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Vallina Estrada, EloyORCID iD iconorcid.org/0000-0002-8204-7798
Publications (4 of 4) Show all publications
Vallina Estrada, E., Zhang, N., Wennerström, H., Danielsson, J. & Oliveberg, M. (2023). Diffusive intracellular interactions: On the role of protein net charge and functional adaptation. Current opinion in structural biology, 81, Article ID 102625.
Open this publication in new window or tab >>Diffusive intracellular interactions: On the role of protein net charge and functional adaptation
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2023 (English)In: Current opinion in structural biology, ISSN 0959-440X, E-ISSN 1879-033X, Vol. 81, article id 102625Article in journal (Refereed) Published
Abstract [en]

A striking feature of nucleic acids and lipid membranes is that they all carry net negative charge and so is true for the majority of intracellular proteins. It is suggested that the role of this negative charge is to assure a basal intermolecular repulsion that keeps the cytosolic content suitably ‘fluid’ for function. We focus in this review on the experimental, theoretical and genetic findings which serve to underpin this idea and the new questions they raise. Unlike the situation in test tubes, any functional protein-protein interaction in the cytosol is subject to competition from the densely crowded background, i.e. surrounding stickiness. At the nonspecific limit of this stickiness is the ‘random’ protein-protein association, maintaining profuse populations of transient and constantly interconverting complexes at physiological protein concentrations. The phenomenon is readily quantified in studies of the protein rotational diffusion, showing that the more net negatively charged a protein is the less it is retarded by clustering. It is further evident that this dynamic protein-protein interplay is under evolutionary control and finely tuned across organisms to maintain optimal physicochemical conditions for the cellular processes. The emerging picture is then that specific cellular function relies on close competition between numerous weak and strong interactions, and where all parts of the protein surfaces are involved. The outstanding challenge is now to decipher the very basics of this many-body system: how the detailed patterns of charged, polar and hydrophobic side chains not only control protein-protein interactions at close- and long-range but also the collective properties of the cellular interior as a whole.

National Category
Biophysics
Identifiers
urn:nbn:se:su:diva-219978 (URN)10.1016/j.sbi.2023.102625 (DOI)001035521800001 ()37331204 (PubMedID)2-s2.0-85162160917 (Scopus ID)
Available from: 2023-08-10 Created: 2023-08-10 Last updated: 2023-08-30Bibliographically approved
Vallina Estrada, E. (2023). Navigating the Cellular Crowd: Physicochemical Properties of Protein Surfaces as Evolved Interaction Guides. (Doctoral dissertation). Stockholm: Department of Biochemistry and Biophysics, Stockholm University
Open this publication in new window or tab >>Navigating the Cellular Crowd: Physicochemical Properties of Protein Surfaces as Evolved Interaction Guides
2023 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The cellular interior is characterised by high concentrations of macromolecules. Compared with dilute conditions, the crowd modifies proteins' ability to fold, diffuse and, ultimately, carry out their biological functions. Cellular fitness depends on ensuring an adequate balance between interactivity and diffusivity.

In this thesis, I discuss how a colloidal description of the cell highlights the central role of electrostatics in protein surface optimisation. By recognising that the modulation of protein-protein interactions concerns the whole proteome, I map the physicochemical preferences of cellular organisms across taxonomic and ecological divisions. Moreover, I propose that all surface residues participate in tuning protein interactions to the correct affinity, within a continuum that spans several orders of magnitude. Finally, I turn to horizontally spreading inteins to gauge the strength of the selective pressures acting on protein surfaces.

