Heterogeneous and Highly Dynamic Interface in Plastocyanin–Cytochrome <i>f</i> Complex Revealed by Site-Specific 2D-IR Spectroscopy

Ramos, Sashary; Sueur, Amanda L. Le; Horness, Rachel E.; Specker, Jonathan T.; Collins, Jessica A; Thibodeau, Katherine E.; Thielges, Megan C.

doi:10.1021/acs.jpcb.8b12157

Cited by 14 publications

(17 citation statements)

References 72 publications

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“…To name a few, these include the homogeneous and inhomogeneous line-broadenings, the anharmonic frequency shift of a given normal mode, the solute–solvent interaction induced spectral diffusion, and mode–mode vibrational coupling constants. As a result, 2D IR and other multidimensional spectroscopy techniques have been used as powerful tools for studying (i) the structure and dynamics of peptides, − proteins, ,,− protein–ligand complexes, DNA, − RNA, and lipid bilayers, , (ii) the energy transfer dynamics between coupled oscillators in condensed phases, ,− (iii) the hydrogen-bonding (H-bonding) structure and dynamics of liquid water and its isotopologues, , (iv) the configurational and H-bonding dynamics of biomolecules, , (v) the molecular exciton dynamics in photovoltaic materials, etc.…”

Section: Introductionmentioning

confidence: 99%

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

et al. 2020

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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 inter-protein 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 allencompassing 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 semi-empirical 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 website (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-theart 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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Section: Introductionmentioning

confidence: 99%

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

et al. 2020

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“…Nuclear magnetic resonance (NMR) studies of biological electron transfer complexes show that the encounter complexes are characterised by very small chemical shift perturbations spread out over relatively large areas of the proteins [93,98]. The interactions that establish ET complexes are therefore highly dynamic, lacking a single well-defined organisation, with any electrostatic interactions and salt-bridges mediated by intervening water molecules [87,99].…”

Section: Interactions Between Pc and Cytb6fmentioning

confidence: 99%

Cytochrome b6f – Orchestrator of photosynthetic electron transfer

Malone¹,

Proctor²,

Hitchcock³

et al. 2021

Biochimica et Biophysica Acta (BBA) - Bioenergetics

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“…This study illustrates site-specific 2D IR spectroscopy as an experimental approach with sufficient spatial and temporal resolution to tackle the complexity of proteins. In addition to the SH3 domain, we have applied the approach to uncover site-dependent involvement of residues in the molecular recognition of Pc and cyt f. 119 Indeed, the intrinsic power of IR spectroscopy lies in its ability to measure rapidly interconverting states at multiple specific locations in a protein with high spatial detail to test if and how each contributes to function. The elucidation of differences in heterogeneity and dynamics throughout a protein, and how they change in a biologically relevant process, is an essential step toward the longer-term aspiration of using biomolecular 2D IR spectroscopy as a routine approach to study protein biophysics.…”

Section: Varying Engagement Of the Sh3 Domain With The Pr Ligandmentioning

confidence: 99%

Section: Site-specific 2d Ir Spectroscopy Uncovers Varying Engagement...mentioning

confidence: 99%

Site-Specific 1D and 2D IR Spectroscopy to Characterize the Conformations and Dynamics of Protein Molecular Recognition

Ramos

Thielges

2019

J. Phys. Chem. B

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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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Heterogeneous and Highly Dynamic Interface in Plastocyanin–Cytochrome f Complex Revealed by Site-Specific 2D-IR Spectroscopy

Cited by 14 publications

References 72 publications

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

Cytochrome b6f – Orchestrator of photosynthetic electron transfer

Site-Specific 1D and 2D IR Spectroscopy to Characterize the Conformations and Dynamics of Protein Molecular Recognition

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