1
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Shirley JC, Baiz CR. MANUSCRIPT Local Crowd, Local Probe: Strengths and Drawbacks of Azidohomoalanine as a Site-Specific Crowding Probe. J Phys Chem B 2024; 128:5310-5319. [PMID: 38806061 DOI: 10.1021/acs.jpcb.4c00712] [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: 05/30/2024]
Abstract
Every residue on a protein can be characterized by its interaction with water, in lack or in excess, as water is the matrix of biological systems. Infrared spectroscopy and the implementation of local azidohomoalanine (AHA) probes allow us to move beyond an ensemble or surface-driven conceptualization of water behavior and toward a granular, site-specific picture. In this paper, we examined the role of crowding in modulating both global and local behavior on the β-hairpin, TrpZip2 using a combination of Fourier-transform infrared spectroscopy (FTIR) spectroscopy, two-dimensional infrared (2D IR) spectroscopy, and molecular dynamics simulations. We found that, at the amino acid level, crowding drove dehydration of both sheet and turn peptide sites as well as free AHA. However, the subpicosecond dynamics showed highly individualized responses based on the local environment. Interestingly, while steady-state FTIR measurements revealed similar responses at the amino-acid level to hard versus soft crowding (dehydration), we found that PEG and glucose had opposite stabilizing and destabilizing effects on the protein secondary structure, emphasizing an important distinction in understanding the impact of crowding on protein structure as well as the role of crowding across length scales.
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Affiliation(s)
- Joseph C Shirley
- Department of Chemistry, University of Texas, Austin 78712, Texas, United States
| | - Carlos R Baiz
- Department of Chemistry, University of Texas, Austin 78712, Texas, United States
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2
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Hunt NT. Biomolecular infrared spectroscopy: making time for dynamics. Chem Sci 2024; 15:414-430. [PMID: 38179520 PMCID: PMC10763549 DOI: 10.1039/d3sc05223k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/24/2023] [Indexed: 01/06/2024] Open
Abstract
Time resolved infrared spectroscopy of biological molecules has provided a wealth of information relating to structural dynamics, conformational changes, solvation and intermolecular interactions. Challenges still exist however arising from the wide range of timescales over which biological processes occur, stretching from picoseconds to minutes or hours. Experimental methods are often limited by vibrational lifetimes of probe groups, which are typically on the order of picoseconds, while measuring an evolving system continuously over some 18 orders of magnitude in time presents a raft of technological hurdles. In this Perspective, a series of recent advances which allow biological molecules and processes to be studied over an increasing range of timescales, while maintaining ultrafast time resolution, will be reviewed, showing that the potential for real-time observation of biomolecular function draws ever closer, while offering a new set of challenges to be overcome.
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Affiliation(s)
- Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York Heslington York YO10 5DD UK
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3
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Richaud AD, Mandal S, Das A, Roche SP. Tunable CH/π Interactions within a Tryptophan Zipper Motif to Stabilize the Fold of Long β-Hairpin Peptides. ACS Chem Biol 2023; 18:2555-2563. [PMID: 37976523 DOI: 10.1021/acschembio.3c00553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The tryptophan zipper (Trpzip) is an iconic folding motif of β-hairpin peptides capitalizing on two pairs of cross-strand tryptophans, each stabilized by an aromatic-aromatic stacking in an edge-to-face (EtF) geometry. Yet, the origins and the contribution of this EtF packing to the unique Trpzip stability remain poorly understood. To address this question of structure-stability relationship, a library of Trpzip hairpins was developed by incorporating readily accessible nonproteinogenic tryptophans of varying electron densities. We found that each EtF geometry was, in fact, stabilized by an intricate combination of XH/π interactions. By tuning the π-electron density of Trpface rings, CH/π interactions are strengthened to gain additional stability. On the contrary, our DFT calculations support the notion that Trpedge modulations are challenging due to their simultaneous paradoxical engagement as H-bond donors in CH/π and acceptors in NH/π interactions.
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Affiliation(s)
- Alexis D Richaud
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Sourav Mandal
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Pashan, Pune 411008, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Pashan, Pune 411008, India
| | - Stéphane P Roche
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
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4
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Brüggemann J, Chekmeneva M, Wolter M, Jacob CR. Structural Dependence of Extended Amide III Vibrations in Two-Dimensional Infrared Spectra. J Phys Chem Lett 2023; 14:9257-9264. [PMID: 37812580 PMCID: PMC10591501 DOI: 10.1021/acs.jpclett.3c02662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 10/05/2023] [Indexed: 10/11/2023]
Abstract
Two-dimensional infrared (2D-IR) spectroscopy is a powerful experimental method for probing the structure and dynamics of proteins in aqueous solution. So far, most experimental studies have focused on the amide I vibrations, for which empirical vibrational exciton models provide a means of interpreting such experiments. However, such models are largely lacking for other regions of the vibrational spectrum. To close this gap, we employ an efficient quantum-chemical methodology for the calculation of 2D-IR spectra, which is based on anharmonic theoretical vibrational spectroscopy with localized modes. We apply this approach to explore the potential of 2D-IR spectroscopy in the extended amide III region. Using calculations for a dipeptide model as well as alanine polypeptides, we show that distinct 2D-IR cross-peaks in the extended amide III region can potentially be used to distinguish α-helix and β-strand structures. We propose that the extended amide III region could be a promising target for future 2D-IR experiments.
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Affiliation(s)
- Julia Brüggemann
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Maria Chekmeneva
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Mario Wolter
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Christoph R. Jacob
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
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5
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Brüggemann J, Wolter M, Jacob CR. Quantum-chemical calculation of two-dimensional infrared spectra using localized-mode VSCF/VCI. J Chem Phys 2022; 157:244107. [PMID: 36586972 DOI: 10.1063/5.0135273] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Computational protocols for the simulation of two-dimensional infrared (2D IR) spectroscopy usually rely on vibrational exciton models which require an empirical parameterization. Here, we present an efficient quantum-chemical protocol for predicting static 2D IR spectra that does not require any empirical parameters. For the calculation of anharmonic vibrational energy levels and transition dipole moments, we employ the localized-mode vibrational self-consistent field (L-VSCF)/vibrational configuration interaction (L-VCI) approach previously established for (linear) anharmonic theoretical vibrational spectroscopy [P. T. Panek and C. R. Jacob, ChemPhysChem 15, 3365-3377 (2014)]. We demonstrate that with an efficient expansion of the potential energy surface using anharmonic one-mode potentials and harmonic two-mode potentials, 2D IR spectra of metal carbonyl complexes and dipeptides can be predicted reliably. We further show how the close connection between L-VCI and vibrational exciton models can be exploited to extract the parameters of such models from those calculations. This provides a novel route to the fully quantum-chemical parameterization of vibrational exciton models for predicting 2D IR spectra.
