Raman spectroscopy of filamentous bacteriophage Ff (fd, M13, f1) incorporating specifically-deuterated alanine and tryptophan side chains. Assignments and structural interpretation

Probing metabolism in mouse embryos using Raman spectroscopy and deuterium tags

The use of deuterated compounds is an interesting opportunity to expand the capabilities of Raman spectroscopy to study metabolism in living cells. Different biological objects have different tolerances to different deuterated compounds, and their metabolic chains may differ. Here, we explore the potential of this approach to probe metabolism in early mouse embryos. We investigated the Raman spectra of mouse embryos at different developmental stages cultured with deuterated amino acids, phenylalanine-d8 and leucine-d10, glucose-d7, and D2O. Embryos after in vitro culture with 20 % v/v D2O demonstrate Raman peak at 2186 cm-1 corresponding to newly synthesized proteins. Deuterated amino acids can slow down the development rate in 4-8 cell stage embryos, and deuterated glucose can be used at 2 mM concentration. For blastocyst, it was possible to achieve 75 % fraction of deuterated phenylalanine, when cultured with glucose, the maximal intensity ratio between CD and CH bands was 13.7 %. To demonstrate the capabilities of Raman spectroscopy reinforced by deuterium labeling, we investigated the short-term effect of cryopreservation and revealed that cryopreservation decreases the amount of saccharides in embryos and does not affect the activity of protein de novo synthesis.

Design of MXene-Based Multiporous Nanosheet Stacking Structures Integrating Multiple Synergistic SERS Enhancements for Ultrasensitive Detection of Chloramphenicol

Motivated by the desire for more sensitivity and stable surface-enhanced Raman scattering (SERS) substrates to trace detect chloramphenicol due to its high toxicity and ubiquity, MXene has attracted increasing attention and is encountering the high-priority task of further observably improving detection sensitivity. Herein, a universal SERS optimization strategy that incorporates NH4VO3 to induce few-layer MXenes assembling into multiporous nanosheet stacking structures was innovatively proposed. The synthesized Nb2C-based multiporous nanosheet stacking structure can achieve a low limit of detection of 10-10 M and a high enhancement factor of 2.6 × 109 for MeB molecules, whose detection sensitivity is improved by 3 orders of magnitude relative to few-layer Nb2C MXenes. Such remarkably enhanced SERS sensitivity mainly originates from the multiple synergistic contributions of the developed physical adsorption, the chemical enhancement, and the conspicuously improved electromagnetic enhancement arising from the intersecting MXenes. Furthermore, the improved SERS sensitivity endows Nb2C-based multiporous structures with the capability to achieve ultrasensitive detection of chloramphenicol with a wide linear range from 100 μg/mL to 1 ng/mL. We believe it is of great significance in conspicuously developing the SERS sensitivity of other MXenes with surficial negative charges and has a great promising perspective for the trace detection of other antibiotics in microsystems.

Raman Multi-Omic Snapshot and Statistical Validation of Structural Differences between Herpes Simplex Type I and Epstein-Barr Viruses

Raman spectroscopy was applied to study the structural differences between herpes simplex virus Type I (HSV-1) and Epstein-Barr virus (EBV). Raman spectra were first collected with statistical validity on clusters of the respective virions and analyzed according to principal component analysis (PCA). Then, average spectra were computed and a machine-learning approach applied to deconvolute them into sub-band components in order to perform comparative analyses. The Raman results revealed marked structural differences between the two viral strains, which could mainly be traced back to the massive presence of carbohydrates in the glycoproteins of EBV virions. Clear differences could also be recorded for selected tyrosine and tryptophan Raman bands sensitive to pH at the virion/environment interface. According to the observed spectral differences, Raman signatures of known biomolecules were interpreted to link structural differences with the viral functions of the two strains. The present study confirms the unique ability of Raman spectroscopy for answering structural questions at the molecular level in virology and, despite the structural complexity of viral structures, its capacity to readily and reliably differentiate between different virus types and strains.

Investigation of the interaction between the functionalized mesoporous silica nanocarriers and bovine serum albumin via multi-spectroscopy

It is well known that the physicochemical properties of nanocarriers, which are closely related to the surface modification of nanoparticles, have crucial impacts on their biological effects. Herein, the interaction between functionalized degradable dendritic mesoporous silica nanoparticles (DDMSNs) and bovine serum albumin (BSA) was investigated for probing into the nanocarriers' potential toxicity using multi-spectroscopy such as ultraviolet/visible (UV/Vis), synchronous fluorescence, Raman and circular dichroism (CD) spectroscopy. BSA, owing to its structural homology and high sequence similarity with HSA, was employed as the model protein to study the interactions with DDMSNs, amino-modified DDMSNs (DDMSNs-NH₂) and hyaluronic acid (HA) coated nanoparticles (DDMSNs-NH₂-HA). It was found that the static quenching behavior of DDMSNs-NH₂-HA to BSA was accompanied by an endothermic and hydrophobic force-driven thermodynamic process, which was confirmed by fluorescence quenching spectroscopic studies and thermodynamic analysis. Furthermore, the conformational variations of BSA upon interaction with nanocarriers were observed by combination of UV/Vis, synchronous fluorescence, Raman and CD spectroscopy. The microstructure of amino residues in BSA changed due to the existence of nanoparticles, for example, the amino residues and hydrophobic groups exposed to microenvironment and the alpha helix (α-helix) content of BSA decreased. Specially, through thermodynamic analysis, the diverse binding modes and driving forces between nanoparticles and BSA were discovered because of different surface modifications on DDMSNs, DDMSNs-NH₂ and DDMSNs-NH₂-HA. We believe that this work can promote the interpretation of mutual impact between nanoparticles and biomolecules, which will be in favor of predicting the biological toxicity of nano-DDS and engineering functionalized nanocarriers.

