1
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Hunt NT. Using 2D-IR Spectroscopy to Measure the Structure, Dynamics, and Intermolecular Interactions of Proteins in H 2O. Acc Chem Res 2024; 57:685-692. [PMID: 38364823 PMCID: PMC10918835 DOI: 10.1021/acs.accounts.3c00682] [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] [Received: 10/30/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/18/2024]
Abstract
Infrared (IR) spectroscopy probes molecular structure at the level of the chemical bond or functional group. In the case of proteins, the most informative band in the IR spectrum is the amide I band, which arises predominantly from the C═O stretching vibration of the peptide link. The folding of proteins into secondary and tertiary structures leads to vibrational coupling between peptide units, generating specific amide I spectral signatures that provide a fingerprint of the macromolecular conformation. Ultrafast two-dimensional IR (2D-IR) spectroscopy allows the amide I band of a protein to be spread over a second frequency dimension in a way that mirrors 2D-NMR methods. This means that amide I 2D-IR spectroscopy produces a spectral map that is exquisitely sensitive to protein structure and dynamics and so provides detailed insights that cannot be matched by IR absorption spectroscopy. As a result, 2D-IR spectroscopy has emerged as a powerful tool for probing protein structure and dynamics over a broad range of time and length scales in the solution phase at room temperature. However, the protein amide I band coincides with an IR absorption from the bending vibration of water (δHOH), the natural biological solvent. To circumvent this problem, protein IR studies are routinely performed in D2O solutions because H/D substitution shifts the solvent bending mode (δDOD) to a lower frequency, revealing the amide I band. While effective, this method raises fundamental questions regarding the impact of the change in solvent mass on the structural or solvation dynamics of the protein and the removal of the energetic resonance between solvent and solute.In this Account, a series of studies applying 2D-IR to study the spectroscopy and dynamics of proteins in H2O-rich solvents is reviewed. A comparison of IR absorption spectroscopy and 2D-IR spectroscopy of protein-containing fluids is used to demonstrate the basis of the approach before a series of applications is presented. These range from measurements of fundamental protein biophysics to recent applications of machine learning to gain insight into protein-drug binding in complex mixtures. An outlook is presented, considering the potential for 2D-IR measurements to contribute to our understanding of protein behavior under near-physiological conditions, along with an evaluation of the obstacles that still need 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, U.K.
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2
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Rutherford SH, Baker MJ, Hunt NT. 2D-IR spectroscopy of proteins in H 2O-A Perspective. J Chem Phys 2023; 158:030901. [PMID: 36681646 DOI: 10.1063/5.0129480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The form of the amide I infrared absorption band provides a sensitive probe of the secondary structure and dynamics of proteins in the solution phase. However, the frequency coincidence of the amide I band with the bending vibrational mode of H2O has necessitated the widespread use of deuterated solvents. Recently, it has been demonstrated that ultrafast 2D-IR spectroscopy allows the detection of the protein amide I band in H2O-based fluids, meaning that IR methods can now be applied to study proteins in physiologically relevant solvents. In this perspective, we describe the basis of the 2D-IR method for observing the protein amide I band in H2O and show how this development has the potential to impact areas ranging from our fundamental appreciation of protein structural dynamics to new applications for 2D-IR spectroscopy in the analytical and biomedical sciences. In addition, we discuss how the spectral response of water, rather than being a hindrance, now provides a basis for new approaches to data pre-processing, standardization of 2D-IR data collection, and signal quantification. Ultimately, we visualize a direction of travel toward the creation of 2D-IR spectral libraries that can be linked to advanced computational methods for use in high-throughput protein screening and disease diagnosis.
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Affiliation(s)
- Samantha H Rutherford
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow G1 1RD, United Kingdom
| | - Matthew J Baker
- School of Medicine, Faculty of Clinical Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York, York YO10 5DD, United Kingdom
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3
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Weng W, Weberg AB, Gera R, Tomson NC, Anna JM. Probing Ligand Effects on the Ultrafast Dynamics of Copper Complexes via Midinfrared Pump-Probe and 2DIR Spectroscopies. J Phys Chem B 2021; 125:12228-12241. [PMID: 34723540 DOI: 10.1021/acs.jpcb.1c06370] [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
The effects of ligand structural variation on the ultrafast dynamics of a series of copper coordination complexes were investigated using polarization-dependent mid-IR pump-probe spectroscopy and two-dimensional infrared (2DIR) spectroscopy. The series consists of three copper complexes [(R3P3tren)CuIIN3]BAr4F (1PR3, R3P3tren = tris[2-(phosphiniminato)ethyl]amine, BAr4F = tetrakis(pentafluorophenyl)borate) where the number of methyl and phenyl groups in the PR3 ligand are systematically varied across the series (PR3 = PMe3, PMe2Ph, PMePh2). The asymmetric stretching mode of azide in the 1PR3 series is used as a vibrational probe of the small-molecule binding site. The results of the pump-probe measurements indicate that the vibrational energy of azide dissipates through intramolecular pathways and that the bulkier phenyl groups lead to an increase in the spatial restriction of the diffusive reorientation of bound azide. From 2DIR experiments, we characterize the spectral diffusion of the azide group and find that an increase in the number of phenyl groups maps to a broader inhomogeneous frequency distribution (Δ2). This indicates that an increase in the steric bulk of the secondary coordination sphere acts to create more distinct configurations in the local environment that are accessible to the azide group. This work demonstrates how ligand structural variation affects the ultrafast dynamics of a small molecular group bound to the metal center, which could provide insight into the structure-function relationship of the copper coordination complexes and transition-metal coordination complexes in general.
