A strongly absorbing class of non-natural labels for probing protein electrostatics and solvation with FTIR and 2D IR spectroscopies

The Long and Short of Coupling and Uncoupling via 2D IR Spectroscopy

Determining dynamic structural changes along with the functional movements in biological systems has been a significant challenge for scientists for several decades. Utilizing vibrational coupling with the aid of 2D IR probe pairs has aided in uncovering structural dynamics and functional roles of chemical moieties involved in actions such as membrane peptide folding and transport, ion and water transport, and drug-protein interactions. Both native and non-native vibrational probe pairs have been developed for infrared studies, and their efficacy has been tested in various systems. With these probe pairs, 2D IR spectroscopy captures frozen snapshots of the structural events involved in biological function through vibrational coupling and correlated spectral diffusion. In this Perspective, different treatments of vibrational coupling and coupling models will be addressed, and a review of some of the specific vibrational probe pairs used to study these coupling mechanisms is presented. Overall, the intrinsic molecular dynamics detected on these ultrafast time scales will provide an atomic level view of how chosen structures traverse reaction paths. Thus, it is important to evaluate and assess the accuracy of the different vibrational coupling models and their consistency with the prediction of different molecular structures.

Unnatural Amino Acids for Biological Spectroscopy and Microscopy

Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.

Anisotropic dynamics of an interfacial enzyme active site observed using tethered substrate analogs and ultrafast 2D IR spectroscopy

Enzymes accelerate the rates of biomolecular reactions by many orders of magnitude compared to bulk solution, and it is widely understood that this catalytic effect arises from a combination of polar pre-organization and electrostatic transition state stabilization. A number of recent reports have also implicated ultrafast (femtosecond-picosecond) timescale motions in enzymatic activity. However, complications arising from spatially-distributed disorder, the occurrence of multiple substrate binding modes, and the influence of hydration dynamics on solvent-exposed active sites still confound many experimental studies. Here we use ultrafast two-dimensional infrared (2D IR) spectroscopy and covalently-tethered substrate analogs to examine dynamical properties of the promiscuous Pyrococcus horikoshii ene-reductase (PhENR) active site in two binding configurations mimicking proposed "inactive" and "reactive" Michaelis complexes. Spectral diffusion measurements of aryl-nitrile substrate analogs reveal an end-to-end tradeoff between fast (sub-ps) and slow (>5 ps) motions. Fermi resonant aryl-azide analogs that sense interactions of coupled oscillators are described. Lineshape and quantum beat analyses of these probes reveal characteristics that correlate with aryl-nitrile frequency fluctuation correlation functions parameters, demonstrating that this anisotropy is an intrinsic property of the water-exposed active site, where countervailing gradients of fast dynamics and disorder in the reactant ground state are maintained near the hydration interface. Our results suggest several plausible factors leading to state-selective rate enhancement and promiscuity in PhENR. This study also highlights a strategy to detect perturbations to vibrational modes outside the transparent window of the mid-IR spectrum, which may be extended to other macromolecular systems.

Effects of the Intramolecular Group and Solvent on Vibrational Coupling Modes and Strengths of Fermi Resonances in Aryl Azides: A DFT Study of 4-Azidotoluene and 4-Azido-N-phenylmaleimide

The high transition dipole strength of the azide asymmetric stretch makes aryl azides good candidates as vibrational probes (VPs). However, aryl azides have complex absorption profiles due to Fermi resonances (FRs). Understanding the origin and the vibrational modes involved in FRs of aryl azides is critically important toward developing them as VPs for studies of protein structures and structural changes in response to their surroundings. As such, we studied vibrational couplings in 4-azidotoluene and 4-azido-N-phenylmaleimide in two solvents, N,N-dimethylacetamide and tetrahydrofuran, to explore the origin and the effects of intramolecular group and solvent on the FRs of aryl azides using density functional theory (DFT) calculations with the B3LYP functional and seven basis sets, 6-31G(d,p), 6-31+G(d,p), 6-31++G(d,p), 6-311G(d,p), 6-311+G(d,p), 6-311++G(d,p), and 6-311++G(df,pd). Two combination bands consisting of the azide symmetric stretch and another mode form strong FRs with the azide asymmetric stretch for both molecules. The FR profile was altered by replacing the methyl group with maleimide. Solvents change the relative peak position and intensity more significantly for 4-azido-N-phenylmaleimide, which makes it a more sensitive VP. Furthermore, the DFT results indicate that a comparison among the results from different basis sets can be used as a means to predict more reliable vibrational spectra.