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Affiliation(s)
- Julia Brüggemann
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Mario Wolter
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
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6
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Askelson PG, Meloni SL, Hoffnagle AM, Anna JM. Resolving the Impact of Hydrogen Bonding on the Phylloquinone Cofactor through Two-Dimensional Infrared Spectroscopy. J Phys Chem B 2022; 126:10120-10135. [PMID: 36444999 DOI: 10.1021/acs.jpcb.2c03556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two-dimensional infrared spectroscopy (2DIR) was applied to phylloquinone (PhQ), an important biological cofactor, to elucidate the impact of hydrogen bonding on the ultrafast dynamics and energetics of the carbonyl stretching modes. 2DIR measurements were performed on PhQ dissolved in hexanol, which served as the hydrogen bonding solvent, and hexane, which served as a non-hydrogen bonding control. Molecular dynamics simulations and quantum chemical calculations were performed to aid in spectral assignment and interpretation. From the position of the peaks in the 2DIR spectra, we extracted the transition frequencies for the fundamental, overtone, and combination bands of hydrogen bonded and non-hydrogen bonded carbonyl groups of PhQ in the 1635-1680 cm-1 region. We find that hydrogen bonding to a single carbonyl group acts to decouple the two carbonyl units of PhQ. Through analysis of the time-resolved 2DIR data, we find that hydrogen bonding leads to faster vibrational relaxation as well as an increase in the inhomogeneous broadening of the carbonyl groups. Overall, this work demonstrates how hydrogen bonding to the carbonyl groups of PhQ presents in the 2DIR spectra, laying the groundwork to use PhQ as a 2DIR probe to characterize the ultrafast fluctuations in the local environment of natural photosynthetic complexes.
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Affiliation(s)
- Phoebe G Askelson
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania19104, United States
| | - Stephen L Meloni
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania19104, United States
| | - Alexander M Hoffnagle
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania19104, United States
| | - Jessica M Anna
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania19104, United States
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7
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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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8
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Abstract
Constantly advancing computer simulations of biomolecules provide huge amounts of data that are difficult to interpret. In particular, obtaining insights into functional aspects of macromolecular dynamics, often related to cascades of transient events, calls for methodologies that depart from the well-grounded framework of equilibrium statistical physics. One of the approaches toward the analysis of complex temporal data which has found applications in the fields of neuroscience and econometrics is Granger causality analysis. It allows determining which components of multidimensional time series are most influential for the evolution of the entire system, thus providing insights into causal relations within the dynamic structure of interest. In this work, we apply Granger analysis to a long molecular dynamics trajectory depicting repetitive folding and unfolding of a mini β-hairpin protein, CLN025. We find objective, quantitative evidence indicating that rearrangements within the hairpin turn region are determinant for protein folding and unfolding. On the contrary, interactions between hairpin arms score low on the causality scale. Taken together, these findings clearly favor the concept of zipperlike folding, which is one of two postulated β-hairpin folding mechanisms. More importantly, the results demonstrate the possibility of a conclusive application of Granger causality analysis to a biomolecular system.
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Affiliation(s)
- Marcin Sobieraj
- Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.,Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Piotr Setny
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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9
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Yang S, Zhang Q, Yang H, Shi H, Dong A, Wang L, Yu S. Progress in infrared spectroscopy as an efficient tool for predicting protein secondary structure. Int J Biol Macromol 2022; 206:175-187. [PMID: 35217087 DOI: 10.1016/j.ijbiomac.2022.02.104] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 12/21/2022]
Abstract
Infrared (IR) spectroscopy is a highly sensitive technique that provides complete information on chemical compositions. The IR spectra of proteins or peptides give rise to nine characteristic IR absorption bands. The amide I bands are the most prominent and sensitive vibrational bands and widely used to predict protein secondary structures. The interference of H2O absorbance is the greatest challenge for IR protein secondary structure prediction. Much effort has been made to reduce/eliminate the interference of H2O, simplify operation steps, and increase prediction accuracy. Progress in sampling and equipment has rendered the Fourier transform infrared (FTIR) technique suitable for determining the protein secondary structure in broader concentration ranges, greatly simplifying the operating steps. This review highlights the recent progress in sample preparation, data analysis, and equipment development of FTIR in A/T mode, with a focus on recent applications of FTIR spectroscopy in the prediction of protein secondary structure. This review also provides a brief introduction of the progress in ATR-FTIR for predicting protein secondary structure and discusses some combined IR methods, such as AFM-based IR spectroscopy, that are used to analyze protein structural dynamics and protein aggregation.
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Affiliation(s)
- Shouning Yang
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | | | - Huayan Yang
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Haimei Shi
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Aichun Dong
- Department of Chemistry and Biochemistry, University of Northern Colorado, Greeley, CO, USA.
| | - Li Wang
- Kweichow Moutai Group, Renhuai, Guizhou 564501, China.
| | - Shaoning Yu
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
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10
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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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11
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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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12
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Nijhawan AK, Chan AM, Hsu DJ, Chen LX, Kohlstedt KL. Resolving Dynamics in the Ensemble: Finding Paths through Intermediate States and Disordered Protein Structures. J Phys Chem B 2021; 125:12401-12412. [PMID: 34748336 PMCID: PMC9096987 DOI: 10.1021/acs.jpcb.1c05820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteins have been found to inhabit a diverse set of three-dimensional structures. The dynamics that govern protein interconversion between structures happen over a wide range of time scales─picoseconds to seconds. Our understanding of protein functions and dynamics is largely reliant upon our ability to elucidate physically populated structures. From an experimental structural characterization perspective, we are often limited to measuring the ensemble-averaged structure both in the steady-state and time-resolved regimes. Generating kinetic models and understanding protein structure-function relationships require atomistic knowledge of the populated states in the ensemble. In this Perspective, we present ensemble refinement methodologies that integrate time-resolved experimental signals with molecular dynamics models. We first discuss integration of experimental structural restraints to molecular models in disordered protein systems that adhere to the principle of maximum entropy for creating a complete set of ensemble structures. We then propose strategies to find kinetic pathways between the refined structures, using time-resolved inputs to guide molecular dynamics trajectories and the use of inference to generate tailored stimuli to prepare a desired ensemble of protein states.