Place, publisher, year, edition, pages
Stockholm: Department of Biochemistry and Biophysics, Stockholm University, 2023. p. 47
Keywords
protein interactions, inteins, physicochemical properties, protein surfaces, evolution, cellular crowding, electrostatics
National Category
Biophysics
Research subject
Biophysics
Identifiers
urn:nbn:se:su:diva-219982 (URN)978-91-8014-408-7 (ISBN)978-91-8014-409-4 (ISBN)
Public defence
2023-09-22, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16B, Stockholm, 09:00 (English)
Opponent
Supervisors
Available from: 2023-08-30 Created: 2023-08-10 Last updated: 2023-08-30Bibliographically approved
Vallina Estrada, E. & Oliveberg, M. (2022). Physicochemical classification of organisms. Proceedings of the National Academy of Sciences of the United States of America, 119(19), Article ID e2122957119.
Open this publication in new window or tab >>Physicochemical classification of organisms
2022 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 119, no 19, article id e2122957119Article in journal (Refereed) Published
Abstract [en]

The hypervariable residues that compose the major part of proteins’ surfaces are generally considered outside evolutionary control. Yet, these “nonconserved” residues determine the outcome of stochastic encounters in crowded cells. It has recently become apparent that these encounters are not as random as one might imagine, but carefully orchestrated by the intracellular electrostatics to optimize protein diffusion, interactivity, and partner search. The most influential factor here is the protein surface-charge density, which takes different optimal values across organisms with different intracellular conditions. In this study, we examine how far the net-charge density and other physicochemical properties of proteomes will take us in terms of distinguishing organisms in general. The results show that these global proteome properties not only follow the established taxonomical hierarchy, but also provide clues to functional adaptation. In many cases, the proteome–property divergence is even resolved at species level. Accordingly, the variable parts of the genes are not as free to drift as they seem in sequence alignment, but present a complementary tool for functional, taxonomic, and evolutionary assignment. 

Keywords
proteome properties, taxonomy, protein electrostatics, intracellular diffusion, functional evolution
National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-206247 (URN)10.1073/pnas.2122957119 (DOI)000854009500015 ()35500111 (PubMedID)2-s2.0-85129401503 (Scopus ID)
Available from: 2022-06-13 Created: 2022-06-13 Last updated: 2023-08-30Bibliographically approved
Wennerström, H., Estrada, E. V., Danielsson, J. & Oliveberg, M. (2020). Colloidal stability of the living cell. Proceedings of the National Academy of Sciences of the United States of America, 117(19), 10113-10121
Open this publication in new window or tab >>Colloidal stability of the living cell
2020 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 117, no 19, p. 10113-10121Article in journal (Refereed) Published
Abstract [en]

Cellular function is generally depicted at the level of functional pathways and detailed structural mechanisms, based on the identification of specific protein-protein interactions. For an individual protein searching for its partner, however, the perspective is quite different: The functional task is challenged by a dense crowd of nonpartners obstructing the way. Adding to the challenge, there is little information about how to navigate the search, since the encountered surrounding is composed of protein surfaces that are predominantly nonconserved or, at least, highly variable across organisms. In this study, we demonstrate from a colloidal standpoint that such a blindfolded intracellular search is indeed favored and has more fundamental impact on the cellular organization than previously anticipated. Basically, the unique polyion composition of cellular systems renders the electrostatic interactions different from those in physiological buffer, leading to a situation where the protein net-charge density balances the attractive dispersion force and surface heterogeneity at close range. Inspection of naturally occurring proteomes and in-cell NMR data show further that the nonconserved protein surfaces are by no means passive but chemically biased to varying degree of net-negative repulsion across organisms. Finally, this electrostatic control explains how protein crowding is spontaneously maintained at a constant level through the intracellular osmotic pressure and leads to the prediction that the extreme in halophilic adaptation is not the ionic-liquid conditions per se but the evolutionary barrier of crossing its physicochemical boundaries.

Keywords
cellular organization, protein-protein interactions, electrostatics, halophilic adaptation, ion screening
National Category
Biological Sciences Chemical Sciences
Identifiers
urn:nbn:se:su:diva-183002 (URN)10.1073/pnas.1914599117 (DOI)000532837500005 ()32284426 (PubMedID)
Available from: 2020-07-01 Created: 2020-07-01 Last updated: 2023-08-10Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0000-0002-8204-7798

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