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Response to crowded conditions reveals compact nucleus for amyloid formation of folded protein

Published online by Cambridge University Press:  19 January 2021

Tony E.R. Werner Open the ORCID record for Tony E.R. Werner [Opens in a new window] ,
Istvan Horvath Open the ORCID record for Istvan Horvath [Opens in a new window]  and
Pernilla Wittung-Stafshede Open the ORCID record for Pernilla Wittung-Stafshede [Opens in a new window]
Tony E.R. Werner
Affiliation:
Department of Biology and Biological Engineering, Chalmers University of Technology, S-41296Gothenburg, Sweden
Istvan Horvath
Affiliation:
Department of Biology and Biological Engineering, Chalmers University of Technology, S-41296Gothenburg, Sweden
Pernilla Wittung-Stafshede*
Affiliation:
Department of Biology and Biological Engineering, Chalmers University of Technology, S-41296Gothenburg, Sweden
*
*Author for correspondence: Pernilla Wittung-Stafshede, E-mail: pernilla.wittung@chalmers.se
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Abstract

Although the consequences of the crowded cell environments may affect protein folding, function and misfolding reactions, these processes are often studied in dilute solutions in vitro. We here used biophysical experiments to investigate the amyloid fibril formation process of the fish protein apo-β-parvalbumin in solvent conditions that mimic steric and solvation aspects of the in vivo milieu. Apo-β-parvalbumin is a folded protein that readily adopts an amyloid state via a nucleation–elongation mechanism. Aggregation experiments in the presence of macromolecular crowding agents (probing excluded volume, entropic effects) as well as small molecule osmolytes (probing solvation, enthalpic effects) revealed that both types of agents accelerate overall amyloid formation, but the elongation step was faster with macromolecular crowding agents but slower in the presence of osmolytes. The observations can be explained by the steric effects of excluded volume favoring assembled states and that amyloid nucleation does not involve monomer unfolding. In contrast, the solvation effects due to osmolyte presence promote nucleation but not elongation. Therefore, the amyloid-competent nuclei must be compact with less osmolytes excluded from the surface than either the folded monomers or amyloid fibers. We conclude that, in contrast to other amyloidogenic folded proteins, amyloid formation of apo-β-parvalbumin is accelerated by crowded cell-like conditions due to a nucleation process that does not involve large-scale protein unfolding.

Keywords

Amyloid formationmacromolecular crowdingosmolyteβ-parvalbuminprotein aggregation
Type
Research Article
Information
QRB Discovery , Volume 2 , 2021 , e2
Creative Commons
Creative Common License - CCCreative Common License - BYCreative Common License - NCCreative Common License - ND
This is an Open Access article, distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives licence (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is unaltered and is properly cited. The written permission of Cambridge University Press must be obtained for commercial re-use or in order to create a derivative work.
Copyright
© The Author(s) 2021. Published by Cambridge University Press

Introduction

The intracellular environment is highly crowded, with an estimate of 80–400 mg ml−1 macromolecules (proteins, lipids, polysaccharides), corresponding to a volume occupancy of 5–40% (Ellis and Minton, Reference Ellis and Minton2003; Kuznetsova et al., Reference Kuznetsova, Turoverov and Uversky2014). Also extracellular space is crowded, where for example blood plasma has a protein concentration of 60–80 mg ml−1 (Leeman et al., Reference Leeman, Choi, Hansson, Storm and Nilsson2018). High concentrations of macromolecules restrict the available molecular space by their mutual impenetrability and repulsive interactions, often termed excluded volume effect. The excluded volume effect is accompanied by increased opportunities for non-specific (chemical or ‘soft’) interactions, increased (heterogeneous) viscosity, reduced macromolecule dynamics, as well as changes in solvent polarity and water activity, which in total describes the macromolecular crowding effect (Gao and Winter, Reference Gao and Winter2015; Davis and Gruebele, Reference Davis and Gruebele2018). The excluded volume effect is an entropic effect in which (due to steric restrictions) compact and assembled protein species are favoured (Ralston, Reference Ralston1990; van den Berg et al., Reference van den Berg, Ellis and Dobson1999; Minton, Reference Minton2001, Reference Minton2005a; Kuznetsova et al., Reference Kuznetsova, Turoverov and Uversky2014). Many in vitro studies of excluded volume effects (using so-called macromolecular crowding agents, for example, sugar-based polymers such as Ficoll and dextran) on protein folding and stability have shown increased folded-state stability and slower unfolding reactions in the presence of macromolecular crowding agents (van den Berg et al., Reference van den Berg, Wain, Dobson and Ellis2000; Ellis, Reference Ellis2001; Christiansen and Wittung-Stafshede, Reference Christiansen and Wittung-Stafshede2013; Christiansen and Wittung-Stafshede, Reference Christiansen and Wittung-Stafshede2014). Notably, macromolecular crowding agents such as Ficoll and dextran are reported to be inert agents with little or no protein interactions; thus, they are useful to specifically study excluded volume effects (Christiansen and Wittung-Stafshede, Reference Christiansen and Wittung-Stafshede2014; Gao and Winter, Reference Gao and Winter2015).

Cellular environments also contain high concentrations of small organic molecules termed osmolytes; so-called ‘protective’ osmolytes are often upregulated (de novo synthesis or import) to cope with water stress, there aiding in equilibration of cellular osmotic pressure (Yancey, Reference Yancey2005; Ignatova and Gierasch, Reference Ignatova and Gierasch2006; Burg and Ferraris, Reference Burg and Ferraris2008; Sukenik et al., Reference Sukenik, Sapir, Gilman-Politi and Harries2013). High amounts of protecting osmolytes increase the viscosity but they also stabilize folded proteins via enthalpic effects as they are specifically excluded from protein surfaces (Timasheff, Reference Timasheff1993, Reference Timasheff2002). Thereby, protective osmolytes affect protein hydration and this results in stabilization of folded and compact protein structures that minimize interactions with the osmolyte, as compared to the many more interactions that are possible in the expanded unfolded state (Liu and Bolen, Reference Liu and Bolen1995; Ignatova and Gierasch, Reference Ignatova and Gierasch2006; Auton and Bolen, Reference Auton and Bolen2007). Taken together, excluded volume effects are entropic in nature (and can be probed using macromolecular crowding agents), whereas solvation effects (probed via small molecule osmolytes) have enthalpic origin. Nonetheless, these systems are complicated and there is more to be revealed; there are for example studies implying that also osmolytes act via entropic forces (Ishrat et al., Reference Ishrat, Hassan, Ahmad and Islam2018).

