Protein molecules often self-assemble by means of non-covalent physical bonds to form extended filaments, such as amyloids, F-actin, intermediate filaments, and many others. The kinetics of filament growth is limited by the disassembly rate, at which inter-protein bonds break due to the thermal motion. Existing models often assume that the thermal dissociation of subunits occurs uniformly along the filament, or even preferentially in the middle, while the well-known propensity of F-actin to depolymerize from one end is mediated by biochemical factors. Here, we show for a very general (and generic) model, using Brownian dynamics simulations and theory, that the breakup location along the filament is strongly controlled by the asymmetry of the binding force about the minimum, as well as by the bending stiffness of the filament. We provide the basic connection between the features of the interaction potential between subunits and the breakup topology. With central-force (that is, fully flexible) bonds, the breakup rate is always maximum in the middle of the chain, whereas for semiflexible or stiff filaments this rate is either a minimum in the middle or flat. The emerging framework provides a unifying understanding of biopolymer fragmentation and depolymerization and recovers earlier results in its different limits.
Skip Nav Destination
Article navigation
21 March 2015
Research Article|
March 19 2015
Fragmentation and depolymerization of non-covalently bonded filaments
A. Zaccone;
A. Zaccone
1Physics Department and Institute for Advanced Study,
Technische Universität München
, 85748 Garching, Germany
Search for other works by this author on:
I. Terentjev;
I. Terentjev
2
Granta Design
, 62 Clifton Rd., Cambridge CB1 7EG, United Kingdom
Search for other works by this author on:
L. Di Michele
;
L. Di Michele
3Cavendish Laboratory,
University of Cambridge
, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
Search for other works by this author on:
E. M. Terentjev
E. M. Terentjev
3Cavendish Laboratory,
University of Cambridge
, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
Search for other works by this author on:
J. Chem. Phys. 142, 114905 (2015)
Article history
Received:
January 13 2015
Accepted:
March 03 2015
Citation
A. Zaccone, I. Terentjev, L. Di Michele, E. M. Terentjev; Fragmentation and depolymerization of non-covalently bonded filaments. J. Chem. Phys. 21 March 2015; 142 (11): 114905. https://doi.org/10.1063/1.4914925
Download citation file:
Pay-Per-View Access
$40.00
Sign In
You could not be signed in. Please check your credentials and make sure you have an active account and try again.
Citing articles via
DeePMD-kit v2: A software package for deep potential models
Jinzhe Zeng, Duo Zhang, et al.
CREST—A program for the exploration of low-energy molecular chemical space
Philipp Pracht, Stefan Grimme, et al.
Freezing point depression of salt aqueous solutions using the Madrid-2019 model
Cintia P. Lamas, Carlos Vega, et al.
Related Content
Kinetics of fragmentation and dissociation of two-strand protein filaments: Coarse-grained simulations and experiments
J. Chem. Phys. (September 2016)
Picosecond dissociation of amyloid fibrils with infrared laser: A nonequilibrium simulation study
J. Chem. Phys. (October 2015)
Cyclic trimer of human cystatin C, an amyloidogenic protein - molecular dynamics and experimental studies
J. Appl. Phys. (May 2018)
Depolymerization of Organosolv Lignin over Silica-alumina Catalysts
Chin. J. Chem. Phys. (August 2016)