Frequency Changes in Terminal Alkynes Provide Strong, Sensitive, and Solvatochromic Raman Probes of Biochemical Environments

The C≡C stretching frequencies of terminal alkynes appear in the "clear" window of vibrational spectra, so they are attractive and increasingly popular as site-specific probes in complicated biological systems like proteins, cells, and tissues. In this work, we collected infrared (IR) absorption and Raman scattering spectra of model compounds, artificial amino acids, and model proteins that contain terminal alkyne groups, and we used our results to draw conclusions about the signal strength and sensitivity to the local environment of both aliphatic and aromatic terminal alkyne C≡C stretching bands. While the IR bands of alkynyl model compounds displayed surprisingly broad solvatochromism, their absorptions were weak enough that alkynes can be ruled out as effective IR probes. The same solvatochromism was observed in model compounds' Raman spectra, and comparisons to published empirical solvent scales (including a linear regression against four meta-aggregated solvent parameters) suggested that the alkyne C≡C stretching frequency mainly reports on local electronic interactions (i.e., short-range electron donor-acceptor interactions) with solvent molecules and neighboring functional groups. The strong solvatochromism observed here for alkyne stretching bands introduces an important consideration for Raman imaging studies based on these signals. Raman signals for alkynes (especially those that are π-conjugated) can be exceptionally strong and should permit alkynyl Raman signals to function as probes at very low concentrations, as compared to other widely used vibrational probe groups like azides and nitriles. We incorporated homopropargyl glycine into a transmembrane helical peptide via peptide synthesis, and we installed p-ethynylphenylalanine into the interior of the Escherichia coli fatty acid acyl carrier protein using a genetic code expansion technique. The Raman spectra from each of these test systems indicate that alkynyl C≡C bands can act as effective and unique probes of their local biomolecular environments. We provide guidance for the best possible future uses of alkynes as solvatochromic Raman probes, and while empirical explanations of the alkyne solvatochromism are offered, open questions about its physical basis are enunciated.

Infrared Spectroscopy Elucidates the Inhibitor Binding Sites in a Metal-Dependent Formate Dehydrogenase

Biological carbon dioxide (CO2 ) reduction is an important step by which organisms form valuable energy-richer molecules required for further metabolic processes. The Mo-dependent formate dehydrogenase (FDH) from Rhodobacter capsulatus catalyzes reversible formate oxidation to CO2 at a bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor. To elucidate potential substrate binding sites relevant for the mechanism, we studied herein the interaction with the inhibitory molecules azide and cyanate, which are isoelectronic to CO2 and charged as formate. We employed infrared (IR) spectroscopy in combination with density functional theory (DFT) and inhibition kinetics. One distinct inhibitory molecule was found to bind to either a non-competitive or a competitive binding site in the secondary coordination sphere of the active site. Site-directed mutagenesis of key amino acid residues in the vicinity of the bis-MGD cofactor revealed changes in both non-competitive and competitive binding, whereby the inhibitor is in case of the latter interaction presumably bound between the cofactor and the adjacent Arg587.

Site-Specific Interrogation of Protein Structure and Stability

To execute their function or activity, proteins need to possess variability in local electrostatic environment, solvent accessibility, structure, and stability. However, assessing any protein property in a site-specific manner is not easy since native spectroscopic signals often lack the needed specificity. One strategy that overcomes this limitation is to use unnatural amino acids that exhibit distinct spectroscopic features. In this chapter, we describe several such unnatural amino acids (UAAs) and their respective applications in site-specific interrogation of protein structure and stability using standard biophysical methods, including circular dichroism (CD), infrared (IR), and fluorescence spectroscopies.