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Affiliation(s)
- Wei Weng
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Alexander B Weberg
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Rahul Gera
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Neil C Tomson
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jessica M Anna
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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4
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Ishiyama T. Energy relaxation dynamics of hydrogen-bonded OH vibration conjugated with free OH bond at an air/water interface. J Chem Phys 2021; 155:154703. [PMID: 34686042 DOI: 10.1063/5.0069618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Vibrational energy relaxation dynamics of the excited hydrogen-bonded (H-bonded) OH conjugated with free OH (OD) at an air/water (for both pure water and isotopically diluted water) interface are elucidated via non-equilibrium ab initio molecular dynamics (NE-AIMD) simulations. The calculated results are compared with those of the excited H-bonded OH in bulk liquid water reported previously. In the case of pure water, the relaxation timescale (vibrational lifetime) of the excited H-bonded OH at the interface is T1 = 0.13 ps, which is slightly larger than that in the bulk (T1 = 0.11 ps). Conversely, in the case of isotopically diluted water, the relaxation timescale of T1 = 0.74 ps in the bulk decreases to T1 = 0.26 ps at the interface, suggesting that the relaxation dynamics of the H-bonded OH are strongly dependent on the surrounding H-bond environments particularly for the isotopically diluted conditions. The relaxation paths and their rates are estimated by introducing certain constraints on the vibrational modes except for the target path in the NE-AIMD simulation to decompose the total energy relaxation rate into contributions to possible relaxation pathways. It is found that the main relaxation pathway in the case of pure water is due to intermolecular OH⋯OH vibrational coupling, which is similar to the relaxation in the bulk. In the case of isotopically diluted water, the main pathway is due to intramolecular stretch and bend couplings, which show more efficient relaxation than in the bulk because of strong H-bonding interactions specific to the air/water interface.
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Affiliation(s)
- Tatsuya Ishiyama
- Department of Applied Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
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5
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Schmidt-Engler JM, von Berg S, Bredenbeck J. Temperature-Dependent Low-Frequency Modes in the Active Site of Bovine Carbonic Anhydrase II Probed by 2D-IR Spectroscopy. J Phys Chem Lett 2021; 12:7777-7782. [PMID: 34374547 DOI: 10.1021/acs.jpclett.1c01453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Enzyme catalysis achieves tremendous rate accelerations. Enzyme reaction centers provide a constraint geometry that preferentially binds an activated form of the substrate and thus lowers the energy barrier. However, this transition state picture neglects the flexibility of proteins and its role in enzymatic catalysis. Especially for proton transfer reactions, it has been suggested that motions of the protein modulate the donor-acceptor distance and prepare a tunneling-ready state. We report the detection of frequency fluctuations of an azide anion (N3-) bound in the active site of the protein carbonic anhydrase II, where a low-frequency mode of the protein has been proposed to facilitate proton transfer over two water molecules during the catalyzed reaction. 2D-IR spectroscopy resolves an underdamped low-frequency mode at about 1 THz (30 cm-1). We find its frequency to be viscosity- and temperature-dependent and to decrease by 6 cm-1 between 230 and 320 K, reporting the softening of the mode's potential.
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Affiliation(s)
- Julian M Schmidt-Engler
- Institute of Biophysics, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany
| | - Sarah von Berg
- Institute of Biophysics, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany
| | - Jens Bredenbeck
- Institute of Biophysics, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany
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6
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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: 11] [Impact Index Per Article: 3.7] [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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7
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Chakrabarty S, Maity S, Yazhini D, Ghosh A. Surface-Directed Disparity in Self-Assembled Structures of Small-Peptide l-Glutathione on Gold and Silver Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:11255-11261. [PMID: 32880182 DOI: 10.1021/acs.langmuir.0c01527] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Despite the key roles of l-glutathiones (GSHs) inbiology and nano-biotechnology, understanding their labile structures and hydrogen bond interactions with nanoparticles has posed a critical challenge to the scientific community. The structural conformation of GSH as a capping layer on gold nanoparticle (AuNP) and silver nanoparticle (AgNP) surfaces is investigated. In this report, we attempt to explore the material-dependent interaction of GSH with different spherical nanoparticle surfaces by employing Fourier transform infrared (FTIR) spectroscopy. The infrared signal of amide I of GSH is studied as a function of different materials' spherical nanoparticles with comparable size. We revealed the β-sheet secondary structure of GSH on AgNPs and the random structure on AuNPs even though both the nanoparticles have comparable shapes and sizes and belong to the same group of the periodic table. The GSH is firmly anchored on the gold and silver surface via the thiol of the cys part. However, our experimental data designate a further interaction with the AgNP surface via the carboxylic acid group of the gly- and glu- end of the molecule. It is observed that enhancement of IR absorption of amide I of GSH is pronounced by a factor of 10 on AuNP but, in contrast, on the same-sized AgNP, the suppression is perceived by a factor of 2, even though both are plasmonic materials with respect to free GSH. This study can be used as a point of reference for understanding the structural conformation of the capping layer on nanoparticle surfaces as well as surface enhancement of the IR absorption of amide I. We would like to emphasize that molecular self-assembly on the nanoparticle surfaces is definitely of very broad interest for chemists working in nearly any subdiscipline, spanning from the nanoparticle-based medicine to surface-enhanced spectroscopy to heterogeneous catalysis, etc.
