Ultrafast infrared spectroscopy of bacteriorhodopsin

Four-dimensional microED of conformational dynamics in protein microcrystals on the femto-to-microsecond timescales

As structural determination of protein complexes approaches atomic resolution, there is an increasing focus on conformational dynamics. Here we conceptualize the combination of two techniques which have become established in recent years: microcrystal electron diffraction and ultrafast electron microscopy. We show that the extremely low dose of pulsed photoemission still enables microED due to the strength of the electron bunching from diffraction of the protein crystals. Indeed, ultrafast electron diffraction experiments on protein crystals have already been demonstrated to be effective in measuring intermolecular forces in protein microcrystals. We discuss difficulties that may arise in the acquisition and processing of data and the overall feasibility of the experiment, paying specific attention to dose and signal-to-noise ratio. In doing so, we outline a detailed workflow that may be effective in minimizing the dose on the specimen. A series of model systems that would be good candidates for initial experiments is provided.

Protein dynamics observed by tunable mid-IR quantum cascade lasers across the time range from 10ns to 1s

We have developed a spectrometer based on tunable quantum cascade lasers (QCLs) for recording time-resolved absorption spectra of proteins in the mid-infrared range. We illustrate its performance by recording time-resolved difference spectra of bacteriorhodopsin in the carboxylic range (1800-1700cm^-1) and on the CO rebinding reaction of myoglobin (1960-1840cm^-1), at a spectral resolution of 1cm^-1. The spectrometric setup covers the time range from 4ns to nearly a second with a response time of 10-15ns. Absorption changes as low as 1×10^-4 are detected in single-shot experiments at t>1μs, and of 5×10^-6 in kinetics obtained after averaging 100 shots. While previous time-resolved IR experiments have mostly been conducted on hydrated films of proteins, we demonstrate here that the brilliance of tunable quantum cascade lasers is superior to perform ns time-resolved experiments even in aqueous solution (H₂O).

Nano-chemical infrared imaging of membrane proteins in lipid bilayers

The spectroscopic characterization of biomolecular structures requires nanometer spatial resolution and chemical specificity. We perform full spatio-spectral imaging of dried purple membrane patches purified from Halobacterium salinarum with infrared vibrational scattering-type scanning near-field optical microscopy (s-SNOM). Using near-field spectral phase contrast based on the Amide I resonance of the protein backbone, we identify the protein distribution with 20 nm spatial resolution and few-protein sensitivity. This demonstrates the general applicability of s-SNOM vibrational nanospectroscopy, with potential extension to a wide range of biomolecular systems.

Implementation of time-resolved step-scan fourier transform infrared (FT-IR) spectroscopy using a kHz repetition rate pump laser

Time-resolved step-scan Fourier transform infrared (FT-IR) spectroscopy has been shown to be invaluable for studying excited-state structures and dynamics in both biological and inorganic systems. Despite the established utility of this method, technical challenges continue to limit the data quality and more wide ranging applications. A critical problem has been the low laser repetition rate and interferometer stepping rate (both are typically 10 Hz) used for data acquisition. Here we demonstrate significant improvement in the quality of time-resolved spectra through the use of a kHz repetition rate laser to achieve kHz excitation and data collection rates while stepping the spectrometer at 200 Hz. We have studied the metal-to-ligand charge transfer excited state of Ru(bipyridine)(3)Cl(2) in deuterated acetonitrile to test and optimize high repetition rate data collection. Comparison of different interferometer stepping rates reveals an optimum rate of 200 Hz due to minimization of long-term baseline drift. With the improved collection efficiency and signal-to-noise ratio, better assignments of the MLCT excited-state bands can be made. Using optimized parameters, carbonmonoxy myoglobin in deuterated buffer is also studied by observing the infrared signatures of carbon monoxide photolysis upon excitation of the heme. We conclude from these studies that a substantial increase in performance of ss-FT-IR instrumentation is achieved by coupling commercial infrared benches with kHz repetition rate lasers.

