Probing dynamics of complex molecular systems with ultrafast 2D IR vibrational echo spectroscopy

Vibrational heavy atom effect on relaxation and solvent shell dynamics in group VIII trimetallic carbonyls

Infrared pump-probe and two-dimensional infrared (2D-IR) spectroscopies were used to study the vibrational dynamics of a homologous set of trimetallic dodecacarbonyls with increasingly heavy atomic masses in tetrahydrofuran solution. The vibrational lifetimes showed some evidence of the vibrational heavy atom effect (VHAE) but were not consistent across the sample set. Spectral diffusion was measured by 2D-IR spectroscopy to investigate whether the changes produced by the VHAE had influenced other aspects of vibrational dynamics. The triiron species was found to be more dynamic on very fast timescales and may exhibit evidence of a transient bridging CO structure. Centerline slope analysis of the high-frequency CO peak for each complex revealed that the vibrational dynamics were subtly but consistently slowed for the compounds with heavier metal atoms.

Two-dimensional ultrafast transient absorption spectrograph covering deep-ultraviolet to visible spectral region optimized for biomolecules

We report on the implementation of a multi-kHz single-shot referenced non-coherent two-dimensional UV spectrograph based on conventional pump-probe geometry. It has the capability to cover a broad spectral region in excitation from 270-to-380 nm and in the detection from 270-to-390 nm and 320-to-720 nm. Other setups features are: an unprecedented time resolution of 33 fs (standard deviation); signals are photometrically corrected; a single-shot noise of <1 mOD. It has the capability to operate with sample volumes as small as few μl which is an accomplishment in studying biological or biomimetic systems. To show its performances and potentials, we report two preliminary studies on the photophysics of phenanthrenes hosted in a multichromophoric antenna system and of aromatic amino acids in a blue-copper azurin.

Bottom-Up Approach to Assess the Molecular Structure of Aqueous Poly(N-Isopropylacrylamide) at Room Temperature via Infrared Spectroscopy

The structure of poly(N-isopropylacrylamide) (PNIPAM) in solution is still an unresolved topic. Here, the PNIPAM structure in water was investigated using a bottom-up approach, involving the monomer, dimer, and trimer, and a combination of infrared (IR) spectroscopies as well as molecular dynamics simulations. The experiments show that the monomer and oligomers exhibit a broad and asymmetric amide I band with two underlying transitions, while PNIPAM presents the same major transitions and a minor one. Analysis of the 2D IR spectra and theoretical modeling of the amide I band indicates that the two transitions of the monomer do not have the same molecular origin as the oligomers and the polymer. In the monomer, the two bands originate from the ultrafast rotation of its ethyl group, which leads to different solvation structures for the various rotational conformers. In the case of the oligomers, the asymmetry and splitting of the amide I band is caused by the vibrational coupling among adjacent amide side chains. Moreover, it is deduced from the simulations that the oligomers have three distinct backbone conformations for neighboring amides. In particular, two of the backbone conformations have a closed and compact structure, while in the third, the backbone is open and elongated. The bottom-up approach allowed us to infer that such backbone conformations exist in PNIPAM as well. Consequently, the two major amide I transitions of the polymer are also assigned to split amide I transitions resulting from the vibrationally coupled nearest-neighboring amides. In contrast, the additional minor transition observed in PNIPAM is assigned to unsolvated amide units of the polymer. The proposed molecular model successfully describes that PNIPAM amide I band changes with temperature in terms of its molecular structure. This new model strongly suggests that PNIPAM does not have a completely random backbone structure, but has distinct backbone conformers between neighboring amides.

Two-dimensional infrared spectroscopic study of cytochrome c peroxidase activity in deep eutectic solvent

Deep eutectic solvents (DESs) prepared by mixing hydrogen-bond donor and acceptor molecules have been found to be of use in several applications. Recently, it was shown that DESs can enhance the peroxidation activity of cytochrome c. Here, to elucidate the effects of DESs on the peroxidase activity of cytochrome c, we carried out linear and nonlinear infrared spectroscopic studies of the CO stretch mode of carbon monoxide cytochrome c (COCytc) in ethylammonium chloride (EAC)/urea DES. The FTIR spectrum of COCytc shows a significant spectral shift upon addition of the DES. The broadening and red-shifting of the CO band are observed in both urea and DES solutions, which are induced by the change of the distal ligands around the heme. Although the FTIR study is sensitive to structural changes in the active site, it does not provide quantitative information about structural dynamics related to the catalytic activity itself. Thus, we carried out two-dimensional IR spectroscopy of the CO mode, which suggests that there is a different conformer that could be related to the enhanced catalytic activity in DES. In particular, the spectral diffusion dynamics of that conformer exhibits quite different behavior. The experimental results lead us to propose a hypothesis that the DES increases the population of the conformer with distal ligand lysines close to the reaction center through the combining effect of urea and EAC, which results in the enhancement of the peroxidase activity of cytochrome c. We anticipate that the present experimental work stimulates future investigations of the effects of DES on biocatalysis.

