1
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Liu J, Gensberger-Reigl S, Zenker H, Schichtl TM, Utz W, Pischetsrieder M. Regioselective analysis of heat-induced conformational changes of β-lactoglobulin by quantitative liquid chromatography-mass spectrometry analysis of chemical labeling kinetics. Food Chem 2024; 460:140716. [PMID: 39106758 DOI: 10.1016/j.foodchem.2024.140716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/08/2024] [Accepted: 07/28/2024] [Indexed: 08/09/2024]
Abstract
β-Lactoglobulin is a main allergen in cow's milk; its allergenicity is strongly impacted by processing. To understand heat-induced epitope-specific effects, the present study analyzed regiospecific conformational changes of heated native β-lactoglobulin variant A (BLG-A). Complementary fluorescence spectroscopy methods indicated two denaturation phases comprising minor sequential conformational changes (25-75 °C) and complete transitions (80-90 °C). Regioselective conformational changes of BLG-A in the native state (25 °C), sequential (70 °C) and complete transition (90 °C) were determined by quantitative liquid chromatography-mass spectrometry analysis of chemical labeling kinetics covering 14 lysine residues and the N-terminus. Conformational changes in two phases were observed for N-terminus, K8 (both N-terminal chain), K60 (β-sheet C), K75 (β-sheet D), K77 (DE loop), K83 (β-sheet E), K100 and K101 (FG loop). The residues K14 (β-sheet A1), K47 (β-sheet B), K69, K70 (both β-sheet D), and K91 (β-sheet F) were not involved in conformational changes.
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Affiliation(s)
- Jiajia Liu
- Food Chemistry, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany.
| | - Sabrina Gensberger-Reigl
- Food Chemistry, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany.
| | - Hannah Zenker
- Food Chemistry, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany.
| | - Theresa Maria Schichtl
- Food Chemistry, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany.
| | - Wolfgang Utz
- Food Chemistry, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany.
| | - Monika Pischetsrieder
- Food Chemistry, Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany; FAU NeW - Research Center New Bioactive Compounds, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany.
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2
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Feng RR, Wang M, Zhang W, Gai F. Unnatural Amino Acids for Biological Spectroscopy and Microscopy. Chem Rev 2024; 124:6501-6542. [PMID: 38722769 DOI: 10.1021/acs.chemrev.3c00944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.
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Affiliation(s)
- Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Manxi Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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3
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Hawkins AP, Edmeades AE, Hutchison CDM, Towrie M, Howe RF, Greetham GM, Donaldson PM. Laser induced temperature-jump time resolved IR spectroscopy of zeolites. Chem Sci 2024; 15:3453-3465. [PMID: 38455000 PMCID: PMC10915812 DOI: 10.1039/d3sc06128k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/29/2024] [Indexed: 03/09/2024] Open
Abstract
Combining pulsed laser heating and time-resolved infrared (TR-IR) absorption spectroscopy provides a means of initiating and studying thermally activated chemical reactions and diffusion processes in heterogeneous catalysts on timescales from nanoseconds to seconds. To this end, we investigated single pulse and burst laser heating in zeolite catalysts under realistic conditions using TR-IR spectroscopy. 1 ns, 70 μJ, 2.8 μm laser pulses from a Nd:YAG-pumped optical parametric oscillator were observed to induce temperature-jumps (T-jumps) in zeolite pellets in nanoseconds, with the sample cooling over 1-3 ms. By adopting a tightly focused beam geometry, T-jumps as large as 145 °C from the starting temperature were achieved, demonstrated through comparison of the TR-IR spectra with temperature dependent IR absorption spectra and three dimensional heat transfer modelling using realistic experimental parameters. The simulations provide a detailed understanding of the temperature distribution within the sample and its evolution over the cooling period, which we observe to be bi-exponential. These results provide foundations for determining the magnitude of a T-jump in a catalyst/adsorbate system from its absorption spectrum and physical properties, and for applying T-jump TR-IR spectroscopy to the study of reactive chemistry in heterogeneous catalysts.
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Affiliation(s)
- Alexander P Hawkins
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory Didcot Oxon OX11 0QX UK
| | - Amy E Edmeades
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory Didcot Oxon OX11 0QX UK
| | - Christopher D M Hutchison
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory Didcot Oxon OX11 0QX UK
| | - Michael Towrie
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory Didcot Oxon OX11 0QX UK
| | - Russell F Howe
- Department of Chemistry, University of Aberdeen Aberdeen AB24 3UE UK
| | - Gregory M Greetham
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory Didcot Oxon OX11 0QX UK
| | - Paul M Donaldson
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory Didcot Oxon OX11 0QX UK
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4
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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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5
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King M, Avaro JT, Peter C, Hauser K, Gebauer D. Solvent-mediated isotope effects strongly influence the early stages of calcium carbonate formation: exploring D 2O vs. H 2O in a combined computational and experimental approach. Faraday Discuss 2022; 235:36-55. [PMID: 35388817 DOI: 10.1039/d1fd00078k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In experimental studies, heavy water (D2O) is employed, e.g., so as to shift the spectroscopic solvent background, but any potential effects of this solvent exchange on reaction pathways are often neglected. While the important role of light water (H2O) during the early stages of calcium carbonate formation has been realized, studies into the actual effects of aqueous solvent exchanges are scarce. Here, we present a combined computational and experimental approach to start to fill this gap. We extended a suitable force field for molecular dynamics (MD) simulations. Experimentally, we utilised advanced titration assays and time-resolved attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy. We find distinct effects in various mixtures of the two aqueous solvents, and in pure H2O or D2O. Disagreements between the computational results and experimental data regarding the stabilities of ion associates might be due to the unexplored role of HDO, or an unprobed complex phase behaviour of the solvent mixtures in the simulations. Altogether, however, our data suggest that calcium carbonate formation might proceed "more classically" in D2O. Also, there are indications for the formation of new structures in amorphous and crystalline calcium carbonates. There is huge potential towards further improving the understanding of mineralization mechanisms by studying solvent-mediated isotope effects, also beyond calcium carbonate. Last, it must be appreciated that H2O and D2O have significant, distinct effects on mineralization mechanisms, and that care has to be taken when experimental data from D2O studies are used, e.g., for the development of H2O-based computer models.
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Affiliation(s)
- Michael King
- Department of Chemistry, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Jonathan T Avaro
- Department of Chemistry, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany.,Empa, Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland
| | - Christine Peter
- Department of Chemistry, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Karin Hauser
- Department of Chemistry, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Denis Gebauer
- Institute of Inorganic Chemistry, Leibniz University of Hannover, Callinstr. 9, 30167 Hannover, Germany.