Oriented suspension mechanics with application to improving flow linear dichroism spectroscopy

Flow linear dichroism is a biophysical spectroscopic technique that exploits the shear-induced alignment of elongated particles in suspension. Motivated by the broad aim of optimizing the sensitivity of this technique, and more specifically by a hand-held synthetic biotechnology prototype for waterborne-pathogen detection, a model of steady and oscillating pressure-driven channel flow and orientation dynamics of a suspension of slender microscopic fibres is developed. The model couples the Fokker-Planck equation for Brownian suspensions with the narrow channel flow equations, the latter modified to incorporate mechanical anisotropy induced by the particles. The linear dichroism signal is estimated through integrating the perpendicular components of the distribution function via an appropriate formula which takes the biaxial nature of the orientation into account. For the specific application of pathogen detection via binding of M13 bacteriophage, it is found that increases in the channel depth are more significant in improving the linear dichroism signal than increases in the channel width. Increasing the channel depth to 2 mm and pressure gradient to 5 × 104 Pa m-1 essentially maximizes the alignment. Oscillating flow can produce nearly equal alignment to steady flow at appropriate frequencies, which has significant potential practical value in the analysis of small sample volumes.

Multifunctional graphene oxide-bacteriophage based porous three-dimensional micro-nanocomposites

Graphene, since its successful exfoliation and characterisation has been continuously drawing extensive research interests due to its potential for a broad range of applications ranging from energy, microelectronics, through polymer fillers and sensors to environmental and biomedical devices. Exploitation of its unique chemical and physical properties for the manufacturing of functional materials, requires careful structural control and scaling-up into three-dimensional morphologies. Here, a facile method is established to create and control the bottom-up self-assembly of graphene oxide nano-sheets via unprecedented integration with a highly versatile bio-ingredient, the filamentous bacteriophage M13, into hierarchical, three-dimensional, porous sponges of GraPhage13. This study explores the interplay of the GraPhage13 structure formation and studies the mechanisms that give rise to the controllable self-assembly. The straightforward fabrication of robust hierarchical micro-nano-architectures further lays a platform for applications in energy storage and conversion, catalysis and sensing.

Study on the Interaction Between Cellulase and Surfactants

The conformations of secondary and tertiary structures of cellulase in the presence of eleven commonly used surfactants were determined by Raman spectroscopy and the results were discussed. The results indicated that anionic surfactants had a stronger influence on the cellulase conformations than nonionic surfactants. Thus anionic surfactants showed a stronger inactivation on the cellulase activity. Furthermore, Zeta potential distributions of cellulase in solutions of surfactants were tested by Dynamic Light Scattering (DLS). The DLS results indicated that the interaction between anionic surfactants and cellulase was attributed to electrostatic attraction. By adding cellulase to a liquid, non-cellulase-containing detergent, the detergency of the liquid detergent could be increased. Further studies on the sample swatches by optical microscopy and scanning electron microscopy (SEM) were undertaken in this paper.

Determining Gender by Raman Spectroscopy of a Bloodstain

The development of novel methods for forensic science is a constantly growing area of modern analytical chemistry. Raman spectroscopy is one of a few analytical techniques capable of nondestructive and nearly instantaneous analysis of a wide variety of forensic evidence, including body fluid stains, at the scene of a crime. In this proof-of-concept study, Raman microspectroscopy was utilized for gender identification based on dry bloodstains. Raman spectra were acquired in mapping mode from multiple spots on a bloodstain to account for intrinsic sample heterogeneity. The obtained Raman spectroscopic data showed highly similar spectroscopic features for female and male blood samples. Nevertheless, support vector machines (SVM) and artificial neuron network (ANN) statistical methods applied to the spectroscopic data allowed for differentiating between male and female bloodstains with high confidence. More specifically, the statistical approach based on a genetic algorithm (GA) coupled with an ANN classification showed approximately 98% gender differentiation accuracy for individual bloodstains. These results demonstrate the great potential of the developed method for forensic applications, although more work is needed for method validation. When this method is fully developed, a portable Raman instrument could be used for the infield identification of traces of body fluids and to obtain phenotypic information about the donor, including gender and race, as well as for the analysis of a variety of other types of forensic evidence.

Sex Determination Based on Raman Spectroscopy of Saliva Traces for Forensic Purposes

The forensic analysis of body fluids has made great strides in recent years. Body fluids can easily be identified, and DNA analysis can be used to link a stain found at a crime scene to a specific person. When no reference DNA profile is available and the recovered DNA does not yield a match in a database, it would be incredibly useful if the evidence could still provide investigators with useful information. Biocatalytic and immunoassays can be used to determine a donor's sex, race, and other phenotypic characteristics. However, these tests depend on chemical reactions and are destructive to the sample. Here, we used Raman spectroscopy and multivariate data analysis to develop a nondestructive technique that could be used at a crime scene to determine the sex of a saliva donor. Our internally cross-validated classification model correctly identified 44 (92%) of the 48 donors used for model training. Subsequent external validation correctly identified 11 (92%) of the 12 donors saved for testing. This proof-of-concept study demonstrates the value of Raman spectroscopy as a forensic tool, and indicates that it can be used to elucidate phenotypic information about a body fluid donor. Future studies will expand to other body fluids and additional donor characteristics, such as race and age.

Gold-Coated M13 Bacteriophage as a Template for Glucose Oxidase Biofuel Cells with Direct Electron Transfer

Glucose oxidase-based biofuel cells are a promising source of alternative energy for small device applications, but still face the challenge of achieving robust electrical contact between the redox enzymes and the current collector. This paper reports on the design of an electrode consisting of glucose oxidase covalently attached to gold nanoparticles that are assembled onto a genetically engineered M13 bacteriophage using EDC-NHS chemistry. The engineered phage is modified at the pIII protein to attach onto a gold substrate and serves as a high-surface-area template. The resulting "nanomesh" architecture exhibits direct electron transfer (DET) and achieves a higher peak current per unit area of 1.2 mA/cm(2) compared to most other DET attachment schemes. The final enzyme surface coverage on the electrode was calculated to be approximately 4.74 × 10(-8) mol/cm(2), which is a significant improvement over most current glucose oxidase (GOx) DET attachment methods.

