Periodic Reporting for period 4 - NEPA (Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines)
Okres sprawozdawczy: 2023-07-01 do 2024-12-31
All living organisms are constructed of proteins that spontaneously combine into nanoscale structures called assemblies. Such assemblies enable life – they give shape and support to cells, connect cells into tissues and organs, and form nanomachines that drive cell division, cell transport, healing, and motility. To produce work, protein assemblies consume energy. How energy inputs drive protein self-organisation, and create “living-like” structures from inanimate molecules, is currently poorly understood.
Better understanding of the fundamental principles of how life emerges at molecular scales could enable us to reprogram assembly phenomena in living organisms when needed, and can guide the design of functional biomimetic assemblies and bio-inspired nano-machines.
Protein assembly includes many interconnected effects that are difficult—or even impossible—to separate from one another in experiment. Luckily, proteins and protein assemblies still must obey the laws of physics and the principles of chemistry. The goal of my grant is to develop computer models, rooted in physics and chemistry, to discover the physical principles of energy-driven protein assemblies in the cell. I focused on the representative examples of the three main ways in which energy is supplied to protein assemblies in the cell: through chemical gradients, chemical reactions of energy-rich molecules, and mechanical forces. The predictions of my models are tested in experiments and used to explain experimental observations, in a close collaboration with experimental colleagues, to deliver an in-depth understanding of the molecular mechanisms that control the emergence of function in energy-driven protein assemblies.
Better understanding of the fundamental principles of how life emerges at molecular scales could enable us to reprogram assembly phenomena in living organisms when needed, and can guide the design of functional biomimetic assemblies and bio-inspired nano-machines.
Protein assembly includes many interconnected effects that are difficult—or even impossible—to separate from one another in experiment. Luckily, proteins and protein assemblies still must obey the laws of physics and the principles of chemistry. The goal of my grant is to develop computer models, rooted in physics and chemistry, to discover the physical principles of energy-driven protein assemblies in the cell. I focused on the representative examples of the three main ways in which energy is supplied to protein assemblies in the cell: through chemical gradients, chemical reactions of energy-rich molecules, and mechanical forces. The predictions of my models are tested in experiments and used to explain experimental observations, in a close collaboration with experimental colleagues, to deliver an in-depth understanding of the molecular mechanisms that control the emergence of function in energy-driven protein assemblies.
The team consisting of postdoctoral scientists, PhD students, scientific interns, and myself, funded by this ERC project, have made substantial progress on the topic. We developed a model for how cell membranes, as well as membrane and cytoplasmic proteins self-organise under chemical gradients, and have explained how these processes help regulate cell volume, form and maintain subcellular compartments, and drive cell reshaping and cell division. We have developed a model for self-organisation of membrane proteins under mechanical forces and chemical patterns. Of particular focus has been such a self-organisation driven far-from-equilibrium via consumption of energy-rich molecules, in collaboration with experimental partners. We believe these studies will help explain how living systems came to be from non-living molecules, and will help drive the creation of synthetic cells. Our studies have also helped better understand self-assembly of extracellular matrix proteins and their reponse to mechanical forces in several different protein systems. We have invested substantial efforts into understanding how active elastic ESCRT-III filaments, driven by consumption of energy rich molecules, perform work to reshape and divide cells across evolution, from archaea, to yeast and plants, which was published in a series of papers with our experimental collaborators. On the methodological side, we have developed a new framework for studying macromolecular self-organisation by i) coupling evolutionary algorithms with molecular simulations, and ii) by coupling the assembly processes to energy consumption and chemical reactions. Finally, we have studied and identified some important general properties of protein assembly out of equilibrium.
The PI and the group have presented the above results at over 150 international meetings, schools, and institute/departmental visits across Europe, the US, and China.
The PI and the group have presented the above results at over 150 international meetings, schools, and institute/departmental visits across Europe, the US, and China.
We established a new framework that couples minimal coarse-grained models for protein assembly to i) gradients in osmolytes, ii) spatio-temporally varying chemical patterns, iii) external mechanical forces, and iv) dynamic formation and breakage of supramolecular bonds to mimic the consumption of energy-rich molecules. Furthermore, a new computational framework that couples evolutionary algorithms and molecular dynamics simulations has been established and applied to the design of chemically consuming protein assemblies. Finally, we have extended and developed new computational tools for modelling cell membrane reshaping, which are substantially more efficient than the current tools and will allow us to couple membrane models to evolutionary algorithms.
Using a combination of the above new methods, we have proposed physical mechanisms for how active elastic ESCRT-III filaments reshape cells in cell trafficking and cell division across evolution, and our predictions have been compared to and tested in experiments. We have further identified the mechanism for self-organisation of FtsZ filament assemblies in bacterial division under chemical patterns and energy consumption, and used it to explain experiments in synthetic systems and living bacteria. We have proposed the physical mechanisms for collective self-organisation of mechanosensitive channels and their implications to cell volume sensing. We have identified a mechanism for protein aggregation under chemical gradients involved in maintenance of subcellular compartments. We have identified a mechanism for passive transport of macromolecules in mechanical gradients. We have identified a new physical mechanism for the control of the size of protein assemblies, and used it to explain experimental data. We have developed a model for self-assembly in non-thermal fluctuating environments.
Using a combination of the above new methods, we have proposed physical mechanisms for how active elastic ESCRT-III filaments reshape cells in cell trafficking and cell division across evolution, and our predictions have been compared to and tested in experiments. We have further identified the mechanism for self-organisation of FtsZ filament assemblies in bacterial division under chemical patterns and energy consumption, and used it to explain experiments in synthetic systems and living bacteria. We have proposed the physical mechanisms for collective self-organisation of mechanosensitive channels and their implications to cell volume sensing. We have identified a mechanism for protein aggregation under chemical gradients involved in maintenance of subcellular compartments. We have identified a mechanism for passive transport of macromolecules in mechanical gradients. We have identified a new physical mechanism for the control of the size of protein assemblies, and used it to explain experimental data. We have developed a model for self-assembly in non-thermal fluctuating environments.