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Affiliation(s)
- Adam K Nijhawan
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Arnold M Chan
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Darren J Hsu
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Lin X Chen
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Kevin L Kohlstedt
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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13
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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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14
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Affiliation(s)
- Peter Hamm
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
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15
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Liu SC, Ying YL, Li WH, Wan YJ, Long YT. Snapshotting the transient conformations and tracing the multiple pathways of single peptide folding using a solid-state nanopore. Chem Sci 2021; 12:3282-3289. [PMID: 34164097 PMCID: PMC8179386 DOI: 10.1039/d0sc06106a] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A fundamental question relating to protein folding/unfolding is the time evolution of the folding of a protein into its precisely defined native structure. The proper identification of transition conformations is essential for accurately describing the dynamic protein folding/unfolding pathways. Owing to the rapid transitions and sub-nm conformation differences involved, the acquisition of the transient conformations and dynamics of proteins is difficult due to limited instrumental resolution. Using the electrochemical confinement effect of a solid-state nanopore, we were able to snapshot the transient conformations and trace the multiple transition pathways of a single peptide inside a nanopore. By combining the results with a Markov chain model, this new single-molecule technique is applied to clarify the transition pathways of the β-hairpin peptide, which shows nonequilibrium fluctuations among several blockage current stages. This method enables the high-throughput investigation of transition pathways experimentally to access previously obscure peptide dynamics, which is significant for understanding the folding/unfolding mechanisms and misfolding of peptides or proteins. A solid-state nanopore based method is described for resolving protein-folding-related problems via snapshotting the folding intermediates and characterizing the kinetics of a single peptide.![]()
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Affiliation(s)
- Shao-Chuang Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China .,Department of Chemistry, East China University of Science and Technology Shanghai 200237 P. R. China
| | - Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China .,Department of Chemistry, East China University of Science and Technology Shanghai 200237 P. R. China
| | - Wei-Hua Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology Shanghai 200237 P. R. China
| | - Yong-Jing Wan
- School of Information Science and Engineering, East China University of Science and Technology Shanghai 200237 P. R. China
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 P. R. China .,Department of Chemistry, East China University of Science and Technology Shanghai 200237 P. R. China
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16
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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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17
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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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18
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Baiz CR, Błasiak B, Bredenbeck J, Cho M, Choi JH, Corcelli SA, Dijkstra AG, Feng CJ, Garrett-Roe S, Ge NH, Hanson-Heine MWD, Hirst JD, Jansen TLC, Kwac K, Kubarych KJ, Londergan CH, Maekawa H, Reppert M, Saito S, Roy S, Skinner JL, Stock G, Straub JE, Thielges MC, Tominaga K, Tokmakoff A, Torii H, Wang L, Webb LJ, Zanni MT. Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction. Chem Rev 2020; 120:7152-7218. [PMID: 32598850 PMCID: PMC7710120 DOI: 10.1021/acs.chemrev.9b00813] [Citation(s) in RCA: 173] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and interprotein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an all-encompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semiempirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository Web site (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-the-art multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future.
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Affiliation(s)
- Carlos R. Baiz
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, U.S.A
| | - Bartosz Błasiak
- Department of Physical and Quantum Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Jens Bredenbeck
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438, Frankfurt am Main, Germany
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Jun-Ho Choi
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Steven A. Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, U.S.A
| | - Arend G. Dijkstra
- School of Chemistry and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, U.K
| | - Chi-Jui Feng
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, U.S.A
| | - Sean Garrett-Roe
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, U.S.A
| | - Nien-Hui Ge
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697-2025, U.S.A
| | - Magnus W. D. Hanson-Heine
- School of Chemistry, University of Nottingham, Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Thomas L. C. Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Kijeong Kwac
- Center for Molecular Spectroscopy and Dynamics, Seoul 02841, Republic of Korea
| | - Kevin J. Kubarych
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, U.S.A
| | - Casey H. Londergan
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041, U.S.A
| | - Hiroaki Maekawa
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697-2025, U.S.A
| | - Mike Reppert
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Shinji Saito
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, 444-8585, Japan
| | - Santanu Roy
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110, U.S.A
| | - James L. Skinner
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, U.S.A
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - John E. Straub
- Department of Chemistry, Boston University, Boston, MA 02215, U.S.A
| | - Megan C. Thielges
- Department of Chemistry, Indiana University, 800 East Kirkwood, Bloomington, Indiana 47405, U.S.A
| | - Keisuke Tominaga
- Molecular Photoscience Research Center, Kobe University, Nada, Kobe 657-0013, Japan
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, U.S.A
| | - Hajime Torii
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, and Department of Optoelectronics and Nanostructure Science, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-Ku, Hamamatsu 432-8561, Japan
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854, U.S.A
| | - Lauren J. Webb
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th Street, STOP A5300, Austin, Texas 78712, U.S.A
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1396, U.S.A
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19
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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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20
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Kwac K, Cho M. Machine learning approach for describing vibrational solvatochromism. J Chem Phys 2020; 152:174101. [DOI: 10.1063/5.0005591] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Kijeong Kwac
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
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21
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Flanagan JC, Baiz CR. Ultrafast pH-jump two-dimensional infrared spectroscopy. OPTICS LETTERS 2019; 44:4937-4940. [PMID: 31613233 DOI: 10.1364/ol.44.004937] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
We present a pH-jump two-dimensional infrared (2D IR) spectrometer to probe pH-dependent conformational changes from nanoseconds to milliseconds. The design incorporates a nanosecond 355 nm source into a pulse-shaper-based 2D IR spectrometer to trigger dissociation of a caged proton prior to probing subsequent conformational changes with femtosecond 2D IR spectroscopy. We observe a blue shift in the amide I mode (C═O stretch) of diglycine induced by protonation of the terminal amine. This method combines the bond-specific structural sensitivity of ultrafast 2D IR with triggered conformational dynamics, providing structural access to multiscale biomolecular transformations such as protein folding.
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22
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Minnes L, Greetham GM, Shaw DJ, Clark IP, Fritzsch R, Towrie M, Parker AW, Henry AJ, Taylor RJ, Hunt NT. Uncovering the Early Stages of Domain Melting in Calmodulin with Ultrafast Temperature-Jump Infrared Spectroscopy. J Phys Chem B 2019; 123:8733-8739. [PMID: 31557034 PMCID: PMC7007250 DOI: 10.1021/acs.jpcb.9b08870] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
The signaling protein
calmodulin (CaM) undergoes a well-known change
in secondary structure upon binding Ca2+, but the structural
plasticity of the Ca2+-free apo state
is linked to CaM functionality. Variable temperature studies of apo-CaM indicate two structural transitions at 46 and 58
°C that are assigned to melting of the C- and N-terminal domains,
respectively, but the molecular mechanism of domain unfolding is unknown.
