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Publications (10 of 59) 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
Nordström, U., Lang, L., Ekhtiari Bidhendi, E., Zetterström, P., Oliveberg, M., Danielsson, J., . . . Marklund, S. L. (2023). Mutant SOD1 aggregates formed in vitro and in cultured cells are polymorphic and differ from those arising in the CNS. Journal of Neurochemistry, 164(1), 77-93
Open this publication in new window or tab >>Mutant SOD1 aggregates formed in vitro and in cultured cells are polymorphic and differ from those arising in the CNS
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2023 (English)In: Journal of Neurochemistry, ISSN 0022-3042, E-ISSN 1471-4159, Vol. 164, no 1, p. 77-93Article in journal (Refereed) Published
Abstract [en]

Mutations in the human Superoxide dismutase 1 (hSOD1) gene are well-established cause of the motor neuron disease ALS. Patients and transgenic (Tg) ALS model mice carrying mutant variants develop hSOD1 aggregates in the CNS. We have identified two hSOD1 aggregate strains, which both transmit spreading template-directed aggregation and premature fatal paralysis when inoculated into adult transgenic mice. This prion-like spread of aggregation could be a primary disease mechanism in SOD1-induced ALS. Human SOD1 aggregation has been studied extensively both in cultured cells and under various conditions in vitro. To determine how the structure of aggregates formed in these model systems related to disease-associated aggregates in the CNS, we used a binary epitope-mapping assay to examine aggregates of hSOD1 variants G93A, G85R, A4V, D90A, and G127X formed in vitro, in four different cell lines and in the CNS of Tg mice. We found considerable variability between replicate sets of in vitro-generated aggregates. In contrast, there was a high similarity between replicates of a given hSOD1 mutant in a given cell line, but pronounced variations between different hSOD1 mutants and different cell lines in both structures and amounts of aggregates formed. The aggregates formed in vitro or in cultured cells did not replicate the aggregate strains that arise in the CNS. Our findings suggest that the distinct aggregate morphologies in the CNS could result from a micro-environment with stringent quality control combined with second-order selection by spreading ability. Explorations of pathogenesis and development of therapeutics should be conducted in models that replicate aggregate structures forming in the CNS.

Keywords
aggregate structure, ALS, amyotrophic lateral sclerosis, neurodegenerative disease, superoxide dismutase 1, protein misfolding, protein aggregation, aggregate strains, aggregate conformation
National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-213524 (URN)10.1111/jnc.15718 (DOI)000890056900001 ()36326589 (PubMedID)2-s2.0-85142644226 (Scopus ID)
Available from: 2023-01-10 Created: 2023-01-10 Last updated: 2023-02-27Bibliographically approved
Wennerström, H. & Oliveberg, M. (2022). On the osmotic pressure of cells. QRB Discovery, 3, Article ID e12.
Open this publication in new window or tab >>On the osmotic pressure of cells
2022 (English)In: QRB Discovery, ISSN 2633-2892, Vol. 3, article id e12Article in journal (Refereed) Published
Abstract [en]

The chemical potential of water provides an essential thermodynamic characterization of the environment of living organisms, and it is of equal significance as the temperature. For cells, is conventionally expressed in terms of the osmotic pressure (πosm). We have previously suggested that the main contribution to the intracellular πosm of the bacterium E. coli is from soluble negatively-charged proteins and their counter-ions. Here, we expand on this analysis by examining how evolutionary divergent cell types cope with the challenge of maintaining πosm within viable values. Complex organisms, like mammals, maintain constant internal πosm ≈ 0.285 osmol, matching that of 0.154 M NaCl. For bacteria it appears that optimal growth conditions are found for similar or slightly higher πosm (0.25-0.4 osmol), despite that they represent a much earlier stage in evolution. We argue that this value reflects a general adaptation for optimising metabolic function under crowded intracellular conditions. Environmental πosm that differ from this optimum require therefore special measures, as exemplified with gram-positive and gram-negative bacteria. To handle such situations, their membrane encapsulations allow for a compensating turgor pressure that can take both positive and negative values, where positive pressures allow increased frequency of metabolic events through increased intracellular protein concentrations. A remarkable exception to the rule of 0.25-0.4 osmol, is found for halophilic archaea with internal πosm ≈ 15 osmol. The internal organization of these archaea differs in that they utilize a repulsive electrostatic mechanism operating only in the ionic-liquid regime to avoid aggregation, and that they stand out from other organisms by having no turgor pressure.

