Revealed by scientists in St. Jude Children’s Research Hospital the complex structure of two proteins associated with Parkinson’s disease, both of which have been linked to late-onset cases. Leucine-rich repeat kinase 2 (LRRK2) is a protein kinase that modifies other proteins in a process called phosphorylation; Rab29, a member of the Rab GTPase family that regulates cellular trafficking, modulates LRRK2 activity. How Rab29 and LRRK2 work synergistically to cause Parkinson’s disease remains unclear. The researchers at St. Jude structures LRRK2 bound to Rab29, revealing mysteries behind LRRK2 regulation and insights with implications for drug design. The job is currently published on Science.
Parkinson’s disease is the second most common neurodegenerative disease after Alzheimer’s disease and affects 1-2% of the population older than 65 years. The genetic link of the disease is known, with approximately 15% of cases showing a family history. While there is a long list of genes associated with the disease, LRRK2 mutations are one of the most common causes. Due to its large size, structural studies of LRRK2 have been cumbersome.
“This protein is very challenging to work with,” said corresponding author Ji Sun, PhD, St. Jude Department of Structural Biology.
Despite the difficulties, Sun and his team presented the first full structure of LRRK2 in 2021 in Cell.
“In that first paper, we obtained the structure of LRRK2, but that structure showed an inactive conformation,” Sun explained. Proteins often have active and inactive forms, which are regulated by different cellular signals. Sometimes, binding to another protein is necessary to induce structural changes that move a protein from an inactive form to an active one. “So, we started to think, ‘We have a LRRK2 factor situation. Can we get active adaptation?'”
Cryo-electron microscopy captures the active state of LRRK2
The search for active adaptation is not as simple as adding Rab29 to LRRK2. LRRK2 can bind to other LRRK2 molecules in a process called oligomerization. This can make a LRRK2 monomer (one unit) into a dimer (two units) -; or larger assemblies. This means that researchers should look for the version that represents the active form. There is also the issue that Rab29 is located on cell membranes.
“In cells, about 90% or more of LRRK2 is cytosolic,” explained Sun, referring to the cytosol, the liquid enclosed in the cell membrane, which contains many of the cell’s components. “A very small amount sits on the surface of the membrane and forms large oligomers. And those are the versions that are active and functional.”
Using cryo-electron microscopy, the researchers, including first author Hanwen Zhu, PhD, St. Jude Department of Structural Biology, determined the first structures of the Rab29-LRRK2 complex. These include monomer (one pair) and dimer (two pairs) structures but also an unexpected tetramer (four pairs). “We are very excited about the structural findings, as they represent the first high-resolution structures of LRRK2 obtained in its active state,” Zhu said.
In this tetramer, we see the active conformation of LRRK2, but in the monomer and dimer complexes, LRRK2 is in the inactive conformation.
Ji Sun, PhD, St. Jude Department of Structural Biology
Understanding the Rab29-LRRK2 complex
These findings show that LRRK2 is activated not only by which proteins it interacts with but also by their spatial arrangement within cells.
“We propose a transition from monomer to tetramer after membrane recruitment,” Sun explained. “Inside the cell, normally inactive monomers or dimers of LRRK2. But when Rab29 recruits LRRK2 to the membrane, the local concentration of LRRK2 increases. This then facilitates the transfer to the tetramer, where LRRK2 becomes active. “
What are the implications of Parkinson’s disease? These structures provide researchers with an atomic-scale map to trace how the various mutations that cause Parkinson’s disease affect movement within this complex.
“All mutations actually favor the active adaptation, meaning they provide new interactions in the active adaptation or disrupt interactions within the inactive adaptation,” Sun said. “The effects of mutations can be seen beautifully in our structures; they are very well explained.”
The importance of such structural studies lies not only in the insight gained but also in their potential application for drug design. For example, the researchers also obtained the structure of LRRK2 in the presence of the drug DNL201. This drug, which underwent a phase 1 clinical trial, locks the protein in an active state, so it was used to confirm their findings that the tetramer is indeed the active one. complex form.
“We have an inactive conformation and an active conformation, so we can monitor the transition from the inactive to active state,” explained Sun. “These structures provide much-needed insights for medicinal chemists to design novel inhibitors against LRRK2 for the treatment of Parkinson’s.”
Authors and funding
The other first author of the study is Francesca Tonelli, University of Dundee. Other authors include Martin Turk, St. Jude, and Dario Alessi, University of Dundee.
The study was supported by grants from the National Institutes of Health (R00HL143037 and R01NS129795), the UK Medical Research Council (MC_UU_00018/1), Aligning Science Across Parkinson’s (ASAP) (ASAP-000463) through the Michael J. Fox Foundation for Parkinson’s Research (MJFF) and ALSAC, the fundraising and awareness organization of St. Jude.
St. Jude Children’s Research Hospital
Zhu, H., and so on. (2023) Rab29-dependent asymmetrical activation of leucine-rich repeat kinase 2. Science. doi.org/10.1126/science.adi9926.
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