Ultrafast structural molecular dynamics investigated with 2D infrared spectroscopy methods

Ultrafast, multi-dimensional infrared (IR) spectroscopy has been advanced in recent years to a versatile analytical tool with a broad range of applications to elucidate molecular structure on ultrafast timescales, and it can be used for samples in a many different environments. Following a short and general introduction on the benefits of 2D IR spectroscopy, the first part of this chapter contains a brief discussion on basic descriptions and conceptual considerations of 2D IR spectroscopy. Outstanding classical applications of 2D IR are used afterwards to highlight the strengths and basic applicability of the method. This includes the identification of vibrational coupling in molecules, characterization of spectral diffusion dynamics, chemical exchange of chemical bond formation and breaking, as well as dynamics of intra- and intermolecular energy transfer for molecules in bulk solution and thin films. In the second part, several important, recently developed variants and new applications of 2D IR spectroscopy are introduced. These methods focus on (i) applications to molecules under two- and three-dimensional confinement, (ii) the combination of 2D IR with electrochemistry, (iii) ultrafast 2D IR in conjunction with diffraction-limited microscopy, (iv) several variants of non-equilibrium 2D IR spectroscopy such as transient 2D IR and 3D IR, and (v) extensions of the pump and probe spectral regions for multi-dimensional vibrational spectroscopy towards mixed vibrational-electronic spectroscopies. In light of these examples, the important open scientific and conceptual questions with regard to intra- and intermolecular dynamics are highlighted. Such questions can be tackled with the existing arsenal of experimental variants of 2D IR spectroscopy to promote the understanding of fundamentally new aspects in chemistry, biology and materials science. The final part of the chapter introduces several concepts of currently performed technical developments, which aim at exploiting 2D IR spectroscopy as an analytical tool. Such developments embrace the combination of 2D IR spectroscopy and plasmonic spectroscopy for ultrasensitive analytics, merging 2D IR spectroscopy with ultra-high-resolution microscopy (nanoscopy), future variants of transient 2D IR methods, or 2D IR in conjunction with microfluidics. It is expected that these techniques will allow for groundbreaking research in many new areas of natural sciences.

Encapsulating Subsite Analogues of the [FeFe]-Hydrogenases in Micelles Enables Direct Water Interactions

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.

Two-dimensional optical spectroscopy of homo- and heterodimers

We theoretically study the two-dimensional (2D) spectroscopy of molecular dimers.

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.

Complexation dynamics of CH3SCN and Li+ in acetonitrile studied by two-dimensional infrared spectroscopy

A chemical exchange 2DIR study of ion–molecule complexation dynamics in electrolyte solutions.

Ultrafast infrared spectroscopy reveals water-mediated coherent dynamics in an enzyme active site

Ultrafast infrared spectroscopy provides insights into the dynamic nature of water in the active sites of catalase and peroxidase enzymes.

Understanding the impact of fast dynamics upon the chemical processes occurring within the active sites of proteins and enzymes is a key challenge that continues to attract significant interest, though direct experimental insight in the solution phase remains sparse. Similar gaps in our knowledge exist in understanding the role played by water, either as a solvent or as a structural/dynamic component of the active site. In order to investigate further the potential biological roles of water, we have employed ultrafast multidimensional infrared spectroscopy experiments that directly probe the structural and vibrational dynamics of NO bound to the ferric haem of the catalase enzyme from Corynebacterium glutamicum in both H₂O and D₂O. Despite catalases having what is believed to be a solvent-inaccessible active site, an isotopic dependence of the spectral diffusion and vibrational lifetime parameters of the NO stretching vibration are observed, indicating that water molecules interact directly with the haem ligand. Furthermore, IR pump–probe data feature oscillations originating from the preparation of a coherent superposition of low-frequency vibrational modes in the active site of catalase that are coupled to the haem ligand stretching vibration. Comparisons with an exemplar of the closely-related peroxidase enzyme family shows that they too exhibit solvent-dependent active-site dynamics, supporting the presence of interactions between the haem ligand and water molecules in the active sites of both catalases and peroxidases that may be linked to proton transfer events leading to the formation of the ferryl intermediate Compound I. In addition, a strong, water-mediated, hydrogen bonding structure is suggested to occur in catalase that is not replicated in peroxidase; an observation that may shed light on the origins of the different functions of the two enzymes.

