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Protein stability and mobility in live cells: Revelation of the intracellular diffusive interaction organization mechanisms
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Biochemical processes inside living cells take place in a confined and highly crowded environment. As such, macromolecular crowding, one of the most important physicochemical properties of cytoplasm, is an essential element of cell physiology. It not only gives rise to steric repulsion, but also promotes non-specific, transient, interactions (referred to as diffusive interactions) between molecules. Since diffusive interactions are a key way to achieving a highly organized intracellular environment, without such interactions, the cell is just “a bag of molecules”. Therefore, understanding how diffusive interactions modulate protein behavior in live cells is of fundamental importance for revealing the mechanisms of molecular recognition, as well as for understanding the cause of protein misfolding diseases.

This thesis focuses on how macromolecular crowding influences the stability and diffusive motions of proteins within living cells by modulating their diffusive interactions. First, we investigated the thermal stability of superoxide dismutase 1 (SOD1), a protein involved in the development of familial amyotrophic lateral sclerosis (ALS), in mammalian and E. coli cells. Intriguingly, the major thermodynamic consequence of macromolecular crowding is due not only to conventional steric repulsions, but primarily to the detailed chemical nature of the diffusive protein interactions in live cells. Secondly, we presented a mutational study of how these diffusive interactions influence the rotation of proteins in the mammalian and bacterial cytosol. The result is a quantitative description of the physicochemical code for the intracellular protein motion, showing that it depends critically on the surface details of protein and the type of the host cell as well. Thirdly, we characterized the impact of  intracellular protein concentration by altering the volume of E. coli cells by osmotic shock. The results obtained show that the intracellular diffusion of proteins is not determined by the chemical properties of the protein surface alone, but also by the frequency of concentration-dependent encounters. Moreover, it appears that eukaryotes and bacteria have achieved fidelity of biological processes through different evolutionary strategies. Overall, these observations have numerous implications for both functional protein design and deciphering the evolution of the surface characteristics of proteins.

Subsequently, we attempted to shed new light on the Hofmeister series, using protein-folding kinetics as observable. The results indicate that the Hofmeister series cannot be explained entirely by the traditional Kosmotropes/Chaotropes classification. Strong hetero-ion pairing cannot be ignored when trying to understand the effects of salts on protein salting-in and salting-out behaviors.

Place, publisher, year, edition, pages
Stockholm: Department of Biochemistry and Biophysics, Stockholm University , 2019. , p. 67
Keywords [en]
diffusive interactions, macromolecular crowding, protein thermodynamic stability, protein mobility, in-cell NMR, Hofmeister series
National Category
Biochemistry and Molecular Biology
Research subject
Biochemistry
Identifiers
URN: urn:nbn:se:su:diva-175632ISBN: 978-91-7797-931-9 (print)ISBN: 978-91-7797-932-6 (electronic)OAI: oai:DiVA.org:su-175632DiVA, id: diva2:1368399
Public defence
2019-12-19, Nordenskiöldsalen, Geovetenskapens hus, Svante Arrhenius väg 12, Stockholm, 10:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript. Paper 5: Manuscript.

Available from: 2019-11-26 Created: 2019-11-07 Last updated: 2019-11-19Bibliographically approved
List of papers
1. Thermodynamics of protein destabilization in live cells
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2015 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 112, no 40, p. 12402-12407Article in journal (Refereed) Published
Abstract [en]

Although protein folding and stability have been well explored under simplified conditions in vitro, it is yet unclear how these basic self-organization events are modulated by the crowded interior of live cells. To find out, we use here in-cell NMR to follow at atomic resolution the thermal unfolding of a beta-barrel protein inside mammalian and bacterial cells. Challenging the view from in vitro crowding effects, we find that the cells destabilize the protein at 37 degrees C but with a conspicuous twist: While the melting temperature goes down the cold unfolding moves into the physiological regime, coupled to an augmented heat-capacity change. The effect seems induced by transient, sequence-specific, interactions with the cellular components, acting preferentially on the unfolded ensemble. This points to a model where the in vivo influence on protein behavior is case specific, determined by the individual protein's interplay with the functionally optimized interaction landscape of the cellular interior.