Typically, macromolecular crowding conditions (large molecules), as well as osmolyte presence (small molecules), thermodynamically favour protein–protein interactions as assembled states will reduce the volume occupancy and number of species in solution. However, the effect on reaction kinetics will depend on conformation and surface-area exposure of rate-limiting steps. Here amyloid formation is interesting as this assembly process involves multiple steps and protein-conformational changes (Chiti and Dobson, Reference Chiti and Dobson2017). Amyloid fibrils are biological polymers composed of monomeric protein units non-covalently assembled through β-strands arranged perpendicularly to the fibril axis, thereby forming a cross-β structure (Chiti and Dobson, Reference Chiti and Dobson2017). Many proteins in all kingdoms of life (Otzen, Reference Otzen2010) can form amyloid fibrils at certain solvent conditions (Chiti and Dobson, Reference Chiti and Dobson2017), and this process is directly related to several human diseases, such as Alzheimer’s disease, Parkinson’s disease and type 2 diabetes (Cooper et al., Reference Cooper, Willis, Clark, Turner, Sim and Reid1987; Jarrett et al., Reference Jarrett, Berger and Lansbury1993; Wakabayashi et al., Reference Wakabayashi, Matsumoto, Takayama, Yoshimoto and Takahashi1997). But there are also proteins that form functional amyloids: for example, biofilms are structures used by bacteria to adhere to surfaces which contain amyloids made of curli proteins (Andersson et al., Reference Andersson, Bengtsson, Evans, Chorell, Sellstedt, Lindgren, Hufnagel, Bhattacharya, Tessier, Wittung-Stafshede, Almqvist and Chapman2013; Evans et al., Reference Evans, Chorell, Taylor, Aden, Gotheson, Li, Koch, Sefer, Matthews, Wittung-Stafshede, Almqvist and Chapman2015). Human functional amyloids include proteins in the signaling pathway leading to necrosis (Li et al., Reference Li, McQuade, Siemer, Napetschnig, Moriwaki, Hsiao, Damko, Moquin, Walz, McDermott, Chan and Wu2012) and in melanosome ultra-structures (Dean and Lee, Reference Dean and Lee2019). Amyloid formation reactions of proteins that start from an intrinsically disordered monomeric state will necessarily involve compaction as the extended polypeptide will form β-structure. Thus for disordered/unfolded proteins, it is reasonable that macromolecular crowding via the excluded volume effect accelerates amyloid formation and this has been observed for aggregation of, for example, α-synuclein (Shtilerman et al., Reference Shtilerman, Ding and Lansbury2002; Uversky et al., Reference Uversky, Cooper, Bower, Li and Fink2002; White et al., Reference White, Buell, Knowles, Welland and Dobson2010), the amyloid-β peptide (Lee et al., Reference Lee, Bird, Shaw, Jean and Vaux2012) and a tau fragment (Zhou et al., Reference Zhou, Fan, Zhu, Shewmaker, Yan, Chen, Chen, Xiao, Guo and Liang2009).

Folded proteins may become amyloidogenic as a result of ligand release, thermal fluctuations, as well as by local or global unfolding (Kuznetsova et al., Reference Kuznetsova, Turoverov and Uversky2014; Chiti and Dobson, Reference Chiti and Dobson2017). It is also possible that assembly of folded proteins (native-like aggregates) occurs prior to structural rearrangements leading to amyloid fibers (Bouchard et al., Reference Bouchard, Zurdo, Nettleton, Dobson and Robinson2000; Plakoutsi et al., Reference Plakoutsi, Taddei, Stefani and Chiti2004; Soldi et al., Reference Soldi, Bemporad, Torrassa, Relini, Ramazzotti, Taddei and Chiti2005; Chiti and Dobson, Reference Chiti and Dobson2017). For folded proteins, it is less straightforward to predict the macromolecular crowding effect on amyloid formation, as the folded states will be stabilized (with respect to unfolding) by macromolecular crowding agents (Jahn and Radford, Reference Jahn and Radford2005; Kuznetsova et al., Reference Kuznetsova, Turoverov and Uversky2014). Indeed, several folded proteins exhibit increased resistance towards amyloid fibril formation in the presence of macromolecular crowding including carbonic anhydrase (Mittal and Singh, Reference Mittal and Singh2014), core histones and insulin (Munishkina et al., Reference Munishkina, Ahmad, Fink and Uversky2008). However, when placed in denaturing conditions, that is, low pH that partially unfolds the proteins and, for core histones and insulin, dissociates the native oligomeric states, macromolecular crowding was found to accelerate aggregation of the proteins mentioned above (Munishkina et al., Reference Munishkina, Ahmad, Fink and Uversky2008; Luo et al., Reference Luo, Kong, Dang, Chen and Liang2016). Acceleration of aggregation by crowding was also shown for partially unfolded apolipoprotein C-II in the absence of lipids (Hatters et al., Reference Hatters, Minton and Howlett2002). Notably, two of these three examples involve proteins with oligomeric native states, and amyloid formation involved oligomer dissociation into monomers as an initial requirement.

To test the effect of macromolecular crowding on an amyloidogenic protein that is folded and monomeric, we turned to G. morhua β-parvalbumin (β-PV). β-PV is an α-helical folded protein capable of binding Mg2+ and/or Ca2+ through two active EF-hand domains (Rall, Reference Rall1996). Upon loss of the metal-ion ligands, which may occur due to low pH protonating the coordinating residues, or the chelating agent, ethylenediaminetetraacetic acid (EDTA), apo-β-PV readily forms amyloid fibrils (Martinez et al., Reference Martinez, Sanchez, Castellanos, Fernandez-Escamilla, Vazquez-Cortes, Fernandez-Rivas and Gasset2015; Castellanos et al., Reference Castellanos, Torres-Pardo, Rodriguez-Perez and Gasset2018). We recently showed that apo-β-PV amyloid formation follows a nucleation–elongation mechanism where the nucleation step involves folded dimers connected by intermolecular disulfide bonds (Werner et al., Reference Werner, Bernson, Esbjorner, Rocha and Wittung-Stafshede2020). The dimers are on path but need to further assemble and/or structurally convert to form competent nuclei that can then be elongated (by monomer and dimer additions) to amyloid fibrils. Thus, the amyloid formation process of apo-β-PV, initiated by assembly of folded proteins, is similar to that reported for only a few other proteins (Bouchard et al., Reference Bouchard, Zurdo, Nettleton, Dobson and Robinson2000; Plakoutsi et al., Reference Plakoutsi, Taddei, Stefani and Chiti2004; Soldi et al., Reference Soldi, Bemporad, Torrassa, Relini, Ramazzotti, Taddei and Chiti2005). Since apo-β-PV is folded, one would predict that macromolecular crowding will slow down amyloid formation by stabilization of the folded monomer. Still, as a folded dimer is on path towards amyloid fibers (Werner et al., Reference Werner, Bernson, Esbjorner, Rocha and Wittung-Stafshede2020), the presence of macromolecular crowding may favor dimers and thereby accelerate nucleation of the amyloid process.