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Affiliation(s)
- Suranjana Chakrabarty
- Department of Condensed Matter Physics and Materials Sciences, S. N. Bose National Centre for Basic Sciences, JD Block, Sector-III, Salt Lake City, Kolkata 700106, India
| | - Swagata Maity
- Department of Condensed Matter Physics and Materials Sciences, S. N. Bose National Centre for Basic Sciences, JD Block, Sector-III, Salt Lake City, Kolkata 700106, India
| | - Darshana Yazhini
- Department of Condensed Matter Physics and Materials Sciences, S. N. Bose National Centre for Basic Sciences, JD Block, Sector-III, Salt Lake City, Kolkata 700106, India
| | - Anup Ghosh
- Department of Condensed Matter Physics and Materials Sciences, S. N. Bose National Centre for Basic Sciences, JD Block, Sector-III, Salt Lake City, Kolkata 700106, India
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8
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Schmidt-Engler JM, Zangl R, Guldan P, Morgner N, Bredenbeck J. Exploring the 2D-IR repertoire of the -SCN label to study site-resolved dynamics and solvation in the calcium sensor protein calmodulin. Phys Chem Chem Phys 2020; 22:5463-5475. [PMID: 32096510 DOI: 10.1039/c9cp06808b] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The calcium sensor protein calmodulin is ubiquitous among eukaryotes. It translates intracellular Ca2+ influx (by a decrease of conformational flexibility) into increased target recognition affinity. Here we demonstrate that by using the IR reporter -SCN in combination with 2D-IR spectroscopy, global structure changes and local dynamics, degree of solvent exposure and protein-ligand interaction can be characterised in great detail. The long vibrational lifetime of the -SCN label allows for centerline slope analysis of the 2D-IR line shape up to 120 ps to deduce the frequency-frequency correlation function (FFCF) of the -SCN label in various states and label positions in the protein. Based on that we show clear differences between a solvent exposed site, the environment close to the Ca2+ binding motif and three highly conserved positions for ligand binding. Furthermore, we demonstrate how these dynamics are affected by conformational change induced by the addition of Ca2+ ions and by interaction with a short helical peptide mimicking protein binding. We show that the binding mode is strongly heterogeneous among the probed key binding methionine residues. SCN's vibrational relaxation is dominated by intermolecular contributions. Changes in the vibrational lifetime upon changing between H2O and D2O buffer therefore provide a robust measure for water accessibility of the label. Characterising -SCN's extinction coefficient, vibrational lifetime in light and heavy water and its FFCF we demonstrate the vast potential it has as a label especially for nonlinear spectroscopies, such as 2D-IR spectroscopy.
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Affiliation(s)
- Julian M Schmidt-Engler
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany.
| | - Rene Zangl
- Johann Wolfgang Goethe-University, Institute of Physical and Theoretical Chemistry, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Patrick Guldan
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany.
| | - Nina Morgner
- Johann Wolfgang Goethe-University, Institute of Physical and Theoretical Chemistry, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Jens Bredenbeck
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany.
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9
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Horch M, Schoknecht J, Wrathall SLD, Greetham GM, Lenz O, Hunt NT. Understanding the structure and dynamics of hydrogenases by ultrafast and two-dimensional infrared spectroscopy. Chem Sci 2019; 10:8981-8989. [PMID: 31762978 PMCID: PMC6857670 DOI: 10.1039/c9sc02851j] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 08/05/2019] [Indexed: 11/21/2022] Open
Abstract
Hydrogenases are valuable model enzymes for sustainable energy conversion approaches using H2, but rational utilization of these base-metal biocatalysts requires a detailed understanding of the structure and dynamics of their complex active sites. The intrinsic CO and CN- ligands of these metalloenzymes represent ideal chromophores for infrared (IR) spectroscopy, but structural and dynamic insight from conventional IR absorption experiments is limited. Here, we apply ultrafast and two-dimensional (2D) IR spectroscopic techniques, for the first time, to study hydrogenases in detail. Using an O2-tolerant [NiFe] hydrogenase as a model system, we demonstrate that IR pump-probe spectroscopy can explore catalytically relevant ligand bonding by accessing high-lying vibrational states. This ultrafast technique also shows that the protein matrix is influential in vibrational relaxation, which may be relevant for energy dissipation from the active site during fast reaction steps. Further insights into the relevance of the active site environment are provided by 2D-IR spectroscopy, which reveals equilibrium dynamics and structural constraints imposed on the H2-accepting intermediate of [NiFe] hydrogenases. Both techniques offer new strategies for uniquely identifying redox-structural states in complex catalytic mixtures via vibrational quantum beats and 2D-IR off-diagonal peaks. Together, these findings considerably expand the scope of IR spectroscopy in hydrogenase research, and new perspectives for the characterization of these enzymes and other (bio-)organometallic targets are presented.
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Affiliation(s)
- Marius Horch
- Department of Chemistry , York Biomedical Research Institute , University of York , Heslington , York , YO10 5DD , UK .
- Institut für Chemie , Technische Universität Berlin , Straße des 17. Juni 135 , Berlin , D-10623 , Germany
| | - Janna Schoknecht
- Institut für Chemie , Technische Universität Berlin , Straße des 17. Juni 135 , Berlin , D-10623 , Germany
| | - Solomon L D Wrathall
- Department of Chemistry , York Biomedical Research Institute , University of York , Heslington , York , YO10 5DD , UK .