Dynamics in the isotropic phase of nematogens using 2D IR vibrational echo measurements on natural-abundance 13CN and extended lifetime probes

The long time scale orientational relaxation of nematogens in the isotropic phase is associated with the randomization of pseudonematic domains, which have a correlation length that grows as the isotropic-to-nematic phase transition temperature is approached from above. Here we begin to address the fast dynamics of the nematogen molecules within the domains using two-dimensional infrared (2D IR) vibrational echo experiments. The problems of performing ultrafast IR experiments in pure liquids are discussed, and solutions are presented. In addition, the issue of short vibrational lifetimes, which limit the ability of 2D IR experiments to examine dynamics over a wide range of times, is addressed. The experiments were performed on the nematogen 4-cyano-4'-pentylbiphenyl (5CB), with the CN stretch initially used as the vibrational probe. Although the CN stretch has a small transition dipole, because the sample is a pure liquid it is necessary to use an exceedingly thin sample to perform the experiments. The small sample volume leads to massive heating effects that distort the results. In addition, the high concentration in the pure liquid can result in vibrational excitation transfer that interferes with the measurements of structural dynamics, and the CN vibrational lifetime is very short (3.6 ps). These problems were overcome by performing the experiments on the natural-abundance (13)CN stretch (5(13)CB), which greatly reduced the absorbance, eliminating the heating problems; also, this stretch has a longer lifetime (7.9 ps). Experiments were also performed on benzonitrile, which showed that the heating problems associated with pure liquids are not unique to 5CB. Again, the problems were eliminated by conducting measurements on the (13)CN stretch, which has an even longer lifetime (20.2 ps) compared with the (12)CN stretch (5.6 ps). Finally, to extend the range of the dynamical measurements, 4-pentyl-4'-thiocyanobiphenyl (5SCB) was synthesized and studied as a dilute solute in 5CB. The CN stretch of 5SCB has a vibrational lifetime of 103 ps, which permits dynamical measurements to 200 ps, revealing the full range of fast structural dynamics in the isotropic phase of 5CB. It is shown that the 5SCB probe reports essentially the same dynamics as 5(13)CB on the short time scale that is observable with the 5(13)CB vibrational probe.

Monitoring the folding of Trp-cage peptide by two-dimensional infrared (2DIR) spectroscopy

Protein folding is one of the most fundamental problems in modern molecular biology. Uncovering the detailed folding mechanism requires methods that can monitor the structures at high temporal and spatial resolution. Two-dimensional infrared (2DIR) spectroscopy is a new tool for studying protein structures and dynamics with high time resolution. Using atomistic molecular dynamics simulations, we illustrate the folding process of Trp-cage along the dominant pathway on the free energy landscape by analyzing nonchiral and chiral coherent 2DIR spectra along the pathway. Isotope labeling is used to reveal residue-specific information. We show that the high resolution structural sensitivity of 2DIR can differentiate the ensemble evolution of protein and thus provides a microscopic picture of the folding process.

Effect of solvent polarity on the vibrational dephasing dynamics of the nitrosyl stretch in an Fe(II) complex revealed by 2D IR spectroscopy

The vibrational dephasing dynamics of the nitrosyl stretching vibration (ν(NO)) in sodium nitroprusside (SNP, Na2[Fe(CN)5NO]·2H2O) are investigated using two-dimensional infrared (2D IR) spectroscopy. The ν(NO) in SNP acts as a model system for the nitrosyl ligand found in metalloproteins which play an important role in the transportation and detection of nitric oxide (NO) in biological systems. We perform a 2D IR line shape study of the ν(NO) in the following solvents: water, deuterium oxide, methanol, ethanol, ethylene glycol, formamide, and dimethyl sulfoxide. The frequency of the ν(NO) exhibits a large vibrational solvatochromic shift of 52 cm(-1), ranging from 1884 cm(-1) in dimethyl sulfoxide to 1936 cm(-1) in water. The vibrational anharmonicity of the ν(NO) varies from 21 to 28 cm(-1) in the solvents used in this study. The frequency-frequency correlation functions (FFCFs) of the ν(NO) in SNP in each of the seven solvents are obtained by fitting the experimentally obtained 2D IR spectra using nonlinear response theory. The fits to the 2D IR line shape reveal that the spectral diffusion time scale of the ν(NO) in SNP varies from 0.8 to 4 ps and is negatively correlated with the empirical solvent polarity scales. We compare our results with the experimentally determined FFCFs of other charged vibrational probes in polar solvents and in the active sites of heme proteins. Our results suggest that the vibrational dephasing dynamics of the ν(NO) in SNP reflect the fluctuations of the nonhomogeneous electric field created by the polar solvents around the nitrosyl and cyanide ligands. The solute solvent interactions occurring at the trans-CN ligand are sensed through the π-back-bonding network along the Fe-NO bond in SNP.

