The key role of the dynamics and flexibility of proteins in functional mechanisms: How computational methods can contribute to their identification

RLF Lin and A Bellaiche and C Etchebest, BIOCHIMIE, 239, 8-26 (2025).

DOI: 10.1016/j.biochi.2025.10.007

Despite its relevance, the well-known paradigm that connects sequence, structure and function still overlooks an important factor: the dynamics of the proteins involved in functional mechanisms. Experimental techniques such as nuclear magnetic resonance and, more recently, cryo- electron microscopy, provide some insight into the conformational diversity of a protein. However, technical difficulties limit their application to the proteome scale. Nevertheless, computational methods are now considered efficient in providing valuable information about the dynamical landscape of a given protein, thereby improving our understanding of its function. Among these methods, molecular dynamics simulations have become very popular and generate a large amount of data that can now be used by Artificial Intelligence approaches for prediction. This paper will describe and discuss the concepts and a few applications of these approaches. (c) 2025 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

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