bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamics of a globular protein and its hydration water studied by neutron scattering and MD simulations
Authors: Chen Sow-Hsin , Lagi Marco , Chu Xiang-qiang , Zhang Yang , Kim Chansoo , Faraone Antonio , Fratini Emiliano , Baglioni Piero
Published: April 2012

This review article describes our neutron scattering experiments made in the past four years for the understanding of the single-particle (hydrogen atom) dynamics of a protein and its hydration water and the strong coupling between them. We found that the key to this strong coupling is the existence of a fragile-to-strong dynamic crossover (FSC) phenomenon occurring at aroundTL= 225±5 K in the hydration water. On lowering of the temperature toward FSC, the structure of hydration water makes a transition from predominantly the high density form (HDL), a more fluid state, to predominantly the low density form (LDL), a less fluid state, derived from the existence of a liquid–liquid critical point at an elevated pressure. We show experimentally that this sudden switch in the mobility of hydration water on Lysozyme, B-DNA and RNA triggers the dynamic transition, at a temperatureTD= 220 K, for these biopolymers. In the glassy state, belowTD, the biopolymers lose their vital conformational flexibility resulting in a substantial diminishing of their biological functions. We also performed molecular dynamics (MD) simulations on a realistic model of hydrated lysozyme powder, which confirms the existence of the FSC and the hydration level dependence of the FSC temperature. Furthermore, we show a striking feature in the short time relaxation (β-relaxation) of protein dynamics, which is the logarithmic decay spanning 3 decades (from ps to ns). The long timeα-relaxation shows instead a diffusive behavior, which supports the liquid-like motions of protein constituents. We then discuss our recent high-resolution X-ray inelastic scattering studies of globular proteins, Lysozyme and Bovine Serum Albumin. We were able to measure the dispersion relations of collective, intra-protein phonon-like excitations in these proteins for the first time. We found that the phonon energies show a marked softening and at the same time their population increases substantially in a certain wave vector range when temperature crosses over theTD. Thus the increase of biological activities aboveTDhas positive correlation with activation of slower and large amplitude collective motions of a protein.
Multivariate statistical evaluation of bone site and sex as parameters for the Fourier transform infrared spectroscopic study of normal bone
Authors: Kourkoumelis Nikolaos , Tzaphlidou Margaret
Published: April 2012

Fourier transform infrared spectroscopy combined with multivariate analysis was performed on a series of bone samples in order to investigate possible differences in the molecular fingerprint based on classification either between different sex and bone sites. Cortical femoral, tibia and ulna samples from five male and five female normal Wistar rats were analysed. PCA analysis classified successfully sex-related spectra since the first three principal components explained 95% of the total variance. This was not the case for bone site-related spectra. In all cases, an important aspect is the ionic exchange of phosphate and carbonate ions.
Dynamic properties of a reconstituted myelin sheath
Authors: Knoll W. , Natali F. , Peters J. , Nanekar R. , Wang C. , Kursula P.
Published: April 2012

Myelin is a multilamellar membrane which, wrapping the nerve axons, increases the efficiency of nervous signal transmission. Indeed, the molecular components of the myelin sheath interact tightly with each other and molecules on the axonal surface to drive myelination, to keep both myelin and the axon intact, and to transduce signals from myelin to the axon and vice versa. Myelin is strongly affected in human demyelinating diseases in both the central and peripheral nervous system (CNS and PNS, respectively). Despite the presence of a well-defined set of myelin-specific proteins, little is known about the structure and the dynamics of these proteins, their interactions with the membrane and their influence on myelin stability. We present here the first neutron scattering results on the dynamics of the myelin sheath in PNS and of the interaction between its constituents. Specifically, the human P2 protein is shown to stabilize the lipid membrane upon binding to it.
S-Layer protein fromLysinibacillus sphaericusJG-A12 as matrix for AuIIIsorption and Au-nanoparticle formation
Authors: Jankowski Ulrike , Merroun Mohamed L. , Selenska-Pobell Sonja , Fahmy Karim
Published: April 2012

The strainLysinibacillus sphaericusJG-A12, isolated from the uranium mining site at Haberland, Saxony (Germany) selectively and reversibly accumulates radionuclides and toxic metals. Metal binding occurs to its surface layer (S-layer) surrounding the cells. Here, we have studied by Fourier-transform infrared (FTIR) spectroscopy the protein structure and stability as a function of AuIIIbinding and the subsequent reductively induced formation of Au-nanoclusters. Similar to previously studied complexes with PdII, Au-treated S-layers become resistant to acid denaturation evidenced by little response of their amide I absorption frequency. However, the strong effect of PdIIexerted on the side chain carboxylate IR absorption intensity is not observed with gold. Particularly after reduction, the carboxyl absorption responds little to acidification and a fraction appears to be protonated already at neutral pH. We ascribe this to a hydrophobic environment of the carboxyl groups after formation of Au-nanoclusters. EXAFS spectra agree with the metallic Au–Au distance but the reduced coordination number indicates that the Au-nanoclusters do not exceed ~2 nm. Thus, the S-layer ofL. sphaericusJG-A12 provides a biotemplate for efficient Au-nanocluster formation in an acid-resistant matrix and independently of cysteins.
Two-dimensional electronic spectroscopy signatures of the glass transition
Authors: Lewis K. L .M. , Myers J. A. , Fuller F. , Tekavec P. F. , Ogilvie J. P.
Published: April 2012