Snapshot of the equilibrium dynamics of a drug bound to HIV-1 reverse transcriptase

The anti-AIDS drug rilpivirine undergoes conformational changes to bind HIV-1 reverse transcriptase (RT), which is an essential enzyme for the replication of HIV. These changes allow it to retain potency against mutations that otherwise would render the enzyme resistant. Here we report that water molecules play an essential role in this binding process. Femtosecond experiments and theory expose the molecular level dynamics of rilpivirine bound to HIV-1 RT. Two nitrile substituents, one on each arm of the drug, are used as vibrational probes of the structural dynamics within the binding pocket. Two-dimensional vibrational echo spectroscopy reveals that one nitrile group is unexpectedly hydrogen-bonded to a mobile water molecule, not identified in previous X-ray structures. Ultrafast nitrile-water dynamics are confirmed by simulations. A higher (1.51 Å) resolution X-ray structure also reveals a water-drug interaction network. Maintenance of a crucial anchoring hydrogen bond may help retain the potency of rilpivirine against pocket mutations despite the structural variations they cause.

Fast dynamics of HP35 for folded and urea-unfolded conditions

The changes in fast dynamics of HP35 with a double CN vibrational dynamics label (HP35-P(2)) as a function of the extent of denaturation by urea were investigated with two-dimensional infrared (2D IR) vibrational echo spectroscopy. Cyanophenylalanine (PheCN) replaces the native phenylalanine at two residues in the hydrophobic core of HP35, providing vibrational probes. NMR data show that HP35-P(2) maintains the native folded structure similar to wild type and that both PheCN residues share essentially the same environment within the peptide. A series of time-dependent 2D IR vibrational echo spectra were obtained for the folded peptide and the increasingly unfolded peptide. Analysis of the time dependence of the 2D spectra yields the system's spectral diffusion, which is caused by the sampling of accessible structures of the peptide under thermal equilibrium conditions. The structural dynamics become faster as the degree of unfolding is increased.

Conformational dynamics and stability of HP35 studied with 2D IR vibrational echoes

Two-dimensional infrared (2D IR) vibrational echo spectroscopy was used to measure the fast dynamics of two variants of chicken villin headpiece 35 (HP35). The CN of cyanophenylalanine residues inserted in the hydrophobic core were used as a vibrational probe. Experiments were performed on both singly (HP35-P) and doubly CN-labeled peptide (HP35-P(2)) within the wild-type sequence, as well as on HP-35 containing a singly labeled cyanophenylalanine and two norleucine mutations (HP35-P NleNle). There is a remarkable similarity between the dynamics measured in singly and doubly CN-labeled HP35, demonstrating that the presence of an additional CN vibrational probe does not significantly alter the dynamics of the small peptide. The substitution of two lysine residues by norleucines markedly improves the stability of HP35 by replacing charged with nonpolar residues, stabilizing the hydrophobic core. The results of the 2D IR experiments reveal that the dynamics of HP35-P are significantly faster than those of HP35-P NleNle. These observations suggest that the slower structural fluctuations in the hydrophobic core, indicating a more tightly structured core, may be an important contributing factor to HP35-P NleNle's increased stability.

