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Retamal-Farfán I, González-Higueras J, Galaz-Davison P, Rivera M, Ramírez-Sarmiento CA. Exploring the structural acrobatics of fold-switching proteins using simplified structure-based models. Biophys Rev 2023; 15:787-799. [PMID: 37681096 PMCID: PMC10480104 DOI: 10.1007/s12551-023-01087-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/22/2023] [Indexed: 09/09/2023] Open
Abstract
Metamorphic proteins are a paradigm of the protein folding process, by encoding two or more native states, highly dissimilar in terms of their secondary, tertiary, and even quaternary structure, on a single amino acid sequence. Moreover, these proteins structurally interconvert between these native states in a reversible manner at biologically relevant timescales as a result of different environmental cues. The large-scale rearrangements experienced by these proteins, and their sometimes high mass interacting partners that trigger their metamorphosis, makes the computational and experimental study of their structural interconversion challenging. Here, we present our efforts in studying the refolding landscapes of two quintessential metamorphic proteins, RfaH and KaiB, using simplified dual-basin structure-based models (SBMs), rigorously footed on the energy landscape theory of protein folding and the principle of minimal frustration. By using coarse-grained models in which the native contacts and bonded interactions extracted from the available experimental structures of the two native states of RfaH and KaiB are merged into a single Hamiltonian, dual-basin SBM models can be generated and savvily calibrated to explore their fold-switch in a reversible manner in molecular dynamics simulations. We also describe how some of the insights offered by these simulations have driven the design of experiments and the validation of the conformational ensembles and refolding routes observed using this simple and computationally efficient models.
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Affiliation(s)
- Ignacio Retamal-Farfán
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, 7820436 Santiago, Chile
- ANID — Millennium Science Initiative Program — Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Jorge González-Higueras
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, 7820436 Santiago, Chile
- ANID — Millennium Science Initiative Program — Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Pablo Galaz-Davison
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, 7820436 Santiago, Chile
- ANID — Millennium Science Initiative Program — Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Maira Rivera
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, 7820436 Santiago, Chile
- Department of Chemistry, Faculty of Science, McGill University, Montreal, Quebec H3A 0B8 Canada
| | - César A. Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, 7820436 Santiago, Chile
- ANID — Millennium Science Initiative Program — Millennium Institute for Integrative Biology (iBio), Santiago, Chile
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