Conformation of bacteriochlorophyll molecules in photosynthetic proteins from purple bacteria.

Fourier transform near-infrared resonance Raman spectroscopy can be used to obtain information on the bacteriochlorophyll a (BChl a) molecules responsible for the redmost absorption band in photosynthetic complexes from purple bacteria. This technique is able to distinguish distortions of the bacteriochlorin macrocycle as small as 0.02 A, and a systematic analysis of those vibrational modes sensitive to BChl a macrocycle conformational changes was recently published [N?veke et al. (1997) J. Raman Spectrosc. 28, 599-604]. The conformation of the two BChl a molecules constituting the primary electron donor in bacterial reaction centers, and of the 850 and 880 nm-absorbing BChl a molecules in the light-harvesting LH2 and LH1 proteins, has been investigated using this technique. From this study it can be concluded that both BChl a molecules of the primary electron donor in the photochemical reaction center are in a conformation close to the relaxed conformation observed for pentacoordinate BChl a in diethyl ether. In contrast, the BChl a molecules responsible for the long-wavelength absorption transition in both LH1 and LH2 antenna complexes are considerably distorted, and furthermore there are noticeable differences between the conformations of the BChl molecules bound to the alpha- and beta-apoproteins. The molecular conformations of the pigments are very similar in all the antenna complexes investigated.     

Investigation of higher order structures of proteins by ultraviolet resonance Raman spectroscopy.

Progress in laser technology and light detection devices have enabled us to explore protein structures and their dynamics by using time-resolved resonance Raman spectroscopy. It is in the last decade that Raman spectra of proteins excited at 200-240 nm have brought about rich structural information. The technological developments in deep UV resonance Raman spectroscopy are reviewed first, and the unique information on proteins obtainable from such spectra are summarized. As an application of this technique to investigations of the higher order structures of proteins, studies on the quaternary structure transition of haemoglobin are described.     

New Insight into Erythrocyte through In Vivo Surface-Enhanced Raman Spectroscopy

The article presents a noninvasive approach to the study of erythrocyte properties by means of a comparative analysis of signals obtained by surface-enhanced Raman spectroscopy (SERS) and resonance Raman spectroscopy (RS). We report step-by-step the procedure for preparing experimental samples containing erythrocytes in their normal physiological environment in a mixture of colloid solution with silver nanoparticles and the procedure for the optimization of SERS conditions to achieve high signal enhancement without affecting the properties of living erythrocytes. By means of three independent techniques, we demonstrate that under the proposed conditions a colloid solution of silver nanoparticles does not affect the properties of erythrocytes. For the first time to our knowledge, we describe how to use the SERS-RS approach to study two populations of hemoglobin molecules inside an intact living erythrocyte: submembrane and cytosolic hemoglobin (Hb_sm and Hb_c). We show that the conformation of Hb_sm differs from the conformation of Hb_c. This finding has an important application, as the comparative study of Hb_sm and Hb_c could be successfully used in biomedical research and diagnostic tests.     

Resonance Raman and EPR of nitrosyl human hemoglobin and chains, carp hemoglobin, and model compounds. Implications for the nitrosyl heme coordination state.

We report the joint resonance Raman (RR) and electron paramagnetic resonance (epr) study of five- and six-coordinate nitrosyl heme model compounds and of the titled nitrosyl hemoproteins. Both epr and RR spectra fall into two types which, in the models, correspond to five- and six-coordinate nitrosyl hemes. However, neither RR nor epr spectroscopy is highly sensitive to the nature of the bond between a nitrosyl heme and a coordinated nitrogenous base, nor do the results of one technique uniformly correlate with those of the other. It is not possible to use epr spectroscopy as a test for the coordination state of a nitrosyl heme. The position of the highest frequency (depolarized) RR band possibly provides such a test. Any breaking of the very weak bond between nitrosyl heme and proximal histidine in T state human HbNO is more a consequence of tertiary structural features unique to the human alphaNO chains than it is of properties of the T quaternary conformation.     

