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 β-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°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.thermodynamics | protein stability | crowding | in vivo | NMR U nlike their static impression in X-ray structures and textbook illustrations, some proteins are tuned to work at marginal structural stability. The advantage of such tuning is that it enables the protein to easily switch from one conformation to another, providing sensitive functional control. A well-known example is the tumor suppressor P53 whose function in gene regulation relies on a complex interplay of local folding-unfolding transitions (1). Likewise, the maturation pathway of the radical scavenger Cu/Zn superoxide dismutase (SOD1) involves a marginally stable apo species that seems required for interorganelle trafficking (2) and effective chaperone-assisted metal loading (3). As an inevitable consequence of such near-equilibrium action, however, the proteins become critically sensitive to perturbations (1): Mutation of SOD1 triggers with full penetrance late-onset neurodegenerative disease even though the causative mutations shift the structural equilibrium only by less than a factor of 3 (4). In the latter case, it is not the loss of native function that poses the acute problem, but rather the promotion of competing disordered SOD1 conformations that eventually exhaust the cellular proteostasis system and end up in pathologic deposits (5-8). Uncovering the rules, capacity and limitations of this delicate interplay between individual proteins and the cellular components (9, 10) requires not only information about the in vivo response to molecular perturbations, but also precise quantification of the structural equilibria at play. The question is then, to what extent are existing data obtained under simplified conditions in vitro transferable to the complex environment in live cells (11)? The answer is not clear cut. Defying predictions from steric crowding effects (11-13), experimental data have shown that cells in some cases stabilize (14-19) and in other cases destabilize (20-25) the native protein structures. In this study, we shed light on these s...

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.in-cell NMR | protein surface properties | intracellular diffusion D espite considerable progress in mapping out how proteins interact functionally through structure and evolved interfaces (1-3), there is yet little known about how proteins interact nonspecifically upon random diffusive encounters (4-10). Although these nonspecific "quinary" (11) interactions are typically weak and short-lived, they are still expected to affect function because of their sheer numbers: Under crowded cellular conditions, they compete with specific binding (6-8), control diffusion (12), and skew structural stability (5,(13)(14)(15)(16)(17)(18)(19). The question is then to what extent this dynamic background of nonspecific interactions is biologically controlled and optimized. Part of the answer is hinted by the tendency of soluble proteins, nucleic acids, and membranes to carry a repulsive net-negative charge (20,21 , and PO 4 2− (22). However, proteins expose also positive, polar, and hydrophobic moieties that operate against the net-negative charge repulsion by engaging in attractive interactions upon diffusive encounters. The strength and duration of these attractive interactions depend on the proteins' detailed surface composition, relative orientations, and ability to adapt complementary shapes. Following Elcock's estimate for the Escherichia coli cytoplasm, each protein experiences at all times approximately five putative interaction partners in its immediate cellular environment (8). Sometimes, mutual fits enable strong functional binding (1, 2), but, most often, the proteins just separate after a brief tête-à-tête (3), in search of higher-affinity partners. A key detail is that the eff...

Intrinsically disordered proteins are abundant in the eukaryotic proteome, and they are implicated in a range of different diseases. However, there is a paucity of experimental data on molecular details of the coupled binding and folding of such proteins. Two interacting and relatively well studied disordered protein domains are the activation domain from the p160 transcriptional co-activator ACTR and the nuclear co-activator binding domain (NCBD) of CREB binding protein. We have analyzed the transition state for their coupled binding and folding by protein engineering and kinetic experiments (Φ-value analysis) and found that it involves weak native interactions between the N-terminal helices of ACTR and NCBD, but is otherwise "disordered-like". Most native hydrophobic interactions in the interface between the two domains form later, after the rate-limiting barrier for association. Linear free energy relationships suggest a cooperative formation of native interactions, reminiscent of the nucleation-condensation mechanism in protein folding.

Background: Intrinsically disordered proteins are common regulators of protein-protein interactions, but little is known about their mechanisms of interaction. Results: Two intrinsically disordered protein domains, from ACTR and CREB-binding protein, interact through rapid association and slow conformational changes. Conclusion: Electrostatics governs the fast association, but the overall reaction is multistep. Significance: The slow conformational search may be common among intrinsically disordered proteins with many binding partners.

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.

All known triterpenes are generated by triterpene synthases (TrTSs) from squalene or oxidosqualene1. This approach is fundamentally different from the biosynthesis of short-chain (C10–C25) terpenes that are formed from polyisoprenyl diphosphates2–4. In this study, two fungal chimeric class I TrTSs, Talaromyces verruculosus talaropentaene synthase (TvTS) and Macrophomina phaseolina macrophomene synthase (MpMS), were characterized. Both enzymes use dimethylallyl diphosphate and isopentenyl diphosphate or hexaprenyl diphosphate as substrates, representing the first examples, to our knowledge, of non-squalene-dependent triterpene biosynthesis. The cyclization mechanisms of TvTS and MpMS and the absolute configurations of their products were investigated in isotopic labelling experiments. Structural analyses of the terpene cyclase domain of TvTS and full-length MpMS provide detailed insights into their catalytic mechanisms. An AlphaFold2-based screening platform was developed to mine a third TrTS, Colletotrichum gloeosporioides colleterpenol synthase (CgCS). Our findings identify a new enzymatic mechanism for the biosynthesis of triterpenes and enhance understanding of terpene biosynthesis in nature.

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Background: Protein-protein interactions often involve intrinsically disordered protein domains. Results: The binding interface between two disordered protein domains is suboptimal, or frustrated, with regard to the energetics. Conclusion:The frustration likely results from the promiscuous binding behavior of these disordered domains. Significance: Suboptimal binding interfaces may be common among intrinsically disordered proteins with multiple binding partners.