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Science and Innovation Campus , Didcot , Oxford , OX110PE , UK
| | - Oliver Lenz
- Institut für Chemie , Technische Universität Berlin , Straße des 17. Juni 135 , Berlin , D-10623 , Germany
| | - Neil T Hunt
- Department of Chemistry , York Biomedical Research Institute , University of York , Heslington , York , YO10 5DD , UK .
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10
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Hume S, Hithell G, Greetham GM, Donaldson PM, Towrie M, Parker AW, Baker MJ, Hunt NT. Measuring proteins in H 2O with 2D-IR spectroscopy. Chem Sci 2019; 10:6448-6456. [PMID: 31341597 PMCID: PMC6611063 DOI: 10.1039/c9sc01590f] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/13/2019] [Indexed: 02/06/2023] Open
Abstract
The amide I infrared band of proteins is highly sensitive to secondary structure, but studies under physiological conditions are prevented by strong, overlapping water absorptions, motivating the widespread use of deuterated solutions. H/D exchange raises fundamental questions regarding the impact of increased mass on protein dynamics, while deuteration is impractical for biomedical or commercial applications of protein IR spectroscopy. We show that 2D-IR spectroscopy can avoid this problem because the 2D-IR amide I signature of proteins dominates that of water even at sub-millimolar protein concentrations. Using equine blood serum as a test system, we investigate the significant implications of being able to measure the spectroscopy and dynamics of proteins in water, demonstrating relevance in areas ranging from fundamental science to the clinic. Measurements of vibrational relaxation dynamics of serum proteins reveals that deuteration slows down the rate of amide I vibrational relaxation by >10%, indicating a dynamic impact of isotopic exchange in some proteins. The unique link between protein secondary structure and 2D-IR amide I lineshape allows differentiation of signals due to albumin and globulin protein fractions in serum leading to measurements of the biomedically-important albumin to globulin ratio (AGR) with an accuracy of ±4% across a clinically-relevant range. Furthermore, we demonstrate that 2D-IR spectroscopy enables differentiation of the structurally similar globulin proteins IgG, IgA and IgM, opening up a straightforward spectroscopic approach to measuring levels of serum proteins that are currently only accessible via biomedical laboratory testing.
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Affiliation(s)
- Samantha Hume
- Department of Physics , University of Strathclyde , SUPA , 107 Rottenrow East , Glasgow , G4 0NG , UK
| | - Gordon Hithell
- Department of Physics , University of Strathclyde , SUPA , 107 Rottenrow East , Glasgow , G4 0NG , UK
| | - Gregory M Greetham
- STFC Central Laser Facility , Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot , OX11 0QX , UK
| | - Paul M Donaldson
- STFC Central Laser Facility , Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot , OX11 0QX , UK
| | - Michael Towrie
- STFC Central Laser Facility , Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot , OX11 0QX , UK
| | - Anthony W Parker
- STFC Central Laser Facility , Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot , OX11 0QX , UK
| | - Matthew J Baker
- WestCHEM , Department of Pure and Applied Chemistry , University of Strathclyde , Technology and Innovation Centre , 99 George Street , Glasgow , G1 1RD , UK
| | - Neil T Hunt
- Department of Chemistry , York Biomedical Research Institute , University of York , Heslington , York , YO10 5DD , UK .
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11
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Pan F, Dashti M, Reynolds MR, Rissanen K, Trant JF, Beyeh NK. Halogen bonding and host-guest chemistry between N-alkylammonium resorcinarene halides, diiodoperfluorobutane and neutral guests. Beilstein J Org Chem 2019; 15:947-954. [PMID: 31164931 PMCID: PMC6541336 DOI: 10.3762/bjoc.15.91] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/03/2019] [Indexed: 12/25/2022] Open
Abstract
Single crystal X-ray structures of halogen-bonded assemblies formed between host N-hexylammonium resorcinarene bromide (1) or N-cyclohexylammonium resorcinarene chloride (2), and 1,4-diiodooctafluorobutane and accompanying small solvent guests (methanol, acetonitrile and water) are presented. The guests’ inclusion affects the geometry of the cavity of the receptors 1 and 2, while the divalent halogen bond donor 1,4-diiodooctafluorobutane determines the overall nature of the halogen bond assembly. The crystal lattice of 1 contains two structurally different dimeric assemblies A and B, formally resulting in the mixture of a capsular dimer and a dimeric pseudo-capsule. 1H and 19F NMR analyses supports the existence of these halogen-bonded complexes and enhanced guest inclusion in solution.