Ribonuclease S dynamics measured using a nitrile label with 2D IR vibrational echo spectroscopy

A nitrile-labeled amino acid, p-cyanophenylalanine, is introduced near the active site of the semisynthetic enzyme ribonuclease S to serve as a probe of protein dynamics and fluctuations. Ribonuclease S is the limited proteolysis product of subtilisin acting on ribonuclease A, and consists of a small fragment including amino acids 1-20, the S-peptide, and a larger fragment including residues 21-124, the S-protein. A series of two-dimensional vibrational echo experiments performed on the nitrile-labeled S-peptide and the RNase S are described. The time-dependent changes in the two-dimensional infrared vibrational echo line shapes are analyzed using the center line slope method to obtain the frequency-frequency correlation function (FFCF). The observations show that the nitrile probe in the S-peptide has dynamics that are similar to, but faster than, those of the single amino acid p-cyanophenylalanine in water. In contrast, the dynamics of the nitrile label when the peptide is bound to form ribonuclease S are dominated by homogeneous dephasing (motionally narrowed) contributions with only a small contribution from very fast inhomogeneous structural dynamics. The results provide insights into the nature of the structural dynamics of the ribonuclease S complex. The equilibrium dynamics of the nitrile labeled S-peptide and the ribonuclease S complex are also investigated by molecular dynamics simulations. The experimentally determined FFCFs are compared to the FFCFs obtained from the molecular dynamics simulations, thereby testing the capacity of simulations to determine the amplitudes and time scales of protein structural fluctuations on fast time scales under thermal equilibrium conditions.

3-picolyl azide adenine dinucleotide as a probe of femtosecond to picosecond enzyme dynamics

Functionally relevant femtosecond to picosecond dynamics in enzyme active sites can be difficult to measure because of a lack of spectroscopic probes that can be located in the active site without altering the behavior of the enzyme. We have developed a new NAD(+) analog 3-Picolyl Azide Adenine Dinucleotide (PAAD(+)), which has the potential to be a general spectroscopic probe for NAD-dependent enzymes. This analog is stable and binds in the active site of a typical NAD-dependent enzyme formate dehydrogenase (FDH) with characteristics similar to those of natural NAD(+). It has an isolated infrared transition with high molar absorptivity that makes it suitable for observing enzyme dynamics using 2D IR spectroscopy. 2D IR experiments show that in aqueous solution, the analog undergoes complete spectral diffusion within hundreds of femtoseconds consistent with the water hydrogen bonding dynamics that would be expected. When bound to FDH in a binary complex, it shows picosecond fluctuations and a large static offset, consistent with previous studies of the binary complexes of this enzyme. These results show that PAAD(+) is an excellent probe of local dynamics and that it should be a general tool for probing the dynamics of a wide range of NAD-dependent enzymes.

Extracting 2D IR frequency-frequency correlation functions from two component systems

The center line slope (CLS) method is often used to extract the frequency-frequency correlation function (FFCF) from 2D IR spectra to delineate dynamics and to identify homogeneous and inhomogeneous contributions to the absorption line shape of a system. While the CLS method is extremely efficient, quite accurate, and immune to many experimental artifacts, it has only been developed and properly applied to systems that have a single vibrational band, or to systems of two species that have spectrally resolved absorption bands. In many cases, the constituent spectra of multiple component systems overlap and cannot be distinguished from each other. This situation creates ambiguity when analyzing 2D IR spectra because dynamics for different species cannot be separated. Here a mathematical formulation is presented that extends the CLS method for a system consisting of two components (chemically distinct uncoupled oscillators). In a single component system, the CLS corresponds to the time-dependent portion of the normalized FFCF. This is not the case for a two component system, as a much more complicated expression arises. The CLS method yields a series of peak locations originating from slices taken through the 2D spectra. The slope through these peak locations yields the CLS value for the 2D spectra at a given T(w). We derive analytically that for two component systems, the peak location of the system can be decomposed into a weighted combination of the peak locations of the constituent spectra. The weighting depends upon the fractional contribution of each species at each wavelength and also on the vibrational lifetimes of both components. It is found that an unknown FFCF for one species can be determined as long as the peak locations (referred to as center line data) of one of the components are known, as well as the vibrational lifetimes, absorption spectra, and other spectral information for both components. This situation can arise when a second species is introduced into a well characterized single species system. An example is a system in which water exists in bulk form and also as water interacting with an interface. An algorithm is presented for back-calculating the unknown FFCF of the second component. The accuracy of the algorithm is tested with a variety of model cases in which all components are initially known. The algorithm successfully reproduces the FFCF for the second component within a reasonable degree of error.