Two-dimensional electronic spectroscopy is a sensitive probe of solvation dynamics. Using a pump–probe geometry with a pulse shaper [Optics Express15(2007), 16681-16689;Optics Express16(2008), 17420-17428], we present temperature dependent 2D spectra of laser dyes dissolved in glass-forming solvents. At low waiting times, the system has not yet relaxed, resulting in a spectrum that is elongated along the diagonal. At longer times, the system loses its memory of the initial excitation frequency, and the 2D spectrum rounds out. As the temperature is lowered, the time scale of this relaxation grows, and the elongation persists for longer waiting times. This can be measured in the ratio of the diagonal width to the anti-diagonal width; the behavior of this ratio is representative of the frequency–frequency correlation function [Optics Letters31(2006), 3354–3356]. Near the glass transition temperature, the relaxation behavior changes. Understanding this change is important for interpreting temperature-dependent dynamics of biological systems.
Elastic scattering studies of aligned DMPC multilayers on different hydrations1
Authors: Trapp Marcus , Juranyi Fanni , Tehei Moeava , van Eijck Lambert , Demé Bruno , Gutberlet Thomas , Peters Judith
Published: April 2012

Biological membranes, consisting mainly of phospholipids and proteins, are organized in a bilayered structure which exhibits dynamical behaviour within time regimes ranging from 10–12s with the motion of alkyl chain defects and 1 s corresponding to collective excitations of the bilayer [Europhysics Letters8(1989), 201–206]. With the prominent role hydration plays on the structural phase behaviour of phospholipids membranes, it is essential for a better description of membranes to understand also the influence of hydration on the dynamics of membrane systems. In the present study we have performed neutron scattering investigations on highly oriented DMPC-d54 multilayers at two different relative humidity (rh) levels. Our results reveal the strong influence of hydration on the local membrane dynamics, i.e., head group dynamics.
Natural monoacetylenes studied by quantum-chemical chemistry
Authors: Roman Maciej , Baranska Malgorzata
Published: April 2012

This study is a part of the project focused on the vibrational analysis of natural mono- and polyacetylenes by using Raman spectroscopy and theoretical calculations. Their vibrational spectra show strong and polarized –C≡C– bands in the region of about 2200 cm–1. Mono- as well as polyacetylenes are supposed to be active in plants yet not available in an isolated form, so theoretical simulation of their vibrational spectra and comparison with the registered ones seems to be an excellent way to confirm or exclude the presence of these compounds in the investigated plants. Such an approach was applied here to analyze polyacetylenes in roots ofCoreopsis grandiflora. According to literature, this plant should contain a monoacetylene substituted by a thiophene ring. Theoretical calculations allowed to confirm this assumption.
Discrimination between healthy and tumor tissues on formalin-fixed paraffin-embedded breast cancer samples using IR imaging
Authors: Bénard Audrey , Desmedt Christine , Durbecq Virginie , Rouas Ghizlane , Larsimont Denis , Sotiriou Christos , Goormaghtigh Erik
Published: April 2012

This work presents a pilot study to illustrate the potential of Fourier transform infrared (FT-IR) imaging in breast cancer research. Using this technique, we have acquired infrared (IR) microspectroscopic images from healthy and cancerous breast tissue section from one patient. First of all, a Studentt-test was applied, showing DNA/RNA spectral region (1400–1000 cm−1) as the most discriminant for the differentiation between healthy and tumor samples. Afterwards, a supervised pattern recognition method, Partial Least Squares (PLS) was used to develop an automated classifier to discriminate the two classes of data. Infrared spectra of independent IR measurements were used to test the classifier. The class identity was correlated with information obtained by histopathologic gold standard. The results showed that more than 95% of the training and validation spectra were correctly identified. We demonstrate that combination between IR microspectroscopic imaging and multivariate data analysis can be used as a complement to present diagnostic tools for breast cancer.
Interaction of thiacloprid with bovine hemoglobin using spectroscopic and molecular modeling methods
Authors: Chen Chang-Yun , Zhao Bo , Wang Zheng-Wu
Published: April 2012

The interaction of thiacloprid (TL) to bovine hemoglobin (BHb) under physiological conditions was investigated by using fluorescence spectroscopy, circular dichroism spectroscopy (CD) and molecular modeling. The fluorescence intensity of BHb decreased regularly with the gradual increasing concentration of TL. It is observed that there was a prominent interaction between TL and BHb. The binding constantsKAat 288, 298 and 308 K obtained are 8.04, 5.26 and 3.08×104l · mol–1, respectively. The standard enthalpy change (ΔH°) and the standard entropy change (ΔS°) are calculated to be –34.54 KJ · mol–1and –25.77 J · mol–1 · K–1, which indicated that hydrogen bonding forces play major role in the interaction between TL and BHb. The alternations of protein secondary structure in the presence of TL were determined by CD spectroscopy. The results revealed that the content of α-helix was decreased from 51.85% in free BHb to 48.14% in TL–BHb complex. Molecular modeling study and our experimental results both showed that the binding mode of TL–BHb complex could be attributed to hydrogen bonding and hydrophobic interaction.
Structural fluctuation of proteins revealed by terahertz time-domain spectroscopy
Authors: Kambara Ohki , Tominaga Keisuke
Published: April 2012