Into the polymer brush regime through the "grafting-to" method: densely polymer-grafted rodlike viruses with an unusual nematic liquid crystal behavior

The current work reports an intriguing discovery of how the force exerted on protein complexes like filamentous viruses by the strong interchain repulsion of polymer brushes can induce subtle changes of the constituent subunits at the molecular scale. Such changes transform into the macroscopic rearrangement of the chiral ordering of the rodlike virus in three dimensions. For this, a straightforward "grafting-to" PEGylation method has been developed to densely graft a filamentous virus with poly(ethylene glycol) (PEG). The grafting density is so high that PEG is in the polymer brush regime, resulting in straight and thick rodlike particles with a thin viral backbone. Scission of the densely PEGylated viruses into fragments was observed due to the steric repulsion of the PEG brush, as facilitated by adsorption onto a mica surface. The high grafting density of PEG endows the virus with an isotropic-nematic (I-N) liquid crystal (LC) phase transition that is independent of the ionic strength and the densely PEGylated viruses enter into the nematic LC phase at much lower virus concentrations. Most importantly, while the intact virus and the one grafted with PEG of low grafting density can form a chiral nematic LC phase, the densely PEGylated viruses only form a pure nematic LC phase. This can be traced back to the secondary to tertiary structural change of the major coat protein of the virus, driven by the steric repulsion of the PEG brush. Quantitative parameters characterising the conformation of the grafted PEG derived from the grafting density or the I-N LC transition are elegantly consistent with the theoretical prediction.

Thermoresponsive Chiral to Nonchiral Ordering Transformation in the Nematic Liquid-Crystal Phase of Rodlike Viruses: Turning the Survival Strategy of a Virus into Valuable Material Properties

The current work investigates the thermoresponsive in situ chiral to nonchiral ordering transformation of a rodlike virus in the naturally assembled state-the chiral nematic liquid crystal (CLC) phase. We take this as an elegant example of reconfigurable self-assembly, through which it is possible to realize in situ transformation from one assembled state to another without disrupting the preformed assembly in general or going through a secondary assembling procedure of the disassembled building blocks. The detailed investigation presented here reveals many unique characteristics of the thermoresponsive 3D chiral ordering of rodlike viruses induced by heat stress. The chiral to nonchiral ordering transformation is highly reversible in the temperature range of up to 60 °C and can be repeated many times. There exists a critical temperature around 40 °C which is independent of the ionic strength and virus concentration. Such reconfigurable ordering in the CLC phase stems from the intrinsic structure change of constituent coat proteins without disrupting the structural integrity of the virus, as revealed by three analytical techniques targeting levels ranging from the molecular, secondary conformation of the constituent proteins to the whole single virus, respectively. Such structural flexibility, also termed polymorphism, is relative to the survival strategies of a biological organism such as the virus and can be transformed into very precious material properties. The potential of the virus-based CLC phase as the chiral matrix to regulate chiro-optical properties of gold nanorods is also presented.

Phage-AgNPs complex as SERS probe for U937 cell identification

The early diagnosis of malignancy is the most critical factor for patient survival and the treatment of cancer. In particular, leukemic cells are highly heterogeneous, and there is a need to develop new rapid and accurate detection systems for early diagnosis and monitoring of minimal residual disease. This study reports the utilization of molecular networks consisting of entire bacteriophage structure, displaying specific peptides, directly assembled with silver nanoparticles as a new Surface Enhanced Raman Spectroscopy (SERS) probe for U937 cells identification in vitro. A 9-mer pVIII M13 phage display library is screened against U937 to identify peptides that selectively recognize these cells. Then, phage clone is assembled with silver nanoparticles and the resulting network is used to obtain a SERS signal on cell-type specific molecular targets. The proposed strategy could be a very sensitive tool for the design of biosensors for highly specific and selective identification of hematological cancer cells and for detection of minimal residual disease in a significant proportion of human blood malignancy.

Accelerated detection of viral particles by combining AC electric field effects and micro-Raman spectroscopy

A detection method that combines electric field-assisted virus capture on antibody-decorated surfaces with the “fingerprinting” capabilities of micro-Raman spectroscopy is demonstrated for the case of M13 virus in water. The proof-of-principle surface mapping of model bioparticles (protein coated polystyrene spheres) captured by an AC electric field between planar microelectrodes is presented with a methodology for analyzing the resulting spectra by comparing relative peak intensities. The same principle is applied to dielectrophoretically captured M13 phage particles whose presence is indirectly confirmed with micro-Raman spectroscopy using NeutrAvidin-Cy3 as a labeling molecule. It is concluded that the combination of electrokinetically driven virus sampling and micro-Raman based signal transduction provides a promising approach for time-efficient and in situ detection of viruses.

