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Siu HW, Hauser K. Observation of Oligomeric States Indicates a High Structural Flexibility Required for the Onset of Polyglutamine Fibrillization. J Phys Chem Lett 2022; 13:4543-4548. [PMID: 35580015 DOI: 10.1021/acs.jpclett.2c00203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Polyglutamine (polyQ) diseases are caused by misfolding and aggregation of expanded polyQ tracts in the affected protein. PolyQ fibrils have been studied in detail; however, less is known about oligomeric precursor states. By a combination of time-resolved temperature-jump (T-jump) infrared (IR) spectroscopy and an appropriately tailored polyQ model peptide, we succeeded in disentangling conformational dynamics in the heterogeneous ensemble of states evolving during aggregation. Individual structural elements could be differentiated by IR-specific signatures, i.e., hairpin monomers, β-structured oligomers, and disordered structure. Submillisecond dynamics were observed for early oligomeric states in contrast to the slow dynamics of fibril growth. We propose that a high structural flexibility of oligomers is required to initiate fibril formation, but not after a fibrillar structure has consolidated and the fibril just grows. Our study reveals that structural flexibility changes at different stages in the aggregation process, from fibril initiation to fibril growth.
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Affiliation(s)
- Ho-Wah Siu
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Karin Hauser
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
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2
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PolyQ aggregation studied by model peptides with intrinsic tryptophan fluorophores. Biophys Chem 2022; 284:106782. [DOI: 10.1016/j.bpc.2022.106782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/15/2022] [Accepted: 02/15/2022] [Indexed: 11/02/2022]
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3
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Klocke JL, Kottke T. A quantum cascade laser setup for studying irreversible photoreactions in H 2O with nanosecond resolution and microlitre consumption. Phys Chem Chem Phys 2020; 22:26459-26467. [PMID: 33185227 DOI: 10.1039/d0cp03164j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Time-resolved infrared spectroscopy on irreversible reactions requires in general an exchange of sample for thousands of acquisitions leading to high sample consumption. Here, we present a setup employing a modern quantum cascade laser (QCL) as a probe light source to record time-resolved difference spectra of irreversible photoreactions in H2O. The combination of the focused QCL with a pressure-tolerant flow cell and a micrometre stage orthogonal to the flow allowed us to drastically reduce the sample consumption. We investigated the irreversible photoreduction of the cofactor flavin mononucleotide (FMN) in H2O, which is a common reaction taking place in biological photoreceptors. A broad time range from 20 nanoseconds to 1 second was accessible, because the approach minimized any signal drift by the flow. Kinetics were recorded at 46 selected wavenumbers consuming 12 microlitres for a complete dataset. The tuning range of 1490-1740 cm-1 included relevant carbonyl vibrations and the region of strong water absorption at around 1650 cm-1. A continuous dataset in the spectral dimension was generated by applying a fit with a sum of Lorentzians. Subsequent global analysis allowed us to resolve reference spectra and kinetics of the photoreaction proceeding from the triplet excited state via the intermediate flavin anion radical to the product, the fully reduced state of FMN. Accordingly, the neutral radical state is not populated in the disproportionation. The approach strongly facilitates the spectroscopic access to irreversible reactions of flavin-containing photoreceptors and photoenzymes with high time resolution and small sample consumption.
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Affiliation(s)
- Jessica L Klocke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
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4
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Siu HW, Heck B, Kovermann M, Hauser K. Template-assisted design of monomeric polyQ models to unravel the unique role of glutamine side chains in disease-related aggregation. Chem Sci 2020; 12:412-426. [PMID: 33552461 PMCID: PMC7863018 DOI: 10.1039/d0sc05299j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/28/2020] [Indexed: 01/28/2023] Open
Abstract
PolyQ model peptides reveal the effect of individual glutamine side chains on fibril formation.