We report temperature-jump time-resolved infrared (IR) spectroscopy
experiments designed to target the first steps in the C-terminal domain
melting transition of human apo-CaM. A comparison
of the nonequilibrium relaxation of apo-CaM with
the more thermodynamically stable holo-CaM, with
4 equiv of Ca2+ bound, shows that domain melting of apo-CaM begins on microsecond time scales with α-helix
destabilization. These observations enable the assignment of previously
reported dynamics of CaM on hundreds of microsecond time scales to
thermally activated melting, producing a complete mechanism for thermal
unfolding of CaM.
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Affiliation(s)
- Lucy Minnes
- Department of Physics, SUPA , University of Strathclyde , Glasgow G4 0NG , United Kingdom
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , United Kingdom
| | | | - Ian P Clark
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , United Kingdom
| | - Robby Fritzsch
- Department of Physics, SUPA , University of Strathclyde , Glasgow G4 0NG , United Kingdom
| | - Michael Towrie
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , United Kingdom
| | - Anthony W Parker
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , United Kingdom
| | | | | | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute , University of York , Heslington, York YO10 5DD , United Kingdom
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23
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Sarkar D, Kang P, Nielsen SO, Qin Z. Non-Arrhenius Reaction-Diffusion Kinetics for Protein Inactivation over a Large Temperature Range. ACS NANO 2019; 13:8669-8679. [PMID: 31268674 PMCID: PMC7384293 DOI: 10.1021/acsnano.9b00068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Understanding protein folding and unfolding has been a long-standing fundamental question and has important applications in manipulating protein activity in biological systems. Experimental investigations of protein unfolding have been predominately conducted by small temperature perturbations (e.g., temperature jump), while molecular simulations are limited to small time scales (microseconds) and high temperatures to observe unfolding. Thus, it remains unclear how fast a protein unfolds irreversibly and loses function (i.e., inactivation) across a large temperature range. In this work, using nanosecond pulsed heating of individual plasmonic nanoparticles to create precise localized heating, we examine the protein inactivation kinetics at extremely high temperatures. Connecting this with protein inactivation measurements at low temperatures, we observe that the kinetics of protein unfolding is less sensitive to temperature change at the higher temperatures, which significantly departs from the Arrhenius behavior extrapolated from low temperatures. To account for this effect, we propose a reaction-diffusion model that modifies the temperature-dependence of protein inactivation by introducing a diffusion limit. Analysis of the reaction-diffusion model provides general guidelines in the behavior of protein inactivation (reaction-limited, transition, diffusion-limited) across a large temperature range from physiological temperature to extremely high temperatures. We further demonstrate that the reaction-diffusion model is particularly useful for designing optimal operating conditions for protein photoinactivation. The experimentally validated reaction-diffusion kinetics of protein unfolding is an important step toward understanding protein-inactivation kinetics over a large temperature range. It has important applications including molecular hyperthermia and calls for future studies to examine this model for other protein molecules.
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Affiliation(s)
- Daipayan Sarkar
- Department of Mechanical Engineering, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - Peiyuan Kang
- Department of Mechanical Engineering, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - Steven O. Nielsen
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - Zhenpeng Qin
- Department of Mechanical Engineering, The University of Texas at Dallas, Richardson, TX 75080, USA
- Department of Bioengineering, The University of Texas at Dallas, Richardson, TX 75080, USA
- Department of Surgery, The University of Texas at Southwestern Medical Center, Dallas, TX 75390, USA
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24
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Ramos S, Thielges MC. Site-Specific 1D and 2D IR Spectroscopy to Characterize the Conformations and Dynamics of Protein Molecular Recognition. J Phys Chem B 2019; 123:3551-3566. [PMID: 30848912 DOI: 10.1021/acs.jpcb.9b00969] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Proteins exist as ensembles of interconverting states on a complex energy landscape. A complete, molecular-level understanding of their function requires knowledge of the populated states and thus the experimental tools to characterize them. Infrared (IR) spectroscopy has an inherently fast time scale that can capture all states and their dynamics with, in principle, bond-specific spatial resolution, and 2D IR methods that provide richer information are becoming more routine. Although application of IR spectroscopy for investigation of proteins is challenged by spectral congestion, the issue can be overcome by site-specific introduction of amino acid side chains that have IR probe groups with frequency-resolved absorptions, which furthermore enables selective characterization of different locations in proteins. Here, we briefly introduce the biophysical methods and summarize the current progress toward the study of proteins. We then describe our efforts to apply site-specific 1D and 2D IR spectroscopy toward elucidation of protein conformations and dynamics to investigate their involvement in protein molecular recognition, in particular mediated by dynamic complexes: plastocyanin and its binding partner cytochrome f, cytochrome P450s and substrates or redox partners, and Src homology 3 domains and proline-rich peptide motifs. We highlight the advantages of frequency-resolved probes to characterize specific, local sites in proteins and uncover variation among different locations, as well as the advantage of the fast time scale of IR spectroscopy to detect rapidly interconverting states. In addition, we illustrate the greater insight provided by 2D methods and discuss potential routes for further advancement of the field of biomolecular 2D IR spectroscopy.
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Affiliation(s)
- Sashary Ramos
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Megan C Thielges
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
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25
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Hogle DG, Cunningham AR, Tucker MJ. Equilibrium versus Nonequilibrium Peptide Dynamics: Insights into Transient 2D IR Spectroscopy. J Phys Chem B 2018; 122:8783-8795. [PMID: 30040900 DOI: 10.1021/acs.jpcb.8b05063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Over the past two decades, two-dimensional infrared (2D IR) spectroscopy has evolved from the theoretical underpinnings of nonlinear spectroscopy as a means of investigating detailed molecular structure on an ultrafast time scale. The combined time and spectral resolution over which spectra can be collected on complex molecular systems has led to the precise structural resolution of dynamic species that have previously been impossible to directly observe through traditional methods. The adoption of 2D IR spectroscopy for the study of protein folding and peptide interactions has provided key details of how small changes in conformations can exert major influences on the activities of these complex molecular systems. Traditional 2D IR experiments are limited to molecules under equilibrium conditions, where small motions and fluctuations of these larger molecules often still lead to functionality. Utilizing techniques that allow the rapid initiation of chemical or structural changes in conjunction with 2D IR spectroscopy, i.e., transient 2D IR, a vast dynamic range becomes available to the spectroscopist uncovering structural content far from equilibrium. Furthermore, this allows the observation of reaction pathways of these macromolecules under quasi- and nonequilibrium conditions.