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6
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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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7
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Kubelka GS, Kubelka J. Multi-Probe Equilibrium Analysis of Gradual (Un)Folding Processes. Methods Mol Biol 2022; 2376:161-171. [PMID: 34845609 DOI: 10.1007/978-1-0716-1716-8_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Studies of small proteins that exhibit noncooperative, gradual (un)folding can offer unique insights into the rarely accessible intermediate stages of the protein folding processes. Detailed experimental characterization of these intermediate states requires approaches that utilize multiple site-specific probes of the local structure. Isotopically edited infrared (IR) spectroscopy has emerged as a powerful methodology capable of providing such high-resolution structural information. Labeling of selected amide carbonyls with 13C results in detectable side-bands of amide I' vibrations, which are sensitive to local conformation and/or solvent exposure without introducing any significant structural perturbation to the protein. Incorporation of isotopically labeled amino acids at specific positions can be achieved by the chemical synthesis of the studied proteins. We describe the basic procedures for synthesis of 13C isotopically edited protein samples, experimental IR spectroscopic measurements and analysis of the site-specific equilibrium thermal unfolding of a small protein from the temperature-dependent IR data.
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Affiliation(s)
- Ginka S Kubelka
- Department of Chemistry, University of Wyoming, Laramie, WY, USA
| | - Jan Kubelka
- Department of Chemistry, University of Wyoming, Laramie, WY, USA.
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8
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Adams ZC, Olson EJ, Lopez-Silva TL, Lian Z, Kim AY, Holcomb M, Zimmermann J, Adhikary R, Dawson PE. Direct observation of peptide hydrogel self-assembly. Chem Sci 2022; 13:10020-10028. [PMID: 36128231 PMCID: PMC9430618 DOI: 10.1039/d1sc06562a] [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: 11/24/2021] [Accepted: 07/14/2022] [Indexed: 11/30/2022] Open
Abstract
The characterization of self-assembling molecules presents significant experimental challenges, especially when associated with phase separation or precipitation. Transparent window infrared (IR) spectroscopy leverages site-specific probes that absorb in the “transparent window” region of the biomolecular IR spectrum. Carbon–deuterium (C–D) bonds are especially compelling transparent window probes since they are non-perturbative, can be readily introduced site selectively into peptides and proteins, and their stretch frequencies are sensitive to changes in the local molecular environment. Importantly, IR spectroscopy can be applied to a wide range of molecular samples regardless of solubility or physical state, making it an ideal technique for addressing the solubility challenges presented by self-assembling molecules. Here, we present the first continuous observation of transparent window probes following stopped-flow initiation. To demonstrate utility in a self-assembling system, we selected the MAX1 peptide hydrogel, a biocompatible material that has significant promise for use in drug delivery and medical applications. C–D labeled valine was synthetically introduced into five distinct positions of the twenty-residue MAX1 β-hairpin peptide. Consistent with current structural models, steady-state IR absorption frequencies and linewidths of C–D bonds at all labeled positions indicate that these side chains occupy a hydrophobic region of the hydrogel and that the motion of side chains located in the middle of the hairpin is more restricted than those located on the hairpin ends. Following a rapid change in ionic strength to initiate self-assembly, the peptide absorption spectra were monitored as function of time, allowing determination of site-specific time constants. We find that within the experimental resolution, MAX1 self-assembly occurs as a cooperative process. These studies suggest that stopped-flow transparent window FTIR can be extended to other time-resolved applications, such as protein folding and enzyme kinetics. To facilitate the characterization of phase-transitioning molecules, site-specific non-perturbative infrared probes are leveraged for continuous observation of the self-assembly of fibrils in a peptide hydrogel following stopped-flow initiation.![]()
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Affiliation(s)
- Zoë C. Adams
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037, USA
| | - Erika J. Olson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037, USA
| | - Tania L. Lopez-Silva
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Zhengwen Lian
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037, USA
| | - Audrey Y. Kim
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037, USA
| | - Matthew Holcomb
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037, USA
| | - Jörg Zimmermann
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037, USA
| | - Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037, USA
| | - Philip E. Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037, USA
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9
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Bozovic O, Jankovic B, Hamm P. Using azobenzene photocontrol to set proteins in motion. Nat Rev Chem 2021; 6:112-124. [PMID: 37117294 DOI: 10.1038/s41570-021-00338-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2021] [Indexed: 02/06/2023]
Abstract
Controlling the activity of proteins with azobenzene photoswitches is a potent tool for manipulating their biological function. With the help of light, it is possible to change binding affinities, control allostery or manipulate complex biological processes, for example. Additionally, owing to their intrinsically fast photoisomerization, azobenzene photoswitches can serve as triggers that initiate out-of-equilibrium processes. Such switching of the activity initiates a cascade of conformational events that can be accessed with time-resolved methods. In this Review, we show how the potency of azobenzene photoswitching can be combined with transient spectroscopic techniques to disclose the order of events and experimentally observe biomolecular interactions in real time. This strategy will further our understanding of how a protein can accommodate, adapt and readjust its structure to answer an incoming signal, revealing more of the dynamical character of proteins.
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10
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Spekowius J, Pfister R, Helbing J. Folding and Unfolding of the Tryptophan Zipper in the Presence of Two Thioamide Substitutions. J Phys Chem B 2021; 125:7662-7670. [PMID: 34232040 DOI: 10.1021/acs.jpcb.1c03327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We studied the stability and folding and unfolding kinetics of the tryptophan zipper, containing different double thioamide subsitutions. Conformation change was triggered by photoisomerization of an integrated AMPP photoswitch in the turn region of the hairpin, and transient spectra were recorded in the deep UV and the mid-IR, covering the time window of the (un)folding transition from picoseconds to tens of microseconds. Thio-substitution of inward-pointing backbone carbonyls was found to strongly destabilize the β-hairpin structures, whereas molecules with two outward pointing thio-carbonyls showed similar or enhanced stability with respect to the unsubstituted sequence, which we attribute to stronger interstrand hydrogen bonding. Thiolation of the two Trp residues closest to the turn can even prevent the opening of the hairpin after cis-trans isomerization of the switch. The circular dichroism due to the two thioamide ππ* transitions is spectrally well-separated from the aromatic tryptophan signal. It changes upon photoswitching, reflecting a local change in coupling and geometry.
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Affiliation(s)
- Jasmin Spekowius
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Rolf Pfister
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Jan Helbing
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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11
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Zhang X, Chen X, Kuroda DG. Computing the frequency fluctuation dynamics of highly coupled vibrational transitions using neural networks. J Chem Phys 2021; 154:164514. [PMID: 33940799 DOI: 10.1063/5.0044911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The description of frequency fluctuations for highly coupled vibrational transitions has been a challenging problem in physical chemistry. In particular, the complexity of their vibrational Hamiltonian does not allow us to directly derive the time evolution of vibrational frequencies for these systems. In this paper, we present a new approach to this problem by exploiting the artificial neural network to describe the vibrational frequencies without relying on the deconstruction of the vibrational Hamiltonian. To this end, we first explored the use of the methodology to predict the frequency fluctuations of the amide I mode of N-methylacetamide in water. The results show good performance compared with the previous experimental and theoretical results. In the second part, the neural network approach is used to investigate the frequency fluctuations of the highly coupled carbonyl stretch modes for the organic carbonates in the solvation shell of the lithium ion. In this case, the frequency fluctuation predicted by the neural networks shows a good agreement with the experimental results, which suggests that this model can be used to describe the dynamics of the frequency in highly coupled transitions.
