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A topic that has attracted considerable interest in recent years is the possibility to perform thermodynamic studies of proteins directly in-cell or in complex environments which mimic the cellular interior. Nuclear magnetic resonance (NMR) could be an attractive technique for these studies but its applicability has so far been limited by technical issues. Here, we demonstrate that 2D NMR methods can be successfully applied to measure thermodynamic parameters provided that a suitable choice of the residues used for the calculation is made. We propose a new parameter, named RAD, which reflects the level of protection of a specific amide proton in the protein core and can guide through the selection of the resonances. We also suggest a way to calibrate the volumes to become independent of technical limitations. The methodology we propose leads to stability curves comparable to that calculated from CD data and provides a new tool for thermodynamic measurements in complex environments. Multidimensional NMR spectroscopy can provide insight into the unfolding of proteins in cells, but may be sensitive to the choice of residue used as a reference. Here 2D 1H-15N NMR is used to obtain thermodynamic parameters of unfolding of Yfh1, relying on an internal standard to normalise peak volumes.

To improve our mechanistic understanding of zinc metalloenzymes, we report a joint computational and experimental study of a minimal carbonic anhydrase (CA) mimic, a 22-residue Zn-finger hydrolase. We combine classical molecular dynamics (MD) simulations, quantum mechanics/molecular mechanics (QM/MM) geometry optimizations, and QM/MM free energy simulations with ambient and high-pressure kinetic measurements to investigate the mechanism of the hydrolysis of the substrate p-nitrophenylacetate (pNPA). The zinc center of the hydrolase prefers a pentacoordinated geometry, as found in most naturally occurring CAs and CA-like enzymes. Two possible mechanisms for the catalytic reaction are investigated. The first one is analogous to the commonly accepted mechanism for CA-like enzymes: a sequential pathway, in which a Zn2+-bound hydroxide acts as a nucleophile and the hydrolysis proceeds through a tetrahedral intermediate. The initial rate-limiting step of this reaction is the nucleophilic attack of the hydroxide...

Changes of the extracellular milieu could affect cellular crowding. To prevent detrimental effects, cells use adaptation mechanisms to react to such conditions. Using fluorescent crowding sensors, we show that the initial response to osmotic stress is fast but imperfect, while the slow response renders cells more tolerant to stress, particularly in the presence of osmolytes.

Biomolekule entstehen und funktionieren in einer dicht gepackten und heterogenen zellularen Umgebung. Diese Bedingungen werden im Reagenzglas oft durch Zugabe kunstlicher makromolekularer “Crowding”-Reagentien imitiert. Dennoch ist es unklar, ob solche Kosolventien tatsachlich die physikalischen und chemischen Eigenschaften der zellularen Umgebung widerspiegeln, da der zellulare “Crowding”-Effekt bisher nicht quantifiziert wurde. Wir haben einen makromolekularen “Crowding”-Sensor, der auf einem FRET-markiertem Polymer basiert, entwickelt, um diese Effekte zu untersuchen. Die Ergebnisse zeigen, dass die Volumenausschlusseffekte zu keiner Kompression des Sensors in der Zelle fuhren. Die durchschnittliche Konformation des Sensors ist dabei ahnlich zu der im verdunnten Puffer sowie im Zell-Lysat. Ferner ist der zellulare “Crowding”-Effekt heterogen verteilt und verandert sich signifikant wahrend eines osmotischen Schocks. Mithilfe dieser Methode lasst sich der zellulare “Crowding”-Effekt als Regulator von biomolekularen Reaktionen systematisch untersuchen.