Multipolar Force Fields for Amide-I Spectroscopy from Conformational Dynamics of the Alanine Trimer

The dynamics and spectroscopy of N-methyl-acetamide (NMA) and trialanine in solution are characterized from molecular dynamics simulations using different energy functions, including a conventional point charge (PC)-based force field, one based on a multipolar (MTP) representation of the electrostatics, and a semiempirical DFT method. For the 1D infrared spectra, the frequency splitting between the two amide-I groups is 10 cm^-1 from the PC, 13 cm^-1 from the MTP, and 47 cm^-1 from self-consistent charge density functional tight-binding (SCC-DFTB) simulations, compared with 25 cm^-1 from experiment. The frequency trajectory required for the frequency fluctuation correlation function (FFCF) is determined from individual normal mode (INM) and full normal mode (FNM) analyses of the amide-I vibrations. The spectroscopy, time-zero magnitude of the FFCF C(t = 0), and the static component Δ₀² from simulations using MTP and analysis based on FNM are all consistent with experiments for (Ala)₃. Contrary to this, for the analysis excluding mode-mode coupling (INM), the FFCF decays to zero too rapidly and for simulations with a PC-based force field, the Δ₀² is too small by a factor of two compared with experiments. Simulations with SCC-DFTB agree better with experiment for these observables than those from PC-based simulations. The conformational ensemble sampled from simulations using PCs is consistent with the literature (including P_II, β, α_R, and α_L), whereas that covered by the MTP-based simulations is dominated by P_II with some contributions from β and α_R. This agrees with and confirms recently reported Bayesian-refined populations based on 1D infrared experiments. FNM analysis together with a MTP representation provides a meaningful model to correctly describe the dynamics of hydrated trialanine.

Ultrafast vibrational dynamics of a solute correlates with dynamics of the solvent

Two-dimensional infrared (2D-IR) spectroscopy is used to measure the spectral dynamics of the metal carbonyl complex cyclopentadienyl manganese tricarbonyl (CMT) in a series of linear alkyl nitriles. 2D-IR spectroscopy provides direct readout of solvation dynamics through spectral diffusion, probing the decay of frequency correlation induced by fluctuations of the solvent environment. 2D-IR simultaneously monitors intramolecular vibrational energy redistribution (IVR) among excited vibrations, which can also be influenced by the solvent through the spectral density rather than the dynamical friction underlying solvation. Here, we report that the CMT vibrational probe reveals solvent dependences in both the spectral diffusion and the IVR time scales, where each slows with increased alkyl chain length. In order to assess the degree to which solute-solvent interactions can be correlated with bulk solvent properties, we compared our results with low-frequency dynamics obtained from optical Kerr effect (OKE) spectroscopy-performed by others-on the same nitrile solvent series. We find excellent correlation between our spectral diffusion results and the orientational dynamics time scales from OKE. We also find a correlation between our IVR time scales and the amplitudes of the low-frequency spectral densities evaluated at the 90-cm^-1 energy difference, corresponding to the gap between the two strong vibrational modes of the carbonyl probe. 2D-IR and OKE provide complementary perspectives on condensed phase dynamics, and these findings provide experimental evidence that at least at the level of dynamical correlations, some aspects of a solute vibrational dynamics can be inferred from properties of the solvent.

Ultrafast vibrational dynamics of the tyrosine ring mode and its application to enkephalin insertion into phospholipid membranes as probed by two-dimensional infrared spectroscopy

Enkephalins are small opioid peptides whose binding conformations are catalyzed by phospholipid membranes. Binding to opioid receptors is determined by the orientation of tyrosine and phenylalanine side chains. In this work, we investigate the effects of different charged phospholipid headgroups on the insertion of the tyrosine side chain into a lipid bilayer using a combination of 2D IR spectroscopy, anharmonic DFT calculations, and third order response function modeling. The insertion is probed by using the ∼1515 cm^-1 tyrosine ring breathing mode, which we found exhibits rich vibrational dynamics on the picosecond timescale. These dynamics include rapid intramolecular vibrational energy redistribution (IVR), where some of the energy ends up in a dark state that shows up as an anharmonically shifted combination band. The waiting-time dependent 2D IR spectra also show an unusual line shape distortion that affects the extraction of the frequency-frequency correlation function (FFCF), which is the dynamic observable of interest that reflects the tyrosine side chain's insertion into the lipid bilayer. We proposed three models to account for this distortion: a hot-state exchange model, a local environment dependent IVR model, and a coherence transfer model. A qualitative analysis of these models suggests that the local environment dependent IVR rate best explains the line shape distortion, while the coherence transfer model best reproduced the effects on the FFCF. Even with these complex dynamics, we found that the tyrosine ring mode's FFCF is qualitatively correlated with the degree of insertion expected from the different phospholipid headgroups.

