Ultrafast Dynamics and Vibrational Relaxation in Six-Coordinate Heme Proteins Revealed by Femtosecond Stimulated Raman Spectroscopy

Neuroglobin Facilitates Neuronal Oxygenation through Tropic Migration under Hypoxia or Anemia in Rat: How Does the Brain Breathe?

The discovery of neuroglobin (Ngb), a brain- or neuron-specific member of the hemoglobin family, has revolutionized our understanding of brain oxygen metabolism. Currently, how Ngb plays such a role remains far from clear. Here, we report a novel mechanism by which Ngb might facilitate neuronal oxygenation upon hypoxia or anemia. We found that Ngb was present in, co-localized to, and co-migrated with mitochondria in the cell body and neurites of neurons. Hypoxia induced a sudden and prominent migration of Ngb towards the cytoplasmic membrane (CM) or cell surface in living neurons, and this was accompanied by the mitochondria. In vivo, hypotonic and anemic hypoxia induced a reversible Ngb migration toward the CM in cerebral cortical neurons in rat brains but did not alter the expression level of Ngb or its cytoplasm/mitochondria ratio. Knock-down of Ngb by RNA interference significantly diminished respiratory succinate dehydrogenase (SDH) and ATPase activity in neuronal N2a cells. Over-expression of Ngb enhanced SDH activity in N2a cells upon hypoxia. Mutation of Ngb at its oxygen-binding site (His64) significantly increased SDH activity and reduced ATPase activity in N2a cells. Taken together, Ngb was physically and functionally linked to mitochondria. In response to an insufficient oxygen supply, Ngb migrated towards the source of oxygen to facilitate neuronal oxygenation. This novel mechanism of neuronal respiration provides new insights into the understanding and treatment of neurological diseases such as stroke and Alzheimer's disease and diseases that cause hypoxia in the brain such as anemia.

Photogrammetry of Ultrafast Excited-State Intramolecular Proton Transfer Pathways in the Fungal Pigment Draconin Red

Proton transfer processes of organic molecules are key to charge transport and photoprotection in biological systems. Among them, excited-state intramolecular proton transfer (ESIPT) reactions are characterized by quick and efficient charge transfer within a molecule, resulting in ultrafast proton motions. The ESIPT-facilitated interconversion between two tautomers (PS and PA) comprising the tree fungal pigment Draconin Red in solution was investigated using a combination of targeted femtosecond transient absorption (fs-TA) and excited-state femtosecond stimulated Raman spectroscopy (ES-FSRS) measurements. Transient intensity (population and polarizability) and frequency (structural and cooling) dynamics of -COH rocking and -C=C, -C=O stretching modes following directed stimulation of each tautomer elucidate the excitation-dependent relaxation pathways, particularly the bidirectional ESIPT progression out of the Franck-Condon region to the lower-lying excited state, of the intrinsically heterogeneous chromophore in dichloromethane solvent. A characteristic overall excited-state PS-to-PA transition on the picosecond timescale leads to a unique "W"-shaped excited-state Raman intensity pattern due to dynamic resonance enhancement with the Raman pump-probe pulse pair. The ability to utilize quantum mechanics calculations in conjunction with steady-state electronic absorption and emission spectra to induce disparate excited-state populations in an inhomogeneous mixture of similar tautomers has broad implications for the modeling of potential energy surfaces and delineation of reaction mechanisms in naturally occurring chromophores. Such fundamental insights afforded by in-depth analysis of ultrafast spectroscopic datasets are also beneficial for future development of sustainable materials and optoelectronics.

Sub-Millisecond Photoinduced Dynamics of Free and EL222-Bound FMN by Stimulated Raman and Visible Absorption Spectroscopies

Time-resolved femtosecond-stimulated Raman spectroscopy (FSRS) provides valuable information on the structural dynamics of biomolecules. However, FSRS has been applied mainly up to the nanoseconds regime and above 700 cm^-1, which covers only part of the spectrum of biologically relevant time scales and Raman shifts. Here we report on a broadband (~200-2200 cm^-1) dual transient visible absorption (visTA)/FSRS set-up that can accommodate time delays from a few femtoseconds to several hundreds of microseconds after illumination with an actinic pump. The extended time scale and wavenumber range allowed us to monitor the complete excited-state dynamics of the biological chromophore flavin mononucleotide (FMN), both free in solution and embedded in two variants of the bacterial light-oxygen-voltage (LOV) photoreceptor EL222. The observed lifetimes and intermediate states (singlet, triplet, and adduct) are in agreement with previous time-resolved infrared spectroscopy experiments. Importantly, we found evidence for additional dynamical events, particularly upon analysis of the low-frequency Raman region below 1000 cm^-1. We show that fs-to-sub-ms visTA/FSRS with a broad wavenumber range is a useful tool to characterize short-lived conformationally excited states in flavoproteins and potentially other light-responsive proteins.