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Affiliation(s)
- David G Hogle
- Department of Chemistry , University of Nevada, Reno , 1664 North Virginia Street , Reno , Nevada 89557 , United States
| | - Amy R Cunningham
- Department of Chemistry , University of Nevada, Reno , 1664 North Virginia Street , Reno , Nevada 89557 , United States
| | - Matthew J Tucker
- Department of Chemistry , University of Nevada, Reno , 1664 North Virginia Street , Reno , Nevada 89557 , United States
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26
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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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27
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Stock G, Hamm P. A non-equilibrium approach to allosteric communication. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170187. [PMID: 29735740 PMCID: PMC5941181 DOI: 10.1098/rstb.2017.0187] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2018] [Indexed: 12/16/2022] Open
Abstract
While the theory of protein folding is well developed, including concepts such as rugged energy landscape, folding funnel, etc., the same degree of understanding has not been reached for the description of the dynamics of allosteric transitions in proteins. This is not only due to the small size of the structural change upon ligand binding to an allosteric site, but also due to challenges in designing experiments that directly observe such an allosteric transition. On the basis of recent pump-probe-type experiments (Buchli et al. 2013 Proc. Natl Acad. Sci. USA110, 11 725-11 730. (doi:10.1073/pnas.1306323110)) and non-equilibrium molecular dynamics simulations (Buchenberg et al. 2017 Proc. Natl Acad. Sci. USA114, E6804-E6811. (doi:10.1073/pnas.1707694114)) studying an photoswitchable PDZ2 domain as model for an allosteric transition, we outline in this perspective how such a description of allosteric communication might look. That is, calculating the dynamical content of both experiment and simulation (which agree remarkably well with each other), we find that allosteric communication shares some properties with downhill folding, except that it is an 'order-order' transition. Discussing the multiscale and hierarchical features of the dynamics, the validity of linear response theory as well as the meaning of 'allosteric pathways', we conclude that non-equilibrium experiments and simulations are a promising way to study dynamical aspects of allostery.This article is part of a discussion meeting issue 'Allostery and molecular machines'.
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Affiliation(s)
- Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, Freiburg, Germany
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Zurich, Switzerland
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28
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Transient two-dimensional vibrational spectroscopy of an operating molecular machine. Nat Commun 2017; 8:2206. [PMID: 29263325 PMCID: PMC5738383 DOI: 10.1038/s41467-017-02278-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 11/16/2017] [Indexed: 01/31/2023] Open
Abstract
Synthetic molecular machines are promising building blocks for future nanoscopic devices. However, the details of their mechanical behaviour are in many cases still largely unknown. A deeper understanding of mechanics at the molecular level is essential for the design and construction of complex nanodevices. Here, we show that transient two-dimensional infrared (T2DIR) spectroscopy makes it possible to monitor the conformational changes of a translational molecular machine during its operation. Translation of a macrocyclic ring from one station to another on a molecular thread is initiated by a UV pulse. The arrival of the shuttling macrocycle at the final station is visible from a newly appearing cross peak between these two moieties. To eliminate spectral congestion in the T2DIR spectra, we use a subtraction method applicable to many other complex molecular systems. The T2DIR spectra indicate that the macrocycle adopts a boat-like conformation at the final station, which contrasts with the chair-like conformation at the initial station. A deeper understanding of the mechanics of molecular machines is limited by the fast motions which are in the nanosecond or picosecond timescale. Here the authors present a real-time observation of structural changes in a rotaxane-based molecular shuttle by transient two-dimensional infrared spectroscopy.
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29
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Kraack JP. Ultrafast structural molecular dynamics investigated with 2D infrared spectroscopy methods. Top Curr Chem (Cham) 2017; 375:86. [PMID: 29071445 DOI: 10.1007/s41061-017-0172-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 10/02/2017] [Indexed: 12/23/2022]
Abstract
Ultrafast, multi-dimensional infrared (IR) spectroscopy has been advanced in recent years to a versatile analytical tool with a broad range of applications to elucidate molecular structure on ultrafast timescales, and it can be used for samples in a many different environments. Following a short and general introduction on the benefits of 2D IR spectroscopy, the first part of this chapter contains a brief discussion on basic descriptions and conceptual considerations of 2D IR spectroscopy. Outstanding classical applications of 2D IR are used afterwards to highlight the strengths and basic applicability of the method. This includes the identification of vibrational coupling in molecules, characterization of spectral diffusion dynamics, chemical exchange of chemical bond formation and breaking, as well as dynamics of intra- and intermolecular energy transfer for molecules in bulk solution and thin films. In the second part, several important, recently developed variants and new applications of 2D IR spectroscopy are introduced. These methods focus on (i) applications to molecules under two- and three-dimensional confinement, (ii) the combination of 2D IR with electrochemistry, (iii) ultrafast 2D IR in conjunction with diffraction-limited microscopy, (iv) several variants of non-equilibrium 2D IR spectroscopy such as transient 2D IR and 3D IR, and (v) extensions of the pump and probe spectral regions for multi-dimensional vibrational spectroscopy towards mixed vibrational-electronic spectroscopies. In light of these examples, the important open scientific and conceptual questions with regard to intra- and intermolecular dynamics are highlighted. Such questions can be tackled with the existing arsenal of experimental variants of 2D IR spectroscopy to promote the understanding of fundamentally new aspects in chemistry, biology and materials science. The final part of the chapter introduces several concepts of currently performed technical developments, which aim at exploiting 2D IR spectroscopy as an analytical tool. Such developments embrace the combination of 2D IR spectroscopy and plasmonic spectroscopy for ultrasensitive analytics, merging 2D IR spectroscopy with ultra-high-resolution microscopy (nanoscopy), future variants of transient 2D IR methods, or 2D IR in conjunction with microfluidics. It is expected that these techniques will allow for groundbreaking research in many new areas of natural sciences.
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Affiliation(s)
- Jan Philip Kraack
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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Ghosh A, Ostrander JS, Zanni MT. Watching Proteins Wiggle: Mapping Structures with Two-Dimensional Infrared Spectroscopy. Chem Rev 2017; 117:10726-10759. [PMID: 28060489 PMCID: PMC5500453 DOI: 10.1021/acs.chemrev.6b00582] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteins exhibit structural fluctuations over decades of time scales. From the picosecond side chain motions to aggregates that form over the course of minutes, characterizing protein structure over these vast lengths of time is important to understanding their function. In the past 15 years, two-dimensional infrared spectroscopy (2D IR) has been established as a versatile tool that can uniquely probe proteins structures on many time scales. In this review, we present some of the basic principles behind 2D IR and show how they have, and can, impact the field of protein biophysics. We highlight experiments in which 2D IR spectroscopy has provided structural and dynamical data that would be difficult to obtain with more standard structural biology techniques. We also highlight technological developments in 2D IR that continue to expand the scope of scientific problems that can be accessed in the biomedical sciences.
