The Impact of Rate Formulations on Stochastic Molecular Motor Dynamics

Abstract

Cells are complex structures which require considerable amounts of organization via transport of large intracellular cargo. While passive diffusion is often sufficiently fast for the transport of smaller cargo, active transport is necessary to organize large structures on the short timescales necessary for biological function. The main mechanism of this transport is by cargo attachment to motors which walk in a directed fashion along intracellular filaments. There are a number of models which seek to describe the motion of motors with attached cargo, from detailed microscopic to coarse phenomenological descriptions. We focus on the intermediate-detailed discrete stochastic hopping models, and explore how cargo transport changes depending on the number of motors, motor interaction, system constraints and rate formulations, which are derived from common thermodynamic assumptions. We find that, despite obeying the same detailed balance constraint, the choice of rate formulation considerably affects the characteristics of the overall motion of the system, with one rate formulation exhibiting novel behavior of loaded motor groups moving faster than a single unloaded motor.

Cooperation and competition in the collective drive by motor proteins: mean active force, fluctuations, and self-load

“…Similar reductions in velocity with increasing spring stiffness have been recently observed in numerical simulations presented in ref. 90. Our theory provides a clear explanation of such observations.…”

“…This journal is © The Royal Society of Chemistry 2023 ref. 90. Our theory provides a clear explanation of such observations.…”

Waiting Time Distributions in Hybrid Models of Motor–Bead Assays: A Concept and Tool for Inference

“…Discrete Markov network models emphasize the changes in the biochemical configuration of the motor protein [11][12][13][14][15], whereas continuous models based on an overdamped Langevin equation focus on the observable diffusive dynamics of the bead [16][17][18][19]. Hybrid models include the dynamics of both assay constituents by coupling the discrete dynamics of the motor with the continuous dynamics of the bead via an effective potential [20][21][22][23][24][25][26][27].…”