Keywords
thermodynamics, protein stability, crowding, in vivo, NMR
National Category
Biological Sciences
Research subject
Biochemistry
Identifiers
urn:nbn:se:su:diva-123537 (URN)10.1073/pnas.1511308112 (DOI)000363125400053 ()
Available from: 2015-11-27 Created: 2015-11-27 Last updated: 2019-11-12Bibliographically approved
2. Physicochemical code for quinary protein interactions in Escherichia coli
Open this publication in new window or tab >>Physicochemical code for quinary protein interactions in Escherichia coli
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2017 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 114, no 23, p. E4556-E4563Article in journal (Refereed) Published
Abstract [en]

How proteins sense and navigate the cellular interior to find their functional partners remains poorly understood. An intriguing aspect of this search is that it relies on diffusive encounters with the crowded cellular background, made up of protein surfaces that are largely nonconserved. The question is then if/how this protein search is amenable to selection and biological control. To shed light on this issue, we examined the motions of three evolutionary divergent proteins in the Escherichia coli cytoplasm by in-cell NMR. The results show that the diffusive in-cell motions, after all, follow simplistic physical-chemical rules: The proteins reveal a common dependence on (i) net charge density, (ii) surface hydrophobicity, and (iii) the electric dipole moment. The bacterial protein is here biased to move relatively freely in the bacterial interior, whereas the human counterparts more easily stick. Even so, the in-cell motions respond predictably to surface mutation, allowing us to tune and intermix the protein's behavior at will. The findings show how evolution can swiftly optimize the diffuse background of protein encounter complexes by just single-point mutations, and provide a rational framework for adjusting the cytoplasmic motions of individual proteins, e.g., for rescuing poor in-cell NMR signals and for optimizing protein therapeutics.

Keywords
in-cell NMR, protein surface properties, intracellular diffusion
National Category
Biological Sciences
Research subject
Biochemistry
Identifiers
urn:nbn:se:su:diva-144791 (URN)10.1073/pnas.1621227114 (DOI)000402703800006 ()28536196 (PubMedID)
Available from: 2017-07-13 Created: 2017-07-13 Last updated: 2019-11-12Bibliographically approved
3. Diffusive protein interactions in human versus bacterial cells
Open this publication in new window or tab >>Diffusive protein interactions in human versus bacterial cells
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(English)Manuscript (preprint) (Other academic)
National Category
Biological Sciences
Research subject
Biochemistry
Identifiers
urn:nbn:se:su:diva-175631 (URN)
Available from: 2019-11-07 Created: 2019-11-07 Last updated: 2019-11-12Bibliographically approved
4. Quantification of the crowding effect on diffusive protein interactions in Escherichia coli by cell-volume modulation
Open this publication in new window or tab >>Quantification of the crowding effect on diffusive protein interactions in Escherichia coli by cell-volume modulation
(English)Manuscript (preprint) (Other academic)
National Category
Biological Sciences
Research subject
Biochemistry
Identifiers
urn:nbn:se:su:diva-175629 (URN)
Available from: 2019-11-07 Created: 2019-11-07 Last updated: 2019-11-15Bibliographically approved
5. Salt effects on protein folding behavior: revealing the molecular origins and limitation of Hofmeister theory
Open this publication in new window or tab >>Salt effects on protein folding behavior: revealing the molecular origins and limitation of Hofmeister theory
(English)Manuscript (preprint) (Other academic)
National Category
Biological Sciences
Research subject
Biochemistry
Identifiers
urn:nbn:se:su:diva-175630 (URN)
Available from: 2019-11-07 Created: 2019-11-07 Last updated: 2019-11-12Bibliographically approved

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