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Affiliation(s)
- Xiaoliu Zhang
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Xiaobing Chen
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Daniel G Kuroda
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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12
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Kumar A, Semwal S, Choudhury J. Emerging Implications of the Concept of Hydricity in Energy‐Relevant Catalytic Processes. Chemistry 2021; 27:5842-5857. [DOI: 10.1002/chem.202004499] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/20/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Abhishek Kumar
- Organometallics & Smart Materials Laboratory Department of Chemistry Indian Institute of, Science Education and Research Bhopal Bhopal 462066 India
| | - Shrivats Semwal
- Organometallics & Smart Materials Laboratory Department of Chemistry Indian Institute of, Science Education and Research Bhopal Bhopal 462066 India
| | - Joyanta Choudhury
- Organometallics & Smart Materials Laboratory Department of Chemistry Indian Institute of, Science Education and Research Bhopal Bhopal 462066 India
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13
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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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14
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Ashwood B, Lewis NHC, Sanstead PJ, Tokmakoff A. Temperature-Jump 2D IR Spectroscopy with Intensity-Modulated CW Optical Heating. J Phys Chem B 2020; 124:8665-8677. [PMID: 32902979 DOI: 10.1021/acs.jpcb.0c07177] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pulsed temperature-jump (T-jump) spectroscopy with infrared (IR) detection has been widely used to study biophysical processes occurring from nanoseconds to ∼1 ms with structural sensitivity. However, many systems exhibit structural dynamics on time scales longer than the millisecond barrier that is set by the time scale for thermal relaxation of the sample. We developed a linear and nonlinear infrared spectrometer coupled to an intensity-modulated continuous wave (CW) laser to probe T-jump-initiated chemical reactions from <1 ms to seconds. Time-dependent modulation of the CW laser leads to a <1 ms heating time as well as a constant final temperature (±3%) for the duration of the heating time. Temperature changes of up to 75 °C in D2O are demonstrated, allowing for nonequilibrium measurements inaccessible to standard pulsed optical T-jump setups. T-jump linear absorption, pump-probe, and two-dimensional IR (2D IR) spectroscopy are applied to the unfolding and refolding of ubiquitin and a model intercalated motif (i-motif) DNA sequence, and analysis of the observed signals is used to demonstrate the limits and utility of each method. Overall, the ability to probe temperature-induced chemical processes from <1 ms to many seconds with 2D IR spectroscopy provides multiple new avenues for time-dependent spectroscopy in chemistry and biophysics.
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Affiliation(s)
- Brennan Ashwood
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Nicholas H C Lewis
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Paul J Sanstead
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
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15
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Hofmann SM, Frost CV, Podewin T, Gailer M, Weber E, Zacharias M, Zinth W, Hoffmann-Röder A. Folding and Unfolding of the Short Light-Triggered β-Hairpin Peptide AzoChignolin Occurs within 100 ns. J Phys Chem B 2020; 124:5113-5121. [PMID: 32479079 DOI: 10.1021/acs.jpcb.0c02021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To map the underlying molecular mechanisms of folding dynamics in proteins, light-operated peptides have emerged as promising tools. In this study, we reveal the complete sequence of light-induced structural changes of AzoChignolin, a short β-hairpin peptide containing an azobenzene photoswitch in its loop region. Light-triggered structural changes were monitored by time-resolved IR spectroscopy. Formation and destruction of the hairpin structure is very fast and occurs within 100 ns for AzoChignolin in methanol. Atomistic molecular dynamics simulations using two explicit solvents, methanol and water, revealed the underlying molecular processes and allowed us to gain further insight into the reaction mechanism. Despite its rapid reaction time, hairpin formation in these solvents is not force-driven by the molecular switch but proceeded via formation of interstrand hydrogen bonds and contacts between aromatic residues. Moreover, the combined experimental and theoretical study demonstrates that the solvent (methanol vs water) does not dictate the velocity of β-hairpin formation in the AzoChignolin peptide comprising only a few hydrophobic residues in the strands.
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Affiliation(s)
- Stefan M Hofmann
- BioMolecular Optics and Center for Integrated Protein Science, Faculty of Physics, Ludwig-Maximilians-Universität München, Oettingenstr. 67, München 80538, Germany
| | - Christina V Frost
- TUM Department of Physics T38, Technical University of Munich, James-Franck-Str. 1, Garching 85748, Germany
| | - Tom Podewin
- Department of Organic Chemistry and Center for Integrated Protein Science, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, München 81377, Germany
| | - Manuel Gailer
- Department of Organic Chemistry and Center for Integrated Protein Science, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, München 81377, Germany
| | - Elisa Weber
- BioMolecular Optics and Center for Integrated Protein Science, Faculty of Physics, Ludwig-Maximilians-Universität München, Oettingenstr. 67, München 80538, Germany
| | - Martin Zacharias
- TUM Department of Physics T38, Technical University of Munich, James-Franck-Str. 1, Garching 85748, Germany
| | - Wolfgang Zinth
- BioMolecular Optics and Center for Integrated Protein Science, Faculty of Physics, Ludwig-Maximilians-Universität München, Oettingenstr. 67, München 80538, Germany
| | - Anja Hoffmann-Röder
- Department of Organic Chemistry and Center for Integrated Protein Science, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, München 81377, Germany
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16
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Avaro JT, Wolf SLP, Hauser K, Gebauer D. Stable Prenucleation Calcium Carbonate Clusters Define Liquid-Liquid Phase Separation. Angew Chem Int Ed Engl 2020; 59:6155-6159. [PMID: 31943581 PMCID: PMC7187218 DOI: 10.1002/anie.201915350] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/07/2020] [Indexed: 01/25/2023]
Abstract
Liquid-liquid phase separation (LLPS) is an intermediate step during the precipitation of calcium carbonate, and is assumed to play a key role in biomineralization processes. Here, we have developed a model where ion association thermodynamics in homogeneous phases determine the liquid-liquid miscibility gap of the aqueous calcium carbonate system, verified experimentally using potentiometric titrations, and kinetic studies based on stopped-flow ATR-FTIR spectroscopy. The proposed mechanism explains the variable solubilities of solid amorphous calcium carbonates, reconciling previously inconsistent literature values. Accounting for liquid-liquid amorphous polymorphism, the model also provides clues to the mechanism of polymorph selection. It is general and should be tested for systems other than calcium carbonate to provide a new perspective on the physical chemistry of LLPS mechanisms based on stable prenucleation clusters rather than un-/metastable fluctuations in biomineralization, and beyond.