Two-dimensional IR spectroscopy of protein dynamics using two vibrational labels: a site-specific genetically encoded unnatural amino acid and an active site ligand

Protein dynamics and interactions in myoglobin (Mb) were characterized via two vibrational dynamics labels (VDLs): a genetically incorporated site-specific azide (Az) bearing unnatural amino acid (AzPhe43) and an active site CO ligand. The Az-labeled protein was studied using ultrafast two-dimensional infrared (2D IR) vibrational echo spectroscopy. CO bound at the active site of the heme serves as a second VDL located nearby. Therefore, it was possible to use Fourier transform infrared (FT-IR) and 2D IR spectroscopic experiments on the Az in unligated Mb and in Mb bound to CO (MbAzCO) and on the CO in MbCO and MbAzCO to investigate the environment and motions of different states of one protein from the perspective of two spectrally resolved VDLs. A very broad bandwidth 2D IR spectrum, encompassing both the Az and CO spectral regions, found no evidence of direct coupling between the two VDLs. In MbAzCO, both VDLs reported similar time scale motions: very fast homogeneous dynamics, fast, ∼1 ps dynamics, and dynamics on a much slower time scale. Therefore, each VDL reports independently on the protein dynamics and interactions, and the measured dynamics are reflective of the protein motions rather than intrinsic to the chemical nature of the VDL. The AzPhe VDL also permitted study of oxidized Mb dynamics, which could not be accessed previously with 2D IR spectroscopy. The experiments demonstrate that the combined application of 2D IR spectroscopy and site-specific incorporation of VDLs can provide information on dynamics, structure, and interactions at virtually any site throughout any protein.

Influence of histidine tag attachment on picosecond protein dynamics

Polyhistidine affinity tags are routinely employed as a convenient means of purifying recombinantly expressed proteins. A tacit assumption is commonly made that His tags have little influence on protein structure and function. Attachment of a His tag to the N-terminus of the robust globular protein myoglobin leads to only minor changes to the electrostatic environment of the heme pocket, as evinced by the nearly unchanged Fourier transform infrared spectrum of CO bound to the heme of His-tagged myoglobin. Experiments employing two-dimensional infrared vibrational echo spectroscopy of the heme-bound CO, however, find that significant changes occur to the short time scale (picoseconds) dynamics of myoglobin as a result of His tag incorporation. The His tag mainly reduces the dynamics on the 1.4 ps time scale and also alters protein motions of myoglobin on the slower, >100 ps time scale, as demonstrated by the His tag's influence on the fluctuations of the CO vibrational frequency, which reports on protein structural dynamics. The results suggest that affinity tags may have effects on protein function and indicate that investigators of affinity-tagged proteins should take this into consideration when investigating the dynamics and other properties of such proteins.

Temperature dependent equilibrium native to unfolded protein dynamics and properties observed with IR absorption and 2D IR vibrational echo experiments

Dynamic and structural properties of carbonmonoxy (CO)-coordinated cytochrome c(552) from Hydrogenobacter thermophilus (Ht-M61A) at different temperatures under thermal equilibrium conditions were studied with infrared absorption spectroscopy and ultrafast two-dimensional infrared (2D IR) vibrational echo experiments using the heme-bound CO as the vibrational probe. Depending on the temperature, the stretching mode of CO shows two distinct bands corresponding to the native and unfolded proteins. As the temperature is increased from low temperature, a new absorption band for the unfolded protein grows in and the native band decreases in amplitude. Both the temperature-dependent circular dichroism and the IR absorption area ratio R(A)(T), defined as the ratio of the area under the unfolded band to the sum of the areas of the native and unfolded bands, suggest a two-state transition from the native to the unfolded protein. However, it is found that the absorption spectrum of the unfolded protein increases its inhomogeneous line width and the center frequency shifts as the temperature is increased. The changes in line width and center frequency demonstrate that the unfolding does not follow simple two-state behavior. The temperature-dependent 2D IR vibrational echo experiments show that the fast dynamics of the native protein are virtually temperature independent. In contrast, the fast dynamics of the unfolded protein are slower than those of the native protein, and the unfolded protein fast dynamics and at least a portion of the slower dynamics of the unfolded protein change significantly, becoming faster as the temperature is raised. The temperature dependence of the absorption spectrum and the changes in dynamics measured with the 2D IR experiments confirm that the unfolded ensemble of conformers continuously changes its nature as unfolding proceeds, in contrast to the native state, which displays a temperature-independent distribution of structures.