The macromolecular crowding agent Ficoll 70 is a sucrose-based branched polymer often used to mimic excluded volume (Zhou et al., Reference Zhou, Rivas and Minton2008; Wang et al., Reference Wang, He and Li2010). Although there may sometimes be exceptions (Nasreen et al., Reference Nasreen, Parray, Ahamad, Ahmad, Ahmed, Alamery, Hussain, Hassan and Islam2020), Ficoll 70 has been shown to only provide steric, excluded volume effects without chemical interactions with proteins (Christiansen et al., Reference Wang, He and Li2010; Christiansen and Wittung-Stafshede, Reference Christiansen and Wittung-Stafshede2013, Reference Christiansen and Wittung-Stafshede2014). Using Ficoll 70, we here show that amyloid formation of apo-β-PV, in contrast to data for folded oligomeric proteins, is promoted by macromolecular crowding. From additional protective osmolyte (glycerol and sucrose) kinetic experiments, it appears that the competent nucleus for amyloid formation is compact, and its formation does not involve large-scale conformational changes. However, addition of monomers during amyloid fibril elongation must involve larger structural conversions (resulting in increased exposure of surface area) as this is retarded by protective osmolytes.

Materials and method

Chemicals

Powders of sucrose (BioXtra, Sigma, St Louis, MO, USA), Ficoll PM 70 (Sigma, St Louis, MO, USA) (70 kDa) and poly(ethylene glycol) (PEG) 35,000 (BioUltra, Sigma, St Louis, MO, USA) (35 kDa) were dissolved in 25 mM Tris-HCl buffer, pH adjusted for 7.4 at 37°C and volume adjusted to desired concentration. Molecular biology grade glycerol (Fisher Scientific, Waltham MA, USA) was used.

Protein preparation

Just prior to aggregation assays of G. morhua β-parvalbumin (A51874, Gad m1), expressed and purified as described in Werner et al. (Reference Werner, Bernson, Esbjorner, Rocha and Wittung-Stafshede2020), the his-tag was removed by treating β-PV with thrombin (35.5 NIH units μmole−1) for 4–5 h at room temperature and 800 RPM shaking followed by size exclusion chromatography (Superdex 75 10/300, GE healthcare, Uppsala, Sweden) in 25 mM Tris-HCl, supplemented with 1 mM CaCl2 to stabilize the monomeric state.

Thioflavin T-aggregation assay

The ThT assay was performed in a quiescent condition at 37°C in 25 mM Tris-HCl (pH 7.4), 150 mM NaCl, 1 mM CaCl2, 5 mM EDTA, 7.7 mM NaN3 and 20 μM recrystallized ThT in 96 well plates. Fluorescence was measured in a plate reader (Fluostar Optima or Fluostar Omega; BMG Labtech, Ortenberg, Germany). Emission was recorded at 480 nm with excitation at 440 nm every 20 min.

Atomic force microscopy

Samples of apo-β-PV fibrils were diluted with Milli-Q water (10 times) and incubated on a freshly cleaved mica for 15 min. The mica was subsequently rinsed five times and dried under a nitrogen gas flow. Intermittent contact mode atomic force microscopy (AFM) in air was used to record the images (NTEGRA Prima setup, NT-MDT) with a single crystal silicon cantilever (TipsNano, NSG01, force constant of ~5.1 N m−1) with a resonance frequency of ~180 kHz. 512-pixel images were acquired with a 0.5-Hz scan rate. Images were analyzed using the WSxM 5.0 software (Horcas et al., Reference Horcas, Fernández, Gómez-Rodríguez, Colchero, Gómez-Herrero and Baro2007).

Circular dichroism spectroscopy

Far-UV circular dichroism (CD) spectra (190–260 nm) of PV monomers (apo- and holo-β-PV) were collected at room temperature (21 ± 1°C) using Chirascan CD spectropolarimeter (Applied Photophysics) in a 1 mm pathlength quartz cuvette. Three scans were collected and averaged with a time-per-point of 2 s, 1 nm bandwith and step size of 1 nm. The buffer signal was subtracted, and intensities converted from millidegrees to mean residue molar ellipticity (degrees M−1 m−1). CD spectra of amyloid fibrils were collected on post-aggregation samples that had been centrifuged at 100 000 g for 5 h, resuspended in 10 mM Tris-HCl, followed by 3 h centrifugation again and final resuspension into 10 mM Tris-HCl (pH 7.8).

Results and discussion

Amyloid formation of apo-β-PV (EDTA added at time zero to remove metal ions) in the presence of Ficoll 70 at 37°C was monitored by the Thioflavin T (ThT) fluorescence assay (Naiki et al., Reference Naiki, Higuchi, Hosokawa and Takeda1989; Xue et al., Reference Xue, Lin, Chang and Guo2017). A significant increase in the speed of aggregation of apo-β-PV was observed when incubated in the presence of 100 and 200 mg ml−1 Ficoll 70 (Fig. 1a), with a reduction of the half-time (time point when ThT fluorescence has reached 50% of its final value) from 32 ± 3 h (buffer), to 11 ± 1 h (100 mg ml−1 Ficoll 70) and 4.5 ± 0.2 h (200 mg ml−1 Ficoll 70). The resulting β-PV amyloid fibrils formed in the presence of Ficoll 70 were found to share the curvilinear appearance of apo-β-PV amyloid fibrils formed in buffer (Fig. 1b,c) and the far-UV CD spectra of amyloid fibers formed with and without Ficoll 70 were identical (Fig. 1d). From inspection of the data in Fig. 1a, it is evident that the lag time is drastically reduced and the slope of the fluorescence rise (i.e. tangent at half-time point) is larger for the two Ficoll 70 conditions. This implies that both nucleation and elongation processes are accelerated in macromolecular crowded solutions. This is in excellent agreement with excluded volume theory that predicts that assembled species are favored when the volume is reduced (Minton, Reference Minton2005b; Ellis and Minton, Reference Ellis and Minton2006). Also more elaborate modelling (including both scaled-particle and transition-state theories) predicts this for systems where the size of the monomer is smaller when in the amyloid fiber than when in the free form (Schreck et al., Reference Schreck, Bridstrup and Yuan2020). Notably, 200 mg ml−1 Ficoll 70 will occupy 13% of the volume based on its partial specific volume value (Christiansen et al., Reference Wang, He and Li2010; Aguilar et al., Reference Aguilar, Weice, Sparrman, Wolf-Watz and Wittung-Stafshede2011) and thus the effective concentration of apo-β-PV is not 30 μM but 34 μM in the presence of 200 mg ml−1 Ficoll 70. However, based on the earlier-determined concentration dependence of apo-β-PV aggregation (Werner et al., Reference Werner, Kumar, Horvath, Scheers and Wittung-Stafshede2018), this small difference in protein concentration does not increase the aggregation speed significantly.

