Structure similarity, difference and variability in the filamentous viruses fd, If1, IKe, Pf1 and Xf. Investigation by laser Raman spectroscopy

Advanced Vibrational Spectroscopy and Bacteriophages Team Up: Dynamic Synergy for Medical and Environmental Applications

Bacteriophages are emerging as a promising alternative in combating antibiotic-resistant bacteria amidst the escalating global antimicrobial resistance crisis. Recently, there has been a notable resurgence of interest in phages, prompting extensive research into their therapeutic potential. Beyond conventional microbiology and virology techniques, such as genomics and proteomics, novel phenotypic and chemical characterization methods are being explored. Among these, there is a growing interest in vibrational spectroscopy, especially in advanced modalities such as surface-enhanced Raman spectroscopy (SERS), tip-enhanced Raman spectroscopy (TERS), and atomic force microscopy-infrared spectroscopy (AFM-IR), which offer improved sensitivity and spatial resolution. This review explores the spectrum of uses of vibrational spectroscopy for bacteriophages, including its role in diagnostics, biosensing, phage detection, assistance in phage-based therapy, and advancing basic research.

Cryo-EM structure of a bacteriophage M13 mini variant

Filamentous bacteriophages package their circular, single stranded DNA genome with the major coat protein pVIII and the minor coat proteins pIII, pVII, pVI, and pIX. Here, we report the cryo-EM structure of a ~500 Å long bacteriophage M13 mini variant. The distal ends of the mini phage are sealed by two cap-like complexes composed of the minor coat proteins. The top cap complex consists of pVII and pIX, both exhibiting a single helix structure. Arg33 of pVII and Glu29 of pIX, located on the inner surface of the cap, play a key role in recognizing the genome packaging signal. The bottom cap complex is formed by the hook-like structures of pIII and pVI, arranged in helix barrels. Most of the inner ssDNA genome adopts a double helix structure with a similar pitch to that of the A-form double-stranded DNA. These findings provide insights into the assembly of filamentous bacteriophages.

Structure of filamentous viruses

Despite filamentous viruses represent an important portion of the universe of viruses, their 3D structures available are quite limited, particularly if compared to the large number of structures of icosahedral viruses present in the Protein Data Bank. As a matter of fact, flexible filamentous viruses cannot be grown as single crystals and past structural studies have mostly been limited to X-ray fiber diffraction or to the determination of the structure of isolated viral proteins. Only very recently, several structures of filamentous viruses have become available, owing to the recent development of cryo-electron microscopy. This technique has given a strong impulse to the field and has allowed the building of reliable molecular models of entire viruses, in some cases at a nearly atomic resolution level. In this paper we briefly describe the architecture of filamentous viruses that infect bacteria, archaea, plants and humans. It is easy to foresee that more new structures of filamentous viruses will become available soon and they will allow a better understanding of the rules underlying the structural organization of these organisms so relevant for the life on our planet.

Equilibrium phase diagram and thermal responses of charged DNA-virus rod-suspensions at low ionic strengths

The collective behavior of DNA is important for exploring new types of bacteria in the means of detection, which is greatly interested in the understanding of interactions between DNAs in living systems. How they self-organize themselves is a physical common phenomenon for broad ranges of thermodynamic systems. In this work, the equilibrium phase diagrams of charged chiral rods (fd viruses) at low ionic strengths (below a few mM) are provided to demonstrate both replicas of (or self-organized) twist orders and replica symmetry breaking near high concentration glass-states. By varying the ionic strengths, it appears that a critical ionic strength is obtained below 1-2 mM salt, where the twist and freezing of nematic domains diverge. Also, the microscopic relaxation is revealed by the ionic strength-dependent effective Debye screening length. At a fixed low ionic strength, the local orientations of twist are shown by two different length scales of optical pitch, in the chiral-nematic N* phase and the helical domains [Formula: see text], for low and high concentration, respectively. RSB occurs in several cases of crossing phase boundary lines in the equilibrium phase diagram of DNA-rod concentration and ionic strength, including long-time kinetic arrests in the presence of twist orders. The different pathways of PATH I, II and III are due to many-body effects of randomized orientations for charged fd rods undergoing long-range electrostatic interactions in bulk elastic medium. In addition, the thermal stability are shown for chiral pitches of the N* phase and the abnormal cooling process of a specific heat in a structural glass. Here, the concentration-driven twist-effects of charged DNA rods are explored using various experimental methods involving image-time correlation, microscopic dynamics in small angle dynamic light scattering, optical activity in second harmonic generation, and differential scanning calorimetry for the glass state.

