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Structure of a large non-crystalline multiprotein assembly by solid-state nuclear magnetic resonance with ultra-fast magic-angle spinning

Periodic Reporting for period 1 - COMPLEX-fastMAS-NMR (Structure of a large non-crystalline multiprotein assembly by solid-state nuclear magnetic resonance with ultra-fast magic-angle spinning)

Reporting period: 2016-01-01 to 2017-12-31

The increasing resistance of pathogens to antibiotic treatment poses a potentially catastrophic threat to public health. There is an emerging need for new drug targets that will be unlikely to bypass by single mutations in bacteria. DNA replication machinery represents a potential candidate: while individual proteins are not conserved among bacteria, replication mechanisms and cascades of interactions are. However, to develop effective drugs, it is crucial to understand not only the atomic structure of these proteins but their weak and transient interactions. In this project, we aimed at the characterisation of large proteins from E. coli replisome using solid-state Nuclear Magnetic Resonance (ssNMR). This rapidly developing method allows to investigate dynamic non-crystalline protein or RNA/DNA samples thus complementing the static information available from the X-ray crystallography or cryo-electron microscopy. The objective of the project was to push the limits of the technique to large biomolecules that can only be obtained in submilligram quantities and/or only with a simple isotope labelling (i.e. without deuteration). To achieve this goal we employed the combination of two unique tools available in the host laboratory: ultra-high magnetic fields and a new generation of probes capable of sample rotation at the so-called magic-angle (MAS) up to 111,111 times per second.
We evaluated the strenghts of the method (in terms of resolution and sensitivity) on a number of proteins, ranging from small model ones (GB1, MNEI) to complex and dynamic protein assemblies: fibrils (HET-s), viral capsids (AP205, HIV-1) or oligomers from E. coli replisome (DnaB), under >100 kHz magic-angle spinning and at the highest magnetic field commercially available. Despite a certain loss in resolution of 1H resonances, we lean towards the full protonation of proteins as a simpler and more general method of sample preparation for solid-state NMR compared to approaches based on extensive deuteration. We demonstrated that large protonated proteins such as those from E. coli replisome can be immobilised by sedimentation, and studied with ssNMR without a significant penalty in resolution. We developed new sensitive methods for the efficient resonance assignment in proteins and ribonucleic acids, which are applicable thanks to improved spectral properties at ultrafast MAS conditions. We also proposed methods to report on proton-proton proximities that allow a determination of three-dimensional structures of fully protonated proteins. New labelling schemes were devised to assist structure modelling of assemblies. These methodological advances were communicated to broad audience of general chemistry and biology journals, and are already exploited in NMR groups world-wide.
We demonstrated the feasibility of structural and interaction studies with ssNMR with > 100 kHz MAS and ultrahigh magnetic fields on fully protonated (13C,15N-labelled) proteins and RNA, with sample amount requirements decreased to less than 0.5 mg. The high sensitivity of the novel 1H-detected techniques allowed site-specific NMR resonance assignment not only in the protein backbone but also in the side-chains, and within only a few weeks of experimental time. The information available from side-chains, previously inaccessible, enables one to determine structural models of proteins with an extensive aid of automated tools. This progress in the ssNMR opens new avenues for atomic-level investigations of proteins and nucleic acids which are critical to cellular processes. Overall, it may contribute to efforts to tackle the drug-resistant pathogens that globally affect public health.
Pushing limits of Solid-state NMR for a deeper insight into large biomolecules