Transparent window 2D IR spectroscopy of proteins

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.

Protein Dynamics by Two-Dimensional Infrared Spectroscopy

Proteins function as ensembles of interconverting structures. The motions span from picosecond bond rotations to millisecond and longer subunit displacements. Characterization of functional dynamics on all spatial and temporal scales remains challenging experimentally. Two-dimensional infrared spectroscopy (2D IR) is maturing as a powerful approach for investigating proteins and their dynamics. We outline the advantages of IR spectroscopy, describe 2D IR and the information it provides, and introduce vibrational groups for protein analysis. We highlight example studies that illustrate the power and versatility of 2D IR for characterizing protein dynamics and conclude with a brief discussion of the outlook for biomolecular 2D IR.

Site-selective dynamics of azidolysozyme

The spectroscopic response of and structural dynamics around all azido-modified alanine residues (AlaN₃) in lysozyme are characterized. It is found that AlaN₃ is a positionally sensitive probe for the local dynamics, covering a frequency range of ∼15 cm^-1 for the center frequency of the line shape. This is consistent with findings from selective replacements of amino acids in PDZ2, which reported a frequency span of ∼10 cm^-1 for replacements of Val, Ala, or Glu by azidohomoalanine. For the frequency fluctuation correlation functions, the long-time decay constants τ₂ range from ∼1 to ∼10 ps, which compares with experimentally measured correlation times of 3 ps. Attaching azide to alanine residues can yield dynamics that decays to zero on the few ps time scale (i.e., static component Δ₀ ∼ 0 ps^-1) or to a remaining, static contribution of ∼0.5 ps^-1 (corresponding to 2.5 cm^-1), depending on the local environment on the 10 ps time scale. The magnitude of the static component correlates qualitatively with the degree of hydration of the spectroscopic probe. Although attaching azide to alanine residues is found to be structurally minimally invasive with respect to the overall protein structure, analysis of the local hydrophobicity indicates that the hydration around the modification site differs for modified and unmodified alanine residues, respectively.

Shot-to-shot 2D IR spectroscopy at 100 kHz using a Yb laser and custom-designed electronics

The majority of 2D IR spectrometers operate at 1-10 kHz using Ti:Sapphire laser technology. We report a 2D IR spectrometer designed around Yb:KGW laser technology that operates shot-to-shot at 100 kHz. It includes a home-built OPA, a mid-IR pulse shaper, and custom-designed electronics with optional on-chip processing. We report a direct comparison between Yb:KGW and Ti:Sapphire based 2D IR spectrometers. Even though the mid-IR pulse energy is much lower for the Yb:KGW driven system, there is an 8x improvement in signal-to-noise over the 1 kHz Ti:Sapphire driven spectrometer to which it is compared. Experimental data is shown for sub-millimolar concentrations of amides. Advantages and disadvantages of the design are discussed, including thermal background that arises at high repetition rates. This fundamental spectrometer design takes advantage of newly available Yb laser technology in a new way, providing a straightforward means of enhancing sensitivity.

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

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.

Site-specific 2D IR spectroscopy: a general approach for the characterization of protein dynamics with high spatial and temporal resolution

The conformational heterogeneity and dynamics of protein side chains contribute to function, but investigating exactly how is hindered by experimental challenges arising from the fast timescales involved and the spatial heterogeneity of protein structures. The potential of two-dimensional infrared (2D IR) spectroscopy for measuring conformational heterogeneity and dynamics with unprecedented spatial and temporal resolution has motivated extensive effort to develop amino acids with functional groups that have frequency-resolved absorptions to serve as probes of their protein microenvironments. We demonstrate the full advantage of the approach by selective incorporation of the probe p-cyanophenylalanine at six distinct sites in a Src homology 3 domain and the application of 2D IR spectroscopy to site-specifically characterize heterogeneity and dynamics and their contribution to cognate ligand binding. The approach revealed a wide range of microenvironments and distinct responses to ligand binding, including at the three adjacent, conserved aromatic residues that form the recognition surface of the protein. Molecular dynamics simulations performed for all the labeled proteins provide insight into the underlying heterogeneity and dynamics. Similar application of 2D IR spectroscopy and site-selective probe incorporation will allow for the characterization of heterogeneity and dynamics of other proteins, how heterogeneity and dynamics are affected by solvation and local structure, and how they might contribute to biological function.