Understanding amyloid fibril formation using protein fragments: structural investigations via vibrational spectroscopy and solid-state NMR

It is well established that amyloid proteins play a primary role in neurodegenerative diseases. Alzheimer’s, Parkinson’s, type II diabetes, and Creutzfeldt-Jakob’s diseases are part of a wider family encompassing more than 50 human pathologies related to aggregation of proteins. Although this field of research is thoroughly investigated, several aspects of fibrillization remain misunderstood, which in turn slows down, or even impedes, advances in treating and curing amyloidoses. To solve this problem, several research groups have chosen to focus on short fragments of amyloid proteins, sequences that have been found to be of great importance for the amyloid formation process. Studying short peptides allows bypassing the complexity of working with full-length proteins and may provide important information relative to critical segments of amyloid proteins. To this end, efficient biophysical tools are required. In this review, we focus on two essential types of spectroscopic techniques, i.e., vibrational spectroscopy and its derivatives (conventional Raman scattering, deep-UV resonance Raman (DUVRR), Raman optical activity (ROA), surface-enhanced Raman spectroscopy (SERS), tip-enhanced Raman spectroscopy (TERS), infrared (IR) absorption spectroscopy, vibrational circular dichroism (VCD)) and solid-state nuclear magnetic resonance (ssNMR). These techniques revealed powerful to provide a better atomic and molecular comprehension of the amyloidogenic process and fibril structure. This review aims at underlining the information that these techniques can provide and at highlighting their strengths and weaknesses when studying amyloid fragments. Meaningful examples from the literature are provided for each technique, and their complementarity is stressed for the kinetic and structural characterization of amyloid fibril formation.     

Pigment binding site properties of two photosystem II antenna proteins. A resonance raman investigation

Two light-harvesting proteins associated with photosystem II of higher plants, namely the major antenna complex LHCIIb and the minor Lhcb4 protein (CP29), have been investigated by resonance Raman spectroscopy. One of the two chlorophylls b and up to five of the six chlorophylls a present in Lhcb4 are shown to adopt similar binding conformations to the (presumably) corresponding molecules in LHCIIb, whereas at least two chlorophylls in the former protein assume unique conformations relative to the bulk complex. The overall conformation of bound xanthophyll molecules is identical in the two antenna proteins, although some small differences are apparent. The pigment binding properties of these two LHCs are discussed, with particular reference to possible structural motifs within this extended family of proteins.     

IR and Raman spectroscopy in the study of carotenoids of <Emphasis Type="Italic">Cladophora rivularis</Emphasis> algae

Using Raman and infrared spectroscopy it has been found that during the normal life of algae (pH changes from 8.0 to 9.0) the content of carotenoids increases and the molecules change their conformation: the contribution of–C=C–bonds of the polyene chain of a carotenoid molecule (Raman spectroscopy) is reduced and the contribution of methyl groups (～2940 cm^–1) and aromatic C–H-plane deformation vibrations (band at 1050 cm^–1) of carotenoid molecules (infrared spectroscopy) decreases as well. It is the opinion of the authors that a change in the extracellular pH within the normal range has no influence on the content of chlorophyll a and b, but tends to increase the content and alter the conformation or structure of carotenoid molecules.     

Introduction to Raman spectrometry]

The frequency shift observed when light is scattered by molecules is called Raman effect. Raman spectroscopy like infrared spectroscopy is a method of studying molecular vibrations. The two methods are complementary, they both give much informations about the structure of molecules and crystals, the nature of chemical bonds and intermolecular interactions. Infrared absorption is allowed if the vibration is accompanied by a variation of electric dipole moment, however Raman scattering will only be observed if a variation of molecular polarizability appears during the vibration. Symetry properties of molecules of crystals lead to the determination of the number of normal vibrational modes and their Raman or infrared activity. The discovery of Laser light source has permitted a great development of Raman instrumentation. Raman spectrometers can easily record the whole spectrum of molecular vibrations (0-4000 cm-1) of samples in solid, liquid or gazeous state. Very small quantities of material are required (several milligrams). Aqueous solutions are easily investigated. Owing to the easy exploration of the low frequency range by modern spectrometers, new areas are opened in the study of the solid state and polymeric chains. Resonance Raman effect allows the spectra of very dilute solutions to be obtained. With the development of rapid scanning systems and electro-optical spectrometers, study of transients species is now possible. Among the physical analysis methods, Raman spectroscopy is now more and more used, and this technic has already been successfully used in numerous biological and biochemical problems.     

