Protein folding, protein dynamics and the topology of self-motions

Hayward, Steven ORCID: https://orcid.org/0000-0001-6959-2604 (2024) Protein folding, protein dynamics and the topology of self-motions. Royal Society Open Science, 11 (9). ISSN 2054-5703

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Abstract

It has long been recognized that segments of the protein main chain are like robotic manipulators and inverse kinematics methods from robotics have been applied to model loops to bridge gaps in protein comparative modelling. The complex internal motion of a redundant manipulator with fixed ends is called a self-motion and its character is determined by the relative position of its ends. Self-motions that are topologically equivalent (homotopic) occupy the same continous region of the configuration space. Topologically inequivalent (non-homotopic) regions are separated by co-regular surfaces and crossing a co-regular surface can result in a sudden dramatic change in the character of the self-motion. It is shown, using a five-residue type I β-turn, that these concepts apply to protein segments and that as the ends of the five-residue segment come closer together, a co-regular surface is crossed, and the structure is locked in to becoming either a type I or type I′ turn. It is also shown that the type II turn is topologically equivalent to the type I′ turn, not the type I turn. These results have implications for both native-state protein dynamics and protein folding.

Item Type:	Article
Additional Information:	Data accessibility statement: The only data used is from the Protein Data Bank (PDB) and can be downloaded fromwww.pdb.org. The PDB codes for the files used are given in the manuscript. The two main algorithms referred to in the manuscript as algorithm 1 and algorithm 2 are available as electronic supplementary material, 1 and 2respectively [22]. These are each a single Matlab source code file that can be run as instructed. Declaration of AI use: I have not used AI-assisted technologies in creating this article. Funding information: No funding has been received for this article
Faculty \ School:	Faculty of Science > School of Computing Sciences
UEA Research Groups:	Faculty of Science > Research Groups > Computational Biology
Related URLs:	https://royalsocietypublishing.org/doi/1...
Depositing User:	LivePure Connector
Date Deposited:	19 Sep 2024 11:30
Last Modified:	25 Sep 2024 18:10
URI:	https://ueaeprints.uea.ac.uk/id/eprint/96777
DOI:	10.1098/rsos.240873

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