Coherent two-dimensional infrared spectroscopy: Quantitative analysis of protein secondary structure in solution

We present a method to quantitatively determine the secondary structure composition of globular proteins using coherent two-dimensional infrared (2DIR) spectroscopy of backbone amide I vibrations (1550–1720 cm−1). Sixteen proteins with known crystal structures were used to construct a library of 2DIR spectra, and the fraction of residues in α-helix, β-sheet, and unassigned conformations was determined by singular value decomposition (SVD) of the measured two-dimensional spectra. The method was benchmarked by removing each individual protein from the set and comparing the composition extracted from 2DIR against the composition determined from the crystal structures. To highlight the increased structural content extracted from 2DIR spectra a similar analysis was also carried out using conventional infrared absorption of the proteins in the library.National Science Foundation (U.S.) (CHE-0616575)National Institutes of Health (U.S.) (CHE-0911107)Agilent Technologie

Visualizing KcsA Conformational Changes upon Ion Binding by Infrared Spectroscopy and Atomistic Modeling

The effect of ion binding in the selectivity filter of the potassium channel KcsA is investigated by combining amide I Fourier-transform infrared spectroscopy with structure-based spectral modeling. Experimental difference IR spectra between K[superscript +]-bound KcsA and Na[superscript +]-bound KcsA are in good qualitative agreement with spectra modeled from structural ensembles generated from molecular dynamics simulations. The molecular origins of the vibrational modes contributing to differences in these spectra are determined not only from structural differences in the selectivity filter but also from the pore helices surrounding this region. Furthermore, the coordination of K[superscript +] or Na[superscript +] to carbonyls in the selectivity filter effectively decouples the vibrations of those carbonyls from the rest of the protein, creating local probes of the electrostatic environment. The results suggest that it is necessary to include the influence of the surrounding helices in discussing selectivity and transport in KcsA and, on a more general level, that IR spectroscopy offers a nonperturbative route to studying the structure and dynamics of ion channels.Vienna Science and Technology Fund (Project VRG10-11)University of Vienna (Research Platform Quantum Phenomena and Nanoscale Biological System

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

© 2020 American Chemical Society. Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and interprotein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an all-encompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semiempirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository Web site (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-the-art multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future

Investigating Ultrafast Condensed-Phase Chemical Dynamics with Coherent Multidimensional Spectroscopy.

Experimental and theoretical studies of ultrafast chemical dynamics in solutionare presented in this work. Condensed-phase chemical reactions are investigated with newly-developed experimental techniques, including non-equilibrium two-dimensional infrared spectroscopy, transient-dispersed vibrational echo spectroscopy, and vibrational Stark-effect spectroscopy. The experiments are aimed at elucidating the complex relationship between molecules and their solvent environment under equilibrium and non-equilibrium conditions. The orientational relaxation rates of hot radical molecules in non-polar solvents were measured with transient-two-dimensional infrared spectroscopy to obtain the vibrational energy relaxation (cooling) rates following a homolytic bond cleavage reaction. Experimental studies of the asymmetric, solvent-caged radical recombination reactions offered new insightsinto the solvent role in determining the branching ratiosand recombination rates in these asymmetric reactions. Dynamic vibrational Stark-effect spectroscopy is demonstrated as a new probe of molecular dynamics in solution. Within this method, a charge-transfer reaction is optically triggered, causing a change in the electric field at the nearby solvent molecules. The vibrational response of the solvent molecules serves to map the electrostatic changes at the chromophore as well as elucidate the dynamics of the molecules within the first solvation shell. The solvent response is measured upon optically triggering an electron-transfer reaction in the solvatochromic dye Betaine-30. The rate of the back-electron transfer, which returns the dye molecules to the ground state, has been measured from the solvent response. In addition to molecular dynamics, two-dimensional infrared spectroscopy can directly access theone- and two-quanta energy levels of the system which directly reports on the anharmonic potential of the molecules. The potential surface of dimanganese decacarbonyl and its photoproducts has been modeled up to fourth order in the normal-mode coordinates using ab-initio electronic structure methods. The energy levels are found to be in agreement with experiment. The vibrational dynamics of dimanganese decacarbonyl are modeled using a Markovian quantum master equation with bilinear system-bath coupling. The model accounts for vibrational relaxation, coherence dephasing, coherence transfer and coherence-population coupling. The transport rates are computed using input from molecular dynamics simulations.Ph.D.ChemistryUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/84620/1/cbaiz_1.pd

Extracting accurate infrared lineshapes from weak vibrational probes at low concentrations

Fourier-transform infrared (FTIR) spectroscopy using vibrational probes is an ideal tool to detect changes in structure and local environments within biological molecules. However, challenges arise when dealing with weak infrared probes, such as thiocyanates, due to their inherent low signal strengths and overlap with solvent bands. In this protocol we demonstrate: • A streamlined approach for the precise extraction of weak infrared absorption lineshapes from a strong solvent background. • A protocol combining a spectral filter, background modeling, and subtraction. • Our methodology successfully extracts the CN stretching mode peak from methyl thiocyanate at remarkably low concentrations (0.25 mM) in water, previously a challenge for FTIR spectroscopy.This approach offers valuable insights and tools for more accurate FTIR measurements using weak vibrational probes. This enhanced precision can potentially enable new approaches to enhance our understanding of protein structure and dynamics in solution

Vibrational Relaxation in EDTA Is Ion-Dependent

Ion binding by carboxylate groups is common in biomolecules such as metalloproteins, but dynamical aspects of ion binding are not fully understood. We present ultrafast spectroscopic measurements of vibrational relaxation in the ion-coordinating carboxylate groups of EDTA, which we use as a model of carboxylate-mediated ion binding, as EDTA binds a series of divalent and trivalent metal ions with high affinity. The measurements are interpreted using a Redfield-based anharmonic model of vibrational relaxation that rationalizes trends in vibrational lifetimes in terms of vibrational energy transfer between EDTA’s asymmetric carboxylate stretching vibrational modes and lower-lying modes. Results show ion-dependent changes in complex structure and dynamics well outside the temporal and spatial resolution of common structural methods and demonstrate how vibrational relaxation measurements may contribute to exploration of ion-binding dynamics on ultrashort length and time scales