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Affiliation(s)
- Jonathan T. Avaro
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Stefan L. P. Wolf
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Karin Hauser
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
| | - Denis Gebauer
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078457KonstanzGermany
- Present address: Institute of Inorganic ChemistryLeibniz University of HannoverCallinstrasse 930167HannoverGermany
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17
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Avaro JT, Wolf SLP, Hauser K, Gebauer D. Stabile Calciumcarbonat‐Pränukleationscluster bestimmen die Flüssig‐flüssig‐Phasenseparation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915350] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Jonathan T. Avaro
- Fachbereich ChemieUniversität Konstanz Universitätsstraße 10 78457 Konstanz Deutschland
| | - Stefan L. P. Wolf
- Fachbereich ChemieUniversität Konstanz Universitätsstraße 10 78457 Konstanz Deutschland
| | - Karin Hauser
- Fachbereich ChemieUniversität Konstanz Universitätsstraße 10 78457 Konstanz Deutschland
| | - Denis Gebauer
- Fachbereich ChemieUniversität Konstanz Universitätsstraße 10 78457 Konstanz Deutschland
- Derzeitige Adresse: Institut für Anorganische ChemieLeibniz Universität Hannover Callinstraße 9 30167 Hannover Deutschland
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18
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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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19
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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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20
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Ihalainen JA, Gustavsson E, Schroeder L, Donnini S, Lehtivuori H, Isaksson L, Thöing C, Modi V, Berntsson O, Stucki-Buchli B, Liukkonen A, Häkkänen H, Kalenius E, Westenhoff S, Kottke T. Chromophore–Protein Interplay during the Phytochrome Photocycle Revealed by Step-Scan FTIR Spectroscopy. J Am Chem Soc 2018; 140:12396-12404. [DOI: 10.1021/jacs.8b04659] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Janne A. Ihalainen
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Emil Gustavsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Lea Schroeder
- Physical and Biophysical Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Serena Donnini
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Heli Lehtivuori
- Nanoscience Center, Department of Physics, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Linnéa Isaksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Christian Thöing
- Physical and Biophysical Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Vaibhav Modi
- Nanoscience Center, Department of Chemistry, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Oskar Berntsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Brigitte Stucki-Buchli
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Alli Liukkonen
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Heikki Häkkänen
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Elina Kalenius
- Nanoscience Center, Department of Chemistry, University of Jyväskylä, Jyväskylä 40014, Finland
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
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21
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Rampp MS, Hofmann SM, Podewin T, Hoffmann-Röder A, Moroder L, Zinth W. Time-resolved infrared studies of the unfolding of a light triggered β-hairpin peptide. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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22
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Salamatova E, Cunha AV, Bloem R, Roeters SJ, Woutersen S, Jansen TLC, Pshenichnikov MS. Hydrophobic Collapse in N-Methylacetamide-Water Mixtures. J Phys Chem A 2018; 122:2468-2478. [PMID: 29425450 PMCID: PMC6028151 DOI: 10.1021/acs.jpca.8b00276] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/02/2018] [Indexed: 11/28/2022]
Abstract
Aqueous N-methylacetamide solutions were investigated by polarization-resolved pump-probe and 2D infrared spectroscopy (2D IR), using the amide I mode as a reporter. The 2D IR results are compared with molecular dynamics simulations and spectral calculations to gain insight into the molecular structures in the mixture. N-Methylacetamide and water molecules tend to form clusters with "frozen" amide I dynamics. This is driven by a hydrophobic collapse as the methyl groups of the N-methylacetamide molecules cluster in the presence of water. Since the studied system can be considered as a simplified model for the backbone of proteins, the present study forms a convenient basis for understanding the structural and vibrational dynamics in proteins. It is particularly interesting to find out that a hydrophobic collapse as the one driving protein folding is observed in such a simple system.
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Affiliation(s)
- Evgeniia Salamatova
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ana V. Cunha
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Robbert Bloem
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Steven J. Roeters
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Sander Woutersen
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Thomas L. C. Jansen
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Maxim S. Pshenichnikov
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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23
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Maj M, Lomont JP, Rich KL, Alperstein AM, Zanni MT. Site-specific detection of protein secondary structure using 2D IR dihedral indexing: a proposed assembly mechanism of oligomeric hIAPP. Chem Sci 2018; 9:463-474. [PMID: 29619202 PMCID: PMC5868010 DOI: 10.1039/c7sc03789a] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/02/2017] [Indexed: 12/19/2022] Open
Abstract
Human islet amyloid polypeptide (hIAPP) aggregates into fibrils through oligomers that have been postulated to contain α-helices as well as β-sheets. We employ a site-specific isotope labeling strategy that is capable of detecting changes in dihedral angles when used in conjunction with 2D IR spectroscopy. The method is analogous to the chemical shift index used in NMR spectroscopy for assigning protein secondary structure. We introduce isotope labels at two neighbouring residues, which results in an increased intensity and positive frequency shift if those residues are α-helical versus a negative frequency shift in β-sheets and turns. The 2D IR dihedral index approach is demonstrated for hIAPP in micelles for which the polypeptide structure is known, using pairs of 13C18O isotope labels L12A13 and L16V17, along with single labeled control experiments. Applying the approach to aggregation experiments performed in buffer, we show that about 27-38% of hIAPP peptides adopt an α-helix secondary structure in the monomeric state at L12A13, prior to aggregation, but not at L16V17 residues. At L16V17, the kinetics are described solely by the monomer and fiber conformations, but at L12A13 the kinetics exhibit a third state that is created by an oligomeric intermediate. Control experiments performed with a single isotope label at A13 exhibit two-state kinetics, indicating that a previously unknown change in dihedral angle occurs at L12A13 as hIAPP transitions from the intermediate to fiber structures. We propose a mechanism for aggregation, in which helices seed oligomer formation via structures analogous to leucine rich repeat proteins.
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Affiliation(s)
- Michał Maj
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , USA .
| | - Justin P Lomont
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , USA .
| | - Kacie L Rich
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , USA .
| | - Ariel M Alperstein
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , USA .
| | - Martin T Zanni
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706-1396 , USA .
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24
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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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25
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Fallah MA, Gerding HR, Scheibe C, Drescher M, Karreman C, Schildknecht S, Leist M, Hauser K. Simultaneous IR-Spectroscopic Observation of α-Synuclein, Lipids, and Solvent Reveals an Alternative Membrane-Induced Oligomerization Pathway. Chembiochem 2017; 18:2312-2316. [PMID: 28980756 DOI: 10.1002/cbic.201700355] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Indexed: 12/15/2022]
Abstract
The intrinsically disordered protein α-synuclein (αS), a known pathogenic factor for Parkinson's disease, can adopt defined secondary structures when interacting with membranes or during fibrillation. The αS-lipid interaction and the implications of this process for aggregation and damage to membranes are still poorly understood. Therefore, we established a label-free infrared (IR) spectroscopic approach to allow simultaneous monitoring of αS conformation and membrane integrity. IR showed its unique sensitivity for identifying distinct β-structured aggregates. A comparative study of wild-type αS and the naturally occurring splicing variant αS Δexon3 yielded new insights into the membrane's capability for altering aggregation pathways.
