Periodic Reporting for period 1 - COMP-O-CELL (Computational Microscopy of Cells)
Berichtszeitraum: 2022-09-01 bis 2025-02-28
Biological cells are the basis of life. As an integral part of cell architecture, cell membranes are central to cell functioning. Comprising a heterogeneous mixture of proteins and lipids, cell membranes constantly adapt their structural organization to regulate cellular processes. Malfunction at the level of lipid-protein interaction is implicated in numerous diseases, so understanding cell membrane organization at the molecular level is of critical importance. Unfortunately, our current understanding is limited, because we lack the methods to study these fluctuating nanoscale assemblies in vivo at the required spatiotemporal resolution.
An important tool for the study of cellular processes is molecular simulation, known as computational microscopy. Computational microscopy has been used to study small membrane patches in isolation, but until now, cell membranes have not been simulated in their ‘natural’ context. I intend to apply computational microscopy at the whole-cell level, to study complex membrane structures and their function within the cellular environment. This requires challenging methodological innovations at the crossroads of biology, physics, and chemistry. In COMP-O-CELL, I will use advanced computational microscopy to study the interplay between membranes and their surroundings in a realistic cellular environment. The main goal is to establish a framework for the simulation, at molecular resolution, of entire cells and cell organelles.
This goal will be realized through three major objectives: (i) to advance the computational microscope by creating a bridge from the molecular to the mesoscale, (ii) to use this improved computational microscope to investigate the driving forces of membrane curvature generation and membrane-cytosol interplay of an entire cell organelle, the mitochondrion, and (iii) to synthesize the advances achieved to simulate − for the first time − a complete cell at molecular resolution.
Why modelling entire cells is important ? First, structural data is a cornerstone of molecular life sciences. We will provide such data for entire cells at unprecedented spatio-temporal resolution. A complete cell model will be key to interpreting experimental measurements performed on real cells. Exciting developments in experimental techniques, such as cryo-ET and mass spectrometry, currently offer unprecedented high-resolution data of molecular compositions and distributions inside the cell, which, together with computational models as proposed in COMP-O-CELL will enhance our understanding of the building blocks of life. Second, complexity is essential. Cellular processes cover a hierarchy of time and length scales, involving millions of interacting molecules. If we can capture the complexity of an entire cell, we can understand its emergent behaviour, and identify lacunae in our knowledge. Fundamental research questions that we will address in this proposal are: To what extent do all constituents interact with each other in the complex cellular environment? Do molecular highways exist across the cell, i.e. pathways with increased mobility, providing fast connections between distant regions? Which type of molecules accumulate or are depleted in proximity to the cellular membranes, to what extent does the cell membrane affect the cytosolic organization, and vice versa? Third, knowledge of cell behaviour can drive biomedical and biotechnological advances. Understanding and combatting disease and engineering artificial cells demand detailed knowledge of processes at the molecular scale. Our computational framework will provide an in-silico test system with a level of realism beyond current model systems. Where do drugs bind, how do dietary restrictions affect cell behaviour, and what is the implication of a protein mutation or modification in a realistic cellular environment? Finally, our ambition to model entire cells will drive the development of advanced modelling tools that will be of use to a broad community of computational scientists interested in cellular processes. The multiscale framework established in COMP-O-CELL can be used, for instance, in creating realistic models for other important organelles such as the thylakoid stacks found in chloroplasts and the internal organelles of eukaryotic cells, as well as in the expanding field of synthetic cells.
An important tool for the study of cellular processes is molecular simulation, known as computational microscopy. Computational microscopy has been used to study small membrane patches in isolation, but until now, cell membranes have not been simulated in their ‘natural’ context. I intend to apply computational microscopy at the whole-cell level, to study complex membrane structures and their function within the cellular environment. This requires challenging methodological innovations at the crossroads of biology, physics, and chemistry. In COMP-O-CELL, I will use advanced computational microscopy to study the interplay between membranes and their surroundings in a realistic cellular environment. The main goal is to establish a framework for the simulation, at molecular resolution, of entire cells and cell organelles.
This goal will be realized through three major objectives: (i) to advance the computational microscope by creating a bridge from the molecular to the mesoscale, (ii) to use this improved computational microscope to investigate the driving forces of membrane curvature generation and membrane-cytosol interplay of an entire cell organelle, the mitochondrion, and (iii) to synthesize the advances achieved to simulate − for the first time − a complete cell at molecular resolution.
Why modelling entire cells is important ? First, structural data is a cornerstone of molecular life sciences. We will provide such data for entire cells at unprecedented spatio-temporal resolution. A complete cell model will be key to interpreting experimental measurements performed on real cells. Exciting developments in experimental techniques, such as cryo-ET and mass spectrometry, currently offer unprecedented high-resolution data of molecular compositions and distributions inside the cell, which, together with computational models as proposed in COMP-O-CELL will enhance our understanding of the building blocks of life. Second, complexity is essential. Cellular processes cover a hierarchy of time and length scales, involving millions of interacting molecules. If we can capture the complexity of an entire cell, we can understand its emergent behaviour, and identify lacunae in our knowledge. Fundamental research questions that we will address in this proposal are: To what extent do all constituents interact with each other in the complex cellular environment? Do molecular highways exist across the cell, i.e. pathways with increased mobility, providing fast connections between distant regions? Which type of molecules accumulate or are depleted in proximity to the cellular membranes, to what extent does the cell membrane affect the cytosolic organization, and vice versa? Third, knowledge of cell behaviour can drive biomedical and biotechnological advances. Understanding and combatting disease and engineering artificial cells demand detailed knowledge of processes at the molecular scale. Our computational framework will provide an in-silico test system with a level of realism beyond current model systems. Where do drugs bind, how do dietary restrictions affect cell behaviour, and what is the implication of a protein mutation or modification in a realistic cellular environment? Finally, our ambition to model entire cells will drive the development of advanced modelling tools that will be of use to a broad community of computational scientists interested in cellular processes. The multiscale framework established in COMP-O-CELL can be used, for instance, in creating realistic models for other important organelles such as the thylakoid stacks found in chloroplasts and the internal organelles of eukaryotic cells, as well as in the expanding field of synthetic cells.
The ultimate microscope, directed at a cell, would reveal the dynamics of all the cell’s components with atomic resolution. In contrast to their real-world counterparts, computational microscopes are currently on the brink of meeting this challenge. In a breakthrough perspective paper, we show how an integrative approach can be employed to model an entire cell, the minimal cell JCVI-syn3A, at full complexity. This step opens the way to interrogate the cell’s spatio-temporal evolution with molecular dynamics simulations, an approach that can be extended to other cell types in the near future.
The tools we develop to enable simulations at the full cell scale, with near-atomic precision, will have an immediate impact on the molecular modeling field, as it will allow for performing so-called in-situ simulations in which a process is studied in its realistic environment. On the longer term, our whole-cell modeling pipeline can be used by, e.g. pharmaceutical companies to explore the action of drugs in the complex setting of a real cell using an in silico platform, potentially saving on downstream testing phases.