Ultrafast Spectroscopies of Nitrophenols and Nitrophenolates in Solution: From Electronic Dynamics and Vibrational Structures to Photochemical and Environmental Implications

Nitrophenols are a group of small organic molecules with significant environmental implications from the atmosphere to waterways. In this work, we investigate a series of nitrophenols and nitrophenolates, with the contrasting ortho-, meta-, and para-substituted nitro group to the phenolic hydroxy or phenolate oxygen site (2/3/4NP or NP^-), implementing a suite of steady-state and time-resolved spectroscopic techniques that include UV/Visible spectroscopy, femtosecond transient absorption (fs-TA) spectroscopy with probe-dependent and global analysis, and femtosecond stimulated Raman spectroscopy (FSRS), aided by quantum calculations. The excitation-dependent (400 and 267 nm) electronic dynamics in water and methanol, for six protonated or deprotonated nitrophenol molecules (three regioisomers in each set), enable a systematic investigation of the excited-state dynamics of these functional "nanomachines" that can undergo nitro-group twisting (as a rotor), excited-state intramolecular or intermolecular proton transfer (donor-acceptor, ESIPT, or ESPT), solvation, and cooling (chromophore) events on molecular timescales. In particular, the meta-substituted compound 3NP or 3NP^- exhibits the strongest charge-transfer character with FSRS signatures (e.g., C-N peak frequency), and thus, does not favor nitroaromatic twist in the excited state, while the ortho-substituted compound 2NP can undergo ESIPT in water and likely generate nitrous acid (HONO) after 267 nm excitation. The delineated mechanistic insights into the nitro-substituent-location-, protonation-, solvent-, and excitation-wavelength-dependent effects on nitrophenols, in conjunction with the ultraviolet-light-induced degradation of 2NP in water, substantiates an appealing discovery loop to characterize and engineer functional molecules for environmental applications.

Absolute excited state molecular geometries revealed by resonance Raman signals

Ultrafast reactions activated by light absorption are governed by multidimensional excited-state (ES) potential energy surfaces (PESs), which describe how the molecular potential varies with the nuclear coordinates. ES PESs ad-hoc displaced with respect to the ground state can drive subtle structural rearrangements, accompanying molecular biological activity and regulating physical/chemical properties. Such displacements are encoded in the Franck-Condon overlap integrals, which in turn determine the resonant Raman response. Conventional spectroscopic approaches only access their absolute value, and hence cannot determine the sense of ES displacements. Here, we introduce a two-color broadband impulsive Raman experimental scheme, to directly measure complex Raman excitation profiles along desired normal modes. The key to achieve this task is in the signal linear dependence on the Frank-Condon overlaps, brought about by non-degenerate resonant probe and off-resonant pump pulses, which ultimately enables time-domain sensitivity to the phase of the stimulated vibrational coherences. Our results provide the tool to determine the magnitude and the sensed direction of ES displacements, unambiguously relating them to the ground state eigenvectors reference frame.

Surface-enhanced Raman spectroscopic analysis of the centrifugally filtered blood serum samples of the hepatitis C patients

BACKGROUND

Previously Raman spectroscopy technique is a use to analyze non-invasive disease related to body fluids.

OBJECTIVES

For the qualitative and quantitative analysis of HCV serum samples surface-enhanced Raman spectroscopy (SERS) based method is developed.

METHOD

Surface-enhanced Raman spectroscopy (SERS) technique is employed for analysis of filtrate portions of blood serum samples of hepatitis C virus (HCV) infected patients and healthy ones by using 50 kDa centrifugal filter device. The filtrate portions of the serum obtained in this way contain proteins smaller than 50 kDa and removal of bigger size protein which allows to acquire SERS spectral features of smaller proteins more effectively which are probably associated with Hepatitis C infection. Moreover, SERS spectral features of the filtrates of different level of viral load including low, medium and high viral loads are compared with SERS spectral features of the filtrate portions of healthy/control serum samples. SERS spectral data sets of different samples are further analyzed by using multivariate data analysis techniques such as principal component analysis (PCA) and partial least square regression (PLSR). Some SERS spectral features are solely observed in the filtrate portions of the serum samples of hepatitis C and their intensities are increased as the level of viral load increases and might be used for HCV diagnosis.

RESULTS

PCA was found helpful for differentiation of SERS spectral data sets of filtrate portions of the serum samples of hepatitis C and healthy persons. The PLSR model helped for the quantification of viral loads in the unknown serum samples with 99 % accuracy.

Exploring the folding energy landscapes of heme proteins using a hybrid AWSEM-heme model

Heme is an active center in many proteins. Here we explore computationally the role of heme in protein folding and protein structure. We model heme proteins using a hybrid model employing the AWSEM Hamiltonian, a coarse-grained forcefield for the protein chain along with AMBER, an all-atom forcefield for the heme. We carefully designed transferable force fields that model the interactions between the protein and the heme. The types of protein-ligand interactions in the hybrid model include thioester covalent bonds, coordinated covalent bonds, hydrogen bonds, and electrostatics. We explore the influence of different types of hemes (heme b and heme c) on folding and structure prediction. Including both types of heme improves the quality of protein structure predictions. The free energy landscape shows that both types of heme can act as nucleation sites for protein folding and stabilize the protein folded state. In binding the heme, coordinated covalent bonds and thioester covalent bonds for heme c drive the heme toward the native pocket. The electrostatics also facilitates the search for the binding site.