Raman and Quantum Yield Studies of Trp48-d5 in Azurin: Closed-Shell and Neutral Radical Species

Isotopologues are valuable vibrational probes that shift features in a vibrational spectrum while preserving the electronic structure of the molecule. We report the vibrational and electronic spectra of perdeuterated tryptophan in solution (l-Trp-d₅), as Trp48-d₅ in azurin, and as the photogenerated neutral tryptophan radical, Trp48-d₅^•, in azurin. The UV resonance Raman bands of the perdeuterated closed-shell tryptophan in solution and in azurin are lower in frequency relative to the protiated counterpart. The observed decrease in frequencies of l-Trp-d₅ bands relative to l-Trp-h₅ enables the analysis of vibrational markers of other amino acids, e.g., phenylalanine, that overlap with some modes of l-Trp-h₅. The Raman intensities vary between l-Trp-d₅ and l-Trp-h₅; these differences likely reflect modifications in normal mode composition upon perdeuteration. Analysis of the W3, W6, and W17 modes suggests that the W3 mode retains its utility as a conformational marker; however, the H-bond markers W6 and W17 appear to be less sensitive upon perdeuteration. The neutral tryptophan radical, Trp48-d₅^•, was generated in azurin with a slightly lower radical quantum yield than for Trp48-h₅^•. The visible resonance Raman spectrum of Trp48-d₅^• is different from that of Trp48-h₅^•, especially in terms of relative intensities, and all assignable peaks decreased in frequency upon perdeuteration. The absorption and emission spectra of the perdeuterated closed-shell and radical species exhibited hypsochromic shifts of less than 1 nm relative to the protiated species. The data presented here indicate that l-Trp-d₅ is a valuable probe of vibrational structure, with minimal modification of photoreactivity and photophysics compared to l-Trp-h₅.

Soft-mode of charged chiral fibrous viruses (fd)

The frictional forces in suspensions vary depending on the size, shape, and the surface of the particles, which are either charged or neutral. For anisotropic particles with no spatial gradient in the order parameter under external parameters, they exhibit either a continuous phase transition or "freezing" of the order parameter fluctuation. They are known as the collective soft-mode, which has a finite cutoff dispersion where the relaxation time diverges. From microscopic dynamics of charged chiral fd-viruses, the soft-mode is revealed with a rotation restoring "twist", obtained from both polarized (VV) and depolarized (VH) small angle dynamic light scattering. Here, I have found the minimum spatial coherence length at a lower I-N binodal concentration, which is due to the reverse of electrostatic repulsive forces with an increase in the concentration of charged chiral rods.

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.

Mechanical stress downregulates MHC class I expression on human cancer cell membrane

In our body, cells are continuously exposed to physical forces that can regulate different cell functions such as cell proliferation, differentiation and death. In this work, we employed two different strategies to mechanically stress cancer cells. The cancer and healthy cell populations were treated either with mechanical stress delivered by a micropump (fabricated by deep X-ray nanolithography) or by ultrasound wave stimuli. A specific down-regulation of Major Histocompatibility Complex (MHC) class I molecules expression on cancer cell membrane compared to different kinds of healthy cells (fibroblasts, macrophages, dendritic and lymphocyte cells) was observed, stimulating the cells with forces in the range of nano-newton, and pressures between 1 and 10 bar (1 bar = 100.000 Pascal), depending on the devices used. Moreover, Raman spectroscopy analysis, after mechanical treatment, in the range between 700–1800 cm⁻¹, indicated a relative concentration variation of MHC class I. PCA analysis was also performed to distinguish control and stressed cells within different cell lines. These mechanical induced phenotypic changes increase the tumor immunogenicity, as revealed by the related increased susceptibility to Natural Killer (NK) cells cytotoxic recognition.

Preliminary investigation of the application of Raman spectroscopy to the prediction of the sensory quality of beef silverside

The potential of Raman spectroscopy for the determination of meat quality attributes has been investigated using data from a set of 52 cooked beef samples, which were rated by trained taste panels. The Raman spectra, shear force and cooking loss were measured and PLS used to correlate the attributes with the Raman data. Good correlations and standard errors of prediction were found when the Raman data were used to predict the panels' rating of acceptability of texture (R(2)=0.71, Residual Mean Standard Error of Prediction (RMSEP)% of the mean (μ)=15%), degree of tenderness (R(2)=0.65, RMSEP% of μ=18%), degree of juiciness (R(2)=0.62, RMSEP% of μ=16%), and overall acceptability (R(2)=0.67, RMSEP% of μ=11%). In contrast, the mechanically determined shear force was poorly correlated with tenderness (R(2)=0.15). Tentative interpretation of the plots of the regression coefficients suggests that the α-helix to β-sheet ratio of the proteins and the hydrophobicity of the myofibrillar environment are important factors contributing to the shear force, tenderness, texture and overall acceptability of the beef. In summary, this work demonstrates that Raman spectroscopy can be used to predict consumer-perceived beef quality. In part, this overall success is due to the fact that the Raman method predicts texture and tenderness, which are the predominant factors in determining overall acceptability in the Western world. Nonetheless, it is clear that Raman spectroscopy has considerable potential as a method for non-destructive and rapid determination of beef quality parameters.

A structural model for the single-stranded DNA genome of filamentous bacteriophage Pf1

The filamentous bacteriophage Pf1, which infects strain PAK of Pseudomonas aeruginosa, is a flexible filament ( approximately 2000 x 6.5 nm) consisting of a covalently closed DNA loop of 7349 nucleotides sheathed by 7350 copies of a 46-residue alpha-helical subunit. The subunit alpha-helices, which are inclined at a small average angle ( approximately 16 degrees ) from the virion axis, are arranged compactly around the DNA core. Orientations of the Pf1 DNA nucleotides with respect to the filament axis are not known. In this work we report and interpret the polarized Raman spectra of oriented Pf1 filaments. We demonstrate that the polarizations of DNA Raman band intensities establish that the nucleotide bases of packaged Pf1 DNA are well ordered within the virion and that the base planes are positioned close to parallel to the filament axis. The present results are combined with a previously proposed projection of the intraviral path of Pf1 DNA [Liu, D. J., and Day, L. A. (1994) Science 265, 671-674] to develop a novel molecular model for the Pf1 assembly.