Fig. 1. Macromolecular crowding agents accelerate amyloid formation but do not affect fiber morphology. ThT fluorescence curves of 30 μM apo-β-PV at 37°C under quiescent conditions in 150 mM NaCl, 1 mM CaCl2, 5 mM EDTA, 25 mM Tris-HCl, pH 7.4 and 0–200 mg ml−1 Ficoll 70 (a) or 0–40 mg ml−1 PEG 35,000 (e). AFM images of fibrils obtained from apo-β-PV alone (b) or in the presence of 100 mg ml−1 Ficoll 70 (c). (d) CD spectra of resulting apo-β-PV amyloid fibers formed with (red) or without (blue) 100 mg ml−1 Ficoll 70 (curves normalized to the same signal at the minimum). (f) CD spectra of 15 μM apo-β-PV at 21°C in 10 mM Tris-HCl, pH 7.8, 1 mM EDTA and 96 μM CaCl2, with (red) 50 mg ml−1 Ficoll 70, or (blue) 20 mg ml−1 PEG, or (grey) without addition (i.e. all prior to aggregation).

Importantly, the Ficoll 70 result implies that the expected excluded-volume effect on the folded-to-unfolded transition of apo-protein monomers is not affecting amyloid formation. Unfortunately, we could not test the effect of Ficoll 70 on apo-β-PV monomer thermal or chemical equilibrium stability, as the apo-form is prone to aggregation during the required experimental time scales. Nonetheless, one expects macromolecular crowding to stabilize the compact folded state relative to the more expanded unfolded state (Christiansen et al., Reference Wang, He and Li2010; Stagg et al., Reference Stagg, Christiansen and Wittung-Stafshede2011; Christiansen and Wittung-Stafshede, Reference Christiansen and Wittung-Stafshede2013; Aden and Wittung-Stafshede, Reference Aden and Wittung-Stafshede2014). Because some studies have shown macromolecular crowding to also modulate folded-state structure (Perham et al., Reference Stagg, Zhang, Cheung and Wittung-Stafshede2007; Stagg et al., Reference Stagg, Zhang, Cheung and Wittung-Stafshede2007; Homouz et al., Reference Homouz, Perham, Samiotakis, Cheung and Wittung-Stafshede2008), we tested the influence of Ficoll 70 on the secondary structure of folded apo-β-PV using far-UV CD within time scales without aggregation. However, we found that the presence of Ficoll 70 did not affect the secondary structure of apo-β-PV (Fig. 1f). Taken together, the effect of Ficoll 70 on apo-β-PV aggregation agrees with folded dimers, stabilized by disulfide bonds (Werner et al., Reference Werner, Bernson, Esbjorner, Rocha and Wittung-Stafshede2020), being key players in a nucleation process that occurs without monomer unfolding. The excluded volume effect due to Ficoll 70 presence favors dimer assembly and, thus, overall aggregation of apo-β-PV into amyloids is accelerated. Also, another macromolecular crowding agent, PEG, accelerated apo-β-PV amyloid formation (Fig. 1e) without affecting apo-β-PV folded structure (Fig. 1f). Although PEG may interact differently with proteins, and not only provide steric effects (Sukenik et al., Reference Sukenik, Politi, Ziserman, Danino, Friedler and Harries2011; Gao and Winter, Reference Gao and Winter2015), the similar results found for PEG and Ficoll 70 (two agents with different chemistry) support that the observed kinetic acceleration is due to excluded volume. Notably, if attractive chemical (soft) interactions between protein and crowding agent were occurring, as noted in a few cases (Mikaelsson et al., Reference Mikaelsson, Aden, Wittung-Stafshede and Johansson2014), such interactions would stabilize the folded monomers and thereby reduce aggregation (which is opposite to our findings).

To specifically test the effect of macromolecular crowding on the amyloid elongation step of apo-β-PV, we performed seeded reactions in which various amounts of preformed sonicated apo-β-PV amyloid fibril seeds were added to monomers. When high amounts of fibril seeds are added, only elongation takes place at early time points and therefore elongation can be exclusively probed. In Fig. 2, we show that seeded reactions (7.5, 15 and 24 μM monomer equivalents of fiber seeds added to 30 μM monomers) is accelerated in the presence of Ficoll 70, as compared to the corresponding seeded reactions in buffer. Again, this can be explained by the excluded volume effect (due to the presence of Ficoll 70) favoring assembled protein states. To elongate, apo-β-PV monomers must structurally convert from the native α-helical structure to the β-strand arrangement in the amyloid fibrils. The observed kinetic acceleration thus show that the macromolecular crowding effect on apo-β-PV monomer stability (folded versus unfolded states) does not kinetically limit the conformational transitions needed for the amyloid fiber elongation process. Analysis of the initial rates in the seeded apo-β-PV experiments reveals that the elongation rate constant is increased by a factor of 1.4–1.5 in the presence of 50 mg ml−1 Ficoll 70 as compared to in buffer (Fig. 2d). This magnitude is in accord with scaled particle theory predictions (thus, based on entropic effects/excluded volume) of amyloid fibril growth: in (White et al., Reference White, Buell, Knowles, Welland and Dobson2010) it was reported that experimental and predicted elongation rates for some different proteins were between 1.2 and 1.8 times faster in 50 mg ml−1 of a macromolecular crowding agents as compared to in buffer.

Fig. 2. Ficoll 70 accelerates, but sucrose slows down, amyloid fiber elongation. ThT aggregation curves of 30 μM apo-β-PV at 37°C under quiescent conditions in 150 mM NaCl, 1 mM CaCl2, 5 mM EDTA, 25 mM Tris-HCl, pH 7.4, with or without 50 mg ml−1 Ficoll 70 or 380 mg ml−1 sucrose, in the presence of 7.5 μM sonicated pre-formed fibrils (PFF) (a), 15 μM PFF (b) or 24 μM PFF (c). (d) Initial slope analysis of the curves (a–c) during the first 2.3 h.

To complement the Ficoll 70 results, which focus on excluded volume, we tested the effect of small molecule protective osmolytes (Kim et al., Reference Kim, Yan and Zhou2006) to assess solvent effects on apo-β-PV amyloid formation. Somewhat surprising, we found that the presence of both sucrose and glycerol (two protective small molecule osmolytes with different chemistry) resulted in faster apo-β-PV amyloid formation (Fig. 3a). The effect was concentration dependent, with higher sucrose or glycerol levels accelerating amyloid formation more. Importantly, the resulting apo-β-PV amyloid fibrils formed in presence of osmolytes appear like those formed in buffer and Ficoll 70 conditions according to far-UV CD (Fig. 3b) and AFM analysis (Fig. 3c,d) Notably, comparing the curves in Fig. 3a and Fig. 1a reveals that the aggregation lag times are not reduced as much, and the slopes (tangents) at the half time points are not as steep, as when apo-β-PV is placed in Ficoll 70, despite the fact that the concentrations of sucrose and glycerol used (in mg ml−1 scale) are higher than the concentrations of Ficoll 70. For example, 380 mg ml−1 sucrose reduced the half time point by a factor two, whereas 200 mg ml−1 Ficoll 70 reduced the half time point by a factor of seven. Thus, excluded volume appears to have a larger effect than osmolyte-mediated hydration changes on the amyloid formation reaction. To better understand this difference, we assessed the effect of one of the osmolytes, sucrose, on the amyloid fibril elongation process of apo-β-PV by performing seeded amyloid formation reactions. We found that in contrast to Ficoll 70, the presence of sucrose reduces the elongation rate as compared to the corresponding reaction in buffer at all three amyloid fiber seed concentrations tested (Fig. 2).

