be different for different motor proteins. We also suggest experiments that can be used to examine the results predicted by the model.

UR - http://www.scopus.com/inward/record.url?scp=0031655432&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0031655432&partnerID=8YFLogxK

M3 - Article

C2 - 9726955

AN - SCOPUS:0031655432

VL - 75

SP - 1529

EP - 1540

JO - Biophysical Journal

JF - Biophysical Journal

SN - 0006-3495

IS - 3

ER -