Physical principles of functional and pathological protein assembly
Lead Research Organisation:
University College London
Department Name: Physics and Astronomy
Abstract
The overarching goal of our group is to gain an in-depth quantitative understanding of how functional and pathological protein assemblies are formed and regulated in nature. In this particular project, we will explore the physical principles of gating of mechanosensitive channels, and the role of biological membranes in catalysing pathological protein aggregation. This will be achieved using coarse-grained computer simulations and the tools of statistical mechanics, in close collaboration with experimentalists.
A fascinating example of functional and dynamic protein reorganisation are mechanosensitive channels (MSCs), which control the flux of solutes in response to mechanical stimuli. One of the outstanding questions concerning the behaviour of MSCs is the mechanistic basis of their gating. Coarse-grained simulations are a unique tool that makes it possible to tackle this problem and test the physics of possible scenarios on experimentally relevant but inaccessible scales. Using computer simulations we will investigate the basic properties of transmembrane channel design needed for efficient gating, and the relationship between the gating activity and system design.
In addition to being important regulators of functional protein assembly, biological membranes can also trigger harmful protein aggregation. For instance, biological membranes are able to catalyse nucleation of pathological amyloid fibrils, abut the mechanism of membrane-mediated protein nucleation is unclear. We will combine our previously developed model for amyloid fibril aggregation, with our coarse-grained membrane model, to investigate how the amyloid fibril nucleation times scale with the fluidity and rigidity of the membrane The same kinetic quantities will be measured by our experimental collaborators using fluorescence kinetic assays and membrane vesicles with different cholesterol content. This combination of simulations and experiments will enable us to reach quantitative mechanistic understanding of the membrane-mediated protein aggregation, and could inform us on how to influence and prevent the related disease-associated processes in a rational manner.
A fascinating example of functional and dynamic protein reorganisation are mechanosensitive channels (MSCs), which control the flux of solutes in response to mechanical stimuli. One of the outstanding questions concerning the behaviour of MSCs is the mechanistic basis of their gating. Coarse-grained simulations are a unique tool that makes it possible to tackle this problem and test the physics of possible scenarios on experimentally relevant but inaccessible scales. Using computer simulations we will investigate the basic properties of transmembrane channel design needed for efficient gating, and the relationship between the gating activity and system design.
In addition to being important regulators of functional protein assembly, biological membranes can also trigger harmful protein aggregation. For instance, biological membranes are able to catalyse nucleation of pathological amyloid fibrils, abut the mechanism of membrane-mediated protein nucleation is unclear. We will combine our previously developed model for amyloid fibril aggregation, with our coarse-grained membrane model, to investigate how the amyloid fibril nucleation times scale with the fluidity and rigidity of the membrane The same kinetic quantities will be measured by our experimental collaborators using fluorescence kinetic assays and membrane vesicles with different cholesterol content. This combination of simulations and experiments will enable us to reach quantitative mechanistic understanding of the membrane-mediated protein aggregation, and could inform us on how to influence and prevent the related disease-associated processes in a rational manner.
Organisations
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| EP/N509577/1 | 01/10/2016 | 24/03/2022 | |||
| 1814851 | Studentship | EP/N509577/1 | 01/10/2016 | 31/12/2020 | Alexandru Paraschiv |
| Description | Throughout my PhD programme, I have developed computational models that allowed the investigation of the biological phenomena associated with membrane proteins. My work focused on developing minimalistic coarse-grained models for mechanosensitive channels, a special class of proteins, responsible for maintaining cell's composition in the optimal parameters, offering it protection in harsh environments. The simulations allowed us to investigate the response of single channels on a cellular membrane as well as the response of multiple interacting channels. We observed that, if there are enough channels to interact, they will show a cooperative closing effect, meaning that their total activity will decrease. This observation is consistent with recent experiments and sheds light on the mechanism behind the regulation of the channel's gating activity. The phenomenon could explain how the cell is protected, and the cell's homeostatis is preserved, even if the concentration of membrane proteins is high and potentially harmful. Additionally, we have also investigated how membrane tension is affected by the presence of membrane linking proteins. Membrane mechanical properties can be measured by locally deforming the membrane and measuring membrane local deformation, for example while deforming the membrane into tubular structures by applying a point force to it. Biological membranes are attached to the underlying cytoskeleton, but so far, the influence of this cytoskeleton on the membrane properties has been widely debated. In this research, we examined how the local organisation of membrane proteins affects the deformation of the membrane as well as the force required to extrude the tubular structures. |
| Exploitation Route | Other researchers could directly use the programs I have developed to simulate a general membrane protein (subject to making the changes required to parametrise for the specific system being investigated). Some of the results can be experimentally tested with single cell microscopy experiments in which the volume of a cell is measured in response to the application of various pressure shocks. Our research could provide insight on how to rationally design synthetic artificial nanosensors and drug-delivery systems. Moreover, the results in the paper related to the extrusion of membrane tethers could be used to better interpret measurements of membrane tension. |
| Sectors | Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
| URL | https://link.aps.org/doi/10.1103/PhysRevLett.124.048102;https://pubmed.ncbi.nlm.nih.gov/33460596/ |
| Description | The work can be used in the private sector to help rationally design artificial nanomechanosensors as well as specific drug-delivery systems. The work I carried out throughout the duration of the PhD programme aims at understanding what governs the activity of mechanosensitive channels, a class of proteins the is responsible for maintaining the cell's composition constant by opening under pressure and allowing the transport of materials across the cellular membrane. It is possible to use the results so design a synthetic version of a nanomechanosensor, finely tuning its activity depending on results obtained in our research. Another possible use is for the design of a targeted drug delivery mechanism, with embedded proteins inside a vesicle that open up when the vesicle encounters the targeted environment. Moreover, the paper on extrusion of membrane tubes in the presence of cytoskeletal linkers sheds light on how the local organisation of proteins affects measurements of membrane tension. This has profound experimental implications, enabling experimentalists from both academic and industrial environments to measure biological membrane properties more accurately. |