Capturing the photo-signaling state of a photoreceptor in a steady-state fashion by binding a transition metal complex

Binding a small molecule to proteins causes conformational changes, but often to a limited extent. Here, we demonstrate that the interaction of a CO-releasing molecule (CORM3) with a photoreceptor photoactive yellow protein (PYP) drives large structural changes in the latter. The interaction of CORM3 and a mutant of PYP, Met100Ala, not only trigger the isomerization of its chromophore, p-coumaric acid, from its anionic trans configuration to a protonated cis configuration, but also increases the content of β-sheet at the cost of α-helix and random coil in the secondary structure of the protein. The CORM3 derived Met100Ala is found to highly resemble the signaling state, which is one of the key photo-intermediates of this photoactive protein, in both protein local conformation and chromophore configuration. The organometallic reagents hold promise as protein engineering tools. This work highlights a novel approach to structurally accessing short lived intermediates of proteins in a steady-state fashion.

Watching Proteins Wiggle: Mapping Structures with Two-Dimensional Infrared Spectroscopy

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.

Extended timescale 2D IR probes of proteins: p-cyanoselenophenylalanine

The importance of dynamics to the function of proteins is well appreciated, but the difficulty in their measurement impedes investigation into their precise role(s). 2D IR spectroscopy is a developing approach for the study of dynamics and has motivated efforts to develop spectrally resolved IR probe groups that enable its application for measuring the dynamics at specific sites in a protein. A challenge with this approach is that the timescales accessible are limited by the vibrational lifetimes of the probes. Toward development of better probes for 2D IR spectroscopy of protein dynamics, we report the characterization of p-cyano-seleno-phenylalanine (CNSePhe), a derivative of the well established IR probe p-cyano-phenylalanine (CNPhe), by FT IR, pump-probe, and 2D IR spectroscopy. The incorporation of the heavy Se atom decouples the CN vibration from the rest in the molecule. Although this leads to a reduction of the transition dipole strength, and thus a reduction in signal intensity, it also dramatically increases the vibrational lifetime, enabling collection of 2D IR spectra for analysis of molecular dynamics on much longer timescales. Interestingly, we also find that the lifetime for CNSePhe shows increased sensitivity to the presence of hydrogen bonding interactions with the CN, suggesting that the probe should be useful for interpretation of CN spectra and possibly for the study of solvation.

Fourier transform spectroscopy in the vibrational fingerprint region with a birefringent interferometer

We introduce a birefringent interferometer for Fourier transform (FT) spectroscopy in the mid-infrared, covering the vibrational fingerprint region (5-10 µm, 1000-2000 cm^-1), which is crucial for molecular identification. Our interferometer employs the crystal calomel (Hg₂Cl₂), which combines high birefringence (n_e-n_o≈0.55) with a broad transparency range (0.38-20 µm). We adopt a design based on birefringent wedges, which is simple and compact and guarantees excellent delay accuracy and long-term stability. We demonstrate FTIR spectroscopy, with a frequency resolution of 3 cm^-1, as well as two-dimensional IR (2DIR) spectroscopy. Our setup can be extended to other spectroscopic modalities such as vibrational circular dichroism and step-scan FT spectroscopy.

The covalently bound diazo group as an infrared probe for hydrogen bonding environments

The bandwidth or position of diazo groups can probe the polarizability and HBA, or density of HBD groups.

Differentiating Two Nitrosylruthenium Isomeric Complexes by Steady-State and Ultrafast Infrared Spectroscopies

The [Ru(II)-NO⁺] group affects the structure and chemical reactivity of nitrosylruthenium(II) complexes. A characteristic infrared absorption band due to the nitrosyl (NO) stretching motion is shown in the frequency region 1800-1900 cm^-1. In this work, linear infrared (IR) and nonlinear IR methods, including pump-probe and two-dimensional (2D) IR, were utilized to study the structures and dynamics of two isomeric nitrosylruthenium complexes [Ru(OAc)(2mqn)₂NO] (H2mqn = 2-methyl-8-quinolinol) in cis and trans isomeric configurations in a weak polar solvent (CDCl₃). Using the NO stretching mode as a vibrational probe, information about local structural dynamics of the Ru complex as well as solvent fluctuation dynamics was obtained. In particular, a "structured" solvent environment is believed to form in the vicinity of the NO group in the case of the cis isomer with the aid of a neighboring OAc ligand, which is the reason for more efficient vibrational relaxation but more inhomogeneously distributed solvent and thus associated slower spectral diffusion. Our results also suggest a more anharmonic potential surface for the NO stretching mode in the less stable trans isomer.