Fig. 3. Osmolytes accelerate the overall amyloid reaction but do not affect amyloid fiber morphology. ThT fluorescence curves of 30 μM apo-β-PV at 37°C under quiescent conditions in 150 mM NaCl, 1 mM CaCl2, 5 mM EDTA, 25 mM Tris-HCl, pH 7.4 and 0–390 mg ml−1 sucrose (blue shades) or 0–566 mg ml−1 glycerol (red shades) (a). CD spectra of resulting apo-β-PV amyloid fibers formed with (red) or without (blue) 190 mg ml−1 sucrose (curves normalized to the same signal at the minimum) (b). AFM images of fibrils obtained from apo-β-PV in the presence of 380 mg ml−1 sucrose (c) or 566 mg ml−1 glycerol (d).

To explain the protective osmolyte results, that is, that non-seeded apo-β-PV amyloid formation is accelerated but apo-β-PV amyloid elongation is retarded by osmolytes, the nucleation step in the amyloid formation process must be promoted by the osmolytes. Protecting osmolytes such as glycerol and sucrose stabilize folded proteins due to their preferential exclusion from the protein surface (Timasheff, Reference Timasheff2002; Ignatova and Gierasch, Reference Ignatova and Gierasch2006; Kim et al., Reference Kim, Yan and Zhou2006). This effect will destabilize expanded unfolded states (that expose more surface area and thus require more osmolyte exclusion) but stabilize compact states of proteins. With this in mind, nucleation of apo-β-PV amyloid formation appears to involve compact structures that are stabilized by the osmolytes. The rate-limiting step for nuclei formation (i.e. the transition state) must also be stabilized by osmolyte presence to result in faster kinetics; thus, nucleation cannot involve large-scale protein unfolding. Again, this result is in accord with folded dimers being key species in apo-β-PV nuclei formation (Werner et al., Reference Werner, Bernson, Esbjorner, Rocha and Wittung-Stafshede2020).

Fibril elongation involves the addition of monomers to the ends of growing amyloids with β-structure. Here structural conversions are needed as apo-β-PV monomers, to be added to growing fibers, are folded with α-helical structure. Conversion from α-helical to β-sheet structure will require transient exposure of an increased protein surface area, which will be disfavored in the presence of the osmolytes due to preferential exclusion effects. The retarding osmolyte effect on apo-β-PV amyloid fiber elongation kinetics agrees with findings on insulin and lysozyme at conditions where the proteins retained some folded structure. For both proteins, slower amyloid fibril elongation was detected in the presence of the protective osmolyte glycine (White et al., Reference White, Buell, Knowles, Welland and Dobson2010).

Conclusions and outlook

Folded proteins, in addition to intrinsically disordered proteins, may form amyloid fibrils and this sometimes results in human diseases. In most cases, folded multimeric proteins must first dissociate to monomers, and the monomers must become structurally perturbed, for amyloid formation to occur. In such cases, macromolecular crowding, as found in living systems, will reduce the aggregation reaction as it stabilizes both folded proteins and multimeric states. Here we analyzed a folded monomeric protein that can assemble to amyloids. We show that the macromolecular crowding agent Ficoll 70 speed up amyloid formation although we start from the folded protein. The results are explained by the fact that apo-β-PV amyloid formation is not initiated by monomer unfolding but is instead promoted by folded dimers (Werner et al., Reference Werner, Bernson, Esbjorner, Rocha and Wittung-Stafshede2020). The complementary experiments with small molecule osmolytes support the conclusion that no unfolding is involved in amyloid nucleation and further demonstrates that the nuclei are compact species stabilized in the osmolyte conditions. The fact that amyloid fiber elongation is accelerated by macromolecular crowding agents but retarded by osmolytes is explained by favorable excluded volume effects and unfavorable solvation effects, respectively, on monomer additions to growing amyloid fibers. Taken together, our study shows the first example of a folded monomeric protein that is augmented to adopt amyloid structures at conditions mimicking those found in living systems. The consequences of cell-like conditions on amyloid formation will depend crucially on mechanisms and structures of involved transient species: in the case of apo-β-PV, aggregation into amyloids is favored by the excluded volume effect as the process involves a compact nucleus that is reached without large-scale polypeptide unfolding.

Excluded volume, here mimicked by macromolecular crowding agents, is definitely an important factor of in vivo conditions. However, other aspects of the cell environment are also at play and may in some cases dominate. In addition to excluded volume and solvation effects (studied here), also nonspecific chemical interactions may take place between macromolecules and hydrophobic forces within macromolecules, for example, DNA, were shown to be affected by cell-like conditions (Feng et al., Reference Feng, Sosa, Martensson, Jiang, Tong, Dorfman, Takahashi, Lincoln, Bustamante, Westerlund and Norden2019). Many more systematic studies of these effects on the molecular-mechanistic level are desired, including studies using mixtures of macromolecular crowding agents, protein crowders, as well as assessing combinations of macromolecular crowding agents and osmolytes; all in combination with new theoretical approaches (Schreck et al., Reference Schreck, Bridstrup and Yuan2020). So far, known amyloidogenic proteins involved in human diseases are intrinsically disordered proteins or folded (often oligomeric) proteins that require partial unfolding/dissociation (i.e. some destabilization) to initiate amyloid formation. Perhaps we may eventually discover that folded proteins, without the need for destabilization, also participate in amyloid diseases, with amyloid initiation triggered by, for example, oxidative stress that cause covalent bonds between folded proteins. In fact, it may emerge that what we today consider ‘well-characterized’ human diseases may involve yet undiscovered amyloid formation that, in turn, is modulated by the cell environment (e.g. crowding, osmolytes).

Author contributions

T.W. and P.W.S. designed the study. T.W. and I.H. performed experiments. T.W., I.H. and P.W.S. analyzed data. P.W.S. wrote the draft article. T.W., I.H. and P.W.S. edited the article.

Financial support

We thank the Knut and Alice Wallenberg Foundation, the Swedish Research Council and the Chalmers Foundation for funding.

Conflicts of interest

The authors declare no conflicts of interest.

Data availability statement

All data are included in the manuscript.