New photointermediates in the two photon signaling pathway of sensory rhodopsin-I

Sensory rhodopsin-I (SRI) functions as a color discriminating receptor in halobacterial phototaxis. SRI exists in the membrane as a molecular complex with a signal transducer protein. Excitation of its thermally stable form, SRI(587), generates a long-lived photointermediate of its photocycle, S(373), and an attractant phototactic response. S(373) decays thermally in a few seconds into SRI(587.) However, when S(373) is excited by UV-blue light, it photoconverts into SRI(587) in less than a second, generating a repellent phototactic response. Only one intermediate of this back-photoreaction, S(b)(510), is known. We studied the back-photoreaction in both native SRI and its transducer free form fSRI by measuring laser flash induced absorption changes of S(373) photoproducts from 100 ns to 1 s in the 350-750 nm range. Using global exponential fitting, we determined the spectra and kinetics of the photointermediates. S(373) and fS(373) when pumped with 355 nm laser light generate in less than 100 ns two intermediate species: a previously undetected species that absorbs maximally at about 410 nm, S(b)(410), and the previously described S(b)(510). These two intermediates appear to be in a rapid equilibrium, which probably entails protonation change of the Schiff base chromophore. At pH 6 this system relaxes to SRI(587) via another intermediate absorbing maximally around 550 nm, which thermally decays back to the ground state. The same intermediates are seen in the presence and absence of transducer; however, the kinetics are affected by binding of the transducer.

Time-resolved mid-infrared spectroscopy: methods and biological applications

Recent developments in time-resolved infrared spectroscopy have paved the way to probe transient intermediates with a high degree of functional group specificity on timescales as short as femtoseconds. This capability has been exploited in studies of biophysical phenomena ranging from protein folding/unfolding to ligand migration in proteins.

Nanosecond retinal structure changes in K-590 during the room-temperature bacteriorhodopsin photocycle: picosecond time-resolved coherent anti-stokes Raman spectroscopy

Time-resolved vibrational spectra are used to elucidate the structural changes in the retinal chromophore within the K-590 intermediate that precedes the formation of the L-550 intermediate in the room-temperature (RT) bacteriorhodopsin (BR) photocycle. Measured by picosecond time-resolved coherent anti-Stokes Raman scattering (PTR/CARS), these vibrational data are recorded within the 750 cm-1 to 1720 cm-1 spectral region and with time delays of 50-260 ns after the RT/BR photocycle is optically initiated by pulsed (< 3 ps, 1.75 nJ) excitation. Although K-590 remains structurally unchanged throughout the 50-ps to 1-ns time interval, distinct structural changes do appear over the 1-ns to 260-ns period. Specifically, comparisons of the 50-ps PTR/CARS spectra with those recorded with time delays of 1 ns to 260 ns reveal 1) three types of changes in the hydrogen-out-of-plane (HOOP) region: the appearance of a strong, new feature at 984 cm-1; intensity decreases for the bands at 957 cm-1, 952 cm-1, and 939 cm-1; and small changes intensity and/or frequency of bands at 855 cm-1 and 805 cm-1; and 2) two types of changes in the C-C stretching region: the intensity increase in the band at 1196 cm-1 and small intensity changes and/or frequency shifts for bands at 1300 cm-1 and 1362 cm-1. No changes are observed in the C = C stretching region, and no bands assignable to the Schiff base stretching mode (C = NH+) mode are found in any of the PTR/CARS spectra assignable to K-590. These PTR/CARS data are used, together with vibrational mode assignments derived from previous work, to characterize the retinal structural changes in K-590 as it evolves from its 3.5-ps formation (ps/K-590) through the nanosecond time regime (ns/K-590) that precedes the formation of L-550. The PTR/CARS data suggest that changes in the torsional modes near the C14-C15 = N bonds are directly associated with the appearance of ns/K-590, and perhaps with the KL intermediate proposed in earlier studies. These vibrational data can be primarily interpreted in terms of the degree of twisting of the C14-C15 retinal bond. Such twisting may be accompanied by changes in the adjacent protein. Other smaller, but nonetheless clear, spectral changes indicate that alterations along the retinal polyene chain also occur. The changes in the retinal structure are preliminary to the deprotonation of the Schiff base nitrogen during the formation of M-412. The time constant for the ps/ns K-590 transformation is estimated from the amplitude change of four vibrational bands in the HOOP region to be 40-70 ns.