Expanded polyglutamine (polyQ) sequences cause numerous neurodegenerative diseases which are accompanied by the formation of polyQ fibrils. The unique role of glutamines in the aggregation onset is undoubtedly accepted and a lot structural data of the fibrils have been acquired, however side-chain specific structural dynamics inducing oligomerization are not well understood yet. To analyze spectroscopically the nucleation process, we designed various template-assisted glutamine-rich β-hairpin monomers mimicking the structural motif of a polyQ fibril. In a top-down strategy, we use a template which forms a well-defined stable hairpin in solution, insert polyQ-rich sequences into each strand and monitor the effects of individual glutamines by NMR, CD and IR spectroscopic approaches. The design was further advanced by alternating glutamines with other amino acids (T, W, E, K), thereby enhancing the solubility and increasing the number of cross-strand interacting glutamine side chains. Our spectroscopic studies reveal a decreasing hairpin stability with increased glutamine content and demonstrate the enormous impact of only a few glutamines – far below the disease threshold – to destabilize structure. Furthermore, we could access sub-ms conformational dynamics of monomeric polyQ-rich peptides by laser-excited temperature-jump IR spectroscopy. Both, the increased number of interacting glutamines and higher concentrations are key parameters to induce oligomerization. Concentration-dependent time-resolved IR measurements indicate an additional slower kinetic phase upon oligomer formation. The here presented peptide models enable spectroscopic molecular analyses to distinguish between monomer and oligomer dynamics in the early steps of polyQ fibril formation and in a side-chain specific manner.
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Affiliation(s)
- Ho-Wah Siu
- Department of Chemistry , University of Konstanz , 78457 Konstanz , Germany . ;
| | - Benjamin Heck
- Department of Chemistry , University of Konstanz , 78457 Konstanz , Germany . ;
| | - Michael Kovermann
- Department of Chemistry , University of Konstanz , 78457 Konstanz , Germany . ;
| | - Karin Hauser
- Department of Chemistry , University of Konstanz , 78457 Konstanz , Germany . ;
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5
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Scheerer D, Chi H, McElheny D, Keiderling TA, Hauser K. Enhanced Sensitivity to Local Dynamics in Peptides by Use of Temperature-Jump IR Spectroscopy and Isotope Labeling. Chemistry 2020; 26:3524-3534. [PMID: 31782580 PMCID: PMC7155074 DOI: 10.1002/chem.201904497] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Indexed: 11/12/2022]
Abstract
Site-specific isotopic labeling of molecules is a widely used approach in IR spectroscopy to resolve local contributions to vibrational modes. The induced frequency shift of the corresponding IR band depends on the substituted masses, as well as on hydrogen bonding and vibrational coupling. The impact of these different factors was analyzed with a designed three-stranded β-sheet peptide and by use of selected 13 C isotope substitutions at multiple positions in the peptide backbone. Single-strand labels give rise to isotopically shifted bands at different frequencies, depending on the specific sites; this demonstrates sensitivity to the local environment. Cross-strand double- and triple-labeled peptides exhibited two resolved bands that could be uniquely assigned to specific residues, the equilibrium IR spectra of which indicated only weak local-mode coupling. Temperature-jump IR laser spectroscopy was applied to monitor structural dynamics and revealed an impressive enhancement of the isotope sensitivity to both local positions and coupling between them, relative to that of equilibrium FTIR spectroscopy. Site-specific relaxation rates were altered upon the introduction of additional cross-strand isotopes. Likewise, the rates for the global β-sheet dynamics were affected in a manner dependent on the distinct relaxation behavior of the labeled oscillator. This study reveals that isotope labels provide not only local structural probes, but rather sense the dynamic complexity of the molecular environment.
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Affiliation(s)
- David Scheerer
- Department of Chemistry, University of Konstanz, 78457, Konstanz, Germany
| | - Heng Chi
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA.,Jiangsu Food and Pharmaceutical Science College, Huai'an, P.R. China
| | - Dan McElheny
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | | | - Karin Hauser
- Department of Chemistry, University of Konstanz, 78457, Konstanz, Germany
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6
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Minnes L, Greetham GM, Shaw DJ, Clark IP, Fritzsch R, Towrie M, Parker AW, Henry AJ, Taylor RJ, Hunt NT. Uncovering the Early Stages of Domain Melting in Calmodulin with Ultrafast Temperature-Jump Infrared Spectroscopy. J Phys Chem B 2019; 123:8733-8739. [PMID: 31557034 PMCID: PMC7007250 DOI: 10.1021/acs.jpcb.9b08870] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
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The signaling protein
calmodulin (CaM) undergoes a well-known change
in secondary structure upon binding Ca2+, but the structural
plasticity of the Ca2+-free apo state
is linked to CaM functionality. Variable temperature studies of apo-CaM indicate two structural transitions at 46 and 58
°C that are assigned to melting of the C- and N-terminal domains,
respectively, but the molecular mechanism of domain unfolding is unknown.
We report temperature-jump time-resolved infrared (IR) spectroscopy
experiments designed to target the first steps in the C-terminal domain
melting transition of human apo-CaM. A comparison
of the nonequilibrium relaxation of apo-CaM with
the more thermodynamically stable holo-CaM, with
4 equiv of Ca2+ bound, shows that domain melting of apo-CaM begins on microsecond time scales with α-helix
destabilization. These observations enable the assignment of previously
reported dynamics of CaM on hundreds of microsecond time scales to
thermally activated melting, producing a complete mechanism for thermal
unfolding of CaM.