Probing the carotenoid content of intact Cyclotella cells by resonance Raman spectroscopy

In this study, we demonstrate the selective in vivo detection of diadinoxanthin (DD) and diatoxanthin (DT) in intact Cyclotella cells using resonance Raman spectroscopy. In these cells, we were able to assess both the content of DD and DT carotenoids relative to chlorophyll and their conformation. In addition, the sensitivity and selectivity of the technique allow us to discriminate between different pools of DD on a structural basis, and to follow their fate as a function of the illumination conditions. We report that the additional DD observed when cells are grown in high-light conditions adopts a more twisted conformation than the lower levels of DD present when the cells are grown in low-light (LL) conditions. Thus, we conclude that this pool of DD is more tightly bound to a protein-binding site, which must differ from the one occupied by the DD present in LL conditions.     

Reflection-mode TERS on Insulin Amyloid Fibrils with Top-Visual AFM Probes

Tip-enhanced Raman spectroscopy provides chemical information while raster scanning samples with topographical detail. The coupling of atomic force microscopy and Raman spectroscopy in top illumination optical setup is a powerful configuration to resolve nanometer structures while collecting reflection mode backscattered signal. Here, we theoretically calculate the field enhancement generated by TER spectroscopy with top illumination geometry and we apply the technique to the characterization of insulin amyloid fibrils. We experimentally confirm that this technique is able to enhance the Raman signal of the polypeptide chain by a factor of 10⁵, thus revealing details down to few molecules resolution.     

Characterization of bacterial spore germination using phase-contrast and fluorescence microscopy, Raman spectroscopy and optical tweezers

This protocol describes a method combining phase-contrast and fluorescence microscopy, Raman spectroscopy and optical tweezers to characterize the germination of single bacterial spores. The characterization consists of the following steps: (i) loading heat-activated dormant spores into a temperature-controlled microscope sample holder containing a germinant solution plus a nucleic acid stain; (ii) capturing a single spore with optical tweezers; (iii) simultaneously measuring phase-contrast images, Raman spectra and fluorescence images of the optically captured spore at 2- to 10-s intervals; and (iv) analyzing the acquired data for the loss of spore refractility, changes in spore-specific molecules (in particular, dipicolinic acid) and uptake of the nucleic acid stain. This information leads to precise correlations between various germination events, and takes 1-2 h to complete. The method can also be adapted to use multi-trap Raman spectroscopy or phase-contrast microscopy of spores adhered on a cover slip to simultaneously obtain germination parameters for multiple individual spores.     

Carotenoid stoichiometry in the LH2 crystal: no spectral evidence for the presence of the second molecule in the alpha/beta-apoprotein dimer

In this work we have investigated the carotenoid-protein interactions in LH2 complexes of Rhodopseudomonas acidophila both in "free in solution" mixed-micelles and in three-dimensional crystals by Raman spectroscopy in resonance with the carotenoid (Car) molecules. We show that the Car molecules when bound to their binding pockets show no significant differences when the complexes are "free in solution" or packed in crystalline arrays. Furthermore, there is no significant wavelength dependence in the Raman spectrum of the Car molecules of LH2. This indicates that there is only one Car configuration in LH2 and thus only one molecule per alpha/beta-heterodimer.     