Keywords
cellular crowding, cellular electrostatic interactions, cellular osmoticpressure, chemical potential of water, functionaladaptation, halophiles
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:su:diva-212108 (URN)10.1017/qrd.2022.3 (DOI)2-s2.0-85135179570 (Scopus ID)
Available from: 2022-12-01 Created: 2022-12-01 Last updated: 2022-12-01Bibliographically 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
Abramsson, M. L., Sahin, C., Hopper, J. T. S., Branca, R. M. M., Danielsson, J., Xu, M., . . . Landreh, M. (2021). Charge Engineering Reveals the Roles of Ionizable Side Chains in Electrospray Ionization Mass Spectrometry. JACS Au, 1(12), 2385-2393
Open this publication in new window or tab >>Charge Engineering Reveals the Roles of Ionizable Side Chains in Electrospray Ionization Mass Spectrometry
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2021 (English)In: JACS Au, E-ISSN 2691-3704, Vol. 1, no 12, p. 2385-2393Article in journal (Refereed) Published
Abstract [en]

In solution, the charge of a protein is intricately linked to its stability, but electrospray ionization distorts this connection, potentially limiting the ability of native mass spectrometry to inform about protein structure and dynamics. How the behavior of intact proteins in the gas phase depends on the presence and distribution of ionizable surface residues has been difficult to answer because multiple chargeable sites are present in virtually all proteins. Turning to protein engineering, we show that ionizable side chains are completely dispensable for charging under native conditions, but if present, they are preferential protonation sites. The absence of ionizable side chains results in identical charge state distributions under native-like and denaturing conditions, while coexisting conformers can be distinguished using ion mobility separation. An excess of ionizable side chains, on the other hand, effectively modulates protein ion stability. In fact, moving a single ionizable group can dramatically alter the gas-phase conformation of a protein ion. We conclude that although the sum of the charges is governed solely by Coulombic terms, their locations affect the stability of the protein in the gas phase.

Keywords
protein folding, gas-phase conformations, ion mobility mass spectrometry
National Category
Chemical Sciences Biological Sciences
Identifiers
urn:nbn:se:su:diva-202027 (URN)10.1021/jacsau.1c00458 (DOI)000746335000003 ()34977906 (PubMedID)
Available from: 2022-02-11 Created: 2022-02-11 Last updated: 2022-07-27Bibliographically approved
Sörensen, T., Leeb, S., Danielsson, J. & Oliveberg, M. (2021). Polyanions Cause Protein Destabilization Similar to That in Live Cells. Biochemistry, 60(10), 735-746
Open this publication in new window or tab >>Polyanions Cause Protein Destabilization Similar to That in Live Cells
2021 (English)In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 60, no 10, p. 735-746Article in journal (Refereed) Published
Abstract [en]

The structural stability of proteins is found to markedly change upon their transfer to the crowded interior of live cells. For some proteins, the stability increases, while for others, it decreases, depending on both the sequence composition and the type of host cell. The mechanism seems to be linked to the strength and conformational bias of the diffusive in-cell interactions, where protein charge is found to play a decisive role. Because most proteins, nucleotides, and membranes carry a net-negative charge, the intracellular environment behaves like a polyanionic (Z:1) system with electrostatic interactions different from those of standard 1:1 ion solutes. To determine how such polyanion conditions influence protein stability, we use negatively charged polyacetate ions to mimic the net-negatively charged cellular environment. The results show that, per Na+ equivalent, polyacetate destabilizes the model protein SOD1barrel significantly more than monoacetate or NaCl. At an equivalent of 100 mM Na+, the polyacetate destabilization of SOD1barrel is similar to that observed in live cells. By the combined use of equilibrium thermal denaturation, folding kinetics, and high-resolution nuclear magnetic resonance, this destabilization is primarily assigned to preferential interaction between polyacetate and the globally unfolded protein. This interaction is relatively weak and involves mainly the outermost N-terminal region of unfolded SOD1barrel. Our findings point thus to a generic influence of polyanions on protein stability, which adds to the sequence-specific contributions and needs to be considered in the evaluation of in vivo data.

National Category
Biochemistry and Molecular Biology
Research subject
Biochemistry
Identifiers
urn:nbn:se:su:diva-185862 (URN)10.1021/acs.biochem.0c00889 (DOI)000636721400001 ()33635054 (PubMedID)2-s2.0-85102963930 (Scopus ID)
Available from: 2020-10-14 Created: 2020-10-14 Last updated: 2022-04-20Bibliographically 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
Leeb, S., Yang, F., Oliveberg, M. & Danielsson, J. (2020). Connecting Longitudinal and Transverse Relaxation Rates in Live-Cell NMR. Journal of Physical Chemistry B, 124(47), 10698-10707
Open this publication in new window or tab >>Connecting Longitudinal and Transverse Relaxation Rates in Live-Cell NMR
2020 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 124, no 47, p. 10698-10707Article in journal (Refereed) Published
Abstract [en]