Complete chemical shift assignment of the ssDNA in the filamentous bacteriophage fd reports on its conformation and on its interface with the capsid shell

The fd bacteriophage is a filamentous virus consisting of a circular single-stranded DNA (ssDNA) wrapped by thousands of copies of a major coat protein subunit (the capsid). The coat protein subunits are mostly α-helical and curved, and are arranged in the capsid in consecutive pentamers related by a translation along the main viral axis and a rotation of ~36° (C5S2 symmetry). The DNA is right-handed and helical, but information on its structure and on its interface with the capsid is incomplete. We present here an approach for assigning the DNA nucleotides and studying its interactions with the capsid by magic-angle spinning solid-state NMR. Capsid contacts with the ssDNA are obtained using a two-dimensional (13)C-(13)C correlation experiment and a proton-mediated (31)P-(13)C polarization transfer experiment, both acquired on an aromatic-unlabeled phage sample. Our results allow us to map the residues that face the interior of the capsid and to show that the ssDNA-capsid interactions are sustained mainly by electrostatic interactions between the positively charged lysine side chains and the phosphate backbone. The use of natural abundance aromatic amino acids in the growth media facilitated the complete assignment of the four nucleotides and the observation of internucleotide contacts. Using chemical shift analysis, our study shows that structural features of the deoxyribose carbons reporting on the sugar pucker are strikingly similar to those observed recently for the Pf1 phage. However, the ssDNA-protein interface is different, and chemical shift markers of base pairing are different. This experimental approach can be utilized in other filamentous and icosahedral bacteriophages, and also in other biomolecular complexes involving structurally and functionally important DNA-protein interactions.

FT-Raman study of deferoxamine and deferiprone exhibits potent amelioration of structural changes in the liver tissues of mice due to aluminum exposure

The present study inform the alterations on major biochemical constituents such as lipids, proteins, nucleic acids and glycogen along with phosphodiester linkages, tryptophan bands, tyrosine doublet, disulfide bridge conformations, aliphatic hydrophobic residue, and salt bridges in liver tissues of mice using Fourier transform Raman spectroscopy. In amide I, amide II and amide III, the area value significant decrease due structural alteration in the protein, glycogen and triglycerides levels but chelating agents DFP and DFO upturned it. Morphology changes by aluminium induced alterations and recovery by chelating agents within liver tissues known by histopathological examination. Concentrations of trace elements were found by ICP-OES. FT-Raman study was revealed to be in agreement with biochemical studies and demonstrate that it can successfully specify the molecular alteration in liver tissues. The tyrosyl doublet ratio I899/I831 decreases more in aluminum intoxicated tissues but treatment with DFP and DFO+DFP brings back to nearer control value. This indicates more variation in the hydrogen bonding of the phenolic hydroxyl group due to aluminum poisoning. The decreased Raman intensity ratio (I3220/I3400) observed in the aluminum induced tissues suggests a decreased water domain size, which could be interpreted in terms of weaker hydrogen-bonded molecular species of water in the aluminum intoxicated liver tissues. Finally, FT-Raman spectroscopy might be a useful tool for obtained successfully to indicate the molecular level changes.

Raman spectroscopy coupled with advanced statistics for differentiating menstrual and peripheral blood

Body fluids are a common and important type of forensic evidence. In particular, the identification of menstrual blood stains is often a key step during the investigation of rape cases. Here, we report on the application of near-infrared Raman microspectroscopy for differentiating menstrual blood from peripheral blood. We observed that the menstrual and peripheral blood samples have similar but distinct Raman spectra. Advanced statistical analysis of the multiple Raman spectra that were automatically (Raman mapping) acquired from the 40 dried blood stains (20 donors for each group) allowed us to build classification model with maximum (100%) sensitivity and specificity. We also demonstrated that despite certain common constituents, menstrual blood can be readily distinguished from vaginal fluid. All of the classification models were verified using cross-validation methods. The proposed method overcomes the problems associated with currently used biochemical methods, which are destructive, time consuming and expensive.

Bacteriophage Associated Silicon Particles: Design and Characterization of a Novel Theranostic Vector with Improved Payload Carrying Potential

There has been extensive research on the use of nanovectors for cancer therapy. Targeted delivery of nanotherapeutics necessitates two important characteristics; the ability to accumulate at the disease locus after overcoming sequential biological barriers and the ability to carry a substantial therapeutic payload. Successful combination of the above two features is challenging, especially in solid porous materials where chemical conjugation of targeting entities on the particle surface will generally prevent successful loading of the therapeutic substance. In this study, we propose a novel strategy for decorating the surface of mesoporous silicon particles with targeting entities (bacteriophage) and gold nanoparticles (AuNP) while maintaining their payload carrying potential. The resulting Bacteriophage Associated Silicon Particles (BASP) demonstrates efficient encapsulation of macromolecules and therapeutic nanoparticles into the porous structures. In vitro targeting data show enhanced targeting efficiency with about four orders of magnitude lower concentration of bacteriophage. In vivo targeting data suggest that BASP maintain their integrity following intravenous administration in mice and display up to three fold higher accumulation in the tumor.

Determination of orientations of aromatic groups in self-assembled peptide fibrils by polarised Raman spectroscopy

In this paper we describe a novel combination of Raman spectroscopy, isotope editing and X-ray scattering as a powerful approach to give detailed structural information on aromatic side chains in peptide fibrils. The orientation of the tyrosine residues in fibrils of the peptide YTIAALLSPYS with respect to the fibril axis has been determined from a combination of polarised Raman spectroscopy and X-ray diffraction measurements. The Raman intensity of selected tyrosine bands collected at different polarisation geometries is related to the values and orientation of the Raman tensor for those specific vibrations. Using published Raman tensor values we solved the relevant expressions for both of the two tyrosine residues present in this peptide. Ring deuteration in one of the two tyrosine side chains allowed for the calculation to be performed individually for both, by virtue of the isotopic shift that eliminates band overlapping. Sample disorder was taken into account by obtaining the distribution of orientations of the samples from X-ray diffraction experiments. The results provide previously unavailable details about the molecular conformation of this peptide, and demonstrate the value of this approach for the study of amyloid fibrils.

