The newly formed Data Reduction and Analysis group at Synchrotron SOLEIL is responsible for the development and implementation of data analysis software and methods for users of the facility. Rapid and efficient data analysis adds value to the users’ experience and efforts will be made by the group to provide simple and rapid tools for this purpose.
We aim to develop cloud-based...
Given a molecular structure, it can be represented as a set of atomic balls, each ball having a van der Waals radius corresponding to the atom type. A ball can be assigned a region of space that contains all the points that are closer (or equally close) to that ball than to any other. Such a region is called a Voronoi cell and the partitioning of space into Voronoi cells is called Voronoi...
Recent breakthroughs in X-ray crystallography, Cryo-EM and complementary approaches resulted in elucidation of many new structures of membrane proteins (MPs) and their complexes. Several classes of MPs, such as microbial rhodopsins, rotary ATPase subunits c, or light harvesting complexes 2, form ring-like assemblies with several lipid molecules trapped inside. Whereas the proteins are usually...
Intrinsically disordered proteins (IDPs) lack well-defined three-dimensional structure in solution under physiological conditions. Despite this they are functional and participate in the regulation of many biological processes, in which disorder can enable interactions of high specificity coupled with low affinity. Phosphorylation is one of the most abundant types of post-translational...
By providing a precise snapshot of the structure of the interface between two protein partners, X-ray crystallography helps identifying point mutations that are likely to strengthen the interaction. However, this technique provides very little information about conformational flexibility, in particular in protein loop fragments. In cases where plasticity may be critical for protein function,...
Short Abstract
Cryo-electron tomography (cryo-ET) is a technique which allows direct visualisation of vitrified biological samples in 3D. In a framework conceptually similar to single particle analysis in cryo-EM, it is possible to achieve high-resolution (subnanometer and beyond!) insights into macromolecules directly within their cellular context by alignment and averaging of multiple...
Many biologically important systems are inherently polydisperse e.g. transient protein-protein complexes, oligomerizing proteins or proteins with different co-existing conformations. Such systems are always in an equilibrium of different species and are therefore heterogenous. Importantly, such systems can’t be meaningfully studied in a holistic sense by physically separating the components of...
Multiple protein sequence alignments are used daily in bioinformatics to annotate and predict the characteristics of currently mass produced sequences. The quality of their results have been assessed many times and have recahed a plateau. Proteins fold into stable three-dimensional structures with a topology much more conserved than sequence. Consequently, it should be advantageous to use this...
The mitochondrial oxidative phosphorylation system (OXPHOS), which includes five protein complexes (CI-V), is the main source of energy in the cell. CI, the largest and first complex, is composed of several protein subunits that are assembled by different assembly factors, such as Acyl-CoA Dehydrogenase Family Member 9 (ACAD9) and Evolutionarily Conserved Signaling Intermediate In Toll Pathway...
Since the conformation of RiboNucleic Acids (RNA) is a key for its function, experimental techniques at different levels of resolution are implemented to determine its structure. Because of the flexibility and the large size of certain RNAs, their structure cannot be determined through high resolution experiments, such as nuclear magnetic resonance (NMR) and X-Ray crystallography. It is...
Cryo-electron microscopy is rapidly emerging as a powerful technique to determine the structures of complex macromolecular systems elusive to other techniques. Since many of these systems are highly dynamical, characterising also their movements is a crucial step to unravel their biological functions. In this talk, I will present an integrative modelling approach to simultaneously determine...
In the recent years a massive amount of raw viral genomic data has been produced and released in sequenced databases, leading to the paradoxical situation of generating the Domain of Unknown Function (DUF), the number one domain in knowledge databases. Together with bio-informatics prediction, the knowledge of the three-dimensional structures of DUF proteins is the key to unveil the full...
The mitochondrial respiratory complex I is the largest of the large mitochondrial respiratory complexes, being roughly 1 MDa in size. Consequently, its assembly process is extremely complicated, requiring multiple assembly factors. Two such factors, acyl-CoA dehydrogenase 9 (ACAD9) and the evolutionarily conserved signalling intermediate in the Toll pathway (ECSIT) appear to act in a complex...
Prediction of protein structures is one of the most important problems of current structural bioinformatics. Many proteins in living organisms form multimeric structures or are involved in the complexes with other biomacromolecules, such as other proteins or small ligands. Prediction of protein structure in the monomeric state is already very challenging and therefore the structures of their...