Monitoring human leukocyte antigen class I molecules by micro-Raman spectroscopy at single-cell level

Human leukocyte antigen (HLA) class I molecules are formed by three immunoglobulin-like domains (alpha1, alpha2, and alpha3) once folded by peptide and beta(2)-microglobulin show the presence of two alpha-helix streams and one beta-sheet limiting the pocket for the antigenic peptide. The loss of HLA class I expression in tumors and virus-infected cells, on one hand, prevents T cell recognition, while on the other hand, it leads to natural killer (NK) cell mediated cytotoxicity. We propose the possibility of using Raman spectroscopy to measure the relative expression of HLA class I molecules at the single-cell level. Raman spectra are recorded for three cell lines (K562, T2, and T3) and monomers (HLA class I folded, unfolded and peptide+beta(2)-microlobulin refolded) using 830 nm laser line. Our data are consistent with the hypothesis that in the Raman spectra, ranging from 1600 to 1800 cm(-1), the intensity variation of cells associated with HLA class I molecules could be measured.

In vivo molecular evaluation of guinea pig skin incisions healing after surgical suture and laser tissue welding using Raman spectroscopy

The healing process in guinea pig skin following surgical incisions was evaluated at the molecular level, in vivo, by the use of Raman spectroscopy. After the incisions were closed either by suturing or by laser tissue welding (LTW), differences in the respective Raman spectra were identified. The study determined that the ratio of the Raman peaks of the amide III (1247 cm(-1)) band to a peak at 1326 cm(-1) (the superposition of elastin and keratin bands) can be used to evaluate the progression of wound healing. Conformational changes in the amide I band (1633-1682 cm(-1)) and spectrum changes in the range of 1450-1520 cm(-1) were observed in LTW and sutured skin. The stages of the healing process of the guinea pig skin following LTW and suturing were evaluated by Raman spectroscopy, using histopathology as the gold standard. LTW skin demonstrated better healing than sutured skin, exhibiting minimal hyperkeratosis, minimal collagen deposition, near-normal surface contour, and minimal loss of dermal appendages. A wavelet decomposition-reconstruction baseline correction algorithm was employed to remove the fluorescence wing from the Raman spectra.

Unfolding thermodynamics of the Delta-domain in the prohead I subunit of phage HK97: determination by factor analysis of Raman spectra

An early step in the morphogenesis of the double-stranded DNA (dsDNA) bacteriophage HK97 is the assembly of a precursor shell (prohead I) from 420 copies of a 384-residue subunit (gp5). Although formation of prohead I requires direct participation of gp5 residues 2-103 (Delta-domain), this domain is eliminated by viral protease prior to subsequent shell maturation and DNA packaging. The prohead I Delta-domain is thought to resemble a phage scaffolding protein, by virtue of its highly alpha-helical secondary structure and a tertiary fold that projects inward from the interior surface of the shell. Here, we employ factor analysis of temperature-dependent Raman spectra to characterize the thermostability of the Delta-domain secondary structure and to quantify the thermodynamic parameters of Delta-domain unfolding. The results are compared for the Delta-domain within the prohead I architecture (in situ) and for a recombinantly expressed 111-residue peptide (in vitro). We find that the alpha-helicity (approximately 70%), median melting temperature (T(m)=58 degrees C), enthalpy (DeltaH(m)=50+/-5 kcal mol(-1)), entropy (DeltaS(m)=150+/-10 cal mol(-1) K(-1)), and average cooperative melting unit (n(c) approximately 3.5) of the in situ Delta-domain are altered in vitro, indicating specific interdomain interactions within prohead I. Thus, the in vitro Delta-domain, despite an enhanced helical secondary structure ( approximately 90% alpha-helix), exhibits diminished thermostability (T(m)=40 degrees C; DeltaH(m)=27+/-2 kcal mol(-1); DeltaS(m)=86+/-6 cal mol(-1) K(-1)) and noncooperative unfolding ( approximately 1) vis-à-vis the in situ Delta-domain. Temperature-dependent Raman markers of subunit side chains, particularly those of Phe and Trp residues, also confirm different local interactions for the in situ and in vitro Delta-domains. The present results clarify the key role of the gp5 Delta-domain in prohead I architecture by providing direct evidence of domain structure stabilization and interdomain interactions within the assembled shell.

Raman spectroscopy of protein pharmaceuticals

Recent advances in optical and spectroscopic technologies have enabled a plethora of Raman spectrometers that are suitable for studies of protein pharmaceuticals. Highly sensitive Raman spectrometers have overcome the handicap of the fundamentally weak Raman effect that hampered their applications to protein pharmaceuticals in the past. These Raman spectrometers can now routinely measure protein therapeutics at the low concentration of 1 mg/mL, which is on par with other spectroscopic methods such as CD, fluorescence and FTIR spectroscopies. In this article, various Raman techniques that can be used for protein pharmaceutical studies are reviewed. Novel Raman marker of proteins discovered from fundamental studies of protein complexes are examined along with established Raman spectra and structure correlations. Examples of Raman spectroscopic studies of protein pharmaceuticals are demonstrated. Future applications of Raman spectroscopy to protein pharmaceuticals are discussed.