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Affiliation(s)
- Fangfang Pan
- College of Chemistry, Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis, Central China Normal University, Luoyu Road 152, Wuhan, Hubei Province, 430079, People's Republic of China
| | - Mohadeseh Dashti
- University of Windsor, Department of Chemistry and Biochemistry, Windsor, Ontario, 401 Sunset Avenue, N9B 3P4, Canada
| | - Michael R Reynolds
- University of Windsor, Department of Chemistry and Biochemistry, Windsor, Ontario, 401 Sunset Avenue, N9B 3P4, Canada
| | - Kari Rissanen
- University of Jyvaskyla, Department of Chemistry, PO Box 35, Jyväskylä, FIN-40014, Finland
| | - John F Trant
- University of Windsor, Department of Chemistry and Biochemistry, Windsor, Ontario, 401 Sunset Avenue, N9B 3P4, Canada
| | - Ngong Kodiah Beyeh
- Oakland University, Department of Chemistry, 146 Library Drive, Rochester, Michigan, 48309-4479, USA
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12
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Edington SC, Halling DB, Bennett SM, Middendorf TR, Aldrich RW, Baiz CR. Non-Additive Effects of Binding Site Mutations in Calmodulin. Biochemistry 2019; 58:2730-2739. [PMID: 31124357 DOI: 10.1021/acs.biochem.9b00096] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite decades of research on ion-sensing proteins, gaps persist in the understanding of ion binding affinity and selectivity even in well-studied proteins such as calmodulin. Site-directed mutagenesis is a powerful and popular tool for addressing outstanding questions about biological ion binding and is employed to selectively deactivate binding sites and insert chromophores at advantageous positions within ion binding structures. However, even apparently nonperturbative mutations can distort the binding dynamics they are employed to measure. We use Fourier transform infrared (FTIR) and ultrafast two-dimensional infrared (2D IR) spectroscopy of the carboxylate asymmetric stretching mode in calmodulin as a mutation- and label-independent probe of the conformational perturbations induced in calmodulin's binding sites by two classes of mutation, tryptophan insertion and carboxylate side-chain deletion, commonly used to study ion binding in proteins. Our results show that these mutations not only affect ion binding but also induce changes in calmodulin's conformational landscape along coordinates not probed by vibrational spectroscopy, remaining invisible without additional perturbation of binding site structure. Comparison of FTIR line shapes with 2D IR diagonal slices provides a clear example of how nonlinear spectroscopy produces well-resolved line shapes, refining otherwise featureless spectral envelopes into more informative vibrational spectra of proteins.
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Affiliation(s)
- Sean C Edington
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - D Brent Halling
- Department of Neuroscience , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Suzanna M Bennett
- Department of Neuroscience , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Thomas R Middendorf
- Department of Neuroscience , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Richard W Aldrich
- Department of Neuroscience , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Carlos R Baiz
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
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13
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Ghosh A, Prasad AK, Chuntonov L. Two-Dimensional Infrared Spectroscopy Reveals Molecular Self-Assembly on the Surface of Silver Nanoparticles. J Phys Chem Lett 2019; 10:2481-2486. [PMID: 30978284 DOI: 10.1021/acs.jpclett.9b00530] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The conformation of molecules, peptides, and proteins, self-assembled into structured monolayers on the surface of metal nanoparticles (NPs), can strongly affect their properties and use in chemical or nanobiomedical applications. Elucidating molecular conformations on the NP surface is highly challenging, and the microscopic details mostly remain elusive. Using polarization-selective third-order two-dimensional ultrafast infrared spectroscopy, we revealed the highly ordered intermolecular structure of γ-tripeptide glutathione on the surface of silver NPs in aqueous solution. Glutathione is an antioxidant thiol abundant in living cells; it is extensively used in NP chemistry and related research. We identified conditions where the interaction of glutathione with the NP surface facilitates formation of a β-sheet-like structure enclosing the NPs. A spectroscopic signature associated with the assembly of β-sheets into an amyloid fibril-like structure was also observed. Remarkably, the interaction with the metal surface promotes formation of a fibril-like structure by a small peptide involving only two amino acids.
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Affiliation(s)
- Anup Ghosh
- Schulich Faculty of Chemistry and Solid State Institute , Technion - Israel Institute of Technology , Haifa 3200003 , Israel
| | - Amit K Prasad
- Schulich Faculty of Chemistry and Solid State Institute , Technion - Israel Institute of Technology , Haifa 3200003 , Israel
| | - Lev Chuntonov
- Schulich Faculty of Chemistry and Solid State Institute , Technion - Israel Institute of Technology , Haifa 3200003 , Israel
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14
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Feng M, Zhao J, Yu P, Wang J. Linear and Nonlinear Infrared Spectroscopies Reveal Detailed Solute-Solvent Dynamic Interactions of a Nitrosyl Ruthenium Complex in Solution. J Phys Chem B 2018; 122:9225-9235. [PMID: 30200757 DOI: 10.1021/acs.jpcb.8b07247] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this work, the solvation of a nitrosyl ruthenium complex, [(CH3)4N][RuCl3(qn)(NO)] (with qn = deprotonated 8-hydroxyquinoline), which is a potential NO-releasing molecule in the bio-environment, was studied in two bio-friendly solvents, namely deuterated dimethyl sulfoxide (dDMSO) and water (D2O). A blue-shifted NO stretching frequency was observed in water with respect to that in dDMSO, which was believed to be due to ligand-solvent hydrogen-bonding interactions, one N═O···D and particularly three Ru-Cl···D, that show competing effects on the NO bond length. The dynamic differences of the NO stretch in these two solvents were further revealed by transient pump-probe IR and two-dimensional IR results: faster vibrational relaxation and faster spectral diffusion (SD) were observed in D2O, confirming stronger solvent-solute interaction and also faster solvent structural dynamics in D2O than in DMSO. Further, a significant non-decaying residual in the SD dynamics was observed in D2O but not in DMSO, suggesting the formation of a stable solvation shell in water due to strong multi-site ligand-solvent hydrogen-bonding interactions, which is in agreement with the observed blue-shifted NO stretching frequency. This work demonstrates that small solvent molecules such as water can form a relatively rigid solvation shell for certain transition metal complexes due to cooperative ligand-solvent interactions and show slower dynamics.
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Affiliation(s)
- Minjun Feng
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P.R. China.,University of Chinese Academy of Sciences , Beijing 100049 , P.R. China
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P.R. China.,University of Chinese Academy of Sciences , Beijing 100049 , P.R. China
| | - Pengyun Yu
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P.R. China.,University of Chinese Academy of Sciences , Beijing 100049 , P.R. China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , P.R. China.,University of Chinese Academy of Sciences , Beijing 100049 , P.R. China
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15
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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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16
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Kumar Das D, Makhal K, Goswami D. Observing ground state vibrational coherence and excited state relaxation dynamics of a cyanine dye in pure solvents. Phys Chem Chem Phys 2018; 20:13400-13411. [DOI: 10.1039/c7cp08605a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using a degenerate pump probe technique at 800 nm, Ground State Vibrational Coherence (GSVC) of a cyanine dye (IR780) is explored in various solvents.
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Affiliation(s)
- Dipak Kumar Das
- Department of Chemistry
- Indian Institute of Technology Kanpur
- Kanpur – 208016
- India
| | - Krishnandu Makhal
- Department of Chemistry
- Indian Institute of Technology Kanpur
- Kanpur – 208016
- India
| | - Debabrata Goswami
- Department of Chemistry
- Indian Institute of Technology Kanpur
- Kanpur – 208016
- India
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17
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Shaw DJ, Hill RE, Simpson N, Husseini FS, Robb K, Greetham GM, Towrie M, Parker AW, Robinson D, Hirst JD, Hoskisson PA, Hunt NT. Examining the role of protein structural dynamics in drug resistance in Mycobacterium tuberculosis. Chem Sci 2017; 8:8384-8399. [PMID: 29619185 PMCID: PMC5863454 DOI: 10.1039/c7sc03336b] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 10/16/2017] [Indexed: 12/12/2022] Open
Abstract
2D-IR spectroscopy reveals a role for protein structural dynamics in antimicrobial-resistance.
Antimicrobial resistance represents a growing global health problem. The emergence of novel resistance mechanisms necessitates the development of alternative approaches to investigate the molecular fundamentals of resistance, leading ultimately to new strategies for counteracting them. To gain deeper insight into antibiotic–target interactions, the binding of the frontline anti-tuberculosis drug isoniazid (INH) to a target enzyme, InhA, from Mycobacterium tuberculosis was studied using ultrafast two-dimensional infrared (2D-IR) spectroscopy and molecular simulations. Comparing wild-type InhA with a series of single point mutations, it was found that binding of the INH–NAD inhibitor to susceptible forms of the enzyme increased the vibrational coupling between residues located in the Rossmann fold co-factor binding site of InhA and suppressed dynamic fluctuations of the enzyme structure. The effect correlated with biochemical assay data, being reduced in the INH-resistant S94A mutant and absent in the biochemically-inactive P193A control. Molecular dynamics simulations and calculations of inter–residue couplings indicate that the changes in coupling and dynamics are not localised to the co-factor binding site, but permeate much of the protein. We thus propose that the resistant S94A mutation circumvents subtle changes in global structural dynamics caused by INH upon binding to the wild-type enzyme that may impact upon the formation of important protein–protein complexes in the fatty acid synthase pathway of M. tuberculosis.
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Affiliation(s)
- Daniel J Shaw
- Department of Physics , University of Strathclyde , SUPA , 107 Rottenrow East , Glasgow , G4 0NG , UK .
| | - Rachel E Hill
- School of Chemistry , University of Nottingham , Nottingham , UK .
| | - Niall Simpson
- Department of Physics , University of Strathclyde , SUPA , 107 Rottenrow East , Glasgow , G4 0NG , UK .
| | - Fouad S Husseini
- School of Chemistry , University of Nottingham , Nottingham , UK .
| | - Kirsty Robb
- Strathclyde Institute of Pharmacy and Biomedical Science , University of Strathclyde , Glasgow , UK .
| | - Gregory M Greetham
- STFC Central Laser Facility , Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Science and Innovation Campus , Didcot , OX110PE , Oxon , UK
| | - Michael Towrie
- STFC Central Laser Facility , Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Science and Innovation Campus , Didcot , OX110PE , Oxon , UK
| | - Anthony W Parker
- STFC Central Laser Facility , Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Science and Innovation Campus , Didcot , OX110PE , Oxon , UK
| | - David Robinson
- Department of Chemistry and Forensics , Nottingham Trent University , Clifton Lane , Nottingham , NG11 8NS , UK
| | - Jonathan D Hirst
- School of Chemistry , University of Nottingham , Nottingham , UK .
| | - Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Science , University of Strathclyde , Glasgow , UK .
| | - Neil T Hunt
- Department of Physics , University of Strathclyde , SUPA , 107 Rottenrow East , Glasgow , G4 0NG , UK .
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18
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Picosecond orientational dynamics of water in living cells. Nat Commun 2017; 8:904. [PMID: 29026086 PMCID: PMC5714959 DOI: 10.1038/s41467-017-00858-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/01/2017] [Indexed: 11/18/2022] Open
Abstract
Cells are extremely crowded, and a central question in biology is how this affects the intracellular water. Here, we use ultrafast vibrational spectroscopy and dielectric-relaxation spectroscopy to observe the random orientational motion of water molecules inside living cells of three prototypical organisms: Escherichia coli, Saccharomyces cerevisiae (yeast), and spores of Bacillus subtilis. In all three organisms, most of the intracellular water exhibits the same random orientational motion as neat water (characteristic time constants ~9 and ~2 ps for the first-order and second-order orientational correlation functions), whereas a smaller fraction exhibits slower orientational dynamics. The fraction of slow intracellular water varies between organisms, ranging from ~20% in E. coli to ~45% in B. subtilis spores. Comparison with the water dynamics observed in solutions mimicking the chemical composition of (parts of) the cytosol shows that the slow water is bound mostly to proteins, and to a lesser extent to other biomolecules and ions. The cytoplasm’s crowdedness leads one to expect that cell water is different from bulk water. By measuring the rotational motion of water molecules in living cells, Tros et al. find that apart from a small fraction of water solvating biomolecules, cell water has the same dynamics as bulk water.