Synthesis and Evaluation of the Sensitivity and Vibrational Lifetimes of Thiocyanate and Selenocyanate Infrared Reporters

Two novel 2'-deoxyadenosine (dA) analogues, Si₂-dA-SCN and Si₂-dA-SeCN, and two novel phenylalanine (Phe) analogues, Boc-Me-PheCH₂SCN and Boc-Me-PheCH₂SeCN, have been synthesized and the thiocyanate (SCN) and selenocyanate (SeCN) functional groups evaluated as vibrational reporters. The syntheses of Si₂-dA-SCN and Si₂-dA-SeCN were accomplished in three steps in 16% and 32% overall yields, respectively, and the syntheses of Boc-Me-PheCH₂SCN and Boc-Me-PheCH₂SeCN were completed in four steps in 8.9% and 2.3% overall yields, respectively. The SCN and SeCN stretch vibrational modes were shown to be sensitive to the local environment by frequency shifts and full-width half-maximum (fwhm) changes in response to tetrahydrofuran (THF) and THF/water solvent mixtures. The vibrational lifetimes of the Si₂-dA-SeCN (237±12 ps) and Boc-Me-PheCH₂SeCN (295±31 ps) in THF solution were determined by ultrafast infrared pump-probe spectroscopy to be 1.5 to 3 times longer than those for Si₂-dA-SCN (140±6 ps) and Boc-Me-PheCH₂SCN (102±4 ps). The longer lifetimes for the SeCN analogues were attributed to the better insulating effects of the heavier selenium atom compared to the sulfur atom. The solvent sensitivity and longer vibrational lifetimes compared to other vibrational reporters suggest that SCN and SeCN vibrational reporters are well suited to studying several dynamic processes including protein and nucleic acid hydration and conformational changes, however stability issues may require post-synthetic modification methods to incorporate these reporters into biomacromolecules.

Kinetics of Reactive Modules Adds Discriminative Dimensions for Selective Cell Imaging

Living cells are chemical mixtures of exceptional interest and significance, whose investigation requires the development of powerful analytical tools fulfilling the demanding constraints resulting from their singular features. In particular, multiplexed observation of a large number of molecular targets with high spatiotemporal resolution appears highly desirable. One attractive road to address this analytical challenge relies on engaging the targets in reactions and exploiting the rich kinetic signature of the resulting reactive module, which originates from its topology and its rate constants. This review explores the various facets of this promising strategy. We first emphasize the singularity of the content of a living cell as a chemical mixture and suggest that its multiplexed observation is significant and timely. Then, we show that exploiting the kinetics of analytical processes is relevant to selectively detect a given analyte: upon perturbing the system, the kinetic window associated to response read-out has to be matched with that of the targeted reactive module. Eventually, we introduce the state-of-the-art of cell imaging exploiting protocols based on reaction kinetics and draw some promising perspectives.

Vibrational spectroscopy of metal carbonyls for bio-imaging and -sensing

Transition metal carbonyls exhibit strong CO absorptions in the 2200–1800 cm⁻¹ region, which is free of interference from other functional groups. This feature has led to their applications in bio-imaging and -sensing, in particular through mid-IR, Raman and more recently, surface-enhanced Raman spectroscopy (SERS).

Applications of two-dimensional infrared spectroscopy

Two-dimensional infrared (2D IR) spectroscopy has recently emerged as a powerful tool with applications in many areas of scientific research. The inherent high time resolution coupled with bond-specific spatial resolution of IR spectroscopy enable direct characterization of rapidly interconverting species and fast processes, even in complex systems found in chemistry and biology. In this minireview, we briefly outline the fundamental principles and experimental procedures of 2D IR spectroscopy. Using illustrative example studies, we explain the important features of 2D IR spectra and their capability to elucidate molecular structure and dynamics. Primarily, this minireview aims to convey the scope and potential of 2D IR spectroscopy by highlighting select examples of recent applications including the use of innate or introduced vibrational probes for the study of nucleic acids, peptides/proteins, and materials.