Analysis of structural changes in permanent waved human hair using Raman spectroscopy

To investigate the mechanism leading to the reduction in tensile strength of permanent waved human hair, the structure of cross-sections at various depths of permanent waved white human hair was directly analyzed without isolating the cuticle and cortex, using Raman spectroscopy. The beta-sheet and/or random coil content (beta/R) and the Amide III(unordered) band intensity existing throughout the cortex region of virgin white human hair remarkably increased, while the alpha-helix (alpha) content slightly decreased by performing the permanent waving treatment. This suggests a secondary structural change from the alpha-helix form to the random coil form in the proteins existing in the microfibril of the cortex region. On the other hand, the S-S band intensity existing in the matrix of the cortex region almost did not change, despite the reduction in the tensile strength of the white human hair following the permanent waving treatment. Moreover, the transmission electron microscope observation shows that the macrofibril (the microfibril and matrix) existing in the cortex region of the virgin white human hair was remarkably disturbed, while the cuticle region was almost unchanged by performing the permanent waving treatment. From these experiments, the authors concluded that some of proteins existing in the cortex region (the microfibril and matrix) of the virgin white human hair were changed, thereby leading to the remarkable reduction in the tensile strength of the white human hair after the permanent waving treatment.

Analysis of internal structure changes in black human hair keratin fibers with aging using Raman spectroscopy

To investigate the internal structure changes in virgin black human hair keratin fibers due to aging, the structure of cross-sections at various depths of virgin black human hair (sections of new growth hair: 2 mm from the scalp) from a group of eight Japanese females in their twenties and another group of eight Japanese females in their fifties were analyzed using Raman spectroscopy. For the first time, we have succeeded in recording the Raman spectra of virgin black human hair, which had been impossible due to high melanin granule content. The key points of this method are to cross-section hair samples to a thickness of 1.50-microm, to select points at various depths of the cortex with the fewest possible melanin granules, and to optimize laser power, cross slit width as well as total acquisition time. The reproducibility of the Raman bands, namely the alpha-helix (alpha) content, the beta-sheet and/or random coil (beta/R) content, the disulfide (--SS--) content, and random coil content of two adjoining cross-sections of a single hair keratin fiber was clearly good. The --SS-- content of virgin black human hair from the Japanese females in their fifties for the cortex region decreased compared with that of the Japanese females in their twenties. On the other hand, the beta/R and alpha contents of the cortex region did not change.

Structural basis of the temperature transition of Pf1 bacteriophage

The filamentous bacteriophage Pf1 undergoes a reversible temperature-dependent transition that is also influenced by salt concentrations. This structural responsiveness may be a manifestation of the important biological property of flexibility, which is necessary for long, thin filamentous assemblies as a protection against shear forces. To investigate structural changes in the major coat protein, one- and two-dimensional solid-state NMR spectra of concentrated solutions of Pf1 bacteriophage were acquired, and the structure of the coat protein determined at 0 degrees C was compared with the structure previously determined at 30 degrees C. Despite dramatic differences in the NMR spectra, the overall change in the coat protein structure is small. Changes in the orientation of the C-terminal helical segment and the conformation of the first five residues at the N-terminus are apparent. These results are consistent with prior studies by X-ray fiber diffraction and other biophysical methods.

Protein structural changes in keratin fibers induced by chemical modification using 2-iminothiolane hydrochloride: A Raman spectroscopic investigation

For the purpose of investigating in detail the influence of chemical modification using 2-iminothiolane hydrochloride (2-IT) on keratin fibers, the structure of cross-sections at various depths of white human hair, treated with 2-IT and then oxidized, was directly analyzed without isolating the cuticle and cortex, using Raman spectroscopy. In particular, the beta-sheet and/or random coil content (beta/R) and the alpha-helix (alpha) content in human hair fibers were estimated by amide I band analysis. The S-S band intensity, amide III (unordered) band intensity, and beta/R content existing from the cuticle region to the center of cortex region of virgin white human hair remarkably increased by performing the chemical modification using 2-IT. On the other hand, not only the S-S band intensity, but also S-O band intensity existing throughout the cortex region of the bleached (damaged) white human hair increased by performing chemical modification using 2-IT. In particular, beta/R content existing throughout the cortex region of the bleached white human hair decreased, while the skeletal C-C stretch (alpha) band intensity at 935 cm(-1) and the alpha content remarkably increased. This indicates a secondary structural change from the random coil form to the alpha-helix form in the proteins existing throughout the cortex region. From these experiments, we concluded that the formation of new disulfide (-SS-) groups resulting from chemical modification using 2-IT induced the secondary structural changes of proteins existing throughout the cortex region.

Deep-UV Raman spectrometer tunable between 193 and 205 nm for structural characterization of proteins

A new deep-UV Raman spectrometer utilizing a laser source tunable between 193 and 205 nm has been designed, built, and characterized. Only selected wavelengths from this range have previously been accessible, by Raman shifting of the second, third, and fourth harmonics of the Nd:YAG fundamental in hydrogen. The apparatus was demonstrated to be a useful tool for characterizing hen egg white lysozyme structural rearrangements at various stages of fibril formation. High-quality deep-UV resonance Raman spectra were obtained for both a protein solution and a highly-scattering gelatinous phase formed by fibrillogenic species. In addition to amide bands, strong contribution of nu(12) and ring-C phenylalanine vibrational modes was observed at excitation wavelengths below 200 nm. Remarkably, the Raman cross-section of these modes revealed dramatic change of lysozyme in response to heat denaturation and fibril formation. These results indicate that phenylalanine could serve as a new deep-UV Raman probe of protein structure.