We have measured spectra of the absorption coefficient and refractive index of hen egg white lysozyme in the wavenumber region from 7 cm–1to 50 cm–1by terahertz (THz) time-domain spectroscopy. From comparison with the results of the inelastic neutron scattering experiment it is concluded that analysis of the THz spectra provides information on the vibrational density of states. We studied temperature dependence of the THz spectra as well as hydration effect on them to discuss structural fluctuation of the protein. We observed dynamical transition at around 210 K for lysozyme.
Structure and stability of D-galactose/D-glucose-binding protein. The role of D-glucose binding and Ca ion depletion
Authors: Stepanenko Olga V. , Povarova Olga I. , Stepanenko Olesya V. , Fonin Alexander V. , Kuznetsova Irina M. , Turoverov Konstantin K. , Staiano Maria , D'Auria Sabato
Published: April 2012

The effects of guanidine hydrochloride (GdnHCl) on the structure and stability of the D-galactose/D-glucose-binding protein fromEscherichia coli(GGBP) and its complex with D-glucose (GGBP/Glc) were investigated by intrinsic protein fluorescence and far-UV circular dichroism (CD). The role of calcium in the stability of the protein structure was also studied. It was shown that the processes of GGBP and GGBP/Glc unfolding induced by GdnHCl followed one-step reversible denaturation mechanism. The obtained data showed that the binding of glucose to GGBP resulted in an increase of the protein stability towards the actions of the GdnHCl which made protein unfolding more cooperative. The stabilities of GGBP alone, GGBP in the presence of glucose, GGBP-depleted calcium (GGBP-Ca), and GGBP/Glc-depleted calcium (GGBP/Glc-Ca) were characterized by difference of Gibbs free energies.
Azure dyes as new photosensitizer prototypes to application in photodynamic therapy againstCandidaspp.
Authors: Moreira Leonardo M. , Lyon Juliana P. , Tursi Suellen M.S. , Trajano Isis , Felipe Monalisa P. , Costa Maricília S. , Rodrigues Máira R. , Codognoto Lúcia , de Oliveira Hueder P.M.
Published: April 2012

Infections caused byCandida albicansare of increasing concern, especially considering immunodepressed patients. The toxicity of most antifungal agents, the great number of cases with recidives, as well as the emergence of resistant samples has provoked the evaluation of new forms of therapy. In this context, the photodynamic therapy (PDT) presents auspicious antimicrobial properties, stimulating the development of trials employing several kinds of photosensitizers. In the present work, the application of different kind of Azure dyes as photosensitizer in PDT againstC. albicanswas evaluated through instrumental measurements of electronic spectroscopy. In fact, the values of optical density were a precise indicator of the growth inhibition of the microorganisms. Indeed, Azures are phenothiazinium derivatives that constitute a very relevant class of compounds with several biomedical applications, such as photoantimicrobial therapy against local bacterial infection, tuberculosis, trypanosomiasis, malaria, Rickettsia, yeasts, viral infectionnand cancer. Azure A, Azure B, Azure A thiocyanate, Azure B BF4, Azure A eosinate are the dyes tested againstC. albicans. The results denoted completely distinct behaviors to the different types of Azure compound evaluated in this work. In fact, Azure A and Azure A eosinate presented significant results when irradiated with 56 J/cm2, since the growth inhibition ofC. albicansreached approximately 60%. This Azure compounds have significant potential to be employed as photosensitizer (PS) in PDT, especially in cases of mucocutaneous candidosis. The spectroscopic evaluation was very effective to the detection of slight alterations in the growth of the microorganisms, denoting that this kind of analysis is an excellent alternative to determine growth inhibition ofCandida albicans. The experimental data are discussed in details in agreement with recent results from literature.
FT-IR spectromicroscopy of mammalian cell cultures during necrosis and apoptosis induced by drugs
Authors: Lamberti Annalisa , Sanges Carmen , Arcari Paolo
Published: April 2012

FT-IR is used in the field of biology and medicine to detect bimolecular changes in disordered cells and tissues. In this report, using FT-IR microscopy, we characterize changes in apoptotic and necrotic Jurkat cells with respect to normal cells. The analysis of deconvoluted regions of the FT-IR spectra showed significant differences compared to the controls in three spectral regions. In particular, the apoptotic cells were characterized by an increase in the absorption at 2925 cm−1, due to the asymmetric CH2-stretching (νasCH2) of membrane lipids whereas the spectral areas ratio (A1654/A1629) of the amide I region indicated an increase in apoptotic cells of more α-helical structures with respect to ofβ-sheet content. Interestingly, apoptotic cells showed the appearance of a peak around 1743 cm¯1,ν(C=O) assigned to acid ester. Because no other similar increase for lipid bands was observed, the increase of A1745is not simply due to an increase in the number of lipid molecules or their density but could also be indicative as marker of apoptosis. These spectral changes were not observed in necrotic Jurkat cells.
Surface- and tip-enhanced Raman spectroscopy of DNA
Authors: Hennemann L. E. , Meixner A. J. , Zhang D.
Published: April 2012

Calf thymus DNA adsorbed on a rough gold substrate or on an atomically smooth gold (111) surface has been investigated by collecting its unique Raman fingerprints using either surface-enhanced Raman scattering (SERS) or tip-enhanced Raman scattering (TERS). A monolayer coverage of DNA strands adsorbed at both the irregular rough edges of evaporated gold grids and at gold nanoparticles is detected by SERS. Highly improved sensitivity down to single DNA strand spectroscopic determination is accomplished by TERS providing an enhancement factor of at least 1400. Based on our experimental results, we propose that TERS is a promising technique to study the DNA–drug molecule interaction on the level of a single DNA strand.
FTIR spectroscopy reveals the concentration dependence of cellular modifications induced by anticancer drugs
Authors: Gasper Régis , Mijatovic Tatjana , Kiss Robert , Goormaghtigh Erik
Published: April 2012