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Affiliation(s)
- Mohammad A Fallah
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Hanne R Gerding
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Christian Scheibe
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Malte Drescher
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Christiaan Karreman
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Stefan Schildknecht
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Marcel Leist
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Karin Hauser
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
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26
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Baldassarre M, Baronio CM, Morozova-Roche LA, Barth A. Amyloid β-peptides 1-40 and 1-42 form oligomers with mixed β-sheets. Chem Sci 2017; 8:8247-8254. [PMID: 29568473 PMCID: PMC5857929 DOI: 10.1039/c7sc01743j] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 10/12/2017] [Indexed: 12/16/2022] Open
Abstract
Two main amyloid-β peptides of different length (Aβ40 and Aβ42) are involved in Alzheimer's disease. Their relative abundance is decisive for the severity of the disease and mixed oligomers may contribute to the toxic species. However, little is know about the extent of mixing. To study whether Aβ40 and Aβ42 co-aggregate, we used Fourier transform infrared spectroscopy in combination with 13C-labeling and spectrum calculation and focused on the amide I vibration, which is sensitive to backbone structure. Mixtures of monomeric labeled Aβ40 and unlabeled Aβ42 (and vice versa) were co-incubated for ∼20 min and their infrared spectrum recorded. The position of the main 13C-amide I' band shifted to higher wavenumbers with increasing admixture of 12C-peptide due to the presence of 12C-amides in the vicinity of 13C-amides. The results indicate that Aβ40 and Aβ42 form mixed oligomers with a largely random distribution of Aβ40 and Aβ42 strands in their β-sheets. The structures of the mixed oligomers are intermediate between those of the pure oligomers. There is no indication that one of the peptides forces the backbone structure of its oligomers on the other peptide when they are mixed as monomers. We also demonstrate that isotope-edited infrared spectroscopy can distinguish aggregation modulators that integrate into the backbone structure of their interaction partner from those that do not. As an example for the latter case, the pro-inflammatory calcium binding protein S100A9 is shown not to incorporate into the β-sheets of Aβ42.
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Affiliation(s)
- Maurizio Baldassarre
- Department of Biochemistry and Biophysics , Stockholm University , Arrhenius Laboratories , 10691 Stockholm , Sweden .
| | - Cesare M Baronio
- Department of Biochemistry and Biophysics , Stockholm University , Arrhenius Laboratories , 10691 Stockholm , Sweden .
| | | | - Andreas Barth
- Department of Biochemistry and Biophysics , Stockholm University , Arrhenius Laboratories , 10691 Stockholm , Sweden .
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27
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Keiderling TA. Sensing site-specific structural characteristics and chirality using vibrational circular dichroism of isotope labeled peptides. Chirality 2017; 29:763-773. [DOI: 10.1002/chir.22749] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 11/07/2022]
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28
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Popp A, Scheerer D, Heck B, Hauser K. Biomolecular dynamics studied with IR-spectroscopy using quantum cascade lasers combined with nanosecond perturbation techniques. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 181:192-199. [PMID: 28364666 DOI: 10.1016/j.saa.2017.03.053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/17/2017] [Accepted: 03/19/2017] [Indexed: 06/07/2023]
Abstract
Early events of protein folding can be studied with fast perturbation techniques triggering non-equilibrium relaxation dynamics. A nanosecond laser-excited pH-jump or temperature-jump (T-jump) was applied to initiate helix folding or unfolding of poly-l-glutamic acid (PGA). PGA is a homopolypeptide with titratable carboxyl side-chains whose protonation degree determines the PGA conformation. A pH-jump was realized by the photochemical release of protons and induces PGA folding due to protonation of the side-chains. Otherwise, the helical conformation can be unfolded by a T-jump. We operated under conditions where PGA does not aggregate and temperature and pH are the regulatory properties of its conformation. The experiments were performed in such a manner that the folding/unfolding jump proceeded to the same PGA conformation. We quantified the increase/decrease in helicity induced by the pH-/T-jump and demonstrated that the T-jump results in a relatively small change in helical content in contrast to the pH-jump. This is caused by the strong pH-dependence of the PGA conformation. The conformational changes were detected by time-resolved single wavelength IR-spectroscopy using quantum cascade lasers (QCL). We could independently observe the kinetics for α-helix folding and unfolding in PGA by using different perturbation techniques and demonstrate the high sensitivity of time-resolved IR-spectroscopy to study protein folding mechanisms.
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Affiliation(s)
- Alexander Popp
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - David Scheerer
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Benjamin Heck
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Karin Hauser
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany.
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29
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Tobias F, Keiderling TA. Role of Side Chains in β-Sheet Self-Assembly into Peptide Fibrils. IR and VCD Spectroscopic Studies of Glutamic Acid-Containing Peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:4653-61. [PMID: 27099990 DOI: 10.1021/acs.langmuir.6b00077] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Poly(glutamic acid) at low pH self-assembles after incubation at higher temperature into fibrils composed of antiparallel sheets that are stacked in a β2-type structure whose amide carbonyls have bifurcated H-bonds involving the side chains from the next sheet. Oligomers of Glu can also form such structures, and isotope labeling has provided insight into their out-of-register antiparallel structure [ Biomacromolecules 2013 , 14 , 3880 - 3891 ]. In this paper we report IR and VCD spectra and transmission electron micrograph (TEM) images for a series of alternately sequenced oligomers, Lys-(Aaa-Glu)5-Lys-NH2, where Aaa was varied over a variety of polar, aliphatic, or aromatic residues. Their spectral and TEM data show that these oligopeptides self-assemble into different structures, both local and morphological, that are dependent on both the nature of the Aaa side chains and growth conditions employed. Such alternate peptides substituted with small or polar residues, Ala and Thr, do not yield fibrils; but with β-branched aliphatic residues, Val and Ile, that could potentially pack with Glu side chains, these oligopeptides do show evidence of β2-stacking. By contrast, for Leu, with longer side chains, only β1-stacking is seen while with even larger Phe side chains, either β-form can be detected separately, depending on preparation conditions. These structures are dependent on high temperature incubation after reducing the pH and in some cases after sonication of initial fibril forms and reincubation. Some of these fibrillar peptides, but not all, show enhanced VCD, which can offer evidence for formation of long, multistrand, often twisted structures. Substitution of Glu with residues having selected side chains yields a variety of morphologies, leading to both β1- and β2-structures, that overall suggests two different packing modes for the hydrophobic side chains depending on size and type.
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Affiliation(s)
- Fernando Tobias
- Department of Chemistry, University of Illinois at Chicago , 845 W. Taylor Street (m/c111), Chicago, Illinois 60607-7061, United States
| | - Timothy A Keiderling
- Department of Chemistry, University of Illinois at Chicago , 845 W. Taylor Street (m/c111), Chicago, Illinois 60607-7061, United States
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30
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Daily MD, Baer MD, Mundy CJ. Divalent Ion Parameterization Strongly Affects Conformation and Interactions of an Anionic Biomimetic Polymer. J Phys Chem B 2016; 120:2198-208. [DOI: 10.1021/acs.jpcb.5b12277] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Michael D. Daily
- Physical
Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Department
of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Marcel D. Baer
- Physical
Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Christopher J. Mundy
- Physical
Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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31
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Sequence, structure, and cooperativity in folding of elementary protein structural motifs. Proc Natl Acad Sci U S A 2015. [PMID: 26216963 DOI: 10.1073/pnas.1506309112] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Residue-level unfolding of two helix-turn-helix proteins--one naturally occurring and one de novo designed--is reconstructed from multiple sets of site-specific (13)C isotopically edited infrared (IR) and circular dichroism (CD) data using Ising-like statistical-mechanical models. Several model variants are parameterized to test the importance of sequence-specific interactions (approximated by Miyazawa-Jernigan statistical potentials), local structural flexibility (derived from the ensemble of NMR structures), interhelical hydrogen bonds, and native contacts separated by intervening disordered regions (through the Wako-Saitô-Muñoz-Eaton scheme, which disallows such configurations). The models are optimized by directly simulating experimental observables: CD ellipticity at 222 nm for model proteins and their fragments and (13)C-amide I' bands for multiple isotopologues of each protein. We find that data can be quantitatively reproduced by the model that allows two interacting segments flanking a disordered loop (double sequence approximation) and incorporates flexibility in the native contact maps, but neither sequence-specific interactions nor hydrogen bonds are required. The near-identical free energy profiles as a function of the global order parameter are consistent with expected similar folding kinetics for nearly identical structures. However, the predicted folding mechanism for the two motifs is different, reflecting the order of local stability. We introduce free energy profiles for "experimental" reaction coordinates--namely, the degree of local folding as sensed by site-specific (13)C-edited IR, which highlight folding heterogeneity and contrast its overall, average description with the detailed, local picture.