Adsorption of S-S containing proteins on a colloidal silver surface studied by surface-enhanced Raman spectroscopy

We present a Raman and surface-enhanced Raman scattering (SERS) study of the following proteins containing S-S group(s): alpha chymotrypsin (alpha-CHT), insulin, lysozyme, oxytocin (OXT), Streptomyces subtilisin inhibitor (SSI), and trypsin inhibitor (STI). The SERS study is performed in order to understand the adsorption mechanism of the above-mentioned proteins on a colloidal silver surface. The SERS spectra presented here show bands associated mainly with aromatic amino acid vibrations. In addition, two distinct vibrations of the -C-S-S-C- fragment are observed in the Raman and SERS spectra, i.e., nu(SS) and nu(CS). The enhancement of the nu(SS) vibration in the SERS spectra yields evidence that the intact disulfide bridge(s) is (are) located near the silver surface. This finding is supported by the presence of the nu(CS) mode(s). The presence of nus(COO-) and nu(C-COO-) in the SERS spectra in the 1384-1399 cm(-1) and 909-939 cm(-1) regions, respectively, indicate that the negatively charged COO- groups (aspartic and glutamic acids) assist in the binding on the positively charged silver surface. The Raman amide I and III bands observed in the 1621-1633 and 1261-1289 cm(-1) ranges, respectively, indicate that the alpha-helical conformation is favored for binding to the surface over the random coil or beta-sheet conformations. In addition, the presence of the imino group of Trp and/or His indicates that these amino acid residues may also bind to the silver sol.

Nonresonant confocal Raman imaging of DNA and protein distribution in apoptotic cells

Nonresonant confocal Raman imaging has been used to map the DNA and the protein distributions in individual single human cells. The images are obtained on an improved homebuilt confocal Raman microscope. After statistical analysis, using singular value decomposition, the Raman images are reconstructed from the spectra covering the fingerprint region. The data are obtained at a step interval of approximately 250 nm and cover a field from 8- to 15- micro m square in size. Dwell times at each pixel are between 0.5 and 2 s, depending on the nature and the state of the cell under investigation. High quality nonresonant Raman images can only be obtained under these conditions using continuous wave high laser powers between 60 and 120 mW. We will present evidence that these laser powers can still safely be used to recover the chemical distributions in fixed cells. The developed Raman imaging method is used to image directly, i.e., without prior labeling, the nucleotide condensation and the protein distribution in the so-called nuclear fragments of apoptotic HeLa cells. In the control (nonapoptotic) HeLa cells, we show, for the first time by Raman microspectroscopy, the presence of the RNA in a cell nucleus.

Structure of the coat protein in fd filamentous bacteriophage particles determined by solid-state NMR spectroscopy

The atomic resolution structure of fd coat protein determined by solid-state NMR spectroscopy of magnetically aligned filamentous bacteriophage particles differs from that previously determined by x-ray fiber diffraction. Most notably, the 50-residue protein is not a single curved helix, but rather is a nearly ideal straight helix between residues 7 and 38, where there is a distinct kink, and then a straight helix with a different orientation between residues 39 and 49. Residues 1-5 have been shown to be mobile and unstructured, and proline 6 terminates the helix. The structure of the coat protein in virus particles, in combination with the structure of the membrane-bound form of the same protein in bilayers, also recently determined by solid-state NMR spectroscopy, provides insight into the viral assembly process. In addition to their roles in molecular biology and biotechnology, the filamentous bacteriophages continue to serve as model systems for the development of experimental methods for determining the structures of proteins in biological supramolecular assemblies. New NMR results include the complete sequential assignment of the two-dimensional polarization inversion spin-exchange at the magic angle spectrum of a uniformly 15N-labeled 50-residue protein in a 1.6 x 107 Da particle in solution, and the calculation of the three-dimensional structure of the protein from orientational restraints with an accuracy equivalent to an rms deviation of approximately 1A.

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.

New structural insights from Raman spectroscopy of proteins and their assemblies

Protein structure and stability are sensitive to and dependent on the local interactions of amino acid side chains. A diverse and important type of side-chain interaction is the hydrogen bond. Although numerous hydrogen bonds are resolved in protein 3-dimensional structures, those of the cysteine sulfhydryl group (S-H) are elusive to high-resolution X-ray and NMR methods. However, the nature and strength of sulfhydryl hydrogen bonds (S-H* * *X) are amenable to investigation by Raman spectroscopy. The power of the Raman method for characterizing S-H* * *X interactions is illustrated by resolving the Raman S-H stretching band for each of the eight cysteines per 666-residue subunit in the trimeric tailspike of icosahedral bacteriophage P22. The Raman sulfhydryl signatures of the wild-type tailspike and eight single-site cysteine to serine mutants reveal a heretofore unrecognized diversity of S-H hydrogen bonds in a native protein. The use of Raman spectroscopy to identify the non-hydrogen-bonded state of the tyrosine phenoxyl group is also described. This unusual and unexpected state occurs for all tyrosines in the assembled capsids of filamentous viruses Ff and Pf1. The Raman spectral signature of the non-hydrogen-bonded tyrosine phenoxyl, which is characterized by an extraordinary Raman Fermi doublet intensity ratio (I850/I830 = 6.7), extends and refines the existing correlation for hydrogen-bonded tyrosines. Finally, a novel Raman signature for tryptophan in the Pf3 filamentous virus is identified, which is proposed as diagnostic of "cation-pi interaction" involving the guanidinium group of Arg 37 as a cation donor and the indolyl ring of Trp 38 as a pi-electron acceptor. These studies demonstrate the power of Raman spectroscopy for investigating the interactions of key side chains in native protein assemblies.