激光拉曼光谱技术在生物分子DNA研究中的应用和进展

激光技术的兴起使拉曼光谱成为激光分析中最活跃的研究领域之一,已被广泛地用于物质成分的分析和分子结构的鉴定。本文综述了拉曼技术在DNA研究中近年来的最新进展,包括：DNA的常规拉曼光谱分析;DNA的激光共振拉曼光谱分析;DNA在金属表面或电极上吸附行为的表面增强拉曼光谱研究;DNA的傅立叶变换拉曼光谱研究等。并对拉曼光谱技术在DNA等生物大分子领域中的研究前景做了进一步的展望。     

Nuclear resonance vibrational spectroscopy--NRVS

The recent, synchrotron-based vibrational technique nuclear resonance vibrational spectroscopy (NRVS) is introduced. The method can be used for a number of M?ssbauer active isotopes including 57Fe, which has yielded most of the results to date. The NRVS experiment can be thought of as M?ssbauer spectroscopy with vibrational sidebands. Importantly, the NRVS experiment provides the complete set of bands corresponding to modes that involve motion of the iron atom. The method has a selectivity reminiscent of that of resonance Raman spectroscopy, but with the significant advantage that NRVS is not subject to the optical selection rules of Raman or infrared spectroscopy. Indeed, NRVS provides the ultimate limit in selectivity because only the vibrational dynamics of the probe nucleus contribute to the observed signal. All iron-ligand modes will be observed, including many that had not been previously observed. For hemes, these include in-plane iron vibrations that have not yet been reported by resonance Raman studies and the iron-imidazole stretch that has not been identified in six-coordinate porphyrins. Other modes that can be investigated include that of heme doming that is expected to be a low-frequency mode. The experimental setup at a beam line and sample requirements for iron-based derivatives are presented. Both powder and polarized single-crystal measurements can be made. The general features of data extraction and analysis are given. Data for heme and heme proteins are given. Examples of assignment of spectra for nitrosyl and carbonyl derivatives are given. These data demonstrate the importance of peripheral substituents on the vibrational spectrum of heme derivatives. Delocalization of modes appears to be common. Although this technique has only been available for a relatively short time, this early progress report indicates that NRVS has significant potential for probing the dynamics of Fe-containing molecules of biological interest.     

Formation of stable polypeptide monolayers at interfaces: controlling molecular conformation and orientation.

The molecular self-organization and structural properties of peptide assemblies at different interfaces, using either amphipathic or hydrophobic polypeptide helices, is described. The two peptides under investigation form stable monolayers on the water surface under the conservation of their molecular conformation, as studied by circular dichroism and polarization-modulation Fourier transform infrared (FTIR) spectroscopy. Using surface plasmon resonance and reflection-absorption FTIR, we show that such molecular layers can be transferred unaltered to solid substrates. Most importantly, the molecular orientation of the hydrophobic helices on solid supports such as gold can be controlled by choosing a particular procedure for the layer formation. The helices were oriented parallel to the interface in Langmuir-Blodgett monolayers, and perpendicular to the interface in self-assembled monolayers. Our reflection-absorption FTIR measurements have delivered for the first time direct experimental evidence for the molecular conformation and orientation of pure peptide monolayers. Suitable reference spectra of polypeptides with defined conformation and orientation are necessary to use this technique for the determination of the molecular orientation of peptides in monomolecular films. We have solved the problem for alpha-helical polypeptides by using bacteriorhodopsin as a reference in combination with synthetic alpha-helices of defined interfacial orientation. The present study shows the possibility of constructing immobilized peptide monolayers with predefined macroscopic properties and molecular structure by choosing the proper polypeptide amino acid sequence, the technique used for layer formation, and the supporting surface properties.     