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Figure 0

Fig. 1. Macromolecular crowding agents accelerate amyloid formation but do not affect fiber morphology. ThT fluorescence curves of 30 μM apo-β-PV at 37°C under quiescent conditions in 150 mM NaCl, 1 mM CaCl2, 5 mM EDTA, 25 mM Tris-HCl, pH 7.4 and 0–200 mg ml−1 Ficoll 70 (a) or 0–40 mg ml−1 PEG 35,000 (e). AFM images of fibrils obtained from apo-β-PV alone (b) or in the presence of 100 mg ml−1 Ficoll 70 (c). (d) CD spectra of resulting apo-β-PV amyloid fibers formed with (red) or without (blue) 100 mg ml−1 Ficoll 70 (curves normalized to the same signal at the minimum). (f) CD spectra of 15 μM apo-β-PV at 21°C in 10 mM Tris-HCl, pH 7.8, 1 mM EDTA and 96 μM CaCl2, with (red) 50 mg ml−1 Ficoll 70, or (blue) 20 mg ml−1 PEG, or (grey) without addition (i.e. all prior to aggregation).

Figure 1

Fig. 2. Ficoll 70 accelerates, but sucrose slows down, amyloid fiber elongation. ThT aggregation curves of 30 μM apo-β-PV at 37°C under quiescent conditions in 150 mM NaCl, 1 mM CaCl2, 5 mM EDTA, 25 mM Tris-HCl, pH 7.4, with or without 50 mg ml−1 Ficoll 70 or 380 mg ml−1 sucrose, in the presence of 7.5 μM sonicated pre-formed fibrils (PFF) (a), 15 μM PFF (b) or 24 μM PFF (c). (d) Initial slope analysis of the curves (a–c) during the first 2.3 h.

Figure 2

Fig. 3. Osmolytes accelerate the overall amyloid reaction but do not affect amyloid fiber morphology. ThT fluorescence curves of 30 μM apo-β-PV at 37°C under quiescent conditions in 150 mM NaCl, 1 mM CaCl2, 5 mM EDTA, 25 mM Tris-HCl, pH 7.4 and 0–390 mg ml−1 sucrose (blue shades) or 0–566 mg ml−1 glycerol (red shades) (a). CD spectra of resulting apo-β-PV amyloid fibers formed with (red) or without (blue) 190 mg ml−1 sucrose (curves normalized to the same signal at the minimum) (b). AFM images of fibrils obtained from apo-β-PV in the presence of 380 mg ml−1 sucrose (c) or 566 mg ml−1 glycerol (d).

Review: Response to crowded conditions reveals compact nucleus for amyloid formation of folded protein — R0/PR1

Published online by Cambridge University Press:  19 January 2021
DOI: https://doi.org/10.1017/qrd.2020.17.pr1 [Opens in a new window]
Bengt J. F. Nordén [Opens in a new window] Chemistry and Chemical Engineering, Chalmers University of Technology, Sweden
Date of review:  27 October 2020
Revision round: 0
Role: reviewer
Recommendation/decision: minor-revision

Conflict of interest statement

Reviewer declares none.

Comments

Comments to Author: Review of QRD-D-20-00022

The authors study amyloid fibril formation rates for apo-β-parvalbumin in solvent conditions that mimic in vivo milieu. This is a challenging problem area as little is still known about causes and consequences of aggregation, folding, elongated fiber formation etc. in amyloid contexts. Specifically, in prion contexts, minor conformational variations between 'bad' and 'not bad' amyloids are very small and the structural origin of toxicity still elusive. Attempts to understand role of cell environment, in particular 'crowding' are therefore highly commendable and of interest to a big audience.

Aggregation in presence of macromolecular crowding agents or smaller-molecule 'osmolytes' show that both types of agents accelerate amyloid formation, but elongation step seams faster in macromolecular crowding than with osmolytes. Authors claim that excluded volume effects favor assembled states (both nuclei and amyloid fibrils), while osmolytes stabilize nuclei formation but not elongation. Therefore, they say, amyloid-competent nuclei must be compact with less exposed surface area than the folded monomers. They also note that in contrast to other amyloidogenic folded proteins, that become more resistant to amyloid formation, aggregation of apo-β-parvalbumin is accelerated by cell-like conditions. The reason for this is claimed to be a nucleation process that does not involve large-scale unfolding events. Although crowding effects have been studied before on amyloids, this seems a first example of a folded protein that forms amyloid structures under cell conditions.

The manuscript reads well and the results are interesting, potentially even of greatest impact. I suggest the ms be accepted once the authors have considered the following comments and amended their paper accordingly.

Comments

1. That assembled species be favoured by reduced volume has been pointed out long ago and also studied in detail both theoretically and experimentally by Minton and co-workers. This is as I see it a simple concentration effect via the law of mass action. The kinetic effects would follow similar increased concentration behaviour. There are as I see them three different causes that may explain in full or in part the observed effects of 'crowding' agents: a) excluded volume (entropic concentration) effects, b) osmotic (including dehydration) effects, c) attractive chemical interactions. Although the manuscript is well written and different effects are somewhat discussed, these three effects should be further discussed. E.g., Ficoll is a roughly globular correspondent to the macromolecular dextran (both dehydrating and both strongly hydrophilic) while, by contrast, PEG is both hydrophilic and hydrophobic. Ficoll has at normal pH a negative charge and is known to 'shield' proteins. I think some arguments are already there , like 'Ficoll 70 did not affect the secondary structure of apo- β-PV' and 'This supports that the observed Ficoll 70 effect is due to excluded volume changes and not chemical interactions.', but they should be articulated more clearly. In 'This magnitude is in accord with scaled particle theory predictions (thus, based on entropic interactions/excluded volume) of amyloid fibril growth' I think, by the way, 'entropic effects' would be more appropriate to say as entropy by definition does not involve interactions.

2. Referring to the previous point, there are several publications some of which ought to be cited and potentially discussed in relation to the effects found for PEG and Ficoll. A) B. Feng PNAS 2019Hydrophobic catalysis and a potential biological role of DNA unstacking where it is demonstrated that in addition to excluded volume and osmolytic effects also direct interactions with hydrophobic moieties are very important. Would hydrophobic interactions with PEG possibly affect the here investigated amyloid reaction? B) Davis & Gruebele 2018 Non‐Steric Interactions Predict the Trend and Steric Interactions the Offset of Protein Stability in Cells. C) Zaslawsky, Mestechkina, Rogozhin J.Chromatography1983. relative hydrophobicities of the proteins, in Ficoll-Dextran biphasic systems D) Nasreen et al Biomolecules 2020. Interactions Under Crowding Milieu: Chemical-Induced Denaturation Biomolecules 2020.

3. The main message of the paper is the unusual behaviour of the apo-beta-PV under cell-like crowded conditions and that nucleation cannot involve large-scale protein unfolding However, it is not explained why this finding could be earth-shattering. It is mentioned in passing that 'the folded dimers, formed transiently, can form inter-protein disulfide bonds'. Is this the reason and then so what?I think the authors should elaborate more on why their finding is important - with some freedom to speculate as Discovery encourages. For example, can the finding of a nucleation process that does not involve large-scale unfolding events indicate mechanistic features that can give a clue about when disease can be expected and potentially also how it may be mitigated or cured?