Large-scale screening to determine the mechanisms of anti-cancer actions of chemical libraries still presents technical challenges that are beyond the capabilities of conventional methods used in cellular or molecular biology. We recently demonstrated in a proof-of-concept study that infrared (IR) spectrum of cells exposed to anticancer drugs could be used to classify their mechanisms of actions. This study highlighted the fact that molecules inducing unique metabolic modifications could be selected for further pharmacological improvements. We show in this paper that drug concentration is an important parameter to be taken into account when analyzing mechanisms of anti-cancer actions by means of FTIR. The data indeed demonstrated that distinct spectral modifications occur in human PC-3 prostate cancer cells when exposed to ouabain at 10 × IC50versus 1 × IC50. Longer incubation times at 1 × IC50never resulted in spectral modifications fitting with those observed at 10 × IC50.
FT-IR spectroscopy supported by PCA–LDA analysis for the study of embryonic stem cell differentiation
Authors: Ami Diletta , Natalello Antonino , Mereghetti Paolo , Neri Tui , Zanoni Mario , Monti Manuela , Doglia Silvia Maria , Redi Carlo Alberto
Published: April 2012

As recently pointed out in the literature, Fourier transform infrared (FT-IR) spectroscopy is emerging as a powerful tool in stem cell research. In this work we characterizedin situby FT-IR microspectroscopy the differentiation of murine embryonic stem cells (ES) to monitor possible changes in the cell macromolecular content during the early stages of differentiation. Undifferentiated and differentiating cells at 4, 7, 9 and 14 days were measured. Data were analyzed by the principal component and subsequent linear discriminant analyses (PCA–LDA) that enabled us to segregate ES cell spectra into well separate clusters and to identify the most significant spectral changes. Important changes in the lipid (3050–2800 cm–1), protein (1700–1600 cm–1) and in the nucleic acid (1050–850 cm–1) absorption regions were observed between days 4 to 7 of differentiation, indicating the appearance – at day 7 – of the new phenotype into cardiomyocyte precursors. Also the presence of DNA/RNA hybrid bands (954 cm–1and 899 cm–1) suggests that the transcriptional switch of the genome started at this stage of differentiation. Particularly noteworthy, we suggest that the 2936 cm–1shoulder we observed could reflect methyl group vibrations thus allowing the detection of variations in methylation levels of the stem cell during differentiation. These infrared results were found to be in agreement with the biochemical characterization of these differentiating cells, underlying the great potential of FT-IR spectroscopy in stem cell research.
Molecular and chemical characterization by Fourier transform infrared spectroscopy of human breast cancer cells with estrogen receptor expressed and not expressed
Authors: Mostaço-Guidolin Leila Büttner , Murakami Luciana Sayuri , Batistuti Marina Ribeiro , Nomizo Auro , Bachmann Luciano
Published: April 2012

The present study was designed to identify and compare the infrared absorption spectra of two human breast cancer cell lines: MCF-7 (estrogen receptor expressed, ER+) and SKBr3 (estrogen receptor non-expressed, ER–). Comparison between SKBr3 and MCF-7 cells revealed differences in the following absorption band areas: 1087 cm–1(DNA), 1397 cm–1(CH3), 1543 cm–1(amide II), 1651 cm–1(amide I), 2924 cm–1(fatty acids). Additionally, peak shifts were observed at 1122 cm–1(RNA), 1397 cm–1(CH3), 1651 cm–1(amide I), 2851 cm–1(fatty acids) and 2962 cm–1(fatty acids). An analysis of the ratio between band areas was conducted, in order to obtain an index that could effectively distinguish between these two cell lines. The following ratios were found: 1650 cm–1/1540 cm–1, 1650 cm–1/1740 cm–1, 1650 cm–1/1084 cm–1and 1120 cm–1/1084 cm–1. This work demonstrates that it is possible to distinguish between MCF-7 and SKBr3 cells through differences in their FTIR spectra. This work enables distinction between two cell lines from the same breast cancer.
Molecular structure of calcium, magnesium, strontium and barium m-nitrobenzoates
Authors: Samsonowicz Mariola
Published: April 2012

The effect of calcium, magnesium, strontium and barium ions on the electronic structure of m-nitrobenzoates was studied. The FT-IR spectra of m-nitrobenzoic acid and its salts were registered, assigned and analyzed. Characteristic shifts and changes in intensities of bands along the metal series were observed. The structures of m-nitrobenzoic acid and its calcium, magnesium, strontium and barium salts were optimized at the B3LYP/LANL2DZ level. Geometric aromaticity indices, atomic charges, dipole moments and energies were also calculated.
Biomedical application of Mössbauer spectroscopy with a high velocity resolution: Revealing of small variations
Authors: Oshtrakh M. I. , Semionkin V. A. , Milder O. B. , Alenkina I. V. , Novikov E. G.
Published: April 2012

Application of Mössbauer spectroscopy with a high velocity resolution for study different hemoglobins, ferritin, its models and chicken liver and spleen as well as normal and lymphoid chicken spleen demonstrated revealing of small variations of hyperfine parameters related to small variations of iron stereochemistry in biomolecules. These data demonstrate that Mössbauer spectroscopy with a high velocity resolution may be useful in biomedical research to distinguish small variations of iron-containing proteins in normal and pathological cases.
Direct identification of potato's fungal phyto-pathogens by Fourier-transform infrared (FTIR) microscopy
Authors: Erukhimovitch V. , Tsror (Lahkim) L. , Hazanovsky M. , Huleihel M.
Published: April 2012