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Affiliation(s)
| | - Joshua S. Ostrander
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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31
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Simulation of the T-jump triggered unfolding and thermal unfolding vibrational spectroscopy related to polypeptides conformation fluctuation. Sci China Chem 2017. [DOI: 10.1007/s11426-016-9055-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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32
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Influence of Glu/Arg, Asp/Arg, and Glu/Lys Salt Bridges on α-Helical Stability and Folding Kinetics. Biophys J 2017; 110:2328-2341. [PMID: 27276251 DOI: 10.1016/j.bpj.2016.04.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 03/17/2016] [Accepted: 04/08/2016] [Indexed: 01/24/2023] Open
Abstract
Using a combination of ultraviolet circular dichroism, temperature-jump transient-infrared spectroscopy, and molecular dynamics simulations, we investigate the effect of salt bridges between different types of charged amino-acid residue pairs on α-helix folding. We determine the stability and the folding and unfolding rates of 12 alanine-based α-helical peptides, each of which has a nearly identical composition containing three pairs of positively and negatively charged residues (either Glu(-)/Arg(+), Asp(-)/Arg(+), or Glu(-)/Lys(+)). Within each set of peptides, the distance and order of the oppositely charged residues in the peptide sequence differ, such that they have different capabilities of forming salt bridges. Our results indicate that stabilizing salt bridges (in which the interacting residues are spaced and ordered such that they favor helix formation) speed up α-helix formation by up to 50% and slow down the unfolding of the α-helix, whereas salt bridges with an unfavorable geometry have the opposite effect. Comparing the peptides with different types of charge pairs, we observe that salt bridges between side chains of Glu(-) and Arg(+) are most favorable for the speed of folding, probably because of the larger conformational space of the salt-bridging Glu(-)/Arg(+) rotamer pairs compared to Asp(-)/Arg(+) and Glu(-)/Lys(+). We speculate that the observed impact of salt bridges on the folding kinetics might explain why some proteins contain salt bridges that do not stabilize the final, folded conformation.
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Slavov C, Yang C, Schweighauser L, Wegner HA, Dreuw A, Wachtveitl J. Ultrafast Excited-State Deactivation Dynamics of Cyclotrisazobenzene-A Novel Type of UV-B Absorber. Chemphyschem 2017; 18:2137-2141. [DOI: 10.1002/cphc.201700384] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/01/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Chavdar Slavov
- Institute of Physical and Theoretical Chemistry; Goethe University; Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Chong Yang
- Interdisciplinary Center for Scientific Computing, IWR; University of Heidelberg; Im Neuenheimer Feld 205 69120 Heidelberg Germany
| | - Luca Schweighauser
- Institute of Organic Chemistry; Justus Liebig University; Heinrich-Buff-Ring 17 35392 Giessen Germany
| | - Hermann A. Wegner
- Institute of Organic Chemistry; Justus Liebig University; Heinrich-Buff-Ring 17 35392 Giessen Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, IWR; University of Heidelberg; Im Neuenheimer Feld 205 69120 Heidelberg Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry; Goethe University; Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
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Abaskharon RM, Gai F. Meandering Down the Energy Landscape of Protein Folding: Are We There Yet? Biophys J 2017; 110:1924-32. [PMID: 27166801 DOI: 10.1016/j.bpj.2016.03.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/18/2016] [Accepted: 03/22/2016] [Indexed: 12/11/2022] Open
Abstract
As judged by a single publication metric, the activity in the protein folding field has been declining over the past 5 years, after enjoying a decade-long growth. Does this development indicate that the field is sunsetting or is this decline only temporary? Upon surveying a small territory of its landscape, we find that the protein folding field is still quite active and many important findings have emerged from recent experimental studies. However, it is also clear that only continued development of new techniques and methods, especially those enabling dissection of the fine details and features of the protein folding energy landscape, will fuel this old field to move forward.
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Affiliation(s)
- Rachel M Abaskharon
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania; The Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania.
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35
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Meuzelaar H, Panman MR, van Dijk CN, Woutersen S. Folding of a Zinc-Finger ββα-Motif Investigated Using Two-Dimensional and Time-Resolved Vibrational Spectroscopy. J Phys Chem B 2016; 120:11151-11158. [PMID: 27723346 DOI: 10.1021/acs.jpcb.6b08883] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small proteins provide good model systems for studying the fundamental forces that control protein folding. Here, we investigate the folding dynamics of the 28-residue zinc-finger mutant FSD-1, which is designed to form a metal-independent folded ββα-motif, and which provides a testing ground for proteins containing a mixed α/β fold. Although the folding of FSD-1 has been actively studied, the folding mechanism remains largely unclear. In particular, it is unclear in what stage of folding the α-helix is formed. To address this issue we investigate the folding mechanism of FSD-1 using a combination of temperature-dependent UV circular dichroism (UV-CD), Fourier transform infrared (FTIR) spectroscopy, two-dimensional infrared (2D-IR) spectroscopy, and temperature-jump (T-jump) transient-IR spectroscopy. Our UV-CD and FTIR data show different thermal melting transitions, indicating multistate folding behavior. Temperature-dependent 2D-IR spectra indicate that the α-helix is the most stable structural element of FSD-1. To investigate the folding/unfolding re-equilibration dynamics of FSD-1, the conformational changes induced by a nanosecond T-jump are probed with transient-IR and transient dispersed-pump-probe (DPP) IR spectroscopy. We observe biexponential T-jump relaxation kinetics (with time constants of 80 ± 13 ns and 1300 ± 100 ns at 322 K), confirming that the folding involves an intermediate state. The IR and dispersed-pump-probe IR spectra associated with the two kinetic components suggest that the folding of FSD-1 involves early formation of the α-helix, followed by the formation of the β-hairpin and hydrophobic contacts.
