Design of novel cyanovirin-N variants by modulation of binding dynamics through distal mutations
Open accessPublished version of a preprint
Abstract
We develop integrated co-evolution and dynamic coupling (ICDC) approach to identify, mutate, and assess distal sites to modulate function. We validate the approach first by analyzing the existing mutational fitness data of TEM-1 β-lactamase and show that allosteric positions co-evolved and dynamically coupled with the active site significantly modulate function. We further apply ICDC approach to identify positions and their mutations that can modulate binding affinity in a lectin, cyanovirin-N (CV-N), that selectively binds to dimannose, and predict binding energies of its variants through Adaptive BP-Dock. Computational and experimental analyses reveal that binding enhancing mutants identified by ICDC impact the dynamics of the binding pocket, and show that rigidification of the binding residues compensates for the entropic cost of binding. This work suggests a mechanism by which distal mutations modulate function through dynamic allostery and provides a blueprint to identify candidates for mutagenesis in order to optimize protein function.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor
Zhang, X., Gureasko, J., Shen, K., Cole, P. A., & Kuriyan, J. (2006) · Cell · doi:10.1016/j.cell.2006.05.013 · Cited by 1,650 · see citing works
Morcos, F., Pagnani, A., Lunt, B., Bertolino, A., Marks, D. S., Sander, C., Zecchina, R., Onuchic, J. N., Hwa, T., & Weigt, M. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1111471108 · Cited by 1,434 · see citing works
Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model
Wang, S., Sun, S., Li, Z., Zhang, R., & Xu, J. (2017) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1005324 · Cited by 931 · see citing works
Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design
Chodera, J. D., & Mobley, D. L. (2013) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-083012-130318 · Cited by 531 · see citing works
Wei, G., Xi, W., Nussinov, R., & Ma, B. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00562 · Cited by 436 · see citing works
Bowman, G. R., & Geissler, P. L. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1209309109 · Cited by 279 · see citing works
The 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
Self-citationOrigins of coevolution between residues distant in protein 3D structures
Anishchenko, I., Ovchinnikov, S., Kamisetty, H., & Baker, D. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1702664114 · Cited by 185 · see citing works
Flagged first, then by citations
- Authors
- Kazan, I. C., Sharma, P., Rahman, M. I., Bobkov, A., Fromme, R., Ghirlanda, G., & Ozkan, S. B.
- Affiliations
- Arizona State University (US)
- Sanford Burnham Prebys Medical Discovery Institute (US)
- Corresponding author
- Ghirlanda, Giovanna
- Ozkan, S Banu
- ORCID
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2022-12-06
- Volume
- 11
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC9725752
- OpenAlex
- W4311549938
- Cited by
- 21
- References
- 9
- Citations by year
- 2026: 1 · 2025: 7 · 2024: 7 · 2023: 6
- FWCI
- 1.63
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Science Foundation (1715591)
- Gordon and Betty Moore Foundation (1901709)
- National Institutes of Health (1R21CA207832-01)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Glycosylation and Glycoproteins Research
- Keywords
- cyanovirin-N, distal mutations, dynamic allostery, TEM-1 beta-lactamase, binding energy prediction, protein mutagenesis
- MeSH terms
- Exercise
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