Analysis of the vibrational spectra of new OH-containing E-4-arylmethylene-3-isochromanones and 3-arylcoumarins

A combined experimental and theoretical approach is presented to structural characterization of fairly large, newly synthesized organic molecules in order to enhance the effectiveness of their instrumental analysis by vibrational spectroscopy. The method consists of measurement of FT-IR and Raman spectra of the reaction products and subsequent ab initio or DFT quantum mechanical calculations (prediction) of the vibrational spectra for any anticipated structural varieties of the synthesized molecules. Comparison of the measured and computed frequencies as well as the observed and simulated spectra is performed to resolve any uncertainties in identifying the reaction products. Vibrational frequency and normal mode calculations based on scaled quantum mechanical (SQM) force fields performed at the DFT/B3LYP/6-31G* level of theory are demonstrated to provide a wealth of information that have been used in this work to ascertain the molecular structure, probable conformation and H-bond properties of three new isochromanone or coumarin derivatives, namely: 3-([2'-hydroxymethyl]-phenyl)-coumarin (1), E-4-(3'-hydroxyphenylmethylene)-3-isochromanone (2), and 2-[(2'-hydroxymethyl)phenyl]-3H-naphto[2,1-b]pyran-3-one (3).     

Vibrational spectroscopic approach to the study of acetylcholine and related compounds

The present review reports the coordinated application of three spectroscopic methods (Raman, infrared(IR) and inelastic electron tunneling spectroscopy (IETS)) in the study of the conformation of Ach and some analogues (beta-MeAch, Mu and Nic) in solid state, aqueous solution and in interaction with a surface. Useful correlated information is obtained by Raman and IR spectroscopies on the conformational possibilities of these molecules in transition from solid state to aqueous solution. With this information in hand as well as on the basis of Raman and IR study of the nonenzymatic hydrolysis of Ach, the first detailed experimental investigation of the interaction of Ach and beta-MeAch adsorbed on a surface (A1203) is realised by the IETS method. The results are used to discuss an interaction analogous to that of Ach with receptor and another one analogous to that of Ach and AchE.     

Vibrational Raman optical activity of proteins,nucleic acids,and viruses

Due to its sensitivity to chirality, Raman optical activity (ROA), which may be measured as a small difference in vibrational Raman scattering from chiral molecules in right- and left-circularly polarized incident light, is a powerful probe of biomolecular structure in solution. Protein ROA spectra provide information on the secondary and tertiary structures of the polypeptide backbone, hydration, side-chain conformation, and structural elements present in denatured states. Nucleic acid ROA spectra yield information on the sugar ring conformation, the base stacking arrangement, and the mutual orientation of the sugar and base rings around the C-N glycosidic linkage. ROA is able to simultaneously probe the structures of both the protein and the nucleic acid components of intact viruses. This article gives a brief account of the theory and measurement of ROA and presents the ROA spectra of a selection of proteins, nucleic acids, and viruses which illustrate the applications of ROA spectroscopy in biomolecular research.     

Functional and spectroscopic characterization of half-liganded iron-zinc hybrid hemoglobin: evidence for conformational plasticity within the T state

Functionally distinct conformations of HbA (human adult hemoglobin) were probed using deoxy and diliganded derivatives of symmetric Fe-Zn hybrids of HbA. To expand the range of accessible structures, different environments were utilized including solution, sol-gel encapsulation, and crystals. Further structural and functional modulation was achieved by the addition of allosteric effectors. Functional characterization included oxygen affinity measurements, CO combination rates, and geminate and bimolecular CO recombination, after photodissociation. The conformational properties were studied using visible resonance Raman spectroscopy as a probe of local tertiary structure at the iron-containing hemes and UV resonance Raman spectroscopy as a probe of elements of the globin known to be sensitive to quaternary structure. The combined results show a pattern in which there is a progression of conformational and functional properties that are consistent with a picture in which the T quaternary structure can accommodate a range of tertiary conformations (plasticity). At one end of the distribution is the equilibrium deoxy T state conformation that has the lowest ligand reactivity. At the other end of the distribution are T state conformations with higher ligand reactivity that exhibit "loosened" T state constraints within the globin including the alpha(1)beta(2) interface and reduced proximal strain at the heme.