Folding–unfolding asymmetry and a RetroFold computational algorithm

We treat protein folding as molecular self-assembly, while unfolding is viewed as disassembly. Fracture is typically a much faster process than self-assembly. Self-assembly is often an exponentially decaying process, since energy relaxes due to dissipation, while fracture is a constant-rate process...

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Bibliographic Details
Published in:Royal Society open science Vol. 10; no. 5; p. 221594
Main Authors: Shityakov, Sergey, Skorb, Ekaterina V., Nosonovsky, Michael
Format: Journal Article
Language:English
Published: England The Royal Society 03.05.2023
Subjects:
Biochemistry, Cellular and Molecular Biology
folding
molecular dynamics
RetroFold algorithm
Trp-cage
unfolding
RetroFold algorithm
molecular dynamics
unfolding
Trp-cage
folding
ISSN:2054-5703, 2054-5703
Online Access:Get full text
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Summary:We treat protein folding as molecular self-assembly, while unfolding is viewed as disassembly. Fracture is typically a much faster process than self-assembly. Self-assembly is often an exponentially decaying process, since energy relaxes due to dissipation, while fracture is a constant-rate process as the driving force is opposed by damping. Protein folding takes two orders of magnitude longer than unfolding. We suggest a mathematical transformation of variables, which makes it possible to view self-assembly as time-reversed disassembly, thus folding can be studied as reversed unfolding. We investigate the molecular dynamics modelling of folding and unfolding of the short Trp-cage protein. Folding time constitutes about 800 ns, while unfolding (denaturation) takes only about 5.0 ns and, therefore, fewer computational resources are needed for its simulation. This RetroFold approach can be used for the design of a novel computation algorithm, which, while approximate, is less time-consuming than traditional folding algorithms.
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ISSN:2054-5703
2054-5703
DOI:10.1098/rsos.221594