Mackereth Lab IECB | Bordeaux | France

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WELCOME to the Mackereth
NMR group

Cameron Mackereth
The lab is focussed on the structural details of how proteins and nucleic acids come together to form complexes. We use a combination of biochemical methods to probe the way in which the pieces of these biomolecules are assembled, but our main technique is nuclear magnetic resonance (NMR) spectroscopy. 

NOESY Structure-4 Structure-3 Structure-2 Structure-1 Structure

Research Overview

There is increasing evidence in support of a model of cellular biochemistry in which most proteins exert their biological role through either transient or relatively stable multi-component macromolecular complexes. The key to understanding the function of these complexes lies in their structural investigation by a variety of biophysical methods. The lab studies molecular details of large protein-nucleic acid macromolecules using a variety of new NMR techniques as well as established biophysical approaches. For large complexes, we utilize a rigid body assembly of individually characterized structures using a combination of methods: domain orientation through the measurement of residual dipolar coupling (RDC) by NMR spectroscopy, overall shape determination by small angle neutron or X-ray scattering (SANS/SAXS), and incorporating molecular contact details from such techniques as NMR paramagnetic spin labelling to acquire information on long-range contacts, as well as in vitro mutational analysis and other binding assays. For smaller proteins and domains, standard NMR-based approaches are used, but with additional insight gained from RDC and spin label information. Equally important to the lab is the traditional strength of NMR as a tool to probe the dynamics of biological samples, the characterization of transient interactions, and the possibility to look at structures that exhibit a significant amount of unstructured elements.

Current projects include:

Proteins involved in RNA processing, especially alternative splicing.
Synthetic foldamer recognition of biomolecules.
Modification of histones. 

*************************************************  NEWS  ***********************************************

We welcome Esther Myriam Nze Mba Ebene to our group as a second-year Masters student (M2) from the Univ. Bordeaux. She will work on connecting RNA-binding domains with artificial linkers.

We also welcome visiting postdoc Sabina Koj from the Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences (Wroclaw, Poland). She will be learning practical aspects of biomolecular NMR.

Previous News Highlights

Current and past lab members

****************************************  RECENT PUBLICATIONS  **************************************

We are excited to present some of our recent work:

A new domain for binding double-stranded RNA. Recent work from a long-standing collaboration with the group of Chris Nelson (Univ. Victoria, Canada) has revealed an RNA-binding behaviour for a nuclear proline isomerase. Using a combination of proteomics, microscopy, molecular biology and NMR spectroscopy we have determined that the N-terminal Basic Tilted Helix Bundle (BTHB) domain of FKBP25 interacts specifically with dsRNA. This association with RNA is required to mediate interactions with several proteins involved in ribosome biogenesis. In addition, RNA-binding is essential for the nucleolar localization of FKBP25.
Dilworth, D., Upadhyay, S.K., Bonnafous, P., Edoo, A.B., Bourbigot, S., Pesek-Jardim, F., Gudavicius, G., Serpa, J., Petrotchenko, E., Borchers, C., Nelson, C.J., Mackereth, C.D. 2017. The basic tilted helix bundle domain of the prolyl isomerase FKBP25 is a novel double-stranded RNA binding module. Nucleic Acids. Res. 45:11989-12004

The difference that a 'G' makes. The family of RBPMS proteins (RNA-binding protein with multiple splicing) all share an RNA-binding Motif (RRM) domain that is required for their cellular function. Using X-ray crystallography, PhD student Heddy Soufari has determined the atomic details of the nucleic acid binding properties of this domain from nematode MEC-8. Using an extensive set of RNA binding studies with C. elegans MEC-8, human RBPMS and Drosophila couch potato, we find that this domain binds tightest to GCAC sequences in target RNA. The initial 'G' is specifically recognized via several key hydrogen bonds between the RNA base and the protein. Due to dimerization, the optimal target is actually two copies of GCAC separated by at least 6 nucleotides. We are continuing to look at the in vitro and in vivo properties of the full-length MEC-8 splicing factor. More details soon!
Soufari, H., Mackereth, C.D. 2017. Conserved binding of GCAC motifs by MEC-8, couch potato and the RBPMS protein family. RNA 23:308-316.

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