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19
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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: 166] [Impact Index Per Article: 23.7] [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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20
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Husseini FS, Robinson D, Hunt NT, Parker AW, Hirst JD. Computing infrared spectra of proteins using the exciton model. J Comput Chem 2017; 38:1362-1375. [PMID: 27868210 PMCID: PMC5434914 DOI: 10.1002/jcc.24674] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 10/22/2016] [Accepted: 10/29/2016] [Indexed: 02/02/2023]
Abstract
The ability to compute from first principles the infrared spectrum of a protein in solution phase representing a biological system would provide a useful connection to atomistic models of protein structure and dynamics. Indeed, such calculations are a vital complement to 2DIR experimental measurements, allowing the observed signals to be interpreted in terms of detailed structural and dynamical information. In this article, we have studied nine structurally and spectroscopically well-characterized proteins, representing a range of structural types. We have simulated the equilibrium conformational dynamics in an explicit point charge water model. Using the resulting trajectories based on MD simulations, we have computed the one and two dimensional infrared spectra in the Amide I region, using an exciton approach, in which a local mode basis of carbonyl stretches is considered. The role of solvent in shifting the Amide I band (by 30 to 50 cm-1 ) is clearly evident. Similarly, the conformational dynamics contribute to the broadening of peaks in the spectrum. The inhomogeneous broadening in both the 1D and 2D spectra reflects the significant conformational diversity observed in the simulations. Through the computed 2D cross-peak spectra, we show how different pulse schemes can provide additional information on the coupled vibrations. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Fouad S Husseini
- School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - David Robinson
- School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Neil T Hunt
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow, G4 0NG, Scotland, United Kingdom
| | - Anthony W Parker
- STFC Rutherford Appleton Laboratory, Central Laser Facility, Harwell Campus, Didcot, OX11 0QX, United Kingdom
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
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21
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Eckert PA, Kubarych KJ. Dynamic Flexibility of Hydrogenase Active Site Models Studied with 2D-IR Spectroscopy. J Phys Chem A 2017; 121:608-615. [PMID: 28032999 DOI: 10.1021/acs.jpca.6b11962] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Hydrogenase enzymes enable organisms to use H2 as an energy source, having evolved extremely efficient biological catalysts for the reversible oxidation of molecular hydrogen. Small-molecule mimics of these enzymes provide both simplified models of the catalysis reactions and potential artificial catalysts that might be used to facilitate a hydrogen economy. We have studied two diiron hydrogenase mimics, μ-pdt-[Fe(CO)3]2 and μ-edt-[Fe(CO)3]2 (pdt = propanedithiolate, edt = ethanedithiolate), in a series of alkane solvents and have observed significant ultrafast spectral dynamics using two-dimensional infrared (2D-IR) spectroscopy. Since solvent fluctuations in nonpolar alkanes do not lead to substantial electrostatic modulations in a solute's vibrational mode frequencies, we attribute the spectral diffusion dynamics to intramolecular flexibility. The intramolecular origin is supported by the absence of any measurable solvent viscosity dependence, indicating that the frequency fluctuations are not coupled to the solvent motional dynamics. Quantum chemical calculations reveal a pronounced coupling between the low-frequency torsional rotation of the carbonyl ligands and the terminal CO stretching vibrations. The flexibility of the CO ligands has been proposed to play a central role in the catalytic reaction mechanism, and our results highlight that the CO ligands are highly flexible on a picosecond time scale.
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Affiliation(s)
- Peter A Eckert
- Department of Chemistry, University of Michigan , 930 N. University Ave., Ann Arbor, Michigan 48109, United States
| | - Kevin J Kubarych
- Department of Chemistry, University of Michigan , 930 N. University Ave., Ann Arbor, Michigan 48109, United States
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22
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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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23
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Fritzsch R, Brady O, Adair E, Wright JA, Pickett CJ, Hunt NT. Encapsulating Subsite Analogues of the [FeFe]-Hydrogenases in Micelles Enables Direct Water Interactions. J Phys Chem Lett 2016; 7:2838-2843. [PMID: 27396585 DOI: 10.1021/acs.jpclett.6b01338] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Encapsulation of subsite analogues of the [FeFe]-hydrogenase enzymes in supramolecular structures has been shown to dramatically increase their catalytic ability, but the molecular basis for this enhancement remains unclear. We report the results of experiments employing infrared absorption, ultrafast infrared pump-probe, and 2D-IR spectroscopy to investigate the molecular environment of Fe2(pdt)(CO)6 (pdt: propanedithiolate) [1] encapsulated in the dispersed alkane phase of a heptane-dodecyltrimethylammonium bromide-water microemulsion. It is demonstrated that 1 is partitioned between two molecular environments, one that closely resembles bulk heptane solution and a second that features direct hydrogen-bonding interactions with water molecules that penetrate the surfactant shell. Our results demonstrate that the extent of water access to the normally water-insoluble subsite analogue 1 can be tuned with micelle size, while IR spectroscopy provides a straightforward tool that can be used to measure and fine-tune the chemical environment of catalyst species in self-assembled structures.
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Affiliation(s)
- Robby Fritzsch
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
| | - Owen Brady
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
| | - Elaine Adair
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
| | - Joseph A Wright
- Energy Materials Laboratory, School of Chemistry, University of East Anglia , Norwich NR4 7TJ, United Kingdom
| | - Christopher J Pickett
- Energy Materials Laboratory, School of Chemistry, University of East Anglia , Norwich NR4 7TJ, United Kingdom
| | - Neil T Hunt
- Department of Physics, University of Strathclyde, SUPA , 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
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24
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Ultrafast Structural Fluctuations of Myoglobin-Bound Thiocyanate and Selenocyanate Ions Measured with Two-Dimensional Infrared Photon Echo Spectroscopy. Chemphyschem 2015; 16:3468-76. [DOI: 10.1002/cphc.201500606] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 08/27/2015] [Indexed: 11/07/2022]
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25
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Campomanes P, Rothlisberger U, Alfonso-Prieto M, Rovira C. The Molecular Mechanism of the Catalase-like Activity in Horseradish Peroxidase. J Am Chem Soc 2015; 137:11170-8. [DOI: 10.1021/jacs.5b06796] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Pablo Campomanes
- Laboratory
of Computational Chemistry and Biochemistry, Institute of Chemical
Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory
of Computational Chemistry and Biochemistry, Institute of Chemical
Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Mercedes Alfonso-Prieto
- Departament de Química Orgànica & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08208 Barcelona, Spain
| | - Carme Rovira
- Departament de Química Orgànica & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08208 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08018 Barcelona, Spain
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26
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27
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Shaw DJ, Adamczyk K, Frederix PWJM, Simpson N, Robb K, Greetham GM, Towrie M, Parker AW, Hoskisson PA, Hunt NT. Multidimensional infrared spectroscopy reveals the vibrational and solvation dynamics of isoniazid. J Chem Phys 2015; 142:212401. [DOI: 10.1063/1.4914097] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- Daniel J. Shaw
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
- Strathclyde Institute for Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, United Kingdom
| | - Katrin Adamczyk
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
| | - Pim W. J. M. Frederix
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
| | - Niall Simpson
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
| | - Kirsty Robb
- Strathclyde Institute for Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, United Kingdom
| | - Gregory M. Greetham
- STFC Rutherford Appleton Laboratory, Central Laser Facility, Research Complex at Harwell, Didcot OX11 0QX, United Kingdom
| | - Michael Towrie
- STFC Rutherford Appleton Laboratory, Central Laser Facility, Research Complex at Harwell, Didcot OX11 0QX, United Kingdom
| | - Anthony W. Parker
- STFC Rutherford Appleton Laboratory, Central Laser Facility, Research Complex at Harwell, Didcot OX11 0QX, United Kingdom
| | - Paul A. Hoskisson
- Strathclyde Institute for Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, United Kingdom
| | - Neil T. Hunt
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
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28
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Simpson N, Adamczyk K, Hithell G, Shaw DJ, Greetham GM, Towrie M, Parker AW, Hunt NT. The effect on structural and solvent water molecules of substrate binding to ferric horseradish peroxidase. Faraday Discuss 2015; 177:163-79. [DOI: 10.1039/c4fd00161c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ultrafast, multi-dimensional infrared spectroscopy, in the form of 2D-IR and pump–probe measurements, has been employed to investigate the effect of substrate binding on the structural dynamics of the horseradish peroxidase (HRP) enzyme. Using nitric oxide bound to the ferric haem of HRP as a sensitive probe of local dynamics, we report measurements of the frequency fluctuations (spectral diffusion) and vibrational lifetime of the NO stretching mode with benzohydroxamic acid (BHA) located in the substrate-binding position at the periphery of the haem pocket, in both D2O and H2O solvents. The results reveal that, with BHA bound to the enzyme, the local structural dynamics are insensitive to H/D exchange. These results are in stark contrast to those found in studies of the substrate-free enzyme, which demonstrated that the local chemical and dynamic environment of the haem ligand is influenced by water molecules. In light of the large changes in solvent accessibility caused by substrate binding, we discuss the potential for varying roles for the solvent in the haem pocket of HRP at different stages along the reaction coordinate of the enzymatic mechanism.
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Affiliation(s)
- Niall Simpson
- Department of Physics
- University of Strathclyde
- SUPA
- Glasgow
- UK
| | | | - Gordon Hithell
- Department of Physics
- University of Strathclyde
- SUPA
- Glasgow
- UK
| | - Daniel J. Shaw
- Department of Physics
- University of Strathclyde
- SUPA
- Glasgow
- UK
| | - Gregory M. Greetham
- Central Laser Facility, Research Complex at Harwell
- STFC Rutherford Appleton Laboratory
- Didcot
- UK
| | - Michael Towrie
- Central Laser Facility, Research Complex at Harwell
- STFC Rutherford Appleton Laboratory
- Didcot
- UK
| | - Anthony W. Parker
- Central Laser Facility, Research Complex at Harwell
- STFC Rutherford Appleton Laboratory
- Didcot
- UK
| | - Neil T. Hunt
- Department of Physics
- University of Strathclyde
- SUPA
- Glasgow
- UK
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