Molecular Motor: Researchers show how cells disentangle clumped proteins

How do cells disentangle clumped, and hence non-functional, proteins? A Dutch-German team including researchers from Heidelberg University explored this question. The researchers describe a molecular machine which pulls on exposed loops of the protein chains and extracts them from the protein aggregate. The research results were published in “Nature”.

The ClpB chaperone pulls an exposed protein chain through its central pore. | Figure: Avellaneda & Tans, AMOLF Amsterdam

Proteins are long, folded chains of amino acids that perform many critical functions in the cell – but only if they are properly folded. In contrast, clumped protein aggregates are not functional and linked to cellular ageing and numerous diseases, including neurodegenerative conditions such as Alzheimer's disease. All organisms have therefore developed molecules capable of disentangling such damaging aggregates. The question is how do these so-called chaperones make these repairs. With the help of the bacterial ClpB chaperone, Dr Mario Avellaneda and Prof. Dr Sander Tams from Amsterdam along with Heidelberg researchers Prof. Dr Bernd Bukau and Associate Professor Dr Axel Mogk found fundamental answers.

The chaperone has a ring-shaped structure and a central, continuous channel. The ClpB grabs an exposed loop of a clumped protein chain protruding from the aggregate and forcibly pulls it through the chaperone's central pore. Although the entire protein clump is too large to pass through the pore, through its pulling action, ClpB can extract individual protein chains from the larger aggregate. “The chaperone works like a motor by moving the chains,” explains Prof. Bukau, whose work group conducts research at the Center for Molecular Biology of Heidelberg University (ZMBH) and the German Cancer Research Center.

After the protein chain is free of the aggregate, it can refold and function normally. By extracting all the chains one by one, the chaperone can fully untangle the entire aggregate. The proteins are extracted in tiny movements that the researchers measured with an "optical tweezers". Their function is based on the fact that light – in the form of focussed laser beams – exerts a force on microscopic objects such as balls of plastic or glass; these objects can thus be moved. Although these beads are significantly larger than proteins, protein chains can be anchored between them and manipulated to measure structural changes. “This way we can determine exactly how the ClpB motor moves the chains,” explains Dr Mogk, a member of Prof. Bukau's team.

Dr Avellaneda and Prof. Tams work at the AMOLF Institute, which pursues fundamental research on physical relationships in complex systems. The work of the German-Dutch cooperation was funded by the German Research Foundation and the Helmholtz Association.

Resaerch Paper: M. J. Avellaneda, K. B. Franke, V. Sunderlikova, B. Bukau, A. Mogk, S. J. Tans: Processive extrusion of polypeptide loops by a Hsp100 disaggregase, Nature 2020

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