Investigation of Preeclampsia Using Raman Spectroscopy

Preeclampsia is associated with increased perinatal morbidity and mortality. There have been numerous efforts to determine preeclampsia biomarkers by means of biophysical, biochemical, and spectroscopic methods. In this study, the preeclampsia and control groups were compared via band component analysis and multivariate analysis using Raman spectroscopy as an alternative technique. The Raman spectra of serum samples were taken from nine preeclamptic, ten healthy pregnant women. The Band component analysis and principal component analysis-linear discriminant analysis were applied to all spectra after a sensitive preprocess step. Using linear discriminant analysis, it was found that Raman spectroscopy has a sensitivity of 78% and a specificity of 90% for the diagnosis of preeclampsia. Via the band component analysis, a significant difference in the spectra of preeclamptic patients was observed when compared to the control group. 19 Raman bands exhibited significant differences in intensity, while 11 of them decreased and eight of them increased. This difference seen in vibrational bands may be used in further studies to clarify the pathophysiology of preeclampsia.

Raman spectroscopic signature of semen and its potential application to forensic body fluid identification

A great potential of Raman spectroscopy for non-destructive, confirmatory identification of body fluids at the crime scene has been reported recently (Virkler and Lednev, Forensic Sci. Int. 2008). However, that analysis was carried out on only one sample of each body fluid and did not take into account any variations that might occur between different donors of the same fluid. This paper reports on the role of heterogeneity within a sample as well as among multiple donors for human semen. Near-infrared (NIR) Raman spectroscopy was used to measure spectra of pure dried human semen samples from multiple donors in a controlled laboratory environment. The major chemical components that contributed to the Raman spectrum of semen were determined and used to tentatively identify the principal spectral components. The issue of potential spectral variations that could arise between different donors of semen was also addressed. Advanced statistical analysis of spectra obtained from multiple spots on dry samples showed that dry semen is heterogeneous and its Raman spectra could be presented as a linear combination of a fluorescent background and three spectral components. The relative contribution of each of the three components varies with donor, so no single spectrum could effectively represent an experimental Raman spectrum of dry semen in a quantitative way. The combination of the three spectral components could be considered to be a spectroscopic signature for semen. This proof-of-concept approach shows the potential for Raman spectroscopy to identify an unknown substance to be semen during forensic analysis.

Raman spectroscopy for monitoring protein structure in muscle food systems

Raman spectroscopy offers structural information about complex solid systems such as muscle food proteins. This spectroscopic technique is a powerful and a non-invasive method for the study of protein changes in secondary structure, mainly quantified, analysing the amide I (1650-1680 cm(- 1)) and amide III (1200-1300 cm(- 1)) regions and C-C stretching band (940 cm(- 1)), as well as modifications in protein local environments (tryptophan residues, tyrosil doublet, aliphatic aminoacids bands) of muscle food systems. Raman spectroscopy has been used to determine structural changes in isolated myofibrillar and connective tissue proteins by the addition of different compounds and by the effect of the conservation process such as freezing and frozen storage. It has been also shown that Raman spectroscopy is particularly useful for monitoring in situ protein structural changes in muscle food during frozen storage. Besides, the possibilities of using protein structural changes of intact muscle to predict the protein functional properties and the sensory attributes of muscle foods have been also investigated. In addition, the application of Raman spectroscopy to study changes in the protein structure during the elaboration of muscle food products has been demonstrated.

Vibrational Analysis of Amino Acids and Short Peptides in Hydrated Media. I. L-glycine and L-leucine

Raman scattering and Fourier-transform infrared (FT-IR) attenuated transmission reflectance (ATR) spectra of two alpha-amino acids (alpha-AAs), i.e., glycine and leucine, were measured in H2O and D2O (at neutral pH and pD). This series of observed vibrational data gave us the opportunity to analyze vibrational features of both AAs in hydrated media by density functional theory (DFT) calculations at the B3LYP/6-31++G* level. Harmonic vibrational modes calculated after geometry optimization on the clusters containing each AA and 12 surrounding water molecules, which represent primary models for hydration scheme of amino acids, allowed us to assign the main observed peaks.

Networks of gold nanoparticles and bacteriophage as biological sensors and cell-targeting agents

Biological molecular assemblies are excellent models for the development of nanoengineered systems with desirable biomedical properties. Here we report an approach for fabrication of spontaneous, biologically active molecular networks consisting of bacteriophage (phage) directly assembled with gold (Au) nanoparticles (termed Au-phage). We show that when the phage are engineered so that each phage particle displays a peptide, such networks preserve the cell surface receptor binding and internalization attributes of the displayed peptide. The spontaneous organization of these targeted networks can be manipulated further by incorporation of imidazole (Au-phage-imid), which induces changes in fractal structure and near-infrared optical properties. The networks can be used as labels for enhanced fluorescence and dark-field microscopy, surface-enhanced Raman scattering detection, and near-infrared photon-to-heat conversion. Together, the physical and biological features within these targeted networks offer convenient multifunctional integration within a single entity with potential for nanotechnology-based biomedical applications.

Raman spectroscopic study of structural changes in Hake (Merluccius merluccius L.) muscle proteins during frozen storage

This paper examines changes in the structure and functionality of fish muscle proteins at frozen storage temperatures known to render very different practical storage lives (-10 and -30 degrees C). Apparent viscosity and dimethylamine (DMA) content showed drastic temperature-related differences during storage. Raman spectroscopy revealed the occurrence of some structural changes involving secondary and tertiary protein structures. The changes in secondary structure were quantified, showing an increase of beta-sheet at the expense of alpha-helix structure. The nuC-H stretching band near 2935 cm(-)(1) increased in intensity, indicating denaturation of the muscle proteins through the exposure of aliphatic hydrophobic groups to the solvent. These structural changes were more pronounced at -10 degrees C but occurred at both storage temperatures, whereas changes in apparent viscosity and DMA only occurred in storage at -10 degrees C. The possible utility of these structural changes for quality assessment is discussed.