Fungi are considered as serious pathogens to many plants and can cause a severe economic damage. The available methods for identification of fungi are time consuming and not always very specific. In the present study we examined the potential of FTIR microscopy for direct detection and identification of different fungal potato pathogens on the surface of potato tubers. Unique spectral bands for each of the examined fungal pathogens appeared in the spectra of naturally infected potatoes. These results strongly support the potential of FTIR microscopy for successful detection and probably discrimination between different fungal pathogens directly from the infected tissue.
High stability of trehalose/maltose binding protein fromThermococcus litoralismakes it a good candidate as a sensitive element in biosensor systems for sugar control
Authors: Povarova Olga I. , Stepanenko Olga V. , Sulatskaya Anna I. , Kuznetsova Irina M. , Turoverov Konstantin K. , Staiano Maria , Vitale Annalisa , D'Auria Sabato
Published: April 2012

Fluorescence and circular dichroism in far-UV region were used to study the stability of trehalose/maltose binding protein (TMBP) from hyper thermophilic archaeonThermococcus litoralisand its complex with glucose (TMBP/Glc). The evaluation of difference between free energy of native and unfolded state for TMBP and TMBP/Glc showed that both of them are several times higher than that of proteins from mesophilic organisms. Due to the high stability and innate ability to bind glucose this protein is a good candidate as a sensitive element in biosensor systems for sugar control.
Low frequency dynamics of lysozyme: A Raman scattering and low temperature specific heat study
Authors: Crupi C. , D'Angelo G. , Wanderlingh U. , Conti Nibali V. , Vasi C.
Published: April 2012

Raman scattering and low temperature specific heat (Cp) measurements have been performed to investigate the low frequency vibrational dynamics of hen egg white dry lysozyme. The occurrence of low energy extra excitations have been revealed both in the light scattering spectrum and in theCp/T3vs. T plot. A perfect agreement in the frequency and temperature position of the Boson Peak in this protein has been observed. At temperature below 3 K it has been found a contribution to the specific heat similar to that revealed in glassy systems. This, together with the other analogies discovered between thermal properties of amorphous and biological systems, suggests the possibility of making the most of the knowledge about the former in order to understand some glassy-like behaviours of proteins.
Raman study of magnesium induced conversion of polyU·polyA duplexes to polyU·polyA·polyU triplexes
Authors: Herrera S. J. Espinoza , Štepánek J.
Published: April 2012

Raman titration experiment with magnesium salt added gradually to aqueous solution of duplexes formed by RNA homopolynucleotides polyU and polyA was performed to reveal its effect on homopolynucleotide complexes. Statistical analysis of obtained spectral set has confirmed the effect already found by less structurally sensitive methods [Nucleic Acids Res.31(17) (2003), 5101–5107] that at sufficiently high concentrations magnesium causes transformation of polyU·polyA duplexes to polyU·polyA·polyU triplexes and single polyA strands. It was found that at relatively high polynucleotide concentrations used in Raman experiment, the threshold magnesium concentration for this effect is above the concentration of duplex basepairs in solution. Due to the strong spectral changes attributed to the varied percentages of duplexes, triplexes and single strands, it was not possible to register weaker direct Raman signs of the magnesium binding to polynucleotide strand.
Development of Raman Imaging System for time-course imaging of single living cells
Authors: Zoladek A. , Pascut F. , Patel P. , Notingher I.
Published: April 2012

Development of novel inverted Raman micro-spectrometer with the ability to perform multi-hours spectral measurements on living cells is presented. Our system combines a Confocal Raman Micro-Spectrometer and Fluorescence Microscope with cell incubator enclosure allowing measurement of cells in extended time period. To illustrate the feasibility of this Raman micro-spectroscopy system forin vitrotime-course studies of cells we performed an experiment where the same group of cells were scanned with the laser at 2 hours intervals between the scans over 8 hours to build Raman spectral images and ensure that no changes occur due to laser damage or environmental conditions. Cell viability test was performed with fluorescence microscopy on exactly the same cells at the end of the time-course Raman measurements.
Rapid-scan FTIR difference spectroscopy applied to ubiquinone reduction in photosynthetic reaction centers: Role of redox mediators
Authors: Mezzetti Alberto
Published: April 2012

Rapid-scan FTIR difference spectroscopy was used to investigate light-induced reduction of the ubiquinone QB, and the oxidation kinetics of QB–and QH2by external mediators in isolated reaction centers (RCs) fromR. sphaeroides. As redox mediators, a Ferrocyanide/N,N,Nʹ,Nʹ-tetramethyl-p-phenylenediamine (TMPD) mixture and an Ascorbate/2,3,5,6-tetramethyl-p-phenylenediamine (DAD) mixture are compared.

Results show that TMPDredrapidly reduces the photoproduced P870+primary donor. The process is fast enough to record rapid-scan FTIR spectra devoid of P870+bands down to 260 K. Results show also that TMPDoxoxidises both QB–and QH2faster than DADox. In particular, QB–is oxidised faster than QH2at all temperatures studied.