Here, we study the stabilities of different naturally fragile mutants of 3' phosphoadenosine 5' phosphosulfate (PAPS) synthases. The goal is to establish a relationship between the stability of the mutants in the cellular environment and their enzymatic activity. In vitro stability measurements have suggested that protein stability is a major factor for cellular PAPS availability [1]. We aim to specifically analyze different cellular factors for in-cell PAPSS stability. One crucial factor is the macromolecular crowding effect. The cell is filled up to a volume of 40 % with macromolecules. Often, artificial macromolecular crowding agents are used to mimic these conditions. We previously studied macromolecular crowding effects via a thermodynamic analysis of the thermal unfolding of ubiquitin [2]. We observed enthalpic stabilization and entropic destabilization forces for all tested crowders. Further, we tested how such artificial cosolutes reflect the physicochemical properties of the complex cellular environment. Therefore, we developed a FRET-based macromolecular crowding sensor to study the crowding effect in living cells [3]. We found that the in-cell crowding effect is distributed heterogeneously and can change significantly upon osmotic stress. In comparison, we now used Fast Relaxation Imaging [4] to study the stability of PAPSS within the cellular environment and compare the results to in vitro crowding studies.References:1. J. Boom, D. Heider, S.R. Martin, A. Pastore, and J.W. Mueller. PAPS synthases - naturally fragile enzymes specifically stabilized by nucleotide binding., J. Biol. Chem. 2012, 287(21):17645-55.2. M. Senske, L. Tork, B. Born, M. Havenith, C. Herrmann, S. Ebbinghaus, J. Am. Chem. Soc. 2014, 136, 9036-9041.3. D. Gnutt, M. Gao, O. Brylski, M. Heyden, S. Ebbinghaus, Angew. Chem Int. Ed. 2015, 54(8):2548-2551.4. S. Ebbinghaus, A. Dhar, J.D. McDonald and M. Gruebele. “Protein folding stability and dynamics imaged in a living cell.” Nature Methods 2010, 7:319-323.

Biomolecules evolve and function in densely crowded and highly heterogeneous cellular environments. Such conditions are often mimicked in the test tube by the addition of artificial macromolecular crowding agents. Still, it is unclear if such cosolutes indeed reflect the physicochemical properties of the cellular environment as the in-cell crowding effect has not yet been quantified. We have developed a macromolecular crowding sensor based on a FRET-labeled polymer to probe the macromolecular crowding effect inside single living cells. Surprisingly, we find that excluded-volume effects, although observed in the presence of artificial crowding agents, do not lead to a compression of the sensor in the cell. The average conformation of the sensor is similar to that in aqueous buffer solution and cell lysate. However, the in-cell crowding effect is distributed heterogeneously and changes significantly upon cell stress. We present a tool to systematically study the in-cell crowding effect as a modulator of biomolecular reactions.

PAPS synthases are bifunctional enzymes providing the cell with the sulfate donor PAPS (3'-phosphoadenosine-5′-phosphosulfate), which is further used by sulfotransferases for modification of several biomolecules (e.g. steroids). Isoform PAPS synthase 2 (PAPSS2) has been shown to be fragile within in vitro experiments, but is stabilized by binding of its endogenous ligands. Mutations affecting its activity lead to disease states like bone and cartilage malformation as well as metabolic diseases. Compared to in vitro conditions, the cellular milieu is crowded by large biopolymers resulting in intermolecular interactions and excluded-volume effects affecting each biopolymer inside the cell.To understand the stability of this large enzyme (70 kDa), we conducted biophysical studies on the individual domains, APS kinase and ATP sulfurylase, as well as the full length protein. Using Fast Relaxation Imaging we studied disease-relevant mutants of PAPSS2 directly within the cell. The data provide novel thermodynamic insights into PAPSS2 stability inside the cellular milieu and its influence on the naturally destabilized protein. These results also unravel new insights into disease mechanisms of PAPSS2 mutations.

Proteins and nucleic acids fold and behave in a highly occupied matrix of macromolecules, the cellular environment. Although this environment is filled up to a volume of 40% with macromolecules, the effect of crowding on biochemical reactions as well as biophysical properties of proteins has been rarely considered. Therefore, studies on macromolecular crowding are mainly conducted using artificially created polymer based substances as mimics of the in cell environment. Still, a common concept how the excluded volume effect in the cell affects protein folding, function and structure is lacking. Understanding these properties will be important to unravel the underlying mechanism of protein misfolding and aggregation as well as the behavior of intrinsically disordered proteins in a living cell.We introduce a FRET based random coil polymer to characterize crowding both in vitro and inside a living cell. We find different compression of the polymer in artificial crowding substances compared to protein crowders such as BSA or oocyte lysate. Injection of the probe inside cells confirms this result and reveals a heterogeneous environment which, on average, shows comparable polymer conformations as in diluted buffer. The polymer conformation is used to quantify crowding differences in the cytosol and the nucleus as well as to identify crowding in cells influenced by different extrinsic conditions. Severe osmotic stress is used to probe compression of the polymer in the highly concentrated cytosolic environment.We conclude that the FRET labelled polymer provides a new approach to investigate and characterize the cellular solvation properties with high spatio-temporal resolution in a variety of systems and identify crowding differences due to the architecture of the cellular matrix. Therefore, it will help to understand how the cell, as the native environment in which proteins evolved, might modulate and tune biomolecule properties and functions.