4. It would have been easier to read the paper if the figure captions had given a hint about what they show. What do the AFM pictures show? Clearly in Fig. 1 that Ficoll does not change the shape of the fibrils. But in Fig 3 what happens in sucrose and glycerol, and what do the differences between them mean, is not so clear.

5. It says based on conserved CD (Figure 1D) "the presence of Ficoll 70 did not affect the secondary structure of apo- β-PV". But what about effect of PEG on CD?

MINOR POINTS

Introduction, 1st page: 'to cope with stress' . What kind of stress, osmotic stress?

based on entropic interactions/excluded volume… better: based on entropic effects/excluded volume…

Conclusion: this sometimes resultshould read this sometimes results

macromolecular crowding speed.. should read macromolecular crowding speeds..

Review: Response to crowded conditions reveals compact nucleus for amyloid formation of folded protein — R0/PR2

Published online by Cambridge University Press:  19 January 2021
DOI: https://doi.org/10.1017/qrd.2020.17.pr2 [Opens in a new window]
Pankaj Bharmoria [Opens in a new window] Applied Chemistry, Chalmers University, Sweden
Date of review:  31 October 2020
Revision round: 0
Role: reviewer
Recommendation/decision: major-revision

Conflict of interest statement

Reviewer declares none.

Comments

Comments to Author: Analysis of the work done: In this work authors have claimed the biomimicking of cell like conditions to accelerate the fibrillation of apo-β-parvalbumin by adding a well-known macromolecularly crowding agent Ficoll 70 where apo-β-parvalbumin undergoes fibrillation without undergoing unfolding step required during conventional in vitro fibrillation of proteins. For comparison authors have also studied fibrillation in the presence of protective osmolytes like glycerol and sucrose which shows long elongation period in comparison to the Fycoll 70.

Authors Comments:

1) The fibrillation of proteins into amyloid-beta without unfolding step is well reported before (Chiti et al.Biophysical Journal, 2005, 89, 4234).Therefore, authors need to explain what is the background of their statement that it's the first report where fibrillation without unfolding step is achieved or protein destabilization is achieved.

2) Authors must cite other relevant references pertaining to effect macromolecular crowding on speeding up the fibrillation (eg. Freire et al. Commun. Mater. 2020, 34) where the fibrillation occurred instantaneously in a natural macromolecular crowding medium.

3) Authors have claimed that they are mimicking the natural macromolecular crowded media (NMCM), however they have used just one crowding agent. On the other hand NMCM is always heterogenous, therefore it would be more correct to use a mixture of crowding agent to support their statement.

4) I am agree with authors comments that excluded volume effect due to molecular crowding can drive protein-protein interactions to form diamers or multimers via disulfide linkage. However, for fibrillation to happen via self-assembly the driving force is generally the hydrophobic or H-bonding interactions. If the unfolding doesn't happen then how did the hydophobic residues present inside the protein core caused fibrillation an if they do not do authors have any evidence of H-bonding interactions.

5) Authors have shown the effect of crowding agent and osmolyte in a counteractive manner separately. It would be more authentic to show their effect in a mixed system. Because biologically in the cell, macromolecules and osmolytes coexists. Therefore, authors are suggested to do another fibrillation experiment in a mixture of macromolecule + osmolyte.

6) Although excluded volume is one of the factor but authors must present some concrete evidence to support their argument. The CD spectra shown in Fig. 1D (at 0 mg Fycol 70 and 50 mg Fycol 70) show no difference. Where are the CD spectra of typical fibrils ? Authors haven't shown any CD spectra corresponding to cross-beta structure even at high concentration of Fycol 70 or osmolytes which they claim are forming fibrils. Just ThT cannot be considered as absolute evidence since many amorphous aggregates also show rise in fluorescence of ThT. AFM images are showing fibrils but in AFM samples are prepared following a long process of washing and drying. Therefore, please show CD spectra of fibrils showing cross-beta structure in solution.

Decision: Acceptable after Major Revision

Recommendation: Response to crowded conditions reveals compact nucleus for amyloid formation of folded protein — R0/PR3

Published online by Cambridge University Press:  19 January 2021
DOI: https://doi.org/10.1017/qrd.2020.17.pr3 [Opens in a new window]
Steven G Boxer Stanford University, United States
Revision round: 0
Role: Associate Editor
Recommendation/decision: major-revision

Comments

Comments to Author: A very recent paper discusses models for exactly the effects being described - it would be very useful for the authors to include this and see whether their results can be described within this physical picture.The reference is: "

Investigating the Effects of Molecular Crowding on the Kinetics of Protein Aggregation”, J.S. Schreck et al. J. Phys. Chem. B, 2020 ASAP.

Reviewer #1: Review of QRD-D-20-00022

The authors study amyloid fibril formation rates for apo-β-parvalbumin in solvent conditions that mimic in vivo milieu. This is a challenging problem area as little is still known about causes and consequences of aggregation, folding, elongated fiber formation etc. in amyloid contexts. Specifically, in prion contexts, minor conformational variations between 'bad' and 'not bad' amyloids are very small and the structural origin of toxicity still elusive. Attempts to understand role of cell environment, in particular 'crowding' are therefore highly commendable and of interest to a big audience.

Aggregation in presence of macromolecular crowding agents or smaller-molecule 'osmolytes' show that both types of agents accelerate amyloid formation, but elongation step seams faster in macromolecular crowding than with osmolytes. Authors claim that excluded volume effects favor assembled states (both nuclei and amyloid fibrils), while osmolytes stabilize nuclei formation but not elongation. Therefore, they say, amyloid-competent nuclei must be compact with less exposed surface area than the folded monomers. They also note that in contrast to other amyloidogenic folded proteins, that become more resistant to amyloid formation, aggregation of apo-β-parvalbumin is accelerated by cell-like conditions. The reason for this is claimed to be a nucleation process that does not involve large-scale unfolding events. Although crowding effects have been studied before on amyloids, this seems a first example of a folded protein that forms amyloid structures under cell conditions.

The manuscript reads well and the results are interesting, potentially even of greatest impact. I suggest the ms be accepted once the authors have considered the following comments and amended their paper accordingly.

