Structural studies of cucumber mosaic virus: Fourier transform infrared spectroscopic studies.

The secondary structure of cucumber mosaic virus (CMV) was investigated in solution using Fourier transform infrared (FT-IR) spectroscopy. The amide I region of intact CMV revealed a doublet at 1671 cm-1 and 1653 cm-1, respectively. In order to isolate the IR bands arising from the protein backbone of CMV, the FT-IR spectra of the RNA component, isolated by phenol-SDS treatment of purified CMV and subsequent precipitation by ethanol, was obtained separately and digitally subtracted from the intact CMV spectra. After digital subtraction, the amide I region contained two bands at 1682 cm-1 and 1644 cm-1. The former band was ascribed to beta-sheet structures, while the later band occurs in the region between alpha-helix and "unordered" structures. Resolution enhancement of the finger print amide I region was accomplished using Fourier self-deconvolution of the digitally subtracted FT-IR spectrum of CMV which further confirmed the presence of anti-parallel beta-sheet structure in the protein coat of CMV. Chou-Fasman predictions on the the coat protein also revealed the presence of beta-sheet structure in agreement with FT-IR studies.

Fusion between retinal rod outer segment membranes and model membranes: a role for photoreceptor peripherin/rds.

Peripherin/rds plays an essential role in the maintenance of photoreceptor rod cell disk membrane structure. The purification of this protein to homogeneity [Boesze-Battaglia, K., et al. (1997) Biochemistry 36, 6835-6846] has allowed us to characterize the functional role of peripherin/rds in the maintenance of rod outer segment (ROS) membrane fusion processes. Utilizing a cell-free fusion assay system, we report that the fusion of R18-labeled ROS plasma membrane (R18-PM) with disk membranes or peripherin/rds-enriched large unilammellar vesicles (LUVs) is inhibited upon trypsinolysis of peripherin/rds. To understand this phenomenon, we tested the ability of a series of overlapping synthetic C-terminal peripherin/rds peptides to mediate model membrane fusion. Within the 63 amino acid long region of the C-terminus, we identified a minimal 15 residue long amino acid sequence (PP-5), which is necessary to promote membrane fusion. PP-5 was able to inhibit R18-PM disk membrane fusion and promoted ANTS/DPX contents mixing in a pure vesicle system. This peptide (PP-5) promoted calcium-induced vesicle aggregation of phosphatidylethanolamine:phosphatidylserine LUVs. FTIR analysis confirmed the structural prediction of this peptide as alpha-helical. When modeled as an alpha-helix, this peptide is amphiphilic with a hydrophobicity index of 0.75 and a hydrophobic moment of 0.59. PP-5 has substantial biochemical and functional homology with other well-characterized membrane fusion proteins. These results demonstrate the necessity for peripherin/rds in ROS membrane fusion, specifically the requirement for an intact C-terminal region of this protein.

Purification and light-dependent phosphorylation of a candidate fusion protein, the photoreceptor cell peripherin/rds.

The proteins peripherin/rds and rom-1 form a protein complex in the rims of photoreceptor outer segment disk membranes. Peripherin/rds plays an essential role in the morphogenesis and maintenance of disk membrane structure, with peripherin/rds gene mutations resulting in photoreceptor cell degeneration. We report two different chromatographic procedures for the purification of native peripherin/rds from bovine photoreceptor cell outer segments and show that the protein is a phosphoprotein that promotes membrane fusion in vitro. During one procedure, peripherin/rds was copurified in association with rom-1 by hyroxylapatite and Mono Q FPLC. During the other, it was purified free from rom-1 by concanavalin-A affinity chromatography and chromatofocusing. Analysis of homogeneous peripherin/rds from the second procedure showed that exposure of photoreceptor outer segments to light resulted in the incorporation of nearly 2 mol of phosphate per mole of peripherin/rds and a concomitant shift in the isoelectric point of the protein. In addition, we found that recombination of purified peripherin/rds into lipid vesicles increased membrane fusion, with more rapid fusion detected with phosphorylated peripherin/rds. In conclusion, studies with purified peripherin/rds reveal that the protein undergoes light-dependent phosphorylation and that it may function in membrane fusion.

Role of cholesterol in the structural order of lens membrane lipids.