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32
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Razavi AM, Voelz VA. Kinetic Network Models of Tryptophan Mutations in β-Hairpins Reveal the Importance of Non-Native Interactions. J Chem Theory Comput 2015; 11:2801-12. [DOI: 10.1021/acs.jctc.5b00088] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Asghar M. Razavi
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Vincent A. Voelz
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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33
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Leitner DM, Buchenberg S, Brettel P, Stock G. Vibrational energy flow in the villin headpiece subdomain: Master equation simulations. J Chem Phys 2015; 142:075101. [DOI: 10.1063/1.4907881] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- David M. Leitner
- Department of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557, USA
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
| | - Sebastian Buchenberg
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, Freiburg, Germany
| | - Paul Brettel
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, Freiburg, Germany
| | - Gerhard Stock
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, Freiburg, Germany
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34
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Anderson BA, Literati A, Ball B, Kubelka J. Temperature dependence of C-terminal carboxylic group IR absorptions in the amide I' region. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 134:473-483. [PMID: 25036456 DOI: 10.1016/j.saa.2014.06.102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 05/13/2014] [Accepted: 06/16/2014] [Indexed: 06/03/2023]
Abstract
Studies of structural changes in peptides and proteins using IR spectroscopy often rely on subtle changes in the amide I' band as a function of temperature. However, these changes can be obscured by the overlap with other absorptions, namely the side-chain and terminal carboxylic groups. The former were the subject of our previous report (Anderson et al., 2014). In this paper we investigate the IR spectra of the asymmetric stretch of α-carboxylic groups for amino acids representing all major types (Gly, Ala, Val, Leu, Ser, Thr, Asp, Glu, Lys, Asn, His, Trp, Pro) as well as the C-terminal groups of three dipeptides (Gly-Gly, Gly-Ala, Ala-Gly) in D₂O at neutral pH. Experimental temperature dependent IR spectra were analyzed by fitting of both symmetric and asymmetric pseudo-Voigt functions. Qualitatively the spectra exhibit shifts to higher frequency, loss in intensity and narrowing with increased temperature, similar to that observed previously for the side-chain carboxylic groups of Asp. The observed dependence of the band parameters (frequency, intensity, width and shape) on temperature is in all cases linear: simple linear regression is therefore used to describe the spectral changes. The spectral parameters vary between individual amino acids and show systematic differences between the free amino acids and dipeptides, particularly in the absolute peak frequencies, but the temperature variations are comparable. The relative variations between the dipeptide spectral parameters are most sensitive to the C-terminal amino acid, and follow the trends observed in the free amino acid spectra. General rules for modeling the α-carboxylic IR absorption bands in peptides and proteins as the function of temperature are proposed.
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Affiliation(s)
- Benjamin A Anderson
- University of Wyoming, 1000 E. University Ave, Laramie, WY 82071, United States
| | - Alex Literati
- University of Wyoming, 1000 E. University Ave, Laramie, WY 82071, United States
| | - Borden Ball
- University of Wyoming, 1000 E. University Ave, Laramie, WY 82071, United States
| | - Jan Kubelka
- University of Wyoming, 1000 E. University Ave, Laramie, WY 82071, United States.
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35
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Popp A, Wu L, Keiderling TA, Hauser K. Effect of hydrophobic interactions on the folding mechanism of β-hairpins. J Phys Chem B 2014; 118:14234-42. [PMID: 25393957 DOI: 10.1021/jp506658x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrophobic interactions are essential in stabilizing protein structures. How they affect the folding pathway and kinetics, however, is less clear. We used time-resolved infrared spectroscopy to study the dynamics of hydrophobic interactions of β-hairpin variants of the sequence Trpzip2 (SWTWENGKWTWK-NH2) that is stabilized by two cross-strand Trp-Trp pairs. The hydrophobicity strength was varied by substituting the tryptophans pairwise by either tyrosines or valines. Relaxation dynamics were induced by a laser-excited temperature jump, which separately probed for the loss of the cross-strand β-hairpin interaction and the rise of the disordered structure. All substitutions tested result in reduced thermal stability, lower transition temperatures, and faster dynamics compared to Trpzip2. However, the changes in folding dynamics depend on the amino acid substituted for Trp. The aromatic substitution of Tyr for Trp results in the same kinetics for the unfolding of sheet and growth of disorder, with similar activation energies, independent of the substitution position. Substitution of Trp with a solely hydrophobic Val results in even faster kinetics than substitution with Tyr but is additionally site-dependent. If the hairpin has a Val pair close to its termini, the rate constants for loss of sheet and gain of disorder are the same, but if the pair is close to the turn, the sheet and disorder components show different relaxation kinetics. The Trp → Val substitutions reveal that hydrophobic interactions alone weakly stabilize the hairpin structure, but adding edge-to-face aromatic interaction strengthens it, and both modify the complex folding process.
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Affiliation(s)
- Alexander Popp
- Biophysical Chemistry, Department of Chemistry, University of Konstanz , 78457 Konstanz, Germany
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36
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Kubelka GS, Kubelka J. Site-Specific Thermodynamic Stability and Unfolding of a de Novo Designed Protein Structural Motif Mapped by 13C Isotopically Edited IR Spectroscopy. J Am Chem Soc 2014; 136:6037-48. [DOI: 10.1021/ja500918k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ginka S. Kubelka
- Department
of Chemistry, University of Wyoming, Laramie, Wyoming 82071, United States
| | - Jan Kubelka
- Department
of Chemistry, University of Wyoming, Laramie, Wyoming 82071, United States
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37
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Anderson BA, Literati A, Ball B, Kubelka J. Temperature dependence of amino acid side chain IR absorptions in the amide I' region. Biopolymers 2014; 101:536-48. [DOI: 10.1002/bip.22416] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 09/05/2013] [Accepted: 09/16/2013] [Indexed: 12/15/2022]
Affiliation(s)
- Benjamin A. Anderson
- Department of Chemistry, University of Wyoming, 1000 E University Ave; Laramie WY 82071
| | - Alex Literati
- Department of Chemistry, University of Wyoming, 1000 E University Ave; Laramie WY 82071
| | - Borden Ball
- Department of Chemistry, University of Wyoming, 1000 E University Ave; Laramie WY 82071
| | - Jan Kubelka
- Department of Chemistry, University of Wyoming, 1000 E University Ave; Laramie WY 82071
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38
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Abstract
Since the first report in 1993 (JACS 115, 5887-5888) of a peptide able to form a monomeric β-hairpin structure in aqueous solution, the design of peptides forming either β-hairpins (two-stranded antiparallel β-sheets) or three-stranded antiparallel β-sheets has become a field of growing interest and activity. These studies have yielded great insights into the principles governing the stability and folding of β-hairpins and antiparallel β-sheets. This chapter provides an overview of the reported β-hairpin/β-sheet peptides focussed on the applied design criteria, reviews briefly the factors contributing to β-hairpin/β-sheet stability, and describes a protocol for the de novo design of β-sheet-forming peptides based on them. Guidelines to select appropriate turn and strand residues and to avoid self-association are provided. The methods employed to check the success of new designed peptides are also summarized. Since NMR is the best technique to that end, NOEs and chemical shifts characteristic of β-hairpins and three-stranded antiparallel β-sheets are given.
