1
|
Singla D, Bhattacharya M. Salt-Induced Dissolution of Protein Aggregates. J Phys Chem B 2022; 126:8760-8770. [PMID: 36283072 DOI: 10.1021/acs.jpcb.2c06555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Protein aggregation is mediated by a complex interplay of noncovalent interactions and is associated with a broad range of aspects from debilitating human diseases to the food industry and therapeutic biotechnology. Deciphering the intricate roles of noncovalent interactions is of paramount importance for the design of effective inhibitory and disaggregation strategies, which remains a formidable challenge. By using a combination of spectroscopic and microscopic tools, here we show that the surfactant-mediated protein aggregation can be modulated by an intriguing interplay of hydrophobic and electrostatic effects. Additionally, our results illuminate the unique role of salt as a potent disaggregation inducer that alters the protein-surfactant electrostatic interactions and triggers the dissolution of preformed protein aggregates resulting in restoring the native protein structure. This unusual salt-induced dissolution and refolding offers a unique approach to regulating the balance between protein self-assembly and disassembly and will offer a potent strategy to design electrostatically targeted inhibitors.
Collapse
Affiliation(s)
- Deepika Singla
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Thapar Technology Campus, Bhadson Road, Patiala, Punjab147004, India
| | - Mily Bhattacharya
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Thapar Technology Campus, Bhadson Road, Patiala, Punjab147004, India
| |
Collapse
|
2
|
Mahapatra S, Sarbahi A, Madhu P, Swasthi HM, Sharma A, Singh P, Mukhopadhyay S. Sub-stoichiometric Hsp104 regulates the genesis and persistence of self-replicable amyloid seeds of Sup35 prion domain. J Biol Chem 2022; 298:102143. [PMID: 35714774 PMCID: PMC9304785 DOI: 10.1016/j.jbc.2022.102143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 11/21/2022] Open
Abstract
Prion-like self-perpetuating conformational conversion of proteins is involved in both transmissible neurodegenerative diseases in mammals and non-Mendelian inheritance in yeast. The transmissibility of amyloid-like aggregates is dependent on the stoichiometry of chaperones such as heat shock proteins (Hsps), including disaggregases. To provide the mechanistic underpinnings of the formation and persistence of prefibrillar amyloid seeds, we investigated the role of substoichiometric Hsp104 on the in vitro amyloid aggregation of the prion domain (NM-domain) of Saccharomyces cerevisiae Sup35. At low substoichiometric concentrations, we show Hsp104 exhibits a dual role: it considerably accelerates the formation of prefibrillar species by shortening the lag phase but also prolongs their persistence by introducing unusual kinetic halts and delaying their conversion into mature amyloid fibers. Additionally, Hsp104-modulated amyloid species displayed a better seeding capability compared to NM-only amyloids. Using biochemical and biophysical tools coupled with site-specific dynamic readouts, we characterized the distinct structural and dynamical signatures of these amyloids. We reveal that Hsp104-remodeled amyloidogenic species are compositionally diverse in prefibrillar aggregates and are packed in a more ordered fashion compared to NM-only amyloids. Finally, we show these Hsp104-remodeled, conformationally distinct NM aggregates display an enhanced autocatalytic self-templating ability that might be crucial for phenotypic outcomes. Taken together, our results demonstrate that substoichiometric Hsp104 promotes compositional diversity and conformational modulations during amyloid formation, yielding effective prefibrillar seeds that are capable of driving prion-like Sup35 propagation. Our findings underscore the key functional and pathological roles of substoichiometric chaperones in prion-like propagation.
Collapse
Affiliation(s)
- Sayanta Mahapatra
- Centre for Protein Science, Design and Engineering; Department of Biological Sciences
| | - Anusha Sarbahi
- Centre for Protein Science, Design and Engineering; Department of Biological Sciences
| | - Priyanka Madhu
- Centre for Protein Science, Design and Engineering; Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Hema M Swasthi
- Centre for Protein Science, Design and Engineering; Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Abhishek Sharma
- CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Priyanka Singh
- CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering; Department of Biological Sciences; Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.
| |
Collapse
|
4
|
Fernandes DD, Bamrah J, Kailasam S, Gomes GNW, Li Y, Wieden HJ, Gradinaru CC. Characterization of Fluorescein Arsenical Hairpin (FlAsH) as a Probe for Single-Molecule Fluorescence Spectroscopy. Sci Rep 2017; 7:13063. [PMID: 29026195 PMCID: PMC5638890 DOI: 10.1038/s41598-017-13427-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 09/21/2017] [Indexed: 01/27/2023] Open
Abstract
In recent years, new labelling strategies have been developed that involve the genetic insertion of small amino-acid sequences for specific attachment of small organic fluorophores. Here, we focus on the tetracysteine FCM motif (FLNCCPGCCMEP), which binds to fluorescein arsenical hairpin (FlAsH), and the ybbR motif (TVLDSLEFIASKLA) which binds fluorophores conjugated to Coenzyme A (CoA) via a phosphoryl transfer reaction. We designed a peptide containing both motifs for orthogonal labelling with FlAsH and Alexa647 (AF647). Molecular dynamics simulations showed that both motifs remain solvent-accessible for labelling reactions. Fluorescence spectra, correlation spectroscopy and anisotropy decay were used to characterize labelling and to obtain photophysical parameters of free and peptide-bound FlAsH. The data demonstrates that FlAsH is a viable probe for single-molecule studies. Single-molecule imaging confirmed dual labeling of the peptide with FlAsH and AF647. Multiparameter single-molecule Förster Resonance Energy Transfer (smFRET) measurements were performed on freely diffusing peptides in solution. The smFRET histogram showed different peaks corresponding to different backbone and dye orientations, in agreement with the molecular dynamics simulations. The tandem of fluorophores and the labelling strategy described here are a promising alternative to bulky fusion fluorescent proteins for smFRET and single-molecule tracking studies of membrane proteins.