Cholesterol may order or disorder phospholipids. The physiological contribution of cholesterol to the structural order of lens membrane lipids was determined. Cholesterol and phospholipid from bovine lens nuclear and cortical tissue were separated by thin layer chromatography. The effect of cholesterol upon the trans to gauche transition of the hydrocarbon chains was assessed by measuring CH2 infrared stretching band frequencies as cholesterol was added back to the phospholipids. Although the relative cholesterol level of nuclear lipid was much higher than that of the cortex (59 vs. 36 mol%, respectively), the structural order of unfractionated nuclear and cortical lipids were similar at physiological temperature. Cholesterol added to lipids devoid of cholesterol produced a sharp biphasic effect on the structural order of nuclear lipids, increasing the trans conformation from 56% to 0 mol% cholesterol to 74% at 18% cholesterol to 41% trans at 59 mol% cholesterol. Cholesterol addition produced a shallow biphasic change in the percentage trans conformation of cortical lipids. Maximum order (about 40% trans conformation) was seen at a cholesterol level equal to that of intact cortical lipid (36 mol%). The physiological role of cholesterol is to increase the structural order of cortical membrane lipid and decrease order in nuclear lipid. The net result is a similarity in the structural order of cortical and nuclear membrane. We suggest that the different response of cortical and nuclear lipids to added cholesterol is linked to differences in the phospholipid composition between these two lens regions. In the absence of cholesterol, nuclear phospholipids are much more highly ordered than those of the cortex.

Lipid-protein interactions in human and bovine lens membranes by Fourier transform Raman and infrared spectroscopies.

In other systems, proteins have been shown to alter the molecular structures of lipids in the cell membrane bilayer. We wished to determine if proteins altered the structure of lens lipids. The structure of lipid hydrocarbon chains in urea purified human lens membrane vesicles containing intrinsic, hydrophobically bound proteins was compared to the structure of lipids in vesicles without protein. Fourier transform Raman spectroscopy was used to characterize lipid and protein structure. To study lipid interactions with extrinsic, surface bound proteins, the lipid structure was compared in bovine lipid vesicles with and without alpha-crystallin bound to the surface of the membrane. Lipid structure was studied using Fourier transform infrared spectroscopy. No change in lipid structure was detected even at protein/lipid weight ratios of two to one. Human lens intrinsic proteins contained a high amount of a helical structure (60%), but did not alter hydrocarbon chain interactions.

Interactions and molecular structure of cardiolipin and beta 2-glycoprotein 1 (beta 2-GP1).

beta 2-GP1 is a serum protein which influences binding of anticardiolipin antibodies to cardiolipin, may influence induction of these antibodies in animals and may play a role in anticardiolipin-mediated thrombosis. Various investigators have proposed that when beta 2-GP1 binds cardiolipin, structural alterations occur in one or both molecules, resulting in exposure of new epitopes for anticardiolipin binding, but there has been no proof that such alterations occur. Utilizing Fourier transform infrared spectroscopy, this study analysed the structure of cardiolipin and beta 2-GP1 alone, then mixed with each other. For pure cardiolipin, analysis of the CH2 stretching, scissoring and carbonyl bands suggested this molecule assumes a hexagonal crystal lattice packing structure in both anhydrous and aqueous samples. Based on the second derivative analysis of the amide 1 band from the beta 2-GP1 protein backbone, as well as Fourier self-deconvolution and curve fit algorithms, beta 2-GP1 was calculated to contain 18% turns, 37% alpha-helix, and 45% beta-sheet structure. beta 2-GP1 binding with cardiolipin results in a significant change in the conformation as well as geometry of the lipid and protein components. This is indicated by a broadening of the CH stretching band and a marked shift in intensity of the carbonyl band of cardiolipin, indicating less hydrogen bonding. There was a decrease in beta-sheet structure of beta 2-GP1 from 46% to 23% and appearance of 26% to 28% random structure. These findings indicate that mixing beta 2-GP1 with cardiolipin results in profound changes in both molecules which might explain the effect of beta 2-GP1 on anticardiolipin binding activity.

Structural characterization of clear human lens lipid membranes by near-infrared Fourier transform Raman spectroscopy.

Regional differences in human lens membrane lipid composition have been documented and could be responsible for alterations in the function of lens membranes. The phospholipid composition of epithelial membranes of human lenses has been shown to be different from that of fiber membranes. To establish lipid composition-membrane structure relationships, we have examined spectroscopically the structure of lipid membranes from human lens epithelium, cortex and nucleus. Near