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ART–RRT: As-Rigid-As-Possible search for protein conformational transition paths

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Abstract

The possible functions of a protein are strongly related to its structural rearrangements in the presence of other molecules or environmental changes. Hence, the evaluation of transition paths of proteins, which encodes conformational changes between stable states, is important since it may reveal the underlying mechanisms of the biochemical processes related to these motions. During the last few decades, different geometry-based methods have been proposed to predict such transition paths. However, in the cases where the solution requires complex motions, these methods, which typically constrain only locally the molecular structures, could produce physically irrelevant solutions involving self-intersection. Recently, we have proposed ART–RRT, an efficient method for finding ligand-unbinding pathways. It relies on the exploration of energy valleys in low-dimensional spaces, taking advantage of some mechanisms inspired from computer graphics to ensure the consistency of molecular structures. This article extends ART–RRT to the problem of finding probable conformational transition between two stable states for proteins. It relies on a bidirectional exploration rooted on the two end states and introduces an original strategy to attempt connections between the explored regions. The resulting method is able to produce at low computational cost biologically realistic paths free from self-intersection. These paths can serve as valuable input to other advanced methods for the study of proteins.

Graphic Abstract 

A better understanding of conformational changes of proteins is important since it may reveal the underlying mechanisms of the biochemical processes related to such motions. Recently, the ART–RRT method has been introduced for finding ligand-unbinding pathways. This article presents an adaptation of the method for finding probable conformational transition between two stable states of a protein. The method is not only computationally cost-effective but also able to produce biologically realistic paths which are free from self-intersection.

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Notes

  1. This one-ring neighbor topology, also called spoke [77], is the only one used in ART–RRT so far.

  2. So far, we set these weights to 1.

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Acknowledgements

We would like to gratefully acknowledge funding from the European Research Council through the ERC Starting Grant No. 307629.

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  1. Université Grenoble Alpes, Inria, CNRS, Laboratoire Jean Kuntzmann, 38000, Grenoble, France

    Minh Khoa Nguyen, Léonard Jaillet & Stéphane Redon

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  1. Minh Khoa Nguyen
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Nguyen, M.K., Jaillet, L. & Redon, S. ART–RRT: As-Rigid-As-Possible search for protein conformational transition paths. J Comput Aided Mol Des 33, 705–727 (2019). https://doi.org/10.1007/s10822-019-00216-w

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