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Affiliation(s)
- Lucy Minnes
- Department of Physics, SUPA , University of Strathclyde , Glasgow G4 0NG , United Kingdom
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , United Kingdom
| | | | - Ian P Clark
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , United Kingdom
| | - Robby Fritzsch
- Department of Physics, SUPA , University of Strathclyde , Glasgow G4 0NG , United Kingdom
| | - Michael Towrie
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , United Kingdom
| | - Anthony W Parker
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , United Kingdom
| | | | | | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute , University of York , Heslington, York YO10 5DD , United Kingdom
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7
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Scheerer D, Chi H, McElheny D, Keiderling TA, Hauser K. Isotopically Site-Selected Dynamics of a Three-Stranded β-Sheet Peptide Detected with Temperature-Jump Infrared-Spectroscopy. J Phys Chem B 2018; 122:10445-10454. [PMID: 30372071 DOI: 10.1021/acs.jpcb.8b08336] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Infrared detected temperature-jump (T-jump) spectroscopy and site-specific isotopic labeling were applied to study a model three-stranded β-sheet peptide with the goal of individually probing the dynamics of strand and turn structural elements. This peptide had two DPro-Gly (pG) turn sequences to stabilize the two component hairpins, which were labeled with 13C═O on each of the Gly residues to resolve them spectroscopically. Labeling the second turn on the amide preceding the DPro (Xxx-DPro amide) provided an alternate turn label as a control. Placing 13C═O labels on specific in-strand residues gave shifted modes that overlap the Xxx-DPro amide I' modes. Their impact could be separated from the turn dynamics by a novel difference transient analysis approach. Fourier-transform infrared spectra were modeled with density functional theory-computations which showed the local, isotope-selected vibrations were effectively uncoupled from the other amide I modes. Our T-jump dynamics results, combined with nuclear magnetic resonance structures and equilibrium spectral measurements, showed the first turn to be most stable and best formed with the slowest dynamics, whereas the second turn and first strand (N-terminus) had similar dynamics, and the third strand (C-terminus) had the fastest dynamics and was the least structured. The relative dynamics of the strands, Xxx-DPro amides, and 13C-labeled Gly residues on the turns also qualitatively corresponded to molecular dynamics (MD) simulations of turn and strand fluctuations. MD trajectories indicated the turns to be bistable, with the first turn being Type I' and the second turn flipping from I' to II'. The differences in relaxation times for each turn and the separate strands revealed that the folding process of this turn-stabilized β-sheet structure proceeds in a multistep process.
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Affiliation(s)
- David Scheerer
- Department of Chemistry , University of Konstanz , 78457 Konstanz , Germany
| | - Heng Chi
- Department of Chemistry , University of Illinois at Chicago , 60607-7061 Chicago , Illinois , United States.,Jiangsu Food and Pharmaceutical Science College , 223003 Huai'an , China
| | - Dan McElheny
- Department of Chemistry , University of Illinois at Chicago , 60607-7061 Chicago , Illinois , United States
| | - Timothy A Keiderling
- Department of Chemistry , University of Illinois at Chicago , 60607-7061 Chicago , Illinois , United States
| | - Karin Hauser
- Department of Chemistry , University of Konstanz , 78457 Konstanz , Germany
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8
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Scheerer D, Chi H, McElheny D, Samer A, Keiderling TA, Hauser K. Role of Aromatic Cross-Links in Structure and Dynamics of Model Three-Stranded β-Sheet Peptides. J Phys Chem A 2018; 122:543-553. [DOI: 10.1021/acs.jpca.7b10190] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- David Scheerer
- Department
of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Heng Chi
- Department
of Chemistry, University of Illinois at Chicago, Chicago, Illinois United States
- Jiangsu Food and Pharmaceutical Science College, Huai’an, China
| | - Dan McElheny
- Department
of Chemistry, University of Illinois at Chicago, Chicago, Illinois United States
| | - Ayesha Samer
- Department
of Chemistry, University of Illinois at Chicago, Chicago, Illinois United States
| | - Timothy A. Keiderling
- Department
of Chemistry, University of Illinois at Chicago, Chicago, Illinois United States
| | - Karin Hauser
- Department
of Chemistry, University of Konstanz, 78457 Konstanz, Germany
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