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Affiliation(s)
- Heleen Meuzelaar
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Matthijs R Panman
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Chris N van Dijk
- 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
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36
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Horvath R, Huff GS, Gordon KC, George MW. Probing the excited state nature of coordination complexes with blended organic and inorganic chromophores using vibrational spectroscopy. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.04.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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37
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Maj M, Ahn C, Błasiak B, Kwak K, Han H, Cho M. Isonitrile as an Ultrasensitive Infrared Reporter of Hydrogen-Bonding Structure and Dynamics. J Phys Chem B 2016; 120:10167-10180. [DOI: 10.1021/acs.jpcb.6b04319] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Michał Maj
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science (IBS) and ‡Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Changwoo Ahn
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science (IBS) and ‡Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Bartosz Błasiak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science (IBS) and ‡Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science (IBS) and ‡Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Hogyu Han
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science (IBS) and ‡Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science (IBS) and ‡Department of Chemistry, Korea University, Seoul 02841, Korea
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38
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Ostrander JS, Serrano AL, Ghosh A, Zanni MT. Spatially Resolved Two-Dimensional Infrared Spectroscopy via Wide-Field Microscopy. ACS PHOTONICS 2016; 3:1315-1323. [PMID: 27517058 PMCID: PMC4976945 DOI: 10.1021/acsphotonics.6b00297] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We report the first wide-field microscope for measuring two-dimensional infrared (2D IR) spectroscopic images. We concurrently collect more than 16 000 2D IR spectra, made possible by a new focal plane array detector and mid-IR pulse shaping, to generate hyperspectral images with multiple frequency dimensions and diffraction-limited spatial resolution. Both frequency axes of the spectra are collected in the time domain by scanning two pairs of femtosecond pulses using a dual acousto-optic modulator pulse shaper. The technique is demonstrated by imaging a mixture of metal carbonyl absorbed polystyrene beads. The differences in image formation between FTIR and 2D IR microscopy are also explored by imaging a patterned USAF test target. We find that our 2D IR microscope has diffraction-limited spatial resolution and enhanced contrast compared to FTIR microscopy because of the nonlinear scaling of the 2D IR signal to the absorptivity coefficient for the vibrational modes. Images generated using off-diagonal peaks, created from vibrational anharmonicities, improve the molecular discrimination and eliminate noise. Two-dimensional wide-field IR microscopy provides information on vibrational lifetimes, molecular couplings, transition dipole orientations, and many other quantities that can be used for creating image contrast to help disentangle and interpret complex and heterogeneous samples. Such experiments made possible could include the study of amyloid proteins in tissues, protein folding in heterogeneous environments, and structural dynamics in devices employing mid-IR materials.
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39
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Zhang XX, Jones KC, Fitzpatrick A, Peng CS, Feng CJ, Baiz CR, Tokmakoff A. Studying Protein-Protein Binding through T-Jump Induced Dissociation: Transient 2D IR Spectroscopy of Insulin Dimer. J Phys Chem B 2016; 120:5134-45. [PMID: 27203447 DOI: 10.1021/acs.jpcb.6b03246] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Insulin homodimer associates through the coupled folding and binding of two partially disordered monomers. We aim to understand this dynamics by observing insulin dimer dissociation initiated with a nanosecond temperature jump using transient two-dimensional infrared spectroscopy (2D IR) of amide I vibrations. With the help of equilibrium FTIR and 2D IR spectra, and through a systematic study of the dependence of dissociation kinetics on temperature and insulin concentration, we are able to decompose and analyze the spectral evolution associated with different secondary structures. We find that the dissociation under all conditions is characterized by two processes whose influence on the kinetics varies with temperature: the unfolding of the β sheet at the dimer interface observed as exponential kinetics between 250 and 1000 μs and nonexponential kinetics between 5 and 150 μs that we attribute to monomer disordering. Microscopic reversibility arguments lead us to conclude that dimer association requires significant conformational changes within the monomer in concert with the folding of the interfacial β sheet. While our data indicates a more complex kinetics, we apply a two-state model to the β-sheet unfolding kinetics to extract thermodynamic parameters and kinetic rate constants. The association rate constant, ka (23 °C) = 8.8 × 10(5) M(-1) s(-1) (pH 0, 20% EtOD), is approximately 3 orders of magnitude slower than the calculated diffusion limited association rate, which is explained by the significant destabilizing effect of ethanol on the dimer state and the highly positive charge of the monomers at this pH.
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Affiliation(s)
- Xin-Xing Zhang
- Department of Chemistry, Institute for Biophysical Dynamics, and the James Franck Institute, The University of Chicago , Chicago, Illinois 60637, United States
| | - Kevin C Jones
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Ann Fitzpatrick
- Department of Chemistry, Institute for Biophysical Dynamics, and the James Franck Institute, The University of Chicago , Chicago, Illinois 60637, United States
| | - Chunte Sam Peng
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Chi-Jui Feng
- Department of Chemistry, Institute for Biophysical Dynamics, and the James Franck Institute, The University of Chicago , Chicago, Illinois 60637, United States
| | - Carlos R Baiz
- Department of Chemistry, Institute for Biophysical Dynamics, and the James Franck Institute, The University of Chicago , Chicago, Illinois 60637, United States
| | - Andrei Tokmakoff
- Department of Chemistry, Institute for Biophysical Dynamics, and the James Franck Institute, The University of Chicago , Chicago, Illinois 60637, United States
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40
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Reppert M, Tokmakoff A. Computational Amide I 2D IR Spectroscopy as a Probe of Protein Structure and Dynamics. Annu Rev Phys Chem 2016; 67:359-86. [DOI: 10.1146/annurev-physchem-040215-112055] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mike Reppert
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637;
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637;
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41
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Ding B, Hilaire MR, Gai F. Infrared and Fluorescence Assessment of Protein Dynamics: From Folding to Function. J Phys Chem B 2016; 120:5103-13. [PMID: 27183318 DOI: 10.1021/acs.jpcb.6b03199] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
While folding or performing functions, a protein can sample a rich set of conformational space. However, experimentally capturing all of the important motions with sufficient detail to allow a mechanistic description of their dynamics is nontrivial since such conformational events often occur over a wide range of time and length scales. Therefore, many methods have been employed to assess protein conformational dynamics, and depending on the nature of the conformational transition in question, some may be more advantageous than others. Herein, we describe our recent efforts, and also those of others, wherever appropriate, to use infrared- and fluorescence-based techniques to interrogate protein folding and functional dynamics. Specifically, we focus on discussing how to use extrinsic spectroscopic probes to enhance the structural resolution of these techniques and how to exploit various cross-linking strategies to acquire dynamic and mechanistic information that was previously difficult to attain.
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Affiliation(s)
- Bei Ding
- Department of Chemistry and ‡The Ultrafast Optical Processes Laboratory, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Mary Rose Hilaire
- Department of Chemistry and ‡The Ultrafast Optical Processes Laboratory, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Feng Gai
- Department of Chemistry and ‡The Ultrafast Optical Processes Laboratory, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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42
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El Khoury Y, Van Wilderen LJGW, Bredenbeck J. Ultrafast 2D-IR spectroelectrochemistry of flavin mononucleotide. J Chem Phys 2016; 142:212416. [PMID: 26049436 DOI: 10.1063/1.4916916] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We demonstrate the coupling of ultrafast two-dimensional infrared (2D-IR) spectroscopy to electrochemistry in solution and apply it to flavin mononucleotide, an important cofactor of redox proteins. For this purpose, we designed a spectroelectrochemical cell optimized for 2D-IR measurements in reflection and measured the time-dependent 2D-IR spectra of the oxidized and reduced forms of flavin mononucleotide. The data show anharmonic coupling and vibrational energy transfer between different vibrational modes in the two redox species. Such information is inaccessible with redox-controlled steady-state FTIR spectroscopy. The wide range of applications offered by 2D-IR spectroscopy, such as sub-picosecond structure determination, IR band assignment via energy transfer, disentangling reaction mixtures through band connectivity in the 2D spectra, and the measurement of solvation dynamics and chemical exchange can now be explored under controlled redox potential. The development of this technique furthermore opens new horizons for studying the dynamics of redox proteins.