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.

The analysis of Merino wool cuticle and cortical cells by Fourier transform Raman spectroscopy

Wool fibers are comprised of proteins known as alpha-keratins and have a complex morphological structure. The major components of this structure, the cuticle and cortical cells, differ in the conformations of their chains as well as their amino acid compositions. High quality Fourier transform Raman spectra of cortical and cuticle cells isolated from fine Merino wool fibers have been obtained. Raman spectroscopy has been shown to be sensitive to the differences in both secondary structure and amino acid composition. The cortical cells were found to be higher in alpha-helical content as compared to the cuticle cells, which had an increased disordered content. Specific information, consistent with amino acid analysis results, regarding cystine, tyrosine, tryptophan, and phenylalnine residues, were obtained for both the cortical and cuticle cells. In addition, the Raman spectra provided information about free thiol groups, amino acids residues with amide group side chains, and residues with protonated carboxyl group side chains. Middle ir transmission spectra of these isolated cells were also obtained. In comparison to the Raman data, the middle ir spectra were found to be not as rich in information.

Epitope structures recognised by antibodies against the major coat protein (g8p) of filamentous bacteriophage fd (Inoviridae)

To map the accessible surface of filamentous bacteriophage fd particles, the epitope structures of polyclonal rabbit serum and three mouse monoclonal antibodies raised against complete phage were analysed. Western blot analysis confirmed the major coat protein, gene VIII product (g8p or pVIII), to be the antigen. Overlapping peptides were synthesised by spot synthesis on cellulose membranes, covering the whole sequence of g8p. Each of the three tested monoclonal antibodies, B62-FE2, B62-GF3/G12 and B62-EA11, reacted with a core epitope covering ten amino acid residues at or near the amino terminus of g8p. The epitope recognised by B62-FE2 consists of the ten N-terminal amino acid residues of g8p. Extension of the amino terminus by various sequences did not inhibit binding, indicating that a terminal amino group is not essential for the interaction. Both B62-GF3/G12 and B62-EA11 recognise internal epitopes covering amino acid residues 3 to 12 of g8p. The epitopes of the polyclonal rabbit serum were also confined to the 12 N-terminal amino acid residues. The contribution of individual amino acid residues to the binding was analysed by a set of peptides containing individual amino acids exchanged by glycine. Accessible residues were Glu2, Asp4, Asp5, Pro6, Lys8, Phe11 and Asp12. The positions of the essential amino acid residues within the epitope are in accordance with a helical conformation of the amino-terminal region of g8p. Further, the results suggest new designs of phage display screening vectors to improve their performance in analysing non-linear epitopes.

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.

Structure of the capsid of Pf3 filamentous phage determined from X-ray fibre diffraction data at 3.1 A resolution

We have recorded X-ray diffraction patterns at 3.1 A resolution from magnetically aligned fibres of the Pf3 strain of filamentous bacteriophage (Inovirus). The patterns are similar to patterns from the higher-temperature form of the Pf1 strain, indicating that the Pf3 and Pf1 virions have the same helix symmetry and similar protein subunit shape. This is of particular interest, given that the primary structures of the two protein subunits are quite different; and the nucleotide/protein subunit ratio in the Pf3 virion is more than twice that in Pf1, indicating important differences in DNA packaging. We have built a molecular model of the Pf3 protein capsid based on the model of Pf1, and refined it against the diffraction data using simulated annealing. The refinement confirms that the two structures are similar, which may reflect a fundamental motif of alpha-helix packing. However, there are some differences between the structures: the Pf3 subunit appears to be completely alpha-helical, beginning at the N terminus, whereas the first few residues of the Pf1 subunit are not helical; and the structure of the C-terminal region of the Pf3 subunit at the inner surface of the tubular capsid indicates that DNA/protein interactions in this virion may involve both aromatic side-chains and positively charged side-chains, whereas those in the Pf1 virion involve predominantly only the latter. In the course of this work, we have developed new approaches to refinement and validation of helical structures with respect to continuous transform fibre diffraction data.

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.

Changes of phage T7 nucleoprotein structure at low ionic strength. A Raman spectroscopic study

To detect changes in DNA and/or protein structures of phage T7 under different ionic strength, Raman spectra of phage T7 have been recorded in solutions of three different NaCl + Tris concentrations. Iterative Jansson-Van Cittert deconvolution, as well as decomposition methods have been used to quantify changes in DNA structure. Significant modifications in ratios of contributions from 675 and 685 per cm vibrations, as well as in the DNA backbone vibrations, characteristic for B-DNA, near 835 per cm frequency have been found. Changes of the base electronic structure were identified in the interval between 1280 and 1400 cm(-1). Estimation of the overall protein structure suggests predominant beta-sheet content.

