Periodic Reporting for period 3 - BioDisOrder (Order and Disorder at the Surface of Biological Membranes.)
Période du rapport: 2021-05-01 au 2022-10-31
Biomolecular surfaces generate functionality in living systems as the cellular membranes that host fundamental heterogeneous processes, including biological signalling, the assembly of biomolecular machinery, the regulation of vesicular exocytosis, the action of drugs. Conventional biophysical and structural methods have obtained extraordinary results in the characterisation of homogeneous systems of pure isolated components, such as conformationally defined biomolecules, but it remains a challenge to understand the properties of highly dynamical systems, particularly those carrying out function through the fine tune between structural order and disorder at the surface of biomembranes.
The vision of BioDisOrder is to innovate structural biology to enable an unprecedented characterisation of biomolecular mechanisms occurring at the surface of biological membranes. These processes are crucial both to function and malfunction in the cell, and cannot be studied using conventional analytical techniques. BioDisOrder is based on multiscale methods intertwining experiments and theory, which provide the key to answer some of the greatest challenges in the study of these processes with particular focus on those associated with neuronal function and pathology. To achieve this ambitious goal, my research team is developing tools based on the combination of nuclear magnetic resonance (NMR) spectroscopy and multiscale molecular simulations, which enable probing the structure, dynamics, thermodynamics and kinetics of complex protein-protein and protein-membrane interactions occurring at the surface of cellular membranes.
The ability to advance both the experimental and theoretical sides, and their combination, is fundamental to define the next generation of methods to achieve our transformative aims. We are exploiting the innovative nature of this multiscale approach by addressing some of the great questions in neuroscience and elucidate the details of how functional and aberrant biological complexity is achieved via the fine tuning between structural order and disorder at the neuronal synapses.
The vision of BioDisOrder is to innovate structural biology to enable an unprecedented characterisation of biomolecular mechanisms occurring at the surface of biological membranes. These processes are crucial both to function and malfunction in the cell, and cannot be studied using conventional analytical techniques. BioDisOrder is based on multiscale methods intertwining experiments and theory, which provide the key to answer some of the greatest challenges in the study of these processes with particular focus on those associated with neuronal function and pathology. To achieve this ambitious goal, my research team is developing tools based on the combination of nuclear magnetic resonance (NMR) spectroscopy and multiscale molecular simulations, which enable probing the structure, dynamics, thermodynamics and kinetics of complex protein-protein and protein-membrane interactions occurring at the surface of cellular membranes.
The ability to advance both the experimental and theoretical sides, and their combination, is fundamental to define the next generation of methods to achieve our transformative aims. We are exploiting the innovative nature of this multiscale approach by addressing some of the great questions in neuroscience and elucidate the details of how functional and aberrant biological complexity is achieved via the fine tuning between structural order and disorder at the neuronal synapses.
Methodological development in BioDisOrder has been focused so far on the employment of artificial intelligence (AI) to analyse nuclear magnetic resonance (NMR) data for characterising the disordered regions of membrane proteins. This has enabled the definition of new approaches to refine the structural ensembles of protein molecules and membranes with significant accuracy, including structure and dynamics of disordered protein regions that are impossible to characterise with current methods. The method included the development of coarse grained MD potentials to enhance the conformational search of disordered regions under the guidance of NMR data (Navarro Paya et al, Life 2020).
We have applied these methodological innovations to different topics in the context of disordered regions of membrane-associated proteins. In particular, we have showed that the disordered binding of alpha-synuclein to the internal plasma membrane enables to stabilise the docking of synaptic vesicles in such a way to contribute to their exocytosis process (Man et al, Nature Communications 2021, 12:927). The interdisciplinary combination of enhanced metadynamics simulations and NMR also enabled to study the conformational transitions leading to the aggregation of the Prion Protein and its pathological mutant T183A (Sanz-Hernandez et al, PNAS 2021, 118: e2019631118). Another successful application of BioDisOrder has enabled a unique structural refinement of the membrane-protein complex between SERCA and PLN (Weber et al eLife 2021, 10:e66226), a key complex for the regulation of the heart cycles. This work was carried out in collaboration with the Veglia lab at the University of Minnesota. The structure of this fundamental complex for the heart function and pathology has represented a top challenge for decades. Previous advancements in this research area enabled to crystallise the SERCA-PLN complex, however, the resulting structure didn't reveal the key N-terminal regulatory domain PLN, which is disordered in the complex. Using the methods developed in BioDisOrder, we obtained the first atomic-resolution ensemble of the complex, including the disordered N-terminal region of PLN that regulate SERCA. The work also clarified how the phosphorylation of Ser 16 of PLN enhances the activity of the SERCA calcium pump in the complex.
We have applied these methodological innovations to different topics in the context of disordered regions of membrane-associated proteins. In particular, we have showed that the disordered binding of alpha-synuclein to the internal plasma membrane enables to stabilise the docking of synaptic vesicles in such a way to contribute to their exocytosis process (Man et al, Nature Communications 2021, 12:927). The interdisciplinary combination of enhanced metadynamics simulations and NMR also enabled to study the conformational transitions leading to the aggregation of the Prion Protein and its pathological mutant T183A (Sanz-Hernandez et al, PNAS 2021, 118: e2019631118). Another successful application of BioDisOrder has enabled a unique structural refinement of the membrane-protein complex between SERCA and PLN (Weber et al eLife 2021, 10:e66226), a key complex for the regulation of the heart cycles. This work was carried out in collaboration with the Veglia lab at the University of Minnesota. The structure of this fundamental complex for the heart function and pathology has represented a top challenge for decades. Previous advancements in this research area enabled to crystallise the SERCA-PLN complex, however, the resulting structure didn't reveal the key N-terminal regulatory domain PLN, which is disordered in the complex. Using the methods developed in BioDisOrder, we obtained the first atomic-resolution ensemble of the complex, including the disordered N-terminal region of PLN that regulate SERCA. The work also clarified how the phosphorylation of Ser 16 of PLN enhances the activity of the SERCA calcium pump in the complex.
Taken together, the research milestones of BioDisOrder aim at a transformative approach in the characterisation of disordered regions of proteins associated with biological membrane. Currently there is a limited ability to study the properties of these regions as their inherent heterogeneity prevents successful methods of structural biology such as X-ray crystallography and cryo-EM. By innovating methods tailored to study structure, dynamics, thermodynamics and kinetics of protein regions that do not possess a defined three-dimensional structure, BioDisOrder will generate a new and unprecedented tool to clarify key biomolecular processes for the function and pathology of the cell.