Results are discussed in the framework of time-resolved infrared studies onR. sphaeroidesRCs, showing advantages/drawbacks of the proposed experimental approach.
Low-frequency dynamics of biological molecules studied by terahertz time-domain spectroscopy
Authors: Kawaguchi Shintaro , Kambara Ohki , Ponseca Jr. Carlito S. , Shibata Mikihiro , Kandori Hideki , Tominaga Keisuke
Published: April 2012

By terahertz (THz) time-domain spectroscopy we have measured low-frequency spectra of amino acid (glycine; Gly), short peptides ((Gly)3and (Gly)4), six globular proteins and bacteriorhodopsin (BR). From the analysis of the THz spectra we defined and obtained the reduced absorption cross sections for these cases, which are proportional to the vibrational density of states. We observed anharmonic behaviors in the low-frequency modes of the short peptides. The globular proteins we investigated show a universal feature in the low-frequency spectra. BR shows the dynamical transition in the temperature dependence of the THz spectrum when the sample is hydrated.
The effect of alkali metal ions on the electronic structure ofp-anisic acid1
Authors: Kalinowska M. , Świsłocka R. , Regulska E. , Lewandowski W.
Published: April 2012

FT-IR (in solid state and solution), FT-Raman, UV and1H,13C NMR spectra of p-methoxybenzoic (p-anisic) acid and lithium, sodium, potassium, rubidium and caesiump-methoxybenzoates (p-anisates) were registered, assigned and analyzed. The structures of anisic acid and Li, Na and Kp-anisates were optimised at the B3LYP/6-311++G** level. The IR spectra and NPA, ChelpG and MK atomic charges were calculated. The effect of metal ions on the electronic charge distribution in ligand was discussed.
In situFTIR studies on mammalian cells
Authors: Wolkers Willem F. , Oldenhof Harriëtte
Published: April 2012

In this work, we describe the application of FTIR spectroscopy to study lipids and proteins, in cellular systems during heating and cooling. Various spectral analysis methods are described to simultaneously study membrane phase behavior and heat-induced protein denaturation in cells. Membrane phase behavior was studied by following the temperature dependence of the CH2stretching vibration bands. Protein denaturation was studied using the amide-I and -III bands. Both amide-I and amide-III band analysis show that heat-induced denaturation of proteins within the cells is typically associated with an increase in extendedβ-sheet structures and a concomitant decrease in α-helical structures.
Frequency domain fluorescence microspectrometry: Application to cellular uptake and drug distribution
Authors: Praus Petr , Kocišová Eva , Mojzeš Peter , Štepánek Josef , Sureau Franck , Turpin Pierre-Yves
Published: April 2012

Time-resolved confocal microspectrofluorometry and fluorescence microimaging were used to monitor how the model antisense oligonucleotide is transported into 3T3 living cells and distributed inside them. Phosphorothioate analog of 15-mer oligothymidylate labeled by ATTO 425 was complexed with Zn(II) 5,10,15,20-tetrakis(4-N-methylpyridyl) porphyrin as an uptake-mediating agent. Homodyne phase-resolved technique based on a high frequency analog modulation of both exciting diode laser and detector image intensifier was used for time-resolved measurements. Decay-time data obtained within a broad range spectral region have provided unique information about the fate of both fluorophores inside the cell.
Towards instantaneous quantitative fluoroimaging drugs determination in body fluids with no added reagents
Authors: Strashnikova Natalia V. , Gershanik Arcady P. , Papiashvili Nona , Khankin Daniel , Cohen-Luria Rivka , Mark Shlomo , Kalisky Yehoshua , Parola Abraham H.
Published: April 2012

Our objective is to develop a simple monitoring technique for rapid, sensitive and quantitative drugs detection in body fluids, with no reagent added and no need for qualified professionals. The user-friendly automatic Fluo-imager will (a) measure the full-range 3D fluorescence map of the inserted fluid sample, (b) determine the chemical nature and concentration of the drugs and (c) transfer the results through internet to the diagnosis center. For these goals the fluorescence measurement data will be examined by neuronal network-pattern recognition software. The software identifies the chemical nature and the appropriate concentration of the drug by comparison of the obtained 3D pattern with the contents of the data bank. One of the problems in the approach under consideration is the high optical density of body fluids in the UV region, which raises difficulties in the fluorescence measurements. In this paper, we have attempted to overcome this problem by means of preliminary dilution. Nevertheless, the problem of subtraction of the fluid fluorescence background still needs to be addressed.
FTIR microspectroscopy of stained cells and tissues. Application in cancer diagnosis
Authors: Pijanka Jacek K. , Stone Nicholas , Cinque Gianfelice , Yang Ying , Kohler Achim , Wehbe Katia , Frogley Mark , Parkes Gary , Parkes Joanne , Dumas Paul , Sandt Christophe , Pittius Daniel G. van , Douce Gillian , Sockalingum Ganesh D. , Sulé-Suso Josep
Published: April 2012

It is widely accepted that FTIR spectroscopy has a huge potential in cancer diagnosis. However further work is required to bring this technique into pathology departments. One of the areas where big efforts will be required is the development of cell spectra databases to be used in the diagnosis of cancer. Presently, unstained cytology and tissue samples are studied with FTIR spectroscopy. However, it is not always possible to identify in unstained samples the types of cells present. In order to achieve this, samples need staining after FTIR spectra have been obtained. We have recently shown it is possible to obtain FTIR spectra of stained cells using a synchrotron source (10.1038/labinvest.2010.8). This allows recording FTIR spectra from cells already characterized by pathologists. In order to further this work, we have now obtained FTIR spectra from stained (Papanicolau or Haematoxylin & Eosin) single cells using a benchtop spectrometer. This would be the logical step towards a clinical application in cancer diagnosis. The data here presented show that staining caused a decreased intensity of the peaks at 2920 cm−1and 2850 cm−1, and the appearance of stronger peaks at 1374 cm−1and 1040 cm−1. The clinical applications are discussed.
Emission lifetime study of fluorescence probes based on G-quadruplex oligonucleotides end-labeled with pyrene moieties
Authors: Cupane A. , Dembska A. , Pedzinski T. , Takenaka S. , Juskowiak B.
Published: April 2012