Excited-State Energy Surfaces in Molecules Revealed by Impulsive Stimulated Raman Excitation Profiles

Photophysical and photochemical processes are ruled by the interplay between transient vibrational and electronic degrees of freedom, which are ultimately determined by the multidimensional potential energy surfaces (PESs). Differences between ground and excited PESs are encoded in the relative intensities of resonant Raman bands, but they are experimentally challenging to access, requiring measurements at multiple wavelengths under identical conditions. Herein, we perform a two-color impulsive vibrational scattering experiment to launch nuclear wavepacket motions by an impulsive pump and record their coupling with a targeted excited-state potential by resonant Raman processes with a delayed probe, generating in a single measurement background-free vibrational spectra across the entire sample absorption. Building on the interference between the multiple pathways resonant with the excited-state manifold that generate the Raman signal, we show how to experimentally tune their relative phase by varying the probe chirp, decoding nuclear displacements along different normal modes and revealing the multidimensional PESs. Our results are validated against time-dependent density functional theory.

Surface enhanced Raman spectroscopy of RNA samples extracted from blood of hepatitis C patients for quantification of viral loads

BACKGROUND

Raman spectroscopy is a promising technique to analyze the body fluids for the purpose of non-invasive disease diagnosis.

OBJECTIVES

To develop a surface-enhanced Raman spectroscopy (SERS) based method for qualitative and quantitative analysis of HCV from blood samples.

METHODS

SERS was employed to characterize the Hepatitis C viral RNA extracted from different blood samples of hepatitis C virus (HCV) infected patients with predetermined viral loads in comparison with total RNA of healthy individuals. The SERS measurements were performed on 27 extracted RNA samples including low viral loads, medium viral loads, high viral loads and healthy/negative viral load samples. For this purpose, silver nanoparticles (Ag NPs) were used as SERS substrates. Furthermore, multivariate data analysis technique, Principal Component Analysis (PCA) and Partial Least Square Regression (PLSR) were also performed on SERS spectral data.

RESULTS

The SERS spectral features due to biochemical changes in the extracted RNA samples associated with the increasing viral loads were established which could be employed for HCV diagnostic purpose. PCA was found helpful for the differentiation between Raman spectral data of RNA extracted from hepatitis infected and healthy blood samples. PLSR model is established for the determination of viral loads in HCV positive RNA samples with 99 % accuracy.

CONCLUSION

SERS can be employed for qualitative and quantitative analysis of HCV from blood samples.

Primary Electronic and Vibrational Dynamics of Cytochrome c Observed by Sub-10 fs NUV Laser Pulses

The primary reaction mechanism of cytochrome c (Cyt c) was elucidated for two redox forms of ferric (oxidized) and ferrous (reduced) Cyt c by measuring their transient absorption (TA) spectra using a homemade sub-10 fs broadband NUV laser pulses system. The TA traces measured in the broad probe wavelength region were analyzed by the global analysis method to study the electronic dynamics. The difference of relaxation dynamics dependent on the excitation bandwidth enabled us to elucidate that the 2.5 ps component in ferrous Cyt c can be assigned to intramolecular vibration energy redistribution and not to vibrational cooling, which was not clear until this work. The temporal resolution of 10 fs observes TA signal modulation caused by the molecular vibration in the time domain, which can be used to calculate the instantaneous frequency of the molecular vibration mode. The observed vibrational dynamics has visualized that the heme structure changes in 0.8 ps for ferric Cyt c and in >1.0 ps for ferrous Cyt c. These estimated lifetimes of vibrational dynamics reflect vibrational relaxation in the ground state of ferric Cyt c and electronic transition from the S2 state to the S1 state in ferrous Cyt c, respectively.

Accessing Excited State Molecular Vibrations by Femtosecond Stimulated Raman Spectroscopy

Excited state vibrations are crucial for determining the photophysical and photochemical properties of molecular compounds. Stimulated Raman scattering can coherently stimulate and probe molecular vibrations with optical pulses, but it is generally restricted to ground state properties. Working under resonance conditions enables cross-section enhancement and selective excitation to a targeted electronic level but is hampered by an increased signal complexity due to the presence of overlapping spectral contributions. Here, we show how detailed information about ground and excited state vibrations can be disentangled by exploiting the relative time delay between Raman and probe pulses to control the excited state population, combined with a diagrammatic formalism to dissect the pathways concurring with the signal generation. The proposed method is then exploited to elucidate the vibrational properties of the ground and excited electronic states in the paradigmatic case of cresyl violet. We anticipate that the presented approach holds the potential for selective mapping of the reaction coordinates pertaining to transient electronic stages implied in photoactive compounds.