Engineering the kinetic stability of a β-trefoil protein by tuning its topological complexity
Kinetic stability, defined as the rate of protein unfolding, is central to determining the functional lifetime of proteins, both in nature and in wide-ranging medical and biotechnological applications. Further, high kinetic stability is generally correlated with high resistance against chemical and...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-02-01
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| Series: | Frontiers in Molecular Biosciences |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmolb.2023.1021733/full |
| _version_ | 1811169233059446784 |
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| author | Delaney M. Anderson Lakshmi P. Jayanthi Shachi Gosavi Elizabeth M. Meiering |
| author_facet | Delaney M. Anderson Lakshmi P. Jayanthi Shachi Gosavi Elizabeth M. Meiering |
| author_sort | Delaney M. Anderson |
| collection | DOAJ |
| description | Kinetic stability, defined as the rate of protein unfolding, is central to determining the functional lifetime of proteins, both in nature and in wide-ranging medical and biotechnological applications. Further, high kinetic stability is generally correlated with high resistance against chemical and thermal denaturation, as well as proteolytic degradation. Despite its significance, specific mechanisms governing kinetic stability remain largely unknown, and few studies address the rational design of kinetic stability. Here, we describe a method for designing protein kinetic stability that uses protein long-range order, absolute contact order, and simulated free energy barriers of unfolding to quantitatively analyze and predict unfolding kinetics. We analyze two β-trefoil proteins: hisactophilin, a quasi-three-fold symmetric natural protein with moderate stability, and ThreeFoil, a designed three-fold symmetric protein with extremely high kinetic stability. The quantitative analysis identifies marked differences in long-range interactions across the protein hydrophobic cores that partially account for the differences in kinetic stability. Swapping the core interactions of ThreeFoil into hisactophilin increases kinetic stability with close agreement between predicted and experimentally measured unfolding rates. These results demonstrate the predictive power of readily applied measures of protein topology for altering kinetic stability and recommend core engineering as a tractable target for rationally designing kinetic stability that may be widely applicable. |
| first_indexed | 2024-04-10T16:39:02Z |
| format | Article |
| id | doaj.art-85e85662cd3f48afac0aa56899356185 |
| institution | Directory Open Access Journal |
| issn | 2296-889X |
| language | English |
| last_indexed | 2024-04-10T16:39:02Z |
| publishDate | 2023-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Molecular Biosciences |
| spelling | doaj.art-85e85662cd3f48afac0aa568993561852023-02-08T09:25:22ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2023-02-011010.3389/fmolb.2023.10217331021733Engineering the kinetic stability of a β-trefoil protein by tuning its topological complexityDelaney M. Anderson0Lakshmi P. Jayanthi1Shachi Gosavi2Elizabeth M. Meiering3Department of Chemistry, University of Waterloo, Waterloo, ON, CanadaSimons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, IndiaSimons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, IndiaDepartment of Chemistry, University of Waterloo, Waterloo, ON, CanadaKinetic stability, defined as the rate of protein unfolding, is central to determining the functional lifetime of proteins, both in nature and in wide-ranging medical and biotechnological applications. Further, high kinetic stability is generally correlated with high resistance against chemical and thermal denaturation, as well as proteolytic degradation. Despite its significance, specific mechanisms governing kinetic stability remain largely unknown, and few studies address the rational design of kinetic stability. Here, we describe a method for designing protein kinetic stability that uses protein long-range order, absolute contact order, and simulated free energy barriers of unfolding to quantitatively analyze and predict unfolding kinetics. We analyze two β-trefoil proteins: hisactophilin, a quasi-three-fold symmetric natural protein with moderate stability, and ThreeFoil, a designed three-fold symmetric protein with extremely high kinetic stability. The quantitative analysis identifies marked differences in long-range interactions across the protein hydrophobic cores that partially account for the differences in kinetic stability. Swapping the core interactions of ThreeFoil into hisactophilin increases kinetic stability with close agreement between predicted and experimentally measured unfolding rates. These results demonstrate the predictive power of readily applied measures of protein topology for altering kinetic stability and recommend core engineering as a tractable target for rationally designing kinetic stability that may be widely applicable.https://www.frontiersin.org/articles/10.3389/fmolb.2023.1021733/fullprotein engineeringkinetic stabilityprotein topologystructure-based modelsβ-trefoillong-range order |
| spellingShingle | Delaney M. Anderson Lakshmi P. Jayanthi Shachi Gosavi Elizabeth M. Meiering Engineering the kinetic stability of a β-trefoil protein by tuning its topological complexity Frontiers in Molecular Biosciences protein engineering kinetic stability protein topology structure-based models β-trefoil long-range order |
| title | Engineering the kinetic stability of a β-trefoil protein by tuning its topological complexity |
| title_full | Engineering the kinetic stability of a β-trefoil protein by tuning its topological complexity |
| title_fullStr | Engineering the kinetic stability of a β-trefoil protein by tuning its topological complexity |
| title_full_unstemmed | Engineering the kinetic stability of a β-trefoil protein by tuning its topological complexity |
| title_short | Engineering the kinetic stability of a β-trefoil protein by tuning its topological complexity |
| title_sort | engineering the kinetic stability of a β trefoil protein by tuning its topological complexity |
| topic | protein engineering kinetic stability protein topology structure-based models β-trefoil long-range order |
| url | https://www.frontiersin.org/articles/10.3389/fmolb.2023.1021733/full |
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