Raman structural markers of tryptophan and histidine side chains in proteins

The Raman spectrum of a protein contains a wealth of information on the structure and interaction of the protein. To extract the structural information from the Raman spectrum, it is necessary to identify and interpret the marker bands that reflect the structure and interaction in the protein. Recently, new Raman structural markers have been proposed for the tryptophan and histidine side chains by examining the spectra-structure correlations of model compounds. Raman structural markers are now available for the conformation, hydrogen bonding, hydrophobic interaction, and cation-pi interaction of the indole ring of Trp. For His, protonation, tautomerism, and metal coordination of the imidazole ring can be studied by using Raman markers. The high-resolution X-ray crystal structures of proteins provide the basis for testing and modifying the Raman structural markers of Trp and His. The structures derived from Raman spectra are generally consistent with the X-ray crystal structures, giving support for the applicability of most Raman structural makers. Possible modifications and limitations to some marker bands are also discussed.

Orientation and interactions of an essential tryptophan (Trp-38) in the capsid subunit of Pf3 filamentous virus

The filamentous bacteriophage Pf3 consists of a covalently closed DNA single strand of 5833 nucleotides sheathed by approximately 2500 copies of a 44-residue capsid subunit. The capsid subunit contains a single tryptophan residue (Trp-38), which is located within the basic C-terminal sequence (-RWIKAQFF) and is essential for virion assembly in vivo. Polarized Raman microspectroscopy has been employed to determine the orientation of the Trp-38 side chain in the native virus structure. The polarized Raman measurements show that the plane of the indolyl ring is tilted by 17 degrees from the virion axis and that the indolyl pseudo-twofold axis is inclined at 46 degrees to the virion axis. Using the presently determined orientation of the indolyl ring and side-chain torsion angles, chi(1) (N-C(alpha)-C(beta)-C(gamma)) and chi(2,1) (C(alpha)-C(beta)-C(gamma)-C(delta1)), we propose a detailed molecular model for the local structure of Trp-38 in the Pf3 virion. The present Pf3 model is consistent with previously reported Raman, ultraviolet-resonance Raman and fluorescence results suggesting an unusual environment for Trp-38 in the virion assembly, probably involving an intrasubunit cation-pi interaction between the guanidinium moiety of Arg-37 and the indolyl moiety of Trp-38. Such a C-terminal Trp-38/Arg-37 interaction may be important for the stabilization of a subunit conformation that is required for binding to the single-stranded DNA genome during virion assembly.

Raman spectroscopy of protein and nucleic acid assemblies

The Raman spectrum of a protein or nucleic acid consists of numerous discrete bands representing molecular normal modes of vibration and serves as a sensitive and selective fingerprint of three-dimensional structure, intermolecular interactions, and dynamics. Recent improvements in instrumentation, coupled with innovative approaches in experimental design, dramatically increase the power and scope of the method, particularly for investigations of large supramolecular assemblies. Applications are considered that involve the use of (a) time-resolved Raman spectroscopy to elucidate assembly pathways in icosahedral viruses, (b) polarized Raman microspectroscopy to determine detailed structural parameters in filamentous viruses, (c) ultraviolet-resonance Raman spectroscopy to probe selective DNA and protein residues in nucleoprotein complexes, and (d) difference Raman methods to understand mechanisms of protein/DNA recognition in gene regulatory and chromosomal complexes.

Intensity of the polarized Raman band at 1340-1345 cm-1 as an indicator of protein alpha-helix orientation: application to Pf1 filamentous virus

Raman spectra of oriented alpha-helical protein molecules exhibit a prominent band near 1340-1345 cm(-)(1), the intensity of which is highly sensitive to molecular orientation. Polarization of the 1340-1345 cm(-)(1) marker is evident in Raman spectra of alpha-helical poly-L-alanine (alphaPLA) and alpha-helical poly-gamma-benzyl-L-glutamate (alphaPBLG). Corresponding polarization is also observed in Raman spectra of the filamentous virus Pf1, which is an assembly of alpha-helical coat protein molecules. In alphaPLA and alphaPBLG, we assign the band to a normal mode of symmetry type E(2) and specifically to a vibration localized in the (O=C)-C(alpha)-H linkages of the main chain peptide group. Although strict helical symmetry does not apply to coat subunits of filamentous viruses, an approximate E(2)-type mode may be presumed to account for a corresponding Raman band of Pf1 and fd filamentous viruses. Spectroscopic studies of N-methylacetamide and isotopically-edited fd viruses support the present assignment of the 1340-1345 cm(-)(1) band. Polarization anisotropy indicates that this band may be exploited as a novel indicator of protein alpha-helix orientation. Application of this approach to the polarized Raman spectrum of Pf1 suggests that, on average, the axis of the alpha-helical coat protein subunit in the native virion structure forms an angle of 20 +/- 10 degrees with respect to the virion axis.

Protein-directed DNA structure. I. Raman spectroscopy of a high-mobility-group box with application to human sex reversal

Protein-directed reorganization of DNA underlies mechanisms of transcription, replication, and recombination. A molecular model for DNA reorganization in the regulation of gene expression is provided by the sequence-specific high-mobility-group (HMG) box. Structures of HMG-box complexes with DNA are characterized by expansion of the minor groove, sharp bending toward the major groove, and local unwinding of the double helix. The Raman vibrational signature of such DNA reorganization has been identified in a study of the SRY HMG box, encoded by the human male-determining region of the Y chromosome. We observe in the human SRY-HMG:DNA complex extraordinarily large perturbations to Raman bands associated with vibrational modes of the DNA backbone and accompanying large increases in intensities of Raman bands attributable to base unstacking. In contrast, DNA major-groove binding, as occurs for the bZIP protein GCN4 [Benevides, J. M., Li, T., Lu, X.-J., Srinivasan, A. R., Olson, W. K., Weiss, M. A., and Thomas, G. J., Jr. (2000) Biochemistry 39, 548-556], perturbs the Raman signature of DNA only marginally. Raman markers of minor-groove recognition in the human SRY-HMG:DNA complex are due primarily to perturbation of specific vibrational modes of deoxyribose moieties and presumably reflect desolvation at the nonpolar interface of protein and DNA. These Raman markers may be diagnostic of protein-induced DNA bending and are proposed as a baseline for comparative analysis of mutations in SRY that cause human sex reversal.