Fast infrared spectroscopy of protein dynamics: advancing sensitivity and selectivity

2D-IR spectroscopy has matured to a powerful technique to study the structure and dynamics of peptides, but its extension to larger proteins is still in its infancy, the major limitations being sensitivity and selectivity. Site-selective information requires measuring single vibrational probes at sub-millimolar concentrations where most proteins are still stable, which is a severe challenge for conventional (FT)IR spectroscopy. Besides its ultrafast time-resolution, a so far largely underappreciated potential of 2D-IR spectroscopy lies in its sensitivity gain. The present paper sets the goals and outlines strategies how to use that sensitivity gain together with properly designed vibrational labels to make IR spectroscopy a versatile tool to study a wide class of proteins.

Site-specific infrared probes of proteins

Infrared spectroscopy has played an instrumental role in the study of a wide variety of biological questions. However, in many cases, it is impossible or difficult to rely on the intrinsic vibrational modes of biological molecules of interest, such as proteins, to reveal structural and environmental information in a site-specific manner. To overcome this limitation, investigators have dedicated many recent efforts to the development and application of various extrinsic vibrational probes that can be incorporated into biological molecules and used to site-specifically interrogate their structural or environmental properties. In this review, we highlight recent advancements in this rapidly growing research area.

β-Isocyanoalanine as an IR probe: comparison of vibrational dynamics between isonitrile and nitrile-derivatized IR probes

An infrared (IR) probe based on isonitrile (NC)-derivatized alanine 1 was synthesized and the vibrational properties of its NC stretching mode were investigated using FTIR and femtosecond IR pump–probe spectroscopy.

Synthesis and Protein Incorporation of Azido-Modified Unnatural Amino Acids

Two new azidophenylalanine residues (3 and 4) have been synthesized and, in combination with 4-azido-L-phenylalanine (1) and 4-azidomethyl-L-phenylalanine (2), form a series of unnatural amino acids (UAAs) containing the azide vibrational reporter at varying distances from the aromatic ring of phenylalanine. These UAAs were designed to probe protein hydration with high spatial resolution by utilizing the large extinction coefficient and environmental sensitivity of the azide asymmetric stretch vibration. The sensitivity of the azide reporters was investigated in solvents that mimic distinct local protein environments. Three of the four azido-modified phenylalanine residues were successfully genetically incorporated into a surface site in superfolder green fluorescent protein (sfGFP) utilizing an engineered, orthogonal aminoacyl-tRNA synthetase in response to an amber codon with high efficiency and fidelity. SDS-PAGE and ESI-Q-TOF mass analysis verified the site-specific incorporation of these UAAs. The observed azide asymmetric stretch in the linear IR spectra of these UAAs incorporated into sfGFP indicated that the azide groups were hydrated in the protein.

General strategy for the bioorthogonal incorporation of strongly absorbing, solvation-sensitive infrared probes into proteins

A high-sensitivity metal-carbonyl-based IR probe is described that can be incorporated into proteins or other biomolecules in very high yield via Click chemistry. A two-step strategy is demonstrated. First, a methionine auxotroph is used to incorporate the unnatural amino acid azidohomoalanine at high levels. Second, a tricarbonyl (η(5)-cyclopentadienyl) rhenium(I) probe modified with an alkynyl linkage is coupled via the Click reaction. We demonstrate these steps using the C-terminal domain of the ribosomal protein L9 as a model system. An overall incorporation level of 92% was obtained at residue 109, which is a surface-exposed residue. Incorporation of the probe into a surface site is shown not to perturb the stability or structure of the target protein. Metal carbonyls are known to be sensitive to solvation and protein electrostatics through vibrational lifetimes and frequency shifts. We report that the frequencies and lifetimes of this probe also depend on the isotopic composition of the solvent. Comparison of the lifetimes measured in H2O versus D2O provides a probe of solvent accessibility. The metal carbonyl probe reported here provides an easy and robust method to label very large proteins with an amino-acid-specific tag that is both environmentally sensitive and a very strong absorber.