In the cytosolic environment, protein crowding and Brownian motions result in numerous transient encounters. Each such encounter event increases the apparent size of the interacting molecules, leading to slower rotational tumbling. The extent of transient protein complexes formed in live cells can conveniently be quantified by an apparent viscosity, based on NMR-detected spin-relaxation measurements, that is, the longitudinal (T-1) and transverse (T-2) relaxation. From combined analysis of three different proteins and surface mutations thereof, we find that T-2 implies significantly higher apparent viscosity than T-1. At first sight, the effect on T-1 and T-2 seems thus nonunifiable, consistent with previous reports on other proteins. We show here that the T-1 and T-2 deviation is actually not a inconsistency but an expected feature of a system with fast exchange between free monomers and transient complexes. In this case, the deviation is basically reconciled by a model with fast exchange between the free-tumbling reporter protein and a transient complex with a uniform 143 kDa partner. The analysis is then taken one step further by accounting for the fact that the cytosolic content is by no means uniform but comprises a wide range of molecular sizes. Integrating over the complete size distribution of the cytosolic interaction ensemble enables us to predict both T-1 and T-2 from a single binding model. The result yields a bound population for each protein variant and provides a quantification of the transient interactions. We finally extend the approach to obtain a correction term for the shape of a database-derived mass distribution of the interactome in the mammalian cytosol, in good accord with the existing data of the cellular composition.

National Category
Chemical Sciences
Identifiers
urn:nbn:se:su:diva-189344 (URN)10.1021/acs.jpcb.0c08274 (DOI)000595542900012 ()33179918 (PubMedID)
Available from: 2021-01-21 Created: 2021-01-21 Last updated: 2022-02-25Bibliographically approved
Leeb, S., Sörensen, T., Yang, F., Xin, M., Oliveberg, M. & Danielsson, J. (2020). Diffusive protein interactions in human versus bacterial cells. Current Research in Structural Biology, 2, 68-78
Open this publication in new window or tab >>Diffusive protein interactions in human versus bacterial cells
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2020 (English)In: Current Research in Structural Biology, E-ISSN 2665-928X, Vol. 2, p. 68-78Article in journal (Refereed) Published
Abstract [en]

Random encounters between proteins in crowded cells are by no means passive, but found to be under selective control. This control enables proteome solubility, helps to optimise the diffusive search for interaction partners, and allows for adaptation to environmental extremes. Interestingly, the residues that modulate the encounters act mesoscopically through protein surface hydrophobicity and net charge, meaning that their detailed signatures vary across organisms with different intracellular constraints. To examine such variations, we use in-cell NMR relaxation to compare the diffusive behaviour of bacterial and human proteins in both human and Escherichia coli cytosols. We find that proteins that ‘stick’ in E. coli are generally less restricted in mammalian cells. Furthermore, the rotational diffusion in the mammalian cytosol is less sensitive to surface-charge mutations. This implies that, in terms of protein motions, the mammalian cytosol is more forgiving to surface alterations than E. coli cells. The cellular differences seem not linked to the proteome properties per se, but rather to a 6-fold difference in protein concentrations. Our results outline a scenario in which the tolerant cytosol of mammalian cells, found in long-lived multicellular organisms, provides an enlarged evolutionary playground, where random protein-surface mutations are less deleterious than in short-generational bacteria.

National Category
Biological Sciences
Research subject
Biochemistry
Identifiers
urn:nbn:se:su:diva-175631 (URN)10.1016/j.crstbi.2020.04.002 (DOI)000658373100007 ()2-s2.0-85096580569 (Scopus ID)
Available from: 2019-11-07 Created: 2019-11-07 Last updated: 2022-12-09Bibliographically approved
Wang, H., Logan, D. T., Danielsson, J. & Oliveberg, M. (2020). Exposing the distinctive modular behavior of β-strands and α-helices in folded proteins. Proceedings of the National Academy of Sciences of the United States of America, 117(46), 28775-28783
Open this publication in new window or tab >>Exposing the distinctive modular behavior of β-strands and α-helices in folded proteins
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 46, p. 28775-28783Article in journal (Refereed) Published
Abstract [en]

Although folded proteins are commonly depicted as simplistic combinations of β-strands and α-helices, the actual properties and functions of these secondary-structure elements in their native contexts are just partly understood. The principal reason is that the behavior of individual β- and α-elements is obscured by the global folding cooperativity. In this study, we have circumvented this problem by designing frustrated variants of the mixed α/β-protein S6, which allow the structural behavior of individual β-strands and α-helices to be targeted selectively by stopped-flow kinetics, X-ray crystallography, and solution-state NMR. Essentially, our approach is based on provoking intramolecular "domain swap." The results show that the α- and β-elements have quite different characteristics: The swaps of β-strands proceed via global unfolding, whereas the α-helices are free to swap locally in the native basin. Moreover, the α-helices tend to hybridize and to promote protein association by gliding over to neighboring molecules. This difference in structural behavior follows directly from hydrogen-bonding restrictions and suggests that the protein secondary structure defines not only tertiary geometry, but also maintains control in function and structural evolution. Finally, our alternative approach to protein folding and native-state dynamics presents a generally applicable strategy for in silico design of protein models that are computationally testable in the microsecond–millisecond regime.

Keywords
structural cooperativity, secondary structure, protein dynamics, protein design
National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-188725 (URN)10.1073/pnas.1920455117 (DOI)000591360600005 ()33148805 (PubMedID)
Available from: 2021-01-19 Created: 2021-01-19 Last updated: 2022-02-25Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0000-0003-1919-7520

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