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Biology subjects

van Oijen, A.

Publications and source records attributed to van Oijen, A..

4 recordsLinked to original sources

Direct single-molecule visualization of Hsp90-mediated relief of a Hsp70-folding block

Hsp70 and Hsp90 are ubiquitous molecular chaperones that cooperate to promote the correct folding and maturation of client proteins. Despite their central role in proteostasis, the molecular mechanisms by which Hsp90 coordinates with Hsp70 to remodel clients remain poorly understood. In particular, how ATP hydrolysis by Hsp90 is coupled to client engagement and conformational change has been a long-standing question. This gap in understanding is largely due to the challenge of visualizing client conformations during the highly dynamic and heterogeneous interactions with the Hsp70/Hsp90 chaperone machinery. To address this, we used a combination of single-molecule fluorescence resonance energy transfer (smFRET) and total internal reflection fluorescence microscopy to observe individual firefly luciferase client proteins as they are sequentially engaged by Hsp70 and Hsp90. Here, we show that Hsp90 reduces rebinding of Hsp70 to folding intermediates while still allowing engagement to misfolded clients, thereby enabling productive refolding in the presence of typically inhibitory concentrations of Hsp70. Furthermore, Hsp90 uses ATP binding and hydrolysis to actively remodel the conformational landscape of the client, promoting controlled folding through localized compaction across multiple regions. These controlled folding events reduce misfolding and are essential for establishing native interdomain contacts. Using smFRET and kinetic simulations, we further demonstrate that heterogeneous Hsp70 binding generates region-specific folding kinetics and conformational dynamics, which are likely driven by variations in the number of available Hsp70-binding sites. This is then exploited during Hsp70/Hsp90-mediated folding to support localized folding of client subdomains, thereby reducing non-native interactions from distal regions to facilitate proper folding of multi-domain proteins.

biophysics↗

The role of auxiliary domains in modulating CHD4 activity suggests mechanistic commonality between enzyme families

CHD4 is an essential, widely conserved ATP-dependent translocase that is also a broad tumour dependency. In common with other SF2-family chromatin remodelling enzymes, it alters chromatin accessibility by repositioning histone octamers. Besides the helicase and adjacent tandem chromodomains and PHD domains, CHD4 features 1000 residues of N- and C-terminal sequence with unknown structure and function. We demonstrate that these regions regulate CHD4 activity through different mechanisms. An N-terminal intrinsically disordered region (IDR) promotes remodelling integrity in a manner that depends on the composition but not sequence of the IDR. The C-terminal region harbours an auto-inhibitory region that contacts the helicase domain. Auto-inhibition is relieved by a previously unrecognized C-terminal SANT-SLIDE domain split by [~]150 residues of disordered sequence, most likely by binding of this domain to substrate DNA. Our data shed light on CHD4 regulation and reveal strong mechanistic commonality between CHD family members, as well as with ISWI-family remodellers.

biochemistry↗

Real-time single-molecule observation of chaperone-assisted protein folding

The ability of Hsp70 molecular chaperones to remodel the conformation of their clients is central to their biological function; however, questions remain regarding the precise molecular mechanisms by which Hsp70 machinery interacts with the client and how this contributes towards efficient protein folding. Here, we used Total Internal Reflection Fluorescence (TIRF) microscopy and single-molecule Fluorescence Resonance Energy Transfer (smFRET) to temporally observe the conformational changes that occur to individual firefly luciferase (Fluc) proteins as they are folded by the bacterial Hsp70 system. For the first time, we observed multiple cycles of chaperone binding-and-release to an individual client during refolding and that high rates of chaperone cycling improves refolding yield. Furthermore, we demonstrate that DnaJ remodels misfolded proteins via a conformational selection mechanism whereas DnaK resolves misfolded states via mechanical unfolding. This study illustrates that the temporal observation of chaperone-assisted folding enables the elucidation of key mechanistic details inaccessible using other approaches.

biochemistry↗

CHD4 slides nucleosomes by decoupling entry- and exit-side DNA translocation

Chromatin remodellers hydrolyse ATP to move nucleosomal DNA against histone octamers. The mechanism, however, is only partially resolved, and unclear if it is conserved among the four remodeller families. Here we use single-molecule assays to examine the mechanism of action of CHD4, which is part of the least well understood family of remodellers. We demonstrate that the binding energy for CHD4-nucleosome complex formation - even in the absence of nucleotide - triggers significant conformational changes in DNA at the entry side, effectively priming the system for remodelling. During remodelling, flanking DNA enters the nucleosome in a continuous, gradual manner but exits in concerted 4-6 base-pair steps. This decoupling of entry- and exit-side translocation suggests that ATP-driven movement of entry-side DNA builds up strain inside the nucleosome that is subsequently released at the exit side by DNA expulsion. We propose a mechanism for nucleosome sliding based on these and published data.

biochemistry↗