Protein dynamics in cytochrome P450 molecular recognition and substrate specificity using 2D IR vibrational echo spectroscopy

Cytochrome (cyt) P450s hydroxylate a variety of substrates that can differ widely in their chemical structure. The importance of these enzymes in drug metabolism and other biological processes has motivated the study of the factors that enable their activity on diverse classes of molecules. Protein dynamics have been implicated in cyt P450 substrate specificity. Here, 2D IR vibrational echo spectroscopy is employed to measure the dynamics of cyt P450(cam) from Pseudomonas putida on fast time scales using CO bound at the active site as a vibrational probe. The substrate-free enzyme and the enzyme bound to both its natural substrate, camphor, and a series of related substrates are investigated to explicate the role of dynamics in molecular recognition in cyt P450(cam) and to delineate how the motions may contribute to hydroxylation specificity. In substrate-free cyt P450(cam), three conformational states are populated, and the structural fluctuations within a conformational state are relatively slow. Substrate binding selectively stabilizes one conformational state, and the dynamics become faster. Correlations in the observed dynamics with the specificity of hydroxylation of the substrates, the binding affinity, and the substrates' molecular volume suggest that motions on the hundreds of picosecond time scale contribute to the variation in activity of cyt P450(cam) toward different substrates.

Dynamics of the folded and unfolded villin headpiece (HP35) measured with ultrafast 2D IR vibrational echo spectroscopy

A series of two-dimensional infrared vibrational echo experiments performed on nitrile-labeled villin headpiece [HP35-(CN)(2)] is described. HP35 is a small peptide composed of three alpha helices in the folded configuration. The dynamics of the folded HP35-(CN)(2) are compared to that of the guanidine-induced unfolded peptide, as well as the nitrile-functionalized phenylalanine (PheCN), which is used to differentiate the peptide dynamic contributions to the observables from those of the water solvent. Because the viscosity of solvent has a significant effect on fast dynamics, the viscosity of the solvent is held constant by adding glycerol. For the folded peptide, the addition of glycerol to the water solvent causes observable slowing of the peptide's dynamics. Holding the viscosity constant as GuHCl is added, the dynamics of unfolded peptide are much faster than those of the folded peptide, and they are very similar to that of PheCN. These observations indicate that the local environment of the nitrile in the unfolded peptide resembles that of PheCN, and the dynamics probed by the CN are dominated by the fluctuations of the solvent molecules, in contrast to the observations on the folded peptide.

Dynamics of a myoglobin mutant enzyme: 2D IR vibrational echo experiments and simulations

Myoglobin (Mb) double mutant T67R/S92D displays peroxidase enzymatic activity in contrast to the wild type protein. The CO adduct of T67R/S92D shows two CO absorption bands corresponding to the A(1) and A(3) substates. The equilibrium protein dynamics for the two distinct substates of the Mb double mutant are investigated by using two-dimensional infrared (2D IR) vibrational echo spectroscopy and molecular dynamics (MD) simulations. The time-dependent changes in the 2D IR vibrational echo line shapes for both of the substates are analyzed using the center line slope (CLS) method to obtain the frequency-frequency correlation function (FFCF). The results for the double mutant are compared to those from the wild type Mb. The experimentally determined FFCF is compared to the FFCF obtained from molecular dynamics simulations, thereby testing the capacity of a force field to determine the amplitudes and time scales of protein structural fluctuations on fast time scales. The results provide insights into the nature of the energy landscape around the free energy minimum of the folded protein structure.

Enhancing signal detection and completely eliminating scattering using quasi-phase-cycling in 2D IR experiments

We demonstrate how quasi-phase-cycling achieved by sub-cycle delay modulation can be used to replace optical chopping in a box-CARS 2D IR experiment in order to enhance the signal size, and, at the same time, completely eliminate any scattering contamination. Two optical devices are described that can be used for this purpose, a wobbling Brewster window and a photoelastic modulator. They are simple to construct, easy to incorporate into any existing 2D IR setup, and have attractive features such as a high optical throughput and a fast modulation frequency needed to phase cycle on a shot-to-shot basis.

Characterization of azido-NAD+ to assess its potential as a two-dimensional infrared probe of enzyme dynamics

Enzyme active-site dynamics at femtosecond to picosecond time scales are of great biochemical importance, but remain relatively unexplored due to the lack of appropriate analytical methods. Two-dimensional infrared (2D IR) spectroscopy is one of the few methods that can examine chemical biological motions at this time scale, but all the IR probes used so far were specific to a few unique enzymes. The lack of IR probes of broader specificity is a major limitation to further 2D IR studies of enzyme dynamics. Here we describe the synthesis of a general IR probe for nicotinamide-dependent enzymes. This azido analog of the ubiquitous cofactor nicotinamide adenine dinucleotide is found to be stable and bind to several dehydrogenases with dissociation constants similar to that for the native cofactor. The infrared absorption spectra of this probe bound to several enzymes indicate that it has significant potential as a 2D IR probe to investigate femtosecond dynamics of nicotinamide-dependent enzymes.