FT-IR spectroscopy of the major coat protein of M13 and Pf1 in the phage and reconstituted into phospholipid systems

FT-IR spectroscopy has been applied to study the secondary structure of the major coat protein of Pf1 and M13 as present in the phage and reconstituted in DOPG and mixed DOPC/DOPG (4/1) bilayers. Infrared absorbance spectra of the samples were examined in dehydrated films and in suspensions of D2O and H2O. The secondary structure of the coat protein is investigated by second-derivative analysis, Fourier self-deconvolution, and curve fitting of the infrared bands in the amide I region (1600-1700 cm-1). It is found that, in dehydrated films of Pf1 and M13 phage, the amide I region contains three bands located at about 1633, 1657, and 1683 cm-1, that are assigned to hydrogen-bonded turn, alpha-helix/random coil, and non-hydrogen-bonded turn, respectively. From a comparison of the infrared spectra in dehydrated film with those in aqueous suspension, the percentages of secondary structure were found with an accuracy of about +/- 5%. For the coat protein of Pf1 phage, the FT-IR quantification gives 69% alpha-helix conformation, 19% turn structure, and 12% random coil structure. For Pf1 coat protein in the membrane-embedded state, the amount of alpha-helix is 57%, whereas 42% is in a turn structure and 1% in a random coil structure. The same assignment strategy was used for the analysis of the data obtained for M13 coat protein reconstitution into phospholipid systems. For M13 coat protein in the phage, this gives 75% alpha-helix conformation, 21% turn structure, and 4% random coil structure.(ABSTRACT TRUNCATED AT 250 WORDS)

Pf1 virus structure: helical coat protein and DNA with paraxial phosphates

The helical path of the DNA in filamentous bacteriophage Pf1 was deduced from different kinds of existing structural information, including results from x-ray fiber diffraction. The DNA has the same pitch, 16 angstroms, as the surrounding helix of protein subunits; the rise and rotation per nucleotides are 6.1 angstroms and 132 degrees, respectively; and the phosphates are 2.5 angstroms from the axis. The DNA in Pf1 is, therefore, the most extended and twisted DNA structure known. On the basis of the DNA structure and extensive additional information about the protein, a model of the virion is proposed. In the model, the DNA bases reach out, into the protein, and the lysine and arginine side chains reach in, between the DNA bases, to stabilize the paraxial phosphate charges; the conformation of the protein subunit is a combination of alpha and 3(10) helices.

Ultraviolet absorbance and circular dichroism of Pf1 virus: nucleotide/subunit ratio of unity, hyperchromic tyrosines and DNA bases, and high helicity in the subunits

Data have been obtained for the Pf1 virion that establish its stoichiometry and conformational features of its DNA and its protein. The absorbance spectrum of the dissociated virus under alkaline denaturing conditions is fit exactly by spectra for DNA and protein at a mole ratio of one nucleotide per protein subunit. This result, together with three previous values by independent methods, establishes that the nucleotide/subunit ratio (n/s) of Pf1 is unity. The absorbance spectrum of DNA in the intact native virus is assigned as the spectrum for heat denatured Pf1 DNA, with epsilon (P) = 8400 M-1 cm-1 at 259 nm. The absorbance spectrum assigned to protein (two tyrosines) in the intact virus has <epsilon (Y)> = 2500 M-1 cm-1 per tyrosine at lambda max of 281.5 nm; this is the most red-shifted and hyperchromic tyrosine spectrum known. The CD spectrum of the intact virus from 250 to 320 nm has no apparent DNA contribution, but has a strong contribution from the red-shifted tyrosine(s). The CD spectrum from 185 to 250 nm has the shape of alpha-helical CD reference spectra, but is perceptibly blue-shifted, with a crossover from negative to positive ellipticity at 199.7 nm, and it has very high amplitudes (e.g. [theta 207.5nm] = -44,000 deg cm2 dmol-1). This spectrum indicates completely helical protein in the virus, with a predominance of alpha-helix and perhaps some 3(10)-helix. The unit n/s ratio, the high absorbance and negligible near-UV CD for the DNA bases, and the high amplitudes for the helical protein are critical input data for the determination of Pf1 virus structure.

Molecular models and structural comparisons of native and mutant class I filamentous bacteriophages Ff (fd, f1, M13), If1 and IKe