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Affiliation(s)
- M Angeles Jiménez
- Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Química Física Rocasolano (IQFR), Serrano 119, 28006, Madrid, Spain,
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39
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Length-dependent conformational transitions of polyglutamine repeats as molecular origin of fibril initiation. Biophys Chem 2014; 185:47-57. [DOI: 10.1016/j.bpc.2013.11.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 11/15/2013] [Accepted: 11/18/2013] [Indexed: 11/16/2022]
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40
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Zeko T, Hannigan SF, Jacisin T, Guberman-Pfeffer MJ, Falcone ER, Guildford MJ, Szabo C, Cole KE, Placido J, Daly E, Kubasik MA. FT-IR Spectroscopy and Density Functional Theory Calculations of 13C Isotopologues of the Helical Peptide Z-Aib6-OtBu. J Phys Chem B 2013; 118:58-68. [DOI: 10.1021/jp408818g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Timothy Zeko
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Steven F. Hannigan
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Timothy Jacisin
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | | | - Eric R. Falcone
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Melissa J. Guildford
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Christopher Szabo
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Kathryn E. Cole
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Jessica Placido
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Erin Daly
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Matthew A. Kubasik
- Department of Chemistry and
Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
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41
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Deeg AA, Rampp MS, Popp A, Pilles BM, Schrader TE, Moroder L, Hauser K, Zinth W. Isomerization- and temperature-jump-induced dynamics of a photoswitchable β-hairpin. Chemistry 2013; 20:694-703. [PMID: 24415361 DOI: 10.1002/chem.201303189] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 10/28/2013] [Indexed: 11/09/2022]
Abstract
Conformational changes in proteins and peptides can be initiated by diverse processes. This raises the question how the variation of initiation mechanisms is connected to differences in folding or unfolding processes. In this work structural dynamics of a photoswitchable β-hairpin model peptide were initiated by two different mechanisms: temperature jump (T-jump) and isomerization of a backbone element. In both experiments the structural changes were followed by time-resolved IR spectroscopy in the nanosecond to microsecond range. When the photoisomerization of the azobenzene backbone switch initiated the folding reaction, pronounced absorption changes related to folding into the hairpin structure were found with a time constant of about 16 μs. In the T-jump experiment kinetics with the same time constant were observed. For both initiation processes the reaction dynamics revealed the same strong dependence of the reaction time on temperature. The highly similar transients in the microsecond range show that the peptide dynamics induced by T-jump and isomerization are both determined by the same mechanism and exclude a downhill-folding process. Furthermore, the combination of the two techniques allows a detailed model for folding and unfolding to be presented: The isomerization-induced folding process ends in a transition-state reaction scheme, in which a high energetic barrier of 48 kJ mol(-1) separates unfolded and folded structures.
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Affiliation(s)
- Andreas A Deeg
- Institute for BioMolecular Optics and Munich Center or Integrated Protein Science CIPSM, University of Munich, Oettingenstrasse 67, 80538 Munich (Germany), Fax: (+49) 89-2180-9202
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42
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Welch WRW, Kubelka J, Keiderling TA. Infrared, vibrational circular dichroism, and Raman spectral simulations for β-sheet structures with various isotopic labels, interstrand, and stacking arrangements using density functional theory. J Phys Chem B 2013; 117:10343-58. [PMID: 23924300 DOI: 10.1021/jp4056126] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Infrared (IR), Raman, and vibrational circular dichroism (VCD) spectral variations for different β-sheet structures were studied using simulations based on density functional theory (DFT) force field and intensity computations. The DFT vibrational parameters were obtained for β-sheet fragments containing nine-amides and constrained to a variety of conformations and strand arrangements. These were subsequently transferred onto corresponding larger β-sheet models, normally consisting of five strands with ten amides each, for spectral simulations. Further extension to fibril models composed of multiple stacked β-sheets was achieved by combining the transfer of DFT parameters for each sheet with dipole coupling methods for interactions between sheets. IR spectra of the amide I show different splitting patterns for parallel and antiparallel β-sheets, and their VCD, in the absence of intersheet stacking, have distinct sign variations. Isotopic labeling by (13)C of selected residues yields spectral shifts and intensity changes uniquely sensitive to relative alignment of strands (registry) for antiparallel sheets. Stacking of multiple planar sheets maintains the qualitative spectral character of the single sheet but evidences some reduction in the exciton splitting of the amide I mode. Rotating sheets with respect to each other leads to a significant VCD enhancement, whose sign pattern and intensity is dependent on the handedness and degree of rotation. For twisted β-sheets, a significant VCD enhancement is computed even for sheets stacked with either the same or opposite alignments and the inter-sheet rotation, depending on the sense, can either further increase or weaken the enhanced VCD intensity. In twisted, stacked structures (without rotation), similar VCD amide I patterns (positive couplets) are predicted for both parallel and antiparallel sheets, but different IR intensity distributions still enable their differentiation. Our simulation results prove useful for interpreting experimental vibrational spectra in terms of β-sheet and fibril structure, as illustrated in the accompanying paper.
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Affiliation(s)
- William R W Welch
- Department of Chemistry, University of Wyoming , Laramie, Wyoming 82071, United States
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43
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Folding of a heterogeneous β-hairpin peptide from temperature-jump 2D IR spectroscopy. Proc Natl Acad Sci U S A 2013; 110:2828-33. [PMID: 23382249 DOI: 10.1073/pnas.1211968110] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We provide a time- and structure-resolved characterization of the folding of the heterogeneous β-hairpin peptide Tryptophan Zipper 2 (Trpzip2) using 2D IR spectroscopy. The amide I' vibrations of three Trpzip2 isotopologues are used as a local probe of the midstrand contacts, β-turn, and overall β-sheet content. Our experiments distinguish between a folded state with a type I' β-turn and a misfolded state with a bulged turn, providing evidence for distinct conformations of the peptide backbone. Transient 2D IR spectroscopy at 45 °C following a laser temperature jump tracks the nanosecond and microsecond kinetics of unfolding and the exchange between conformers. Hydrogen bonds to the peptide backbone are loosened rapidly compared with the 5-ns temperature jump. Subsequently, all relaxation kinetics are characterized by an observed 1.2 ± 0.2-μs exponential. Our time-dependent 2D IR spectra are explained in terms of folding of either native or nonnative contacts from a common compact disordered state. Conversion from the disordered state to the folded state is consistent with a zip-out folding mechanism.