Ultraviolet-resonance raman spectroscopy of the filamentous virus Pf3: interactions of Trp 38 specific to the assembled virion subunit

The class II filamentous virus Pf3 packages a circular single-stranded DNA genome of approximately 5833 [corrected] nucleotides within a cylindrical capsid constructed from approximately 2500 [corrected] copies of a 44 residue alpha-helical subunit. The single tryptophan residue (Trp 38) of the capsid subunit is located within a basic C-terminal sequence (.R(+)WIK(+)AQFF). The local environment of Trp 38 in the native Pf3 assembly has been investigated using 229 nm excited ultraviolet-resonance Raman (UVRR) spectroscopy and fluorescence spectroscopy. Trp 38 exhibits an anomalous UVRR signature in Pf3, including structure-diagnostic Raman bands (763, 1228, 1370, and 1773 cm(-)(1)) that are greatly displaced from corresponding Raman markers observed in either detergent-disassembled Pf3, class I filamentous viruses, most globular proteins, or aqueous L-TRP. An unusual and highly quenched fluorescence spectrum is also observed for Trp 38. These distinctive UVRR and fluorescence signatures together reflect interactions of the Trp 38 side chain that are specific to the native PF3 assembly. The experimental results on PF3 and supporting spectroscopic data from other proteins of known three-dimensional structure favor a model in which pi electrons of the Trp 38 indolyl ring interact specifically with a basic side chain of the subunit C-terminal sequence. Residues Arg 37 AND Lys 40 are plausible candidates for the proposed cation-pi interaction of Trp 38. The present study suggests that raman spectroscopy may be a generally useful probe of interactions between the indolyl pi-electron system of tryptophan and electropositive groups in proteins and their assemblies.

Raman markers of nonaromatic side chains in an alpha-helix assembly: Ala, Asp, Glu, Gly, Ile, Leu, Lys, Ser, and Val residues of phage fd subunits

The study of filamentous virus structure by Raman spectroscopy requires accurate band assignments. In previous work, site- and residue-specific isotope substitutions were implemented to elucidate definitive assignments for Raman bands arising from vibrational modes of the alpha-helical coat protein main chain and aromatic side chains in the class I filamentous phage, fd [Overman, S. A., and Thomas, G. J., Jr. (1995) Biochemistry 34, 5440-5451; Overman, S. A., and Thomas, G. J., Jr. (1998) Biochemistry 37, 5654-5665]. Here, we extend the previous methods and expand the assignment scheme to identify Raman markers of nonaromatic side chains of the coat protein in the native fd assembly. This has been accomplished by Raman analysis of 11 different fd isotopomers selectively incorporating deuterium at specific sites in either alanine, aspartic acid, glutamic acid, glycine, isoleucine, leucine, lysine, serine, or valine residues of the coat protein. Raman markers are also identified for the corresponding deuterated side chains. In combination with previous assignments, the results provide a comprehensive understanding of coat protein contributions to the Raman signature of the fd virion and validate Raman markers assigned to the packaged single-stranded DNA genome. The findings described here show that nonaromatic side chains contribute prolifically to the fd Raman signature, that marker bands for specific nonaromatics differ in general from those observed in corresponding polypeptides and amino acids, and that the frequencies and intensities of many nonaromatic markers are sensitive to secondary and higher-order structures. Nonaromatic markers within the 1200-1400 cm-1 interval also interfere seriously with the diagnostic Raman amide III band that is normally exploited in secondary structure analysis. Implications of these findings for the assessment of protein conformation by Raman spectroscopy are considered.

Effects of temperature and Y21M mutation on conformational heterogeneity of the major coat protein (pVIII) of filamentous bacteriophage fd

Solid-state NMR spectroscopy was used to analyze the conformational heterogeneity of the major coat protein (pVIII) of filamentous bacteriophage fd. Both one and two-dimensional solid-state NMR spectra of magnetically aligned samples of fd bacteriophage reveal that an increase in temperature and a single site substitution (Tyr21 to Met, Y21M) reduce the conformational heterogeneity observed throughout wild-type pVIII. The NMR results are consistent with previous studies indicating that conformational flexibility in the hinge-bend segment that links the amphipathic and hydrophobic helices in the membrane-bound form of the protein plays an essential role during phage assembly, which involves a major change in the tertiary, but not secondary, structure of the coat protein.

Orientations of tyrosines 21 and 24 in coat subunits of Ff filamentous virus: determination by Raman linear intensity difference spectroscopy and implications for subunit packing

Virions of the Ff group of bacteriophages (fd, f1, M13) are morphologically identical filaments (approximately 6-nm diameter x approximately 880-nm length) in which a covalently closed, single-stranded DNA genome is sheathed by approximately 2700 copies of a 50-residue alpha-helical subunit (pVIII). Orientations of pVIII tyrosines (Tyr21 and Tyr24) with respect to the filament axis have been determined by Raman linear intensity difference (RLID) spectroscopy of flow-oriented mutant virions in which the tyrosines were independently mutated to methionine. The results show that the twofold axis of the phenolic ring (C1-C4 line) of Tyr21 is inclined at 39.5 +/- 1.4 degrees from the virion axis, and that of Tyr24 is inclined at 43.7 +/- 0.6 degrees. The orientation determined for the Tyr21 phenol ring is close to that of a structural model previously proposed on the basis of fiber x-ray diffraction results (Protein Data Bank, identification code 1IFJ). On the other hand, the orientation determined for the Tyr24 phenol ring differs from the diffraction-based model by a 40 degrees rotation about the Calpha-Cbeta bond. The RLID results also indicate that each tyrosine mutation does not greatly affect the orientation of either the remaining tyrosine or single tryptophan (Trp26) of pVIII. On the basis of these results, a refined model is proposed for the coat protein structure in Ff.