Fluorescence lifetime study of two probes abbreviated as Py-Htelom-Py and Py-TBA-Py, carrying pyrene moieties at both termini and sequences of Human telomere and Thrombin Binding Aptamer, respectively are reported. The effect of potassium ion on the photophysical processes was examined in order to elucidate factors that facilitate the production of excimer emission. Emission kinetics data indicated that the relative orientation of pyrene and neighboring nucleobase (guanine, adenine, thymine) plays a crucial role in determining both the rate of electron-transfer quenching of pyrene excited state and the efficiency of excimer emission.
Resistance to irradiation of micro-algae growing in the storage pools of a nuclear reactor investigated by NMR and neutron spectroscopies
Authors: Rivasseau Corinne , Farhi Emmanuel , Gromova Marina , Ollivier Jacques , Bligny Richard
Published: April 2012

A green Chlorophycean micro-alga surviving high irradiation doses has been discovered in the storage pools of a nuclear reactor. Investigating the mechanisms sustaining its properties is of peculiar interest. Metabolic impact of irradiation on the micro-alga as well as structural macromolecular impact were investigated using nuclear magnetic resonance and neutron backscattering spectroscopy. Carbohydrate, amino acid and organic acid content studied as a function of the irradiation dose revealed an intense protein repair activity. Resilience was extracted according to irradiation dose and compared to that of other extremophile species.
A modular Raman microspectroscopy system for biological tissue analysis
Authors: Wang Shuang , Zhao Jianhua , Lui Harvey , He Qingli , Zeng Haishan
Published: April 2012

Raman spectroscopy has been used as a sensitive tool for studying biological tissue and evaluating disease. In many applications, microscopic level resolution spectral analysis is desirable. And this has been performed mostly by expensive commercial confocal micro-Raman systems. In this research, we present a simple method for building an economical and modular Raman microspectroscopy system that combines a microscope with a Raman spectrometer using an optical fiber bundle. The bundle with a circular collection end is positioned at an image plane of the microscope to collect Raman signals from the interested micro-location on the sample. The light delivery end is specially configured so that its 37 fibers are arranged along a straight line to fit into the spectrometer entrance slit. This configuration improves light collection efficiency and maintains high spectral resolution. To battle the great background autofluorescence and Raman signals that could originate from the microscope slides and optics due to the non-confocal set-up of our simplified system, conventional normal-incident illumination is replaced by oblique illumination at 45° degrees and the microscope slides are coated with gold. We demonstrated the usefulness of the system by measuring micro-Raman spectra from different skin layers on vertical sections of normal skin tissue samples.
Vibrational analysis of boldine hydrochloride using QM/MM approach
Authors: Misra Neeraj , Siddiqui Shamoon Ahmad , Srivastava Ruby , Pandey Anoop Kumar , Jain Sudha
Published: April 2012

A complete vibrational analysis was performed on the molecular structure of boldine hydrochloride using QM/MM method. The equilibrium geometry, harmonic vibrational frequencies and infrared intensities were calculated by QM/MM method with B3LYP/6-31G(d) and universal force field (UFF) combination using ONIOM code. We found the geometry obtained by the QM/MM method to be very accurate, and we can use this rapid method in place of time consuming ab initio methods for large molecules. A detailed interpretation of the infrared spectra of boldine hydrochloride is reported. The scaled theoretical wave numbers are in perfect agreement with the experimental values. The FT-IR spectra of boldine hydrochloride in the region 4000–500 cm–1were recorded in CsI (solid phase) and in chloroform with concentration 5 and 10 mg/ml.
Fourier transform infrared and near-infrared spectroscopic methods for the detection of toxic Diethylene Glycol (DEG) contaminant in glycerin based cough syrup
Authors: Ahmed M. Khalique , McLeod Michael P. , Nézivar Jean , Giuliani Allison W.
Published: April 2012

Recently there have been reports of the contamination of cough syrups with Diethylene Glycol (DEG). The consumption of such cough syrups has devastating effects on the health. In this paper we report evidence that Fourier transform infrared (FT-IR) and near-infrared (NIR) spectroscopic techniques are viable, simple, cost effective, rapid and fool proof methods for the identification and quantification of DEG in glycerin based cough syrups. The FT-IR and NIR spectra of the glycerin based cough syrup and up to 50:50 mixtures of DEG in cough syrup are recorded. The major peaks in the FT-IR spectrum of the cough syrup are assigned to the OH stretching (∼3300 cm−1), CH stretching (∼2900 cm−1), CH bending (1500–1200 cm−1) and C–O stretching (1200–900 cm−1) vibrational modes. In the FT-IR spectra of the mixtures, DEG contribute distinct peaks due to the vibrations of the C–O (920 cm−1) and OC2H4(892 cm−1) moieties of its backbone and form the basis of the DEG detection and quantification. The prominent peaks of the NIR spectra of cough syrup and DEG are assigned to the first overtones of OH and CH, and to the combination of OH and CH fundamental vibrations. Both FT-IR and NIR Partial Least Square (PLS) calibrations produced correlation coefficients of 0.98.
Spectral properties and factors determining high quantum yield of thioflavin T incorporated in amyloid fibrils
Authors: Sulatskaya A. I. , Turoverov K. K. , Kuznetsova I. M.
Published: April 2012