2D IR spectroscopy reveals the role of water in the binding of channel-blocking drugs to the influenza M2 channel

Water is an integral part of the homotetrameric M2 proton channel of the influenza A virus, which not only assists proton conduction but could also play an important role in stabilizing channel-blocking drugs. Herein, we employ two dimensional infrared (2D IR) spectroscopy and site-specific IR probes, i.e., the amide I bands arising from isotopically labeled Ala30 and Gly34 residues, to probe how binding of either rimantadine or 7,7-spiran amine affects the water dynamics inside the M2 channel. Our results show, at neutral pH where the channel is non-conducting, that drug binding leads to a significant increase in the mobility of the channel water. A similar trend is also observed at pH 5.0 although the difference becomes smaller. Taken together, these results indicate that the channel water facilitates drug binding by increasing its entropy. Furthermore, the 2D IR spectral signatures obtained for both probes under different conditions collectively support a binding mechanism whereby amantadine-like drugs dock in the channel with their ammonium moiety pointing toward the histidine residues and interacting with a nearby water cluster, as predicted by molecular dynamics simulations. We believe these findings have important implications for designing new anti-influenza drugs.

An alternative structural isoform in amyloid-like aggregates formed from thermally denatured human γD-crystallin

The eye lens protein γD-crystallin contributes to cataract formation in the lens. In vitro experiments show that γD-crystallin has a high propensity to form amyloid fibers when denatured, and that denaturation by acid or UV-B photodamage results in its C-terminal domain forming the β-sheet core of amyloid fibers. Here, we show that thermal denaturation results in sheet-like aggregates that contain cross-linked oligomers of the protein, according to transmission electron microscopy and SDS-PAGE. We use two-dimensional infrared spectroscopy to show that these aggregates have an amyloid-like secondary structure with extended β-sheets, and use isotope dilution experiments to show that each protein contributes approximately one β-strand to each β-sheet in the aggregates. Using segmental (13) C labeling, we show that the organization of the protein's two domains in thermally induced aggregates results in a previously unobserved structure in which both the N-terminal and C-terminal domains contribute to β-sheets. We propose a model for the structural organization of the aggregates and attribute the recruitment of the N-terminal domain into the fiber structure to intermolecular cross linking.

Vibrational dynamics and solvatochromism of the label SCN in various solvents and hemoglobin by time dependent IR and 2D-IR spectroscopy

The vibrational label SCN is used to report on local structural dynamics in a protein revealing spectral diffusion on a picosecond scale. The SCN spectra are compared to the response of methylthiocyanate in solvents with different polarity and hydrogen-bonding capabilities.

Amyloid fiber formation in human γD-Crystallin induced by UV-B photodamage

γD-Crystallin is an abundant structural protein of the lens that is found in native and modified forms in cataractous aggregates. We establish that UV-B irradiation of γD-Crystallin leads to structurally specific modifications and precipitation via two mechanisms: amorphous aggregates and amyloid fibers. UV-B radiation causes cleavage of the backbone, in large measure near the interdomain interface, where side chain oxidations are also concentrated. 2D IR spectroscopy and expressed protein ligation localize fiber formation exclusively to the C-terminal domain of γD-Crystallin. The native β-sandwich domains are not retained upon precipitation by either mechanism. The similarities between the amyloid forming pathways when induced by either UV-B radiation or low pH suggest that the propensity for the C-terminal β-sandwich domain to form amyloid β-sheets determines the misfolding pathway independent of the mechanism of denaturation.

Site-specific measurements of lipid membrane interfacial water dynamics with multidimensional infrared spectroscopy

One route to accessing site-specific dynamical information available with ultrafast multidimensional infrared spectroscopy is the development of robust and versatile vibrational probes. Here we synthesize and characterize a vibrationally labeled cholesterol derivative, (cholesteryl benzoate) chromium tricarbonyl, to probe model lipid membranes, focusing specifically on the membrane-water interface. Utilizing FTIR and polarized-ATR spectroscopies, we determine the location of the chromium tricarbonyl motif to be situated at the water-membrane interface with an orientation of 46 ± 2° relative to the vector normal to the membrane surface. We test the dynamical sensitivity of the (cholesteryl benzoate) chromium tricarbonyl label with two different nonlinear infrared spectroscopy methods, both of which show that the probe is well-suited to the study of membrane dynamics as well as the dynamics of water at the membrane interface. The metal carbonyl vibrational probe located at the surface of a bicelle exhibits spectral diffusion dynamics induced by membrane hydration water that is roughly three times slower than observed using a nearly identical vibrational probe in bulk water.