Amide modes of the alpha-helix: Raman spectroscopy of filamentous virus fd containing peptide 13C and 2H labels in coat protein subunits

The filamentous virus fd consists of a single-stranded DNA genome sheathed by 2700 copies of a 50-residue alpha-helical subunit (protein pVIII) and serves as a model assembly of alpha-helices. To advance vibrational assignments for the alpha-helix, we have investigated Raman spectra of fd virions containing 13C and 2H (deuterium) labels at various main-chain sites of the pVIII subunits. 13C was introduced at specific peptide carbonyls, while deuterium was introduced at selected alpha-carbon (Calpha) and amide nitrogen positions. Interpretation of the Raman spectra reveals a previously unrecognized alpha-helix band in the spectral interval 730-745 cm-1, tentatively assigned to a carbonyl in-plane bending mode (amide IV). Experimental evidence has also been obtained for a distinctive alpha-helix marker near 1345 cm-1, assigned to a coupled Calpha-H bending and Calpha-C stretching mode. The fd virions containing 13C-labeled carbonyls exhibit unexpectedly complex amide I profiles, consisting of multiple band components. Amide I splitting resulting from 13C substitution of carbonyls is attributed to decoupling of transition-dipole interactions normally occurring in the extended pVIII helix. The present study identifies novel conformation-dependent Raman bands in a native alpha-helix assembly, confirms amide I and amide III assignments proposed previously for filamentous viruses, and facilitates new Raman assignments for the packaged ssDNA. The alpha-helix markers identified here should also be useful in conformation analyses of other proteins by Raman spectroscopy.

Conformation, stability, and active-site cysteine titrations of Escherichia coli D26A thioredoxin probed by Raman spectroscopy

The active-site cysteines (Cys 32 and Cys 35) of Escherichia coli thioredoxin are oxidized to a disulfide bridge when the protein mediates substrate reduction. In reduced thioredoxin, Cys 32 and Cys 35 are characterized by abnormally low pKa values. A conserved side chain, Asp 26, which is sterically accessible to the active site, is also essential to oxidoreductase activity. pKa values governing cysteine thiol-thiolate equilibria in the mutant thioredoxin, D26A, have been determined by direct Raman spectrophotometric measurement of sulfhydryl ionizations. The results indicate that, in D26A thioredoxin, both sulfhydryls titrate with apparent pKa values of 7.5+/-0.2, close to values measured previously for wild-type thioredoxin. Sulfhydryl Raman markers of D26A and wild-type thioredoxin also exhibit similar band shapes, consistent with minimal differences in respective cysteine side-chain conformations and sulfhydryl interactions. The results imply that neither the Cys 32 nor Cys 35 SH donor is hydrogen bonded directly to Asp 26 in the wild-type protein. Additionally, the thioredoxin main-chain conformation is largely conserved with D26A mutation. Conversely, the mutation perturbs Raman bands diagnostic of tryptophan (Trp 28 and Trp 31) orientations and leads to differences in their pH dependencies, implying local conformational differences near the active site. We conclude that, although the carboxyl side chain of Asp 26 neither interacts directly with active-site cysteines nor is responsible for their abnormally low pKa values, the aspartate side chain may play a role in determining the conformation of the enzyme active site.

Structure and interactions of the single-stranded DNA genome of filamentous virus fd: investigation by ultraviolet resonance raman spectroscopy

The filamentous bacteriophage fd is a member of the Ff class of Inovirus, which includes phages f1 and M13. Ultraviolet resonance Raman (UVRR) spectra of fd have been obtained using excitation wavelengths of 257, 244, 238, and 229 nm. Excitation at 257 nm selectively enhances Raman markers of the packaged single-stranded (ss) DNA genome, while excitation at the shorter wavelengths favors the detection of Raman signals from coat protein aromatics, particularly tryptophan (W26) and tyrosine residues (Y21 and Y24) of the viral coat subunit (pVIII). The principal findings are the following: (1) Distinctive markers of dA, dC, dG, and dT residues of the packaged genome are identified in UVRR spectra of fd excited at 257 and 244 nm, despite the low DNA mass composition (12%) of the virion. (2) Raman bands of the bases of packaged ssDNA show extraordinary resonance Raman hypochromism. Raman intensity losses as large as 80% of the parent DNA nucleotide intensities are observed. This is interpreted as evidence of extensive short-range interactions involving bases of the packaged genome. (3) Conversely, Raman bands of tryptophan and tyrosine residues of the coat protein generally exhibit strong hyperchromism. Typically, Raman markers of the aromatic amino acids are about 3-fold more intense in the UVRR spectrum of fd than in spectra of the free amino acids. The very high Raman cross sections for residues Y21, Y24, and W26 are indicative of unusual hydrophobic environments in the viral assembly. (4) UVRR band shifts that accompany the transfer of fd from H2O to D2O solution indicate that bases of the packaged ssDNA are readily exchanged by the solvent. Similarly, the indole N1H group of W26 is accessible to solvent, as shown by N1H --> N1D exchange in D2O solution. (5) The UVRR markers of the packaged fd genome confirm the conclusion reached previously from off-resonance Raman studies that fd DNA nucleosides favor the C3'-endo/anti conformation, rather than the C2'-endo/anti conformation that is characteristic of the lowest energy structure of DNA. We conclude that nucleoside conformations of the packaged fd genome are influenced by the specific organization of ssDNA and coat protein subunits in the native virion assembly.