Diffusive Dynamics of Bacterial Proteome as a Proxy of Cell Death

Daniele Di Baria,b,c, Stepan Timrd,e,f, Marianne Guiralg, Marie-Thérèse Giudici-Orticonig, Tilo Seydelc, Christian Beckc, Caterina Petrilloa, Philippe Derreumauxd,e,j , Simone Melchionnah,i, Fabio Sterponed,e,∗, Judith Petersb,c,j,∗, Alessandro Paciaronia,∗

a Dipartimento di Fisica e Geologia, Università degli Studi di Perugia,
b Université Grenoble Alpes, CNRS, Laboratoire Interdisciplinaire de Physique,
c Institut Laue-Langevin, Grenoble, France
d Laboratoire de Biochimie Théorique (UPR 9080), CNRS, Université de Paris Cité,
e Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild,
f J. Heyrovsky Institute of Physical Chemistry, Czech Academy of Sciences,
g Laboratoire de Bioénergétique et Ingénierie des Protéines, BIP, CNRS, Aix-Marseille Université,
h ISC-CNR, Dipartimento di Fisica, Università Sapienza,
i Lexma Technology 1337 Massachusetts Avenue, Arlington, MA, 02476, USA
j Institut Universitaire de France

See the full published paper : Di Bari et al., ACS Central Science. 2023, 9, 1, 93–102 

What is happening to the proteome of a bacterium like Escherichia coli when it is heated above the temperature of cell death? For a long time, it was hypothesized that a so-called proteome catastrophe happens when going beyond denaturation, where most of the proteins unfold in a narrow range of temperatures [1, 2].
With the help of incoherent neutron scattering, we were able to find out that on the contrary, only a very small fraction (less than 10 %) of proteins unfold around this temperature, in accordance with first findings by Leuenberger et al. [3] and Mateus et al. [4]. It appears in addition that the dynamical state of the proteome of E. coli, which could be determined from our neutron scattering data taken on the high resolution spectrometer IN16B of the Institut Laue Langevin (ILL), is an excellent proxy for temperature-dependent bacterial metabolism and death. Indeed, the global diffusive dynamics within the proteome is first increasing when coming close to the optimal growth temperature of the cells and just above, when crossing the cell death temperature, it drops significantly (see Figure 1).

Figure 1. Apparent self-diffusion coefficient, DG, of an average protein in the E. coli cytoplasm as a function of temperature.

To better understand in detail what is driving the cell death, we have undertaken in parallel multiscale (coarse-grained and all-atom) MD simulations of whole cells. The coarse-grained simulations contained 197 proteins of 35 different species, mimicking the protein composition of the E. coli cytoplasm [5]. Figure 2 shows a pictorial representation of the coarse-grained cytoplasm system, the schematic strategy of the back-map, and the temperature scans for the folded and unfolded versions of the atomistic systems. The combination of the two techniques permitted to formulate a new hypothesis to explain the observations: the studies show that when these few proteins unfold, they alter the dynamic properties of the cell medium, increasing the local viscosity considerably. The molecular reason for this effect is simple: when a protein unfolds, it becomes a long, flexible spaghetti that interacts with neighbouring macromolecules to form a kind of gel. Could this increase in viscosity be enough to block certain vital metabolic reactions controlled by local diffusivity and hasten cell death?
The international group of researchers is pursuing the investigation of such questions by studying now cells which live in very different environments.

Figure 2. Coarse-grained and all-atom simulations of E. coli cytoplasm

[1] K.A. Dill, K. Ghosh, J.D. Schmit, Physical limits of cells and proteomes, PNAS, 108 (2011) 17876-17882.
[2] K. Ghosh, K. Dill, Cellular proteomes have broad distributions of protein stability, Biophys J, 99 (2010) 3996-4002.
[3] P. Leuenberger, S. Ganscha, A. Kahraman, V. Cappelletti, P.J. Boersema, C. von Mering, M. Claassen, P. Picotti, Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability, Science, 355 (2017).
[4] A. Mateus, J. Bobonis, N. Kurzawa, F. Stein, D. Helm, J. Hevler, A. Typas, M.M. Savitski, Thermal proteome profiling in bacteria: probing protein state in vivo, Mol Syst Biol, 14 (2018) e8242.
[5] S.R. McGuffee, A.H. Elcock, Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm, PLoS Comput Biol, 6 (2010) e1000694.

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