Benzthiazole dye thioflavin T (ThT) is widely used for studying amyloid fibrils structure and formation. Nevertheless, till now there is no common opinion concerning molecular mechanisms of ThT binding to amyloid fibrils and the reasons of dramatic increase of its fluorescence quantum yield on incorporation into amyloid fibrils. Our data prove that ThT molecules incorporate in amyloid fibrils in monomeric form and there is no ground to suppose the formation of ThT dimers, eximers, or micelles. It was shown that the increase of quantum yield of ThT incorporated in amyloid fibrils is caused by restriction of benzthiazole and aminobenzene rings torsion fluctuations about each other.
Structural analysis of proteins by isotope-edited FTIR spectroscopy
Authors: Tatulian Suren A.
Published: April 2012

Structure determination of multidomain proteins or protein–membrane complexes is one of the most challenging tasks in modern structural biology. High-resolution techniques, like NMR or X-ray crystallography, are limited to molecules of moderate size or those that can be crystallized easily. Both methods encounter serious technical obstacles in structural analysis of protein–membrane systems. This work describes an emerging biophysical technique that combines segmental isotope labeling of proteins with Fourier transform infrared (FTIR) spectroscopy, which provides site-specific structural information on proteins and allows structural characterization of protein–membrane complexes. Labeling of a segment of the protein with13C results in infrared spectral resolution of the labeled and unlabeled parts and thus allows identification of structural changes in specific domains/segments of the protein that accompany functional transitions. Segmental isotope labeling also allows determination of the precise configuration of protein–membrane complexes by polarized attenuated total reflection FTIR (ATR–FTIR) spectroscopy. These new developments offer solutions to functionally important site-specific structural changes in proteins and protein–membrane complexes that are hard to approach using conventional methods.
Structural organization of DNA–protein complexes of chromatin studied by vibrational and electronic circular dichroism
Authors: Polyanichko Alexander , Wieser Helmut
Published: April 2012

Structure and functioning of chromatin is determined by interactions of DNA with numerous nuclear proteins. The most abundant and yet not completely understood non-histone chromosomal proteins are those belonging to a High Mobility Group (HMG) namely HMGB1. The interplay of this protein on DNA with linker histone H1 and other proteins determines both structure and functioning of the chromatin. A combination of UV and IR absorption and circular dichroism (CD) spectroscopy was applied to investigate the structure and formation of large supramolecular DNA–protein complexes. This combination of techniques was used to overcome limitations of UV-CD (ECD) spectroscopy due to considerable light scattering in such solutions. Based on the analysis of FTIR and UV circular dichroism spectra and AFM imaging the interaction of DNA with high-mobility group non-histone chromatin protein HMGB1 and linker histone H1 was studied.
Influence of growth conditions on hydrophobicity ofLactobacillus acidophilusandBifidobacterium lactiscells and characteristics by FT-IR spectra
Authors: Shakirova Laisana , Auzina Lilija , Zikmanis Peteris , Gavare Marita , Grube Mara
Published: April 2012

In this study we have found, that the values of cell surface hydrophobicity (CSH) ofL. acidophilusLA5 andB. lactisBb12 cells change in response to varied growth conditions – phase of growth, concentration or type of carbon source, presence of oxygen. An evaluation of FT-IR spectra using cluster and quantitative analyses revealed substantial changes of the chemical composition depending on the CSH level ofL. acidophilusLA5 andB. lactisBb12 cells. Decrease of the carbohydrate level was observed in proportion to the increased CSH values alongside with the elevated protein content of more hydrophobic cells of both cultures. The results of present study could help to specify the appropriate physiological state and environment forL. acidophilusLA5 andB. lactisBb12 to ensure their probiotic properties.
The FT-IR, FT-Raman,1H and13C NMR study on molecular structure of sodium(I), calcium(II), lanthanum(III) and thorium(IV) cinnamates
Authors: Kalinowska M. , Lewandowski W. , Swislocka R. , Regulska E.
Published: April 2012

In this work the effect of sodium(I), calcium(II), lanthanum(III) and thorium(IV) ions on the electronic structure of cinnamic acid (phenylacrylic acid) was studied. In this research: infrared (FT-IR), Raman (FT-Raman), nuclear magnetic resonance (1H,13C NMR) were used. In the series of Na(I)→ Ca(II)→ La(III)→ Th(IV) cinnamates: (1) systematic shifts of several bands in the FT-IR and FT-Raman spectra, and (2) regular chemical shifts of protons1H and13C nuclei were observed.
Interaction of porphyrin/oligonucleotide complex with liposomes studied by drop coating deposition Raman spectroscopy
Authors: Kocišová E. , Procházka M. , Štepánek J. , Mojzeš P.
Published: April 2012

Drop coating deposition Raman (DCDR) microspectroscopy was used to investigate interaction of the complexed cationic copper 5,10,15,20-tetrakis(1-methyl-4-pyridyl) porphyrin (CuP) and phosphorothioate analog of dT15oligonucleotide with liposomes, the lipid composition of which imitated the natural plasmatic membrane. Great advantage of dried drops on DCDR plates over a solution sample is that the specific drying process on the special hydrophobic surface efficiently separates liposomes from small species in the solvent. In our case, liposomes with bound CuP/oligonucleotide complexes formed a ring at the edge part of the dried drop while dried solution of this complex remained inside this ring. High quality spectra measured from the ring by using Raman confocal microspectrometer revealed unperturbed arrangement of lipid chains by the drying process, partial binding of the CuP/oligonucleotide complexes to liposomes, and a certain reorientation of lipid chains as a consequence of this interaction.