Project acronym BayCellS
Project A Bayesian Framework for Cellular Structural Biology
Researcher (PI) Michael Nilges
Host Institution (HI) INSTITUT PASTEUR
Country France
Call Details Advanced Grant (AdG), LS1, ERC-2011-ADG_20110310
Summary The functioning of a single cell or organism is governed by the laws of chemistry and physics. The bridge from biology to chemistry and physics is provided by structural biology: to understand the functioning of a cell, it is necessary to know the atomic structure of macromolecular assemblies, which may contain hundreds of components. To characterise the structures of the increasingly large and often flexible complexes, high resolution structure determination (as was possible for example for the ribosome) will likely stay the exception, and multiple sources of structural data at multiple resolutions are employed. Integrating these data into one consistent picture poses particular difficulties, since data are much more sparse than in high resolution methods, and the data sets from heterogeneous sources are of highly different and unknown quality and may be mutually inconsistent, and that data are in general averaged over large ensembles and long times. Molecular modelling, a crucial element of any structure determination, plays an even more important role in these multi-scale and multi-technique approaches, not only to obtain structures from the data, but also to evaluate their reliability. This proposal is to develop a consistent framework for this highly complex data integration problem, principally based on Bayesian probability theory. Appropriate models for the major types data types used in hybrid approaches will be developed, as well as representations to include structural knowledge for the components of the complexes, at multiple scales. The new methods will be applied to a series of problems with increasing complexity, going from the determination of protein complexes with high resolution information, over low resolution structures based on protein-protein interaction data such as the nuclear pore, to the genome organisation in the nucleus.
Summary
The functioning of a single cell or organism is governed by the laws of chemistry and physics. The bridge from biology to chemistry and physics is provided by structural biology: to understand the functioning of a cell, it is necessary to know the atomic structure of macromolecular assemblies, which may contain hundreds of components. To characterise the structures of the increasingly large and often flexible complexes, high resolution structure determination (as was possible for example for the ribosome) will likely stay the exception, and multiple sources of structural data at multiple resolutions are employed. Integrating these data into one consistent picture poses particular difficulties, since data are much more sparse than in high resolution methods, and the data sets from heterogeneous sources are of highly different and unknown quality and may be mutually inconsistent, and that data are in general averaged over large ensembles and long times. Molecular modelling, a crucial element of any structure determination, plays an even more important role in these multi-scale and multi-technique approaches, not only to obtain structures from the data, but also to evaluate their reliability. This proposal is to develop a consistent framework for this highly complex data integration problem, principally based on Bayesian probability theory. Appropriate models for the major types data types used in hybrid approaches will be developed, as well as representations to include structural knowledge for the components of the complexes, at multiple scales. The new methods will be applied to a series of problems with increasing complexity, going from the determination of protein complexes with high resolution information, over low resolution structures based on protein-protein interaction data such as the nuclear pore, to the genome organisation in the nucleus.
Max ERC Funding
2 130 212 €
Duration
Start date: 2012-05-01, End date: 2017-04-30
Project acronym SBPSSHS
Project Structural Basis of Protein Synthesis System of Human Cell
Researcher (PI) Marat Yusupov
Host Institution (HI) CENTRE EUROPEEN DE RECHERCHE EN BIOLOGIE ET MEDECINE
Country France
Call Details Advanced Grant (AdG), LS1, ERC-2011-ADG_20110310
Summary This project will elucidate the structure and mechanism of ribosome function through the determination of high resolution crystal structures of human ribosome functional complexes. Currently, the only high resolution crystal structures available for the ribosome functional complexes are bacterial ribosomes containing mRNA, tRNAs in E, P and A sites and several translation factors. Recently, we have determined at medium resolution the first eukaryotic ribosome structure. Saccharomyces cerevisaiae ribosomes have been chosen for the first step of the study because they have been extensively investigated in our laboratory by biochemical methods and by x-ray analysis.
Step One: We will improve the quality of the crystals and determine the ribosome structure of yeast at atomic resolution (about 3Å resolution). These conditions will be used for an investigation of the ribosome functional complexes in order to better understand the detailed mechanism of the translocation of large molecules (tRNA and mRNA) on the ribosome.
Step Two: Ribosomes from human HeLa cells will be investigated via crystallization and x-ray structure determination. Ribosome functional complexes developed on yeast systems will be used as models for the creation and structural investigation of human ribosome complexes. Available biochemical data will provide a framework for the interpretation of structural information which will be obtained.
The aims:
To determine the atomic resolution crystal structure of the yeast ribosome as a model for all eukaryotic ribosome x-ray studies.
To obtain crystals and determine the structure of 80S ribosome from HeLa cells.
To determine the structure of the ribosome complexes with mRNA and tRNA in ratcheted and non-ratcheted states in order to describe the mechanism of translocation.
To determine structure of the ribosome initiation complex with an internal ribosomal entry site mRNA.
To obtain crystals and to determine the structures of 40S initiation complexes.
Summary
This project will elucidate the structure and mechanism of ribosome function through the determination of high resolution crystal structures of human ribosome functional complexes. Currently, the only high resolution crystal structures available for the ribosome functional complexes are bacterial ribosomes containing mRNA, tRNAs in E, P and A sites and several translation factors. Recently, we have determined at medium resolution the first eukaryotic ribosome structure. Saccharomyces cerevisaiae ribosomes have been chosen for the first step of the study because they have been extensively investigated in our laboratory by biochemical methods and by x-ray analysis.
Step One: We will improve the quality of the crystals and determine the ribosome structure of yeast at atomic resolution (about 3Å resolution). These conditions will be used for an investigation of the ribosome functional complexes in order to better understand the detailed mechanism of the translocation of large molecules (tRNA and mRNA) on the ribosome.
Step Two: Ribosomes from human HeLa cells will be investigated via crystallization and x-ray structure determination. Ribosome functional complexes developed on yeast systems will be used as models for the creation and structural investigation of human ribosome complexes. Available biochemical data will provide a framework for the interpretation of structural information which will be obtained.
The aims:
To determine the atomic resolution crystal structure of the yeast ribosome as a model for all eukaryotic ribosome x-ray studies.
To obtain crystals and determine the structure of 80S ribosome from HeLa cells.
To determine the structure of the ribosome complexes with mRNA and tRNA in ratcheted and non-ratcheted states in order to describe the mechanism of translocation.
To determine structure of the ribosome initiation complex with an internal ribosomal entry site mRNA.
To obtain crystals and to determine the structures of 40S initiation complexes.
Max ERC Funding
2 466 000 €
Duration
Start date: 2012-04-01, End date: 2017-03-31