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44
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Culik RM, Jo H, DeGrado WF, Gai F. Using thioamides to site-specifically interrogate the dynamics of hydrogen bond formation in β-sheet folding. J Am Chem Soc 2012; 134:8026-9. [PMID: 22540162 PMCID: PMC3354031 DOI: 10.1021/ja301681v] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Thioamides are sterically almost identical to their oxoamide counterparts, but they are weaker hydrogen bond acceptors. Therefore, thioamide amino acids are excellent candidates for perturbing the energetics of backbone-backbone H-bonds in proteins and hence should be useful in elucidating protein folding mechanisms in a site-specific manner. Herein, we validate this approach by applying it to probe the dynamic role of interstrand H-bond formation in the folding kinetics of a well-studied β-hairpin, tryptophan zipper. Our results show that reducing the strength of the peptide's backbone-backbone H-bonds, except the one directly next to the β-turn, does not change the folding rate, suggesting that most native interstrand H-bonds in β-hairpins are formed only after the folding transition state.
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Affiliation(s)
- Robert M Culik
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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45
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Kobus M, Lieder M, Nguyen PH, Stock G. Simulation of transient infrared spectra of a photoswitchable peptide. J Chem Phys 2012; 135:225102. [PMID: 22168727 DOI: 10.1063/1.3664747] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In transient infrared (IR) experiments, a molecular system may be photoexcited in a nonstationary conformational state, whose time evolution is monitored via IR spectroscopy with high temporal and structural resolution. As a theoretical formulation of these experiments, this work derives explicit expressions for transient one- and two-dimensional IR spectra and discusses various levels of approximation and sampling strategies. Adopting a photoswitchable octapeptide in water as a representative example, nonequilibrium molecular dynamics simulations are performed and the photoinduced conformational dynamics and associated IR spectra are discussed in detail. Interestingly, it is found that the time scales of dynamics and spectra may differ from residue to residue by up to an order of magnitude. Considering merely the cumulative spectrum of all residues, the contributions of the individual residues largely compensate each other, which may explain the surprisingly small frequency shifts and short photoproduct rise times found in experiment. Even when a localized amide I mode is probed (e.g., via isotope labeling), the vibrational frequency shift is shown to depend in a complicated way on the conformation of the entire peptide as well as on the interaction with the solvent. In this context, various issues concerning the interpretation of transient IR spectra and conformational dynamics in terms of a few exponential time scales are discussed.
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Affiliation(s)
- Maja Kobus
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
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46
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Yamamoto S, Kaminský J, Bouř P. Structure and Vibrational Motion of Insulin from Raman Optical Activity Spectra. Anal Chem 2012; 84:2440-51. [DOI: 10.1021/ac2032436] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Shigeki Yamamoto
- Institute of Organic Chemistry and
Biochemistry, Academy of Sciences, Flemingovo
nám. 2, 166 10, Prague 6, Czech Republic
| | - Jakub Kaminský
- Institute of Organic Chemistry and
Biochemistry, Academy of Sciences, Flemingovo
nám. 2, 166 10, Prague 6, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and
Biochemistry, Academy of Sciences, Flemingovo
nám. 2, 166 10, Prague 6, Czech Republic
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47
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Impact ofβ-Turn Sequence onβ-Hairpin Dynamics Studied with Infrared-Detected Temperature Jump. ACTA ACUST UNITED AC 2012. [DOI: 10.1155/2012/102423] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Folding dynamics forβ-structure loss and disordered structure gain were studied in a modelβ-hairpin peptide based on Cochran’s tryptophan zipper peptide Trpzip2, but with an altered Thr-Gly (TG) turn sequence, that is, SWTWETGKWTWK, using laser-induced temperature-jump (T-jump) kinetics with IR detection. As has been shown previously, the TG turn sequence reduces the thermodynamicβ-hairpin stability as compared to the Asn-Gly sequence used in Trpzip2 (TZ2-NG). In this study, we found that the TG-turn slows down the overall relaxation dynamics as compared to TZ2-NG, which were studied at higher temperatures where the time constants show little difference between relaxation of theβ-strand and the disordered conformation. These time constants become equivalent at lower temperatures for TZ2-TG than was seen for TZ2-NG. The correlation of thermodynamic stability and rates of relaxation suggests that the change from NG to TG turn results in a slowing of folding, lowerkf, with less change of the unfolding rate,ku, assuming two state behavior at higher temperatures.
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48
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Xu Y, Du D, Oyola R. Infrared study of the stability and folding kinetics of a series of β-hairpin peptides with a common NPDG turn. J Phys Chem B 2011; 115:15332-8. [PMID: 22136248 DOI: 10.1021/jp2046867] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The thermal stability and folding kinetics of a series of 15-residue β-hairpins with a common Type I [3:5] NPDG turn were studied using Fourier transform infrared spectroscopy (FTIR) and laser-induced temperature jump (T-jump) with infrared detection, respectively. Mutations at positions 3, 5, or 13 in the peptide sequence SEXYXNPDGTWTXTE, where X represents the position of mutation, were performed to study the roles of hydrophobic interactions in determining the thermodynamic and kinetic properties of β-hairpin folding. The thermal stability studies show a broad thermal folding/unfolding transition for all the peptides. T-jump studies indicate that these β-hairpin peptides fold in less than 2 μs. In addition, both folding and unfolding rate constants decrease with increasing strength of hydrophobic interactions. Kinetically, the hydrophobic interactions have more significant influence on the unfolding rate than the folding rate. Φ-value analysis indicates that the hydrophobic interactions between the side chains are mainly formed at the latter part of the transition-state region during the folding process. In summary, the results suggest that the formation of the native structure of these β-hairpins depends on the correct topology of the hydrophobic cluster. Besides the formation of the turn region as a key process for folding as suggested by previous studies, a hydrophobic collapse process may also play a crucial role during β-hairpin folding.
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Affiliation(s)
- Yao Xu
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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49
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Nguyen PH, Staudt H, Wachtveitl J, Stock G. Real Time Observation of Ultrafast Peptide Conformational Dynamics: Molecular Dynamics Simulation vs Infrared Experiment. J Phys Chem B 2011; 115:13084-92. [DOI: 10.1021/jp207945p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Phuong H. Nguyen
- Laboratoire de Biochimie Theorique - UPR 9080, Institut de Biologie Physico-Chimique, 13, rue Pierre et Marie Curie, F-75005 Paris, France
| | - Heike Staudt
- Institute of Physical and Theoretical Chemistry, Goethe University, 60438 Frankfurt, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University, 60438 Frankfurt, Germany
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
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50
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Wu L, McElheny D, Setnicka V, Hilario J, Keiderling TA. Role of different β-turns in β-hairpin conformation and stability studied by optical spectroscopy. Proteins 2011; 80:44-60. [DOI: 10.1002/prot.23140] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 06/28/2011] [Accepted: 07/21/2011] [Indexed: 12/28/2022]
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