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Affiliation(s)
- Youssef El Khoury
- Institut für Biophysik, Johann Wolfgang Goethe-Universität, Max-von-Laue-Strasse 1, 60438 Frankfurt am Main, Germany
| | - Luuk J G W Van Wilderen
- Institut für Biophysik, Johann Wolfgang Goethe-Universität, Max-von-Laue-Strasse 1, 60438 Frankfurt am Main, Germany
| | - Jens Bredenbeck
- Institut für Biophysik, Johann Wolfgang Goethe-Universität, Max-von-Laue-Strasse 1, 60438 Frankfurt am Main, Germany
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43
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Baiz CR, Tokmakoff A. Structural disorder of folded proteins: isotope-edited 2D IR spectroscopy and Markov state modeling. Biophys J 2016; 108:1747-1757. [PMID: 25863066 DOI: 10.1016/j.bpj.2014.12.061] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 12/05/2014] [Accepted: 12/19/2014] [Indexed: 01/14/2023] Open
Abstract
The conformational heterogeneity of the N-terminal domain of the ribosomal protein L9 (NTL91-39) in its folded state is investigated using isotope-edited two-dimensional infrared spectroscopy. Backbone carbonyls are isotope-labeled ((13)C=(18)O) at five selected positions (V3, V9, V9G13, G16, and G24) to provide a set of localized spectroscopic probes of the structure and solvent exposure at these positions. Structural interpretation of the amide I line shapes is enabled by spectral simulations carried out on structures extracted from a recent Markov state model. The V3 label spectrum indicates that the β-sheet contacts between strands I and II are well folded with minimal disorder. The V9 and V9G13 label spectra, which directly probe the hydrogen-bond contacts across the β-turn, show significant disorder, indicating that molecular dynamics simulations tend to overstabilize ideally folded β-turn structures in NTL91-39. In addition, G24-label spectra provide evidence for a partially disordered α-helix backbone that participates in hydrogen bonding with the surrounding water.
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Affiliation(s)
- Carlos R Baiz
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois.
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44
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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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45
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Abstract
Two-dimensional infrared (2D IR) spectroscopy has recently emerged as a powerful tool with applications in many areas of scientific research. The inherent high time resolution coupled with bond-specific spatial resolution of IR spectroscopy enable direct characterization of rapidly interconverting species and fast processes, even in complex systems found in chemistry and biology. In this minireview, we briefly outline the fundamental principles and experimental procedures of 2D IR spectroscopy. Using illustrative example studies, we explain the important features of 2D IR spectra and their capability to elucidate molecular structure and dynamics. Primarily, this minireview aims to convey the scope and potential of 2D IR spectroscopy by highlighting select examples of recent applications including the use of innate or introduced vibrational probes for the study of nucleic acids, peptides/proteins, and materials.
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Affiliation(s)
- Amanda L Le Sueur
- Department of Chemistry, Indiana University, Bloomington, Indiana, 47405, USA.
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46
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Stevenson P, Tokmakoff A. Distinguishing gramicidin D conformers through two-dimensional infrared spectroscopy of vibrational excitons. J Chem Phys 2015; 142:212424. [PMID: 26049444 PMCID: PMC4401804 DOI: 10.1063/1.4917321] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 03/31/2015] [Indexed: 11/14/2022] Open
Abstract
Gramicidin D is a short peptide which dimerizes to form helical pores, adopting one of two conformations in the process. These conformations differ primarily in number of residues per turn and the hydrogen-bond registry between rungs of the helix. Using amide I 2D infrared (IR) and FTIR, we have demonstrated that it is possible to distinguish between the different conformers of gramicidin D in solution. We show that the spectra observed for this helical peptide bear no resemblance to the spectra of α- or 310-helices and that while the FTIR spectra appear similar to spectra of β-sheets, 2D IR reveals that the observed resonances arise from vibrational modes unlike those observed in β-sheets. We also present an idealized model which reproduces the experimental data with high fidelity. This model is able to explain the polarization-dependence of the experimental 2D IR data. Using this model, we show the coupling between the rungs of the helix dominates the spectra, and as a consequence of this, the number of residues per turn can greatly influence the amide I spectra of gramicidin D.
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Affiliation(s)
- Paul Stevenson
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
| | - Andrei Tokmakoff
- Department of Chemistry, James Frank Institute, and The Institute for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, USA
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47
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Zerze GH, Uz B, Mittal J. Folding thermodynamics ofβ-hairpins studied by replica-exchange molecular dynamics simulations. Proteins 2015; 83:1307-15. [DOI: 10.1002/prot.24827] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 04/24/2015] [Accepted: 04/29/2015] [Indexed: 01/21/2023]
Affiliation(s)
- Gül H. Zerze
- Department of Chemical and Biomolecular Engineering; Lehigh University; Bethlehem Pennsylvania 18015
| | - Bilge Uz
- Department of Chemical and Biomolecular Engineering; Lehigh University; Bethlehem Pennsylvania 18015
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering; Lehigh University; Bethlehem Pennsylvania 18015
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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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Koziol KL, Johnson PJM, Stucki-Buchli B, Waldauer SA, Hamm P. Fast infrared spectroscopy of protein dynamics: advancing sensitivity and selectivity. Curr Opin Struct Biol 2015; 34:1-6. [PMID: 25900180 DOI: 10.1016/j.sbi.2015.03.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 03/27/2015] [Accepted: 03/31/2015] [Indexed: 01/08/2023]
Abstract
2D-IR spectroscopy has matured to a powerful technique to study the structure and dynamics of peptides, but its extension to larger proteins is still in its infancy, the major limitations being sensitivity and selectivity. Site-selective information requires measuring single vibrational probes at sub-millimolar concentrations where most proteins are still stable, which is a severe challenge for conventional (FT)IR spectroscopy. Besides its ultrafast time-resolution, a so far largely underappreciated potential of 2D-IR spectroscopy lies in its sensitivity gain. The present paper sets the goals and outlines strategies how to use that sensitivity gain together with properly designed vibrational labels to make IR spectroscopy a versatile tool to study a wide class of proteins.
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Affiliation(s)
- Klemens L Koziol
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Philip J M Johnson
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Brigitte Stucki-Buchli
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Steven A Waldauer
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland.
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Affiliation(s)
- Qiang Shao
- Drug Discovery and Design
Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
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