Photoinduced volume changes associated with the early transformations of bacteriorhodopsin: a laser-induced optoacoustic spectroscopy study

Volume changes associated with the primary photochemistry of bacteriorhodopsin (BR) were measured by temperature-dependent laser-induced optoacoustic spectroscopy (LIOAS). Excitation was performed with 8-ns flashes establishing a photoequilibrium between the BR and the K states (BR<-->hvK). The concentration of K at the end of the laser pulse, which is an important parameter for the calculation of the volume change per molecule from the LIOAS data, was determined by flash photolysis with optical detection under the specific conditions (concentration, photon density) of the LIOAS experiment. Temperature-dependent measurements yielded a linear dependency of the ratio of the optoacoustic signals for BR and for a calorimetric reference (CoCl2) with the cubic thermal expansion coefficient beta of water. From the slope of this linear ratio a contraction of 11 cm3/mol was determined.

Picosecond infrared studies of the dynamics of the photosynthetic reaction center

The changes in the vibrational transitions of the protein and redox cofactors of the photosynthetic reaction center were examined by picosecond infrared spectroscopy. The spectra in the vibrational mid-infrared region (1800-1550 cm-1) of hydrated and partially dehydrated reaction centers were investigated from 50 ps to 4 ns after photoinitiation of the electron transfer. Features in the infrared difference spectra were identified with both protein and redox cofactor vibrational modes and correlated with electron transfer events whose kinetics were measured in the infrared and visible regions. The observed protein response is confined to a few amide I transitions (1644 cm-1, 1661 cm-1, 1665 cm-1) and carboxylic residues (1727 cm-1). About 85% of the observed signal corresponded to alterations in the cofactor-associated ester and keto carbonyls. The amide I and carboxylic transitions appeared prior to 50 ps, suggesting that the primary electron transfer event is coupled with a specific piece of the protein backbone and to glutamic or aspartic residues nearby the special pair. Infrared absorption changes accompanying bacteriochlorophyll-dimer cation formation dominated the signal at all times investigated. Infrared spectral changes observed in hydrated and partially dehydrated reaction centers were distinctly different; a band at 1665 cm-1 with a spectral width of 6 cm-1 in the hydrated protein, corresponding to a protein amide I bleach, was not present in the dehydrated film. These differences are discussed in terms of the markedly different electron transfer kinetics observed in the presence of water.

Picosecond dynamics of bacteriorhodopsin, probed by time-resolved infrared spectroscopy

The photoinduced reaction cycle of bacteriorhodopsin (BR) has been studied by means of a recently developed picosecond infrared spectroscopic method at ambient temperature. BR - K difference spectra between 1560 and 1700 cm-1 have been recorded at delay times from 100 ps to 14 ns. The spectrum remains unchanged during this period. The negative difference OD band at 1660 cm-1 indicates the peptide backbone responds within 50 ps. A survey in the region of carboxylic side chain absorption around 1740 cm-1 reveals that perturbations of those groups, present in low-temperature FTIR spectra, are not observable within 10 ns, suggesting a slow conformational change.

FTIR difference spectroscopy of bacteriorhodopsin: toward a molecular model

Bacteriorhodopsin (bR) is a light-driven proton pump whose function includes two key membrane-based processes, active transport and energy transduction. Despite extensive research on bR and other membrane proteins, these processes are not fully understood on the molecular level. In the past ten years, the introduction of Fourier transform infrared (FTIR) difference spectroscopy along with related techniques including time-resolved FTIR difference spectroscopy, polarized FTIR, and attenuated total reflection FTIR has provided a new approach for studying these processes. A key step has been the utilization of site-directed mutagenesis to assign bands in the FTIR difference spectrum to the vibrations of individual amino acid residues. On this basis, detailed information has been obtained about structural changes involving the retinylidene chromophore and protein during the bR photocycle. This includes a determination of the protonation state of the four membrane-embedded Asp residues, identification of specific structurally active amino acid residues, and the detection of protein secondary structural changes. This information is being used to develop an increasingly detailed picture of the bR proton pump mechanism.