Comments

1. That assembled species be favoured by reduced volume has been pointed out long ago and also studied in detail both theoretically and experimentally by Minton and co-workers. This is as I see it a simple concentration effect via the law of mass action. The kinetic effects would follow similar increased concentration behaviour. There are as I see them three different causes that may explain in full or in part the observed effects of 'crowding' agents: a) excluded volume (entropic concentration) effects, b) osmotic (including dehydration) effects, c) attractive chemical interactions. Although the manuscript is well written and different effects are somewhat discussed, these three effects should be further discussed. E.g., Ficoll is a roughly globular correspondent to the macromolecular dextran (both dehydrating and both strongly hydrophilic) while, by contrast, PEG is both hydrophilic and hydrophobic. Ficoll has at normal pH a negative charge and is known to 'shield' proteins. I think some arguments are already there , like 'Ficoll 70 did not affect the secondary structure of apo- β-PV' and 'This supports that the observed Ficoll 70 effect is due to excluded volume changes and not chemical interactions.', but they should be articulated more clearly. In 'This magnitude is in accord with scaled particle theory predictions (thus, based on entropic interactions/excluded volume) of amyloid fibril growth' I think, by the way, 'entropic effects' would be more appropriate to say as entropy by definition does not involve interactions.

2. Referring to the previous point, there are several publications some of which ought to be cited and potentially discussed in relation to the effects found for PEG and Ficoll. A) B. Feng PNAS 2019Hydrophobic catalysis and a potential biological role of DNA unstacking where it is demonstrated that in addition to excluded volume and osmolytic effects also direct interactions with hydrophobic moieties are very important. Would hydrophobic interactions with PEG possibly affect the here investigated amyloid reaction? B) Davis & Gruebele 2018 Non‐Steric Interactions Predict the Trend and Steric Interactions the Offset of Protein Stability in Cells. C) Zaslawsky, Mestechkina, Rogozhin J.Chromatography1983. relative hydrophobicities of the proteins, in Ficoll-Dextran biphasic systems D) Nasreen et al Biomolecules 2020. Interactions Under Crowding Milieu: Chemical-Induced Denaturation Biomolecules 2020.

3. The main message of the paper is the unusual behaviour of the apo-beta-PV under cell-like crowded conditions and that nucleation cannot involve large-scale protein unfolding However, it is not explained why this finding could be earth-shattering. It is mentioned in passing that 'the folded dimers, formed transiently, can form inter-protein disulfide bonds'. Is this the reason and then so what?I think the authors should elaborate more on why their finding is important - with some freedom to speculate as Discovery encourages. For example, can the finding of a nucleation process that does not involve large-scale unfolding events indicate mechanistic features that can give a clue about when disease can be expected and potentially also how it may be mitigated or cured?

4. It would have been easier to read the paper if the figure captions had given a hint about what they show.What do the AFM pictures show?Clearly in Fig. 1 that Ficoll does not change the shape of the fibrils. But in Fig 3 what happens in sucrose and glycerol, and what do the differences between them mean, is not so clear.

5. It says based on conserved CD (Figure 1D) "the presence of Ficoll 70 did not affect the secondary structure of apo- β-PV". But what about effect of PEG on CD?

MINOR POINTS

Introduction, 1st page: 'to cope with stress' . What kind of stress, osmotic stress?

based on entropic interactions/excluded volume… better: based on entropic effects/excluded volume…

Conclusion: this sometimes resultshould read this sometimes results

macromolecular crowding speed.. should read macromolecular crowding speeds..

Reviewer #2: Analysis of the work done: In this work authors have claimed the biomimicking of cell like conditions to accelerate the fibrillation of apo-β-parvalbumin by adding a well-known macromolecularly crowding agent Ficoll 70 where apo-β-parvalbumin undergoes fibrillation without undergoing unfolding step required during conventional in vitro fibrillation of proteins. For comparison authors have also studied fibrillation in the presence of protective osmolytes like glycerol and sucrose which shows long elongation period in comparison to the Fycoll 70.

Authors Comments:

1) The fibrillation of proteins into amyloid-beta without unfolding step is well reported before (Chiti et al.Biophysical Journal, 2005, 89, 4234).Therefore, authors need to explain what is the background of their statement that it's the first report where fibrillation without unfolding step is achieved or protein destabilization is achieved.

2) Authors must cite other relevant references pertaining to effect macromolecular crowding on speeding up the fibrillation (eg. Freire et al. Commun. Mater. 2020, 34) where the fibrillation occurred instantaneously in a natural macromolecular crowding medium.

3) Authors have claimed that they are mimicking the natural macromolecular crowded media (NMCM), however they have used just one crowding agent. On the other hand NMCM is always heterogenous, therefore it would be more correct to use a mixture of crowding agent to support their statement.

4) I am agree with authors comments that excluded volume effect due to molecular crowding can drive protein-protein interactions to form diamers or multimers via disulfide linkage. However, for fibrillation to happen via self-assembly the driving force is generally the hydrophobic or H-bonding interactions. If the unfolding doesn't happen then how did the hydophobic residues present inside the protein core caused fibrillation an if they do not do authors have any evidence of H-bonding interactions.

5) Authors have shown the effect of crowding agent and osmolyte in a counteractive manner separately. It would be more authentic to show their effect in a mixed system. Because biologically in the cell, macromolecules and osmolytes coexists. Therefore, authors are suggested to do another fibrillation experiment in a mixture of macromolecule + osmolyte.

6) Although excluded volume is one of the factor but authors must present some concrete evidence to support their argument. The CD spectra shown in Fig. 1D (at 0 mg Fycol 70 and 50 mg Fycol 70) show no difference. Where are the CD spectra of typical fibrils ? Authors haven't shown any CD spectra corresponding to cross-beta structure even at high concentration of Fycol 70 or osmolytes which they claim are forming fibrils. Just ThT cannot be considered as absolute evidence since many amorphous aggregates also show rise in fluorescence of ThT. AFM images are showing fibrils but in AFM samples are prepared following a long process of washing and drying. Therefore, please show CD spectra of fibrils showing cross-beta structure in solution.

Decision: Acceptable after Major Revision

Review: Response to crowded conditions reveals compact nucleus for amyloid formation of folded protein — R1/PR4

Published online by Cambridge University Press:  19 January 2021
DOI: https://doi.org/10.1017/qrd.2020.17.pr4 [Opens in a new window]
Pankaj Bharmoria [Opens in a new window] Applied Chemistry, Chalmers University, Sweden
Date of review:  03 December 2020
Revision round: 1
Role: reviewer
Recommendation/decision: accept

Conflict of interest statement

Reviewer declares none.

Comments

Comments to Author: I think authors have addressed the comments nicely. The have added the CD spectra required to show the cross-Beta structure upon fibrillation and also answered other queries raised in my previous review report.

I give my consent for publication of this work

Recommendation: Response to crowded conditions reveals compact nucleus for amyloid formation of folded protein — R1/PR5

Published online by Cambridge University Press:  19 January 2021
DOI: https://doi.org/10.1017/qrd.2020.17.pr5 [Opens in a new window]
Steven G Boxer Stanford University, United States
Revision round: 1
Role: Associate Editor
Recommendation/decision: accept

Comments

Comments to Author: Reviewer #2: I think authors have addressed the comments nicely. The have added the CD spectra required to show the cross-Beta structure upon fibrillation and also answered other queries raised in my previous review report.

I give my consent for publication of this work