Collapse
Affiliation(s)
- Dennis D Fernandes
- Department of Physics, University of Toronto, Toronto, Ontario, M5S 1A7, Canada.
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, L5L 1C6, Canada.
| | - Jasbir Bamrah
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, L5L 1C6, Canada
| | - Senthilkumar Kailasam
- Alberta RNA Research & Training Institute, Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta, T1K 3M4, Canada
| | - Gregory-Neal W Gomes
- Department of Physics, University of Toronto, Toronto, Ontario, M5S 1A7, Canada
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, L5L 1C6, Canada
| | - Yuchong Li
- Department of Physics, University of Toronto, Toronto, Ontario, M5S 1A7, Canada
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, L5L 1C6, Canada
| | - Hans-Joachim Wieden
- Alberta RNA Research & Training Institute, Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta, T1K 3M4, Canada
| | - Claudiu C Gradinaru
- Department of Physics, University of Toronto, Toronto, Ontario, M5S 1A7, Canada.
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, L5L 1C6, Canada.
| |
Collapse
|
5
|
Jain N, Narang D, Bhasne K, Dalal V, Arya S, Bhattacharya M, Mukhopadhyay S. Direct Observation of the Intrinsic Backbone Torsional Mobility of Disordered Proteins. Biophys J 2017; 111:768-774. [PMID: 27558720 DOI: 10.1016/j.bpj.2016.07.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/14/2016] [Accepted: 07/20/2016] [Indexed: 12/20/2022] Open
Abstract
The fundamental backbone dynamics of unfolded proteins arising due to intrinsic ϕ-ψ dihedral angle fluctuations dictate the course of protein folding, binding, assembly, and function. These internal fluctuations are also critical for protein misfolding associated with a range of human diseases. However, direct observation and unambiguous assignment of this inherent dynamics in chemically denatured proteins is extremely challenging due to various experimental limitations. To directly map the backbone torsional mobility in the ϕ-ψ dihedral angle space, we used a model intrinsically disordered protein, namely, α-synuclein, that adopts an expanded state under native conditions. We took advantage of nonoccurrence of tryptophan in α-synuclein and created a number of single-tryptophan variants encompassing the entire polypeptide chain. We then utilized highly sensitive picosecond time-resolved fluorescence depolarization measurements that allowed us to discern the site-specific torsional relaxation at a low protein concentration under physiological conditions. For all the locations, the depolarization kinetics exhibited two well-separated rotational-correlation-time components. The shorter, subnanosecond component arises due to the local mobility of the indole side chain, whereas the longer rotational-correlation-time component (1.37 ± 0.15 ns), independent of global tumbling, represents a characteristic timescale for short-range conformational exchange in the ϕ-ψ dihedral space. This correlation time represents an intrinsic timescale for torsional relaxation and is independent of position, which is expected for an extended polypeptide chain having little or no propensity to form persistent structures. We were also able to capture this intrinsic timescale at the N-terminal unstructured domain of the prion protein. Our estimated timescale of the segmental mobility is similar to that of unfolded proteins studied by nuclear magnetic resonance in conjunction with molecular dynamics simulations. Our results have broader implications for a diverse range of functionally and pathologically important intrinsically disordered proteins and disordered regions.
Collapse
Affiliation(s)
- Neha Jain
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, S.A.S. Nagar, Mohali, Punjab, India
| | - Dominic Narang
- Centre for Protein Science, Design, and Engineering, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, S.A.S. Nagar, Mohali, Punjab, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, S.A.S. Nagar, Mohali, Punjab, India
| | - Karishma Bhasne
- Centre for Protein Science, Design, and Engineering, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, S.A.S. Nagar, Mohali, Punjab, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, S.A.S. Nagar, Mohali, Punjab, India
| | - Vijit Dalal
- Centre for Protein Science, Design, and Engineering, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, S.A.S. Nagar, Mohali, Punjab, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, S.A.S. Nagar, Mohali, Punjab, India
| | - Shruti Arya
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, S.A.S. Nagar, Mohali, Punjab, India
| | - Mily Bhattacharya
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, S.A.S. Nagar, Mohali, Punjab, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design, and Engineering, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, S.A.S. Nagar, Mohali, Punjab, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, S.A.S. Nagar, Mohali, Punjab, India; Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, S.A.S. Nagar, Mohali, Punjab, India.
| |
Collapse
|