The role of protein dynamics in the evolution of new enzyme function
Abstract
Enzymes must be ordered to allow the stabilization of transition states by their active sites, yet dynamic enough to adopt alternative conformations suited to other steps in their catalytic cycles. The biophysical principles that determine how specific protein dynamics evolve and how remote mutations affect catalytic activity are poorly understood. Here we examine a 'molecular fossil record' that was recently obtained during the laboratory evolution of a phosphotriesterase from Pseudomonas diminuta to an arylesterase. Analysis of the structures and dynamics of nine protein variants along this trajectory, and three rationally designed variants, reveals cycles of structural destabilization and repair, evolutionary pressure to 'freeze out' unproductive motions and sampling of distinct conformations with specific catalytic properties in bi-functional intermediates. This work establishes that changes to the conformational landscapes of proteins are an essential aspect of molecular evolution and that change in function can be achieved through enrichment of preexisting conformational sub-states.
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Dynamic interconversion between multiple conformations underpins the functions of integral membrane proteins in all domains of life.
“Dynamic interconversion between multiple conformations underpins the functions of integral membrane proteins in all domains of life (Campbell et al., 2016; Cournia et al., 2015; Shaw et al., 2010; Boehr et al., 2009).”
From Sampling alternative conformational states of transporters and receptors with AlphaFold2 (2022) · cites this paper as Campbell et al., 2016
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Sampling alternative conformational states of transporters and receptors with AlphaFold2
del Alamo, D., Sala, D., Mchaourab, H. S., & Meiler, J. (2022) · eLife · doi:10.7554/elife.75751 · Cited by 511 · see citing works
“Dynamic interconversion between multiple conformations underpins the functions of integral membrane proteins in all domains of life ( Campbell et al., 2016 ; Cournia et al., 2015 ; Shaw et al., 2010 ; Boehr et al., 2009 ).”
BackgroundThe Role of Conformational Dynamics and Allostery in Modulating Protein Evolution
Campitelli, P., Modi, T., Kumar, S., & Ozkan, S. B. (2020) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-052118-115517 · Cited by 190 · see citing works
Dashnyam, P., Mudududdla, R., Hsieh, T.-J., Lin, T.-C., Lin, H.-Y., Chen, P.-Y., Hsu, C.-Y., & Lin, C.-H. (2018) · Scientific Reports · doi:10.1038/s41598-018-34678-z · Cited by 108 · see citing works
Protein multiple conformations prediction using multi-objective evolution algorithm
Hou, M.-H., Jin, S.-R., Cui, X.-Y., Peng, C.-X., Zhao, K.-L., Song, L., & Zhang, G.-J. (2023) · doi:10.1101/2023.04.21.537776 · Cited by 29 · see citing works
- Authors
- Campbell, E., Kaltenbach, M., Correy, G. J., Carr, P. D., Porebski, B. T., Livingstone, E. K., Afriat-Jurnou, L., Buckle, A. M., Weik, M., Hollfelder, F., Tokuriki, N., & Jackson, C. J.
- Affiliations
- Australian National University (AU)
- University of British Columbia (CA)
- Monash University (AU)
- Centre National de la Recherche Scientifique (FR)
- University of Cambridge (GB)
- Corresponding author
- Tokuriki, Nobuhiko
- Jackson, Colin J
- ORCID
- Venue
- Nature Chemical Biology
- Published
- 2016-09-12
- Volume
- 12
- Issue
- 11
- Pages
- 944-950
- ISSN
- 1552-4450 (ISSN-L)
- 1552-4469
- OpenAlex
- W2520187496
- Cited by
- 311
- References
- 61
- Citations by year
- 2026: 15 · 2025: 28 · 2024: 36 · 2023: 43 · 2022: 30 · 2021: 30 · 2020: 38 · 2019: 31 · 2018: 34 · 2017: 21 · 2016: 5
- FWCI
- 15.76
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Chemical Biology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Enzyme Catalysis and Immobilization
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- protein dynamics, enzyme evolution, phosphotriesterase, arylesterase, Pseudomonas diminuta, directed protein evolution, conformational landscape, transition state stabilization, rational protein design
- MeSH terms
- Carboxylic Ester Hydrolases, Protein Conformation, Pseudomonas, Evolution, Molecular, Phosphoric Triester Hydrolases, Biocatalysis
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