Periodic Reporting for period 1 - CHAPLIN (Chaperone action - a thermodynamic view)
Reporting period: 2023-05-01 to 2025-10-31
The goal of the proposed study is to obtain a fundamental understanding of the molecular mechanism and thermodynamics of chaperone action. Chaperones are critical components of all organisms and serve to ensure a healthy state of the proteome. The proposal concerns a class of chaperones that increases the solubility of client proteins. The activity of these chaperones exhibits a number of crucial but poorly understood features; for instance, there is a remarkable specificity in action combined with promiscuous recognition across sequence space. These features are challenging to achieve through molecular design and raise the question of the general physical principles which govern chaperone activity.
Our research aims to reach a general understanding, beyond specific effects, and we will study nine binary combinations of three chaperones and three client proteins. Our strategy is to first characterize in detail the aqueous solubility and self-assembly of each chaperone alone including the phase behaviour. With this knowledge, and our existing deep understanding of client self-assembly, we turn to chaperone action to study the thermodynamics of chaperone-client mixtures to determine the phase behaviour, structure of chaperone-client co-assemblies, the mixing stoichiometry and quantitative equilibrium parameters. We use state-of-the art scattering, spectroscopy, and microscopy methods and develop new methodology.
Common to the field is a mechanical view and search for specific sites in chaperone and client proteins that mediate their mutual interaction, but the promiscuity makes us question whether such sites exist. We take a new approach, not pursued by others in the field, in that we search for general molecular and thermodynamic principles of chaperone action. Our results may guide the design of small molecules that operate according to the same principles, which can serve as therapeutics toward some of the most devastating diseases affecting humans.
Our research aims to reach a general understanding, beyond specific effects, and we will study nine binary combinations of three chaperones and three client proteins. Our strategy is to first characterize in detail the aqueous solubility and self-assembly of each chaperone alone including the phase behaviour. With this knowledge, and our existing deep understanding of client self-assembly, we turn to chaperone action to study the thermodynamics of chaperone-client mixtures to determine the phase behaviour, structure of chaperone-client co-assemblies, the mixing stoichiometry and quantitative equilibrium parameters. We use state-of-the art scattering, spectroscopy, and microscopy methods and develop new methodology.
Common to the field is a mechanical view and search for specific sites in chaperone and client proteins that mediate their mutual interaction, but the promiscuity makes us question whether such sites exist. We take a new approach, not pursued by others in the field, in that we search for general molecular and thermodynamic principles of chaperone action. Our results may guide the design of small molecules that operate according to the same principles, which can serve as therapeutics toward some of the most devastating diseases affecting humans.
Published work:
1. On the micelle formation of DNAJB6b.
Carlsson A, Olsson U, Linse S. QRB Discov. 2023 Aug 15;4:e6. doi: 10.1017/qrd.2023.4.
The human chaperone DNAJB6b increases the solubility of proteins involved in protein aggregation diseases and suppresses the nucleation of amyloid structures. Due to such favourable properties, DNAJB6b has gained increasing attention over the past decade. The understanding of how DNAJB6b operates on a molecular level may aid the design of inhibitors against amyloid formation. In this work, fundamental aspects of DNAJB6b self-assembly have been examined, providing a basis for future experimental designs and conclusions. The results imply the formation of large chaperone clusters in a concentration-dependent manner. Microfluidic diffusional sizing (MDS) was used to evaluate how DNAJB6b average hydrodynamic radius varies with concentration. We found that, in 20 mM sodium phosphate buffer, 0.2 mM EDTA, at pH 8.0 and room temperature, DNAJB6b displays a micellar behaviour, with a critical micelle concentration (CMC) of around 120 nM. The average hydrodynamic radius appears to be concentration independent between ∼10 μM and 100 μM, with a mean radius of about 12 nm. The CMC found by MDS is supported by native agarose gel electrophoresis and the size distribution appears bimodal in the DNAJB6b concentration range ∼100 nM to 4 μM.