The filamentous bacteriophages are flexible rods about 1 to 2 microns long and 6 nm in diameter, with a helical shell of protein subunits surrounding a DNA core. The approximately 50-residue coat protein subunit is largely alpha-helix and the axis of the alpha-helix makes a small angle with the axis of the virion. The protein shell can be considered in three sections: the outer surface, occupied by the N-terminal region of the subunit, rich in acidic residues that interact with the surrounding solvent and give the virion a low isoelectric point; the interior of the shell, including a 19-residue stretch of apolar side-chains, where protein subunits interact mainly with each other; and the inner surface, occupied by the C-terminal region of the subunit, rich in basic residues that interact with the DNA core. The fact that virtually all protein side-chain interactions are between different subunits in the coat protein array, rather than within subunits, makes this a useful model system for studies of interactions between alpha-helix subunits in a macromolecular assembly. We describe molecular models of the class I filamentous bacteriophages. This class includes strains fd, f1, M13 (these 3 very similar strains are members of the Ff group), If1 and IKe. Our model of fd has been refined to fit quantitative X-ray fibre diffraction data to 30 A resolution in the meridional direction and 7 A resolution in the equatorial direction. A simulated 3.3 A resolution diffraction pattern from this model has the same general distribution of intensity as the experimental diffraction pattern. The observed diffraction data at 7 A resolution are fitted much better by the calculated diffraction pattern of our molecular model than by that of a model in which the alpha-helix subunit is represented by a rod of uniform density. The fact that our fd model explains the fd diffraction data is only part of our structure analysis. The atomic details of the model are supported by non-diffraction data, in part previously published and in part newly reported here. These data include information about permitted or forbidden side-chain replacements, about the effect of chemical modification, and about spectroscopic experiments.(ABSTRACT TRUNCATED AT 400 WORDS)

Secondary structure of M13 coat protein in phospholipids studied by circular dichroism, Raman, and Fourier transform infrared spectroscopy

There is considerable uncertainty about the precise secondary structure adopted by the M13 coat protein when embedded in a phospholipid bilayer. Circular dichroism (CD) spectroscopy suggests that a major change in the structure of the coat protein occurs upon membrane insertion. It is reported that the structure of the protein in the membrane has only about 50% alpha-helix, the rest being mainly in a beta-sheet conformation, whereas the protein is almost completely alpha-helical when intact in the phage. In this study we have undertaken a spectroscopic analysis using Fourier transform infrared, Raman, and CD spectroscopy to characterize the secondary structure of M13 coat protein when present in membranes consisting of dioleoylphosphatidylglycerol and dimyristoylphosphatidylglycerol. In sharp contrast to earlier CD studies, our results indicate that the coat protein in its membrane-embedded state has a very high alpha-helical content with virtually no beta-sheet structures present. This result indicates that the structures of the coat protein when intact in the phage or when embedded in the membrane are similar. Although our results differ from earlier CD studies, they are consistent with a recent NMR study, which showed that the M13 coat protein in sodium dodecyl sulfate micelles is primarily alpha-helical with no evidence for beta-sheet structure [Henry, G. D., & Sykes, B.D. (1992) Biochemistry 31, 5284-5297]. These results lead to the conclusion that the M13 coat protein can insert from the membrane-bound state into a virus particle with a similar secondary structure, without large energy implications.(ABSTRACT TRUNCATED AT 250 WORDS)

A Raman spectroscopic study of acetylcholine receptor-rich membranes from Torpedo marmorata. Interaction of the receptor with carbamylcholine and (+)-tubocurarine

Raman spectroscopy is used to determine structural features of alkali-treated subsynaptic membrane fragments from Torpedo marmorata electric organ, rich in native functional AcChR. Distinct vibrations attributable to the membrane proteins and lipids were identified and studied before and after addition of the agonist carbamylcholine and the competitive antagonist (+)-tubocurarine. The protein secondary structure determined by using amide-I polypeptide vibrational analysis, indicates 47% alpha-helices, 25% beta-sheets, 18% turns and 11% undefined structure. The secondary structure of the AcChR molecule was not subject to large modifications upon addition of carbamylcholine. But, the presence of the (+)-tubocurarine leads to detectable changes in the amide-I region which might be interpreted as reflecting different contributions of alpha-helices and turns in the secondary structure. In addition, Raman spectra provide information about the environment of aromatic amino acids (tyrosine and tryptophan), the (C-C) bonds, the CH2 and CH3 groups of aliphatic side chains, as well as the disulfide (S-S) and cystein (C-S) bonds. The tyrosines seem 'exposed' to the aqueous medium. The Raman spectra of the AcChR-carbamylcholine complex suggest 'exposed' tryptophans, while those of the unliganded membrane-bound AcChR or of the receptor with (+)-tubocurarine are shown 'buried'. The disulfide bridges in the AcChR subunits show identical conformation in the absence and presence of carbamylcholine. On the contrary, considerable changes are found in the AcChR-(+)-tubocurarine complex. Carbamylcholine and especially (+)-tubocurarine decrease lipid fluidity.

Subunit conformational changes accompanying bacteriophage P22 capsid maturation

In double-stranded DNA bacteriophages, packaging of dsDNA requires the transformation of a precursor procapsid into a mature viral capsid. Lattice expansion and release of scaffolding subunits accompanying DNA packaging. Three-dimensional structures of procapsid and mature phage lattices demonstrate that the capsid transformation involves substantial changes in subunit environment. Since this transformation occurs without subunit dissociation, it represents a transition between at least two stable subunit conformations. Using Raman spectroscopy, we have identified changes in coat protein secondary structure and side-chain environments which accompany the capsid transformation. The subunits of procapsid shells contain only 2.0 +/- 0.4% more alpha-helix and less beta-sheet than those of mature capsids; however, numerous side chains are substantially altered by the transformation, including tyrosines, tryptophans, phenylalanines, and aliphatics, which are widely distributed through the subunit sequence. We propose, therefore, that procapsid expansion is accomplished through the relative motion of coat subunit domains with little change in secondary structure. Such hinge-bending conformational transitions may couple ATP-dependent dsDNA condensation with shell expansion.