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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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Al-Mualem ZA, Baiz CR. Generative Adversarial Neural Networks for Denoising Coherent Multidimensional Spectra. J Phys Chem A 2022; 126:3816-3825. [PMID: 35668543 DOI: 10.1021/acs.jpca.2c02605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Ultrafast spectroscopy often involves measuring weak signals and long data acquisition times. Spectra are typically collected as a "pump-probe" spectrum by measuring differences in intensity across laser shots. Shot-to-shot intensity fluctuations are most often the primary source of noise in ultrafast spectroscopy. Here, we present a novel approach for denoising ultrafast two-dimensional infrared (2D IR) spectra using conditional generative adversarial neural networks (cGANNs). The cGANN approach is able to eliminate shot-to-shot noise and reconstruct the line shapes present in the noisy input spectrum. We present a general approach for training the cGANN using matched pairs of noisy and clean synthetic 2D IR spectra based on the Kubo-line shape model for a three-level system. Experimental shot-to-shot laser noise is added to synthetic spectra to recreate the noise profile present in measured experimental spectra. The cGANNs can recover line shapes from synthetic 2D IR spectra with signal-to-noise ratios as low as 2:1, while largely preserving the key features such as center frequencies, line widths, and diagonal elongation. In addition, we benchmark the performance of the cGANN using experimental 2D IR spectra of an ester carbonyl vibrational probe and demonstrate that, by applying the cGANN denoising approach, we can extract the frequency-frequency time correlation function (FFCF) from reconstructed spectra using a nodal-line slope analysis. Finally, we provide a set of practical guidelines for extending the denoising method to other coherent multidimensional spectroscopies.
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Affiliation(s)
- Ziareena A Al-Mualem
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Carlos R Baiz
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
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Thielges MC. Transparent window 2D IR spectroscopy of proteins. J Chem Phys 2021; 155:040903. [PMID: 34340394 PMCID: PMC8302233 DOI: 10.1063/5.0052628] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/21/2021] [Indexed: 02/01/2023] Open
Abstract
Proteins are complex, heterogeneous macromolecules that exist as ensembles of interconverting states on a complex energy landscape. A complete, molecular-level understanding of their function requires experimental tools to characterize them with high spatial and temporal precision. Infrared (IR) spectroscopy has an inherently fast time scale that can capture all states and their dynamics with, in principle, bond-specific spatial resolution. Two-dimensional (2D) IR methods that provide richer information are becoming more routine but remain challenging to apply to proteins. Spectral congestion typically prevents selective investigation of native vibrations; however, the problem can be overcome by site-specific introduction of amino acid side chains that have vibrational groups with frequencies in the "transparent window" of protein spectra. This Perspective provides an overview of the history and recent progress in the development of transparent window 2D IR of proteins.
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Affiliation(s)
- Megan C. Thielges
- Department of Chemistry, Indiana University, Bloomington,
Indiana 47405, USA
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Abstract
This review examines low-frequency vibrational modes of proteins and their coupling to enzyme catalytic sites. That protein motions are critical to enzyme function is clear, but the kinds of motions present in proteins and how they are involved in function remain unclear. Several models of enzyme-catalyzed reaction suggest that protein dynamics may be involved in the chemical step of the catalyzed reaction, but the evidence in support of such models is indirect. Spectroscopic studies of low-frequency protein vibrations consistently show that there are underdamped modes of the protein with frequencies in the tens of wavenumbers where overdamped behavior would be expected. Recent studies even show that such underdamped vibrations modulate enzyme active sites. These observations suggest that increasingly sophisticated spectroscopic methods will be able to unravel the link between low-frequency protein vibrations and enzyme function.
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Hume S, Greetham GM, Donaldson PM, Towrie M, Parker AW, Baker MJ, Hunt NT. 2D-Infrared Spectroscopy of Proteins in Water: Using the Solvent Thermal Response as an Internal Standard. Anal Chem 2020; 92:3463-3469. [PMID: 31985198 PMCID: PMC7145279 DOI: 10.1021/acs.analchem.9b05601] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Ultrafast
two-dimensional infrared (2D-IR) spectra can now be obtained
in a matter of seconds, opening up the possibility of high-throughput
screening applications of relevance to the biomedical and pharmaceutical
sectors. Determining quantitative information from 2D-IR spectra recorded
on different samples and different instruments is however made difficult
by variations in beam alignment, laser intensity, and sample conditions.