Probing the folding of mini-protein Beta3s by two-dimensional infrared spectroscopy; simulation study

We propose to use infrared coherent two-dimensional correlation spectroscopy (2DCS) to characterize the folding mechanism of the mini-protein Beta3s. In this study Beta3s was folded by molecular dynamics (MD) simulation and intermediate conformational ensembles were identified. The one and two-dimensional correlation spectrum was calculated for the intermediate and native states of the mini-protein. A direct structure-spectra relationship was determined by analysis of conformational properties and specific residue contributions. We identified the structural origin of diagonal and off-diagonal peaks in the 2DCS spectra for the native and intermediate conformational ensembles in the folding mechanism. This work supports the implementation of computational techniques in conjunction with experimental 2DCS to study the folding mechanism of proteins. In addition to exploring the folding mechanism the work presented here can be applied in combination with experiment to refine and validate current molecular dynamics force fields.

PACS Codes: 87.15.Cc, 87.15.hm, 87.15.hp

2D-IR study of a photoswitchable isotope-labeled alpha-helix

A series of photoswitchable, alpha-helical peptides were studied using two-dimensional infrared spectroscopy (2D-IR). Single-isotope labeling with (13)C(18)O at various positions in the sequence was employed to spectrally isolate particular backbone positions. We show that a single (13)C(18)O label can give rise to two bands along the diagonal of the 2D-IR spectrum, one of which is from an amide group that is hydrogen-bonded internally, or to a solvent molecule, and the other from a non-hydrogen-bonded amide group. The photoswitch enabled examination of both the folded and unfolded state of the helix. For most sites, unfolding of the peptide caused a shift of intensity from the hydrogen-bonded peak to the non-hydrogen-bonded peak. The relative intensity of the two diagonal peaks gives an indication of the fraction of molecules hydrogen-bonded at a certain location along the sequence. As this fraction varies quite substantially along the helix, we conclude that the helix is not uniformly folded. Furthermore, the shift in hydrogen bonding is much smaller than the change of helicity measured by CD spectroscopy, indicating that non-native hydrogen-bonded or mis-folded loops are formed in the unfolded ensemble.

Simulation of four-wave mixing signals by a perturbative approach: application to ultrafast two-dimensional infrared spectroscopy

We propose an alternative method for the calculation of the phase-matched contributions, which are responsible for the third-order optical signals measured in four-wave mixing experiments. In particular, we extend the strong field dissipation theory of Meier and Tannor [J. Chem. Phys. 111, 3365 (1999)] to the case of a perturbative treatment with respect to the exciting laser fields. Our approach is based on an analytical expression of the third-order density matrix and hence it does not require to verify numerically the irrelevance of higher order terms or the calculation of a spatial Fourier transform. In order to illustrate this method, we simulate the experimental signal measured in femtosecond two-dimensional infrared (2D-IR) vibrational spectroscopy. We consider an intramolecular anharmonic vibrational mode modeled by a Morse potential and coupled to a dissipative bath of harmonic oscillators. We calculate the 2D-IR correlation spectrum and we discuss the influence of the population decay on the line shapes. In particular, we compare two situations, one where only pure dephasing processes are considered, and another one where phase losses due to population relaxation are also taken into account. We show that the shape of the peaks observed in a 2D-IR correlation spectrum differs in these two cases, and therefore this difference appears as a signature of population decay and gives information on the importance of pure dephasing processes in phase loss mechanisms.

Site-specific difference 2D-IR spectroscopy of bacteriorhodopsin

We demonstrate the extension of the principle of difference Fourier transform infrared (FTIR) spectroscopy to difference 2D-IR spectroscopy. To this end, we measure difference 2D-IR spectra of the protein bacteriorhodopsin in its early J- and K-intermediates. By comparing with the static 2D-IR spectrum of the protonated Schiff base of all-trans retinal, we demonstrate that the 2D-IR spectrum of the all-trans retinal chromophore in bacteriorhodopsin can be measured with the background from the remainder of the protein completely suppressed. We discuss several models to interpret the detailed line shape of the difference 2D-IR spectrum.