2. The Ability of DNAJB6b to Suppress Amyloid Formation Depends on the Chaperone Aggregation State.
Carlsson A, Axell E, Emanuelsson C, Olsson U, Linse S. ACS Chem Neurosci. 2024 May 1;15(9):1732-1737. doi: 10.1021/acschemneuro.4c00120.
For many chaperones, a propensity to self-assemble correlates with function. The highly efficient amyloid suppressing chaperone DNAJB6b has been reported to oligomerize. A key question is whether the DNAJB6b self-assemblies or their subunits are active units in the suppression of amyloid formation. Here, we address this question using a nonmodified chaperone. We use the well-established aggregation kinetics of the amyloid β 42 peptide (Aβ42) as a readout of the amyloid suppression efficiency. The experimental setup relies on the slow dissociation of DNAJB6b assemblies upon dilution. We find that the dissociation of the chaperone assemblies correlates with its ability to suppress fibril formation. Thus, the data show that the subunits of DNAJB6b assemblies rather than the large oligomers are the active forms in amyloid suppression. Our results provide insights into how DNAJB6b operates as a chaperone and illustrate the importance of established assembly equilibria and dissociation rates for the design of kinetic experiments.
1. On the micelle formation of DNAJB6b.
Carlsson A, Olsson U, Linse S. QRB Discov. 2023 Aug 15;4:e6. doi: 10.1017/qrd.2023.4.
The human chaperone DNAJB6b increases the solubility of proteins involved in protein aggregation diseases and suppresses the nucleation of amyloid structures. Due to such favourable properties, DNAJB6b has gained increasing attention over the past decade. The understanding of how DNAJB6b operates on a molecular level may aid the design of inhibitors against amyloid formation. In this work, fundamental aspects of DNAJB6b self-assembly have been examined, providing a basis for future experimental designs and conclusions. The results imply the formation of large chaperone clusters in a concentration-dependent manner. Microfluidic diffusional sizing (MDS) was used to evaluate how DNAJB6b average hydrodynamic radius varies with concentration. We found that, in 20 mM sodium phosphate buffer, 0.2 mM EDTA, at pH 8.0 and room temperature, DNAJB6b displays a micellar behaviour, with a critical micelle concentration (CMC) of around 120 nM. The average hydrodynamic radius appears to be concentration independent between ∼10 μM and 100 μM, with a mean radius of about 12 nm. The CMC found by MDS is supported by native agarose gel electrophoresis and the size distribution appears bimodal in the DNAJB6b concentration range ∼100 nM to 4 μM.
2. The Ability of DNAJB6b to Suppress Amyloid Formation Depends on the Chaperone Aggregation State.
Carlsson A, Axell E, Emanuelsson C, Olsson U, Linse S. ACS Chem Neurosci. 2024 May 1;15(9):1732-1737. doi: 10.1021/acschemneuro.4c00120.
For many chaperones, a propensity to self-assemble correlates with function. The highly efficient amyloid suppressing chaperone DNAJB6b has been reported to oligomerize. A key question is whether the DNAJB6b self-assemblies or their subunits are active units in the suppression of amyloid formation. Here, we address this question using a nonmodified chaperone. We use the well-established aggregation kinetics of the amyloid β 42 peptide (Aβ42) as a readout of the amyloid suppression efficiency. The experimental setup relies on the slow dissociation of DNAJB6b assemblies upon dilution. We find that the dissociation of the chaperone assemblies correlates with its ability to suppress fibril formation. Thus, the data show that the subunits of DNAJB6b assemblies rather than the large oligomers are the active forms in amyloid suppression. Our results provide insights into how DNAJB6b operates as a chaperone and illustrate the importance of established assembly equilibria and dissociation rates for the design of kinetic experiments.
We have established
1) the critical micelle concentration of DNAJB6b
2) that subunits rather than chaperone oligomers are active in amyloid suppression
1) the critical micelle concentration of DNAJB6b
2) that subunits rather than chaperone oligomers are active in amyloid suppression