Recently, we demonstrated that 2D-IR spectroscopy of the protein amide
I band can be performed in aqueous (H2O) rather than deuterated
(D2O) solvents, and we now report a method that uses the
magnitude of the associated thermal response of H2O as
an internal normalization standard for 2D-IR spectra. Using the water
response, which is temporally separated from the protein signal, to
normalize the spectra allows significant reduction of the impact of
measurement-to-measurement fluctuations on the data. We demonstrate
that this normalization method enables creation of calibration curves
for measurement of absolute protein concentrations and facilitates
reproducible difference spectroscopy methodologies. These advances
make significant progress toward the robust data handling strategies
that will be essential for the realization of automated spectral analysis
tools for large scale 2D-IR screening studies of protein-containing
solutions and biofluids.
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Affiliation(s)
- Samantha Hume
- Department of Physics, SUPA , University of Strathclyde , 107 Rottenrow East , Glasgow G4 0NG , U.K
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus, Didcot OX11 0QX , U.K
| | - Paul M Donaldson
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus, Didcot OX11 0QX , U.K
| | - Michael Towrie
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus, Didcot OX11 0QX , U.K
| | - Anthony W Parker
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus, Didcot OX11 0QX , U.K
| | - Matthew J Baker
- WestCHEM, Department of Pure and Applied Chemistry , University of Strathclyde , Technology and Innovation Centre, 99 George Street , Glasgow G1 1RD , U.K
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute , University of York , Heslington, York YO10 5DD , U.K
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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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Kiefer LM, Kubarych KJ. Two-dimensional infrared spectroscopy of coordination complexes: From solvent dynamics to photocatalysis. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.05.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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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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Ding F, Peng W, Peng YK. Biophysical exploration of protein-flavonol recognition: effects of molecular properties and conformational flexibility. Phys Chem Chem Phys 2017; 18:11959-71. [PMID: 27095486 DOI: 10.1039/c5cp07754k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The current work explores the biomolecular recognition of a series of flavonols by a protein and then uncovers the influences of the structural features of flavonols and the protein's own characteristics, e.g. the dynamics and flexibility, on the bioavailability of flavonols by using the pivotal biomacromolecule hemoglobin as a model. The experimental results revealed that flavonol may lead to a notable decrease in the steady-state fluorescence intensity of the β-37 Trp residue, and in the meantime the R-T transition of the protein transpired. Such noncovalent recognition forms the ground-state adduct, with an association intensity of 3.991 × 10(4) M(-1) in the reaction process, which has already been authenticated by the detailed analysis of time-resolved fluorescence and UV/vis absorption spectra. Furthermore, flavonol can form hydrogen bonds and π-conjugation effects with several amino acid residues on the polypeptide chain, for example, Trp-37, Arg-40, Asp-99 and Asn-102, and this event would induce self-regulation of the compact, regular conformation of the protein to a certain extent, which explicitly corroborates the results of circular dichroism. According to the study of molecular docking and structure-activity relationships, we could see that the recognition capacities of the protein-flavonols are inversely interrelated with the C log P values of the flavonol molecules. Moreover, the properties of the substituents in the structural B-ring unit of flavonols, i.e. polarity, position and number, will also prominently affect the degree of affinity and bioavailability of the protein-flavonol complexes. The analytical results of molecular dynamics (MD) simulation testified that the discussions of the structure-activity relationships are entirely logical, and the conformations of the amino acid residues forming noncovalent interactions tend to be stable in the MD simulation, as further elucidated from the dynamics data. Plainly, molecular recognition of the protein-flavonols might noticeably cause relatively large changes in protein flexibility, and then manifest different recognition strengths and corresponding biological activities. This issue will be carefully validated by the interpretation of root-mean-square fluctuation.
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Affiliation(s)
- Fei Ding
- College of Agriculture and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China. and Department of Chemistry, China Agricultural University, Beijing 100193, China and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Wei Peng
- College of Agriculture and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China. and College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Yu-Kui Peng
- Center for Food Quality Supervision & Testing, Ministry of Agriculture, College of Food Science & Engineering, Northwest A&F University, Yangling 712100, China
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Biological effects of α-adrenergic phentolamine on erythrocyte hemeprotein: Molecular insights from biorecognition behavior, protein dynamics and flexibility. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 171:75-84. [PMID: 28482223 DOI: 10.1016/j.jphotobiol.2017.04.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 04/26/2017] [Accepted: 04/27/2017] [Indexed: 12/31/2022]
Abstract
Phentolamine is one of the most representative nonselective α-adrenoreceptor blocking agents, which have been proved to be owned various pharmacological actions. Unfortunately, whether erythrocytes in the veins intervene in biological behaviors of such drug are largely obscured. With the aid of multiple biophysical techniques, this scenario was to detailed explore the potential biorecognition between phentolamine and the hemeprotein in the cytosol of erythrocytes, and the influences of dynamic characters of protein during the bioreaction. Steady-state and time-resolved fluorescence data manifested that the biomolecular recognition of phentolamine by hemeprotein was processed through the biopolymer-drug adduct with a moderate strength of 104M-1. Such procedure causes a reduction in fluorescence intensity of the aromatic tryptophan (Trp) residues, and the R-T transition of the globular protein occurred concurrently. Circular dichroism demonstrated the conclusions of fluorescence essays, viz. biorecognition can induce fairly structural transformation (self-regulation) of protein conformation. Furthermore, one could find that a specific domain for phentolamine is located at the polypeptide chains α1β2 interface, and hydrogen bonds, π-conjugated and hydrophobic effects are discovered to be held the lowest energy state of the biomacromolecule-drug biosystem, which overtly matches the outcomes of wet experiments. Meanwhile, several crucial residues such as Trp-37 and Arg-40 were confirmed to have directly noncovalent interactions with phentolamine, and the effect of the heme group on the biomolecule-drug recognition is minimal. Further analyses of molecular dynamics simulation supported that the inherent protein flexibility may notably elicit alterations in some key noncovalent bonds between biomacromolecule and drug during the dynamic biointeraction, which might primarily be attributed to the torsion of drug structure and the conformational changes of essential residues. Undoubtedly, this research will not only help to thoroughly unearth the pharmacological profiles of phentolamine, but to elaborate the impacts of the intrinsic features (i.e. dynamics and flexibility) of critically cellular proteins on the biological conducts of active α-adrenergic blockers.
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Hithell G, González-Jiménez M, Greetham GM, Donaldson PM, Towrie M, Parker AW, Burley GA, Wynne K, Hunt NT. Ultrafast 2D-IR and optical Kerr effect spectroscopy reveal the impact of duplex melting on the structural dynamics of DNA. Phys Chem Chem Phys 2017; 19:10333-10342. [DOI: 10.1039/c7cp00054e] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Changes in the structural and solvation dynamics of DNA upon duplex melting are observed by 2D-IR and optical Kerr-effect spectroscopies.
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Affiliation(s)
- Gordon Hithell
- Department of Physics, University of Strathclyde, SUPA
- Glasgow
- UK
| | | | - Gregory M. Greetham
- STFC Central Laser Facility, Research Complex at Harwell, Harwell Science and Innovation Campus
- Didcot
- UK
| | - Paul M. Donaldson
- STFC Central Laser Facility, Research Complex at Harwell, Harwell Science and Innovation Campus
- Didcot
- UK
| | - Michael Towrie
- STFC Central Laser Facility, Research Complex at Harwell, Harwell Science and Innovation Campus
- Didcot
- UK
| | - Anthony W. Parker
- STFC Central Laser Facility, Research Complex at Harwell, Harwell Science and Innovation Campus
- Didcot
- UK
| | - Glenn A. Burley
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street
- Glasgow
- UK
| | - Klaas Wynne
- School of Chemistry, WestCHEM, University of Glasgow
- Glasgow
- UK
| | - Neil T. Hunt
- Department of Physics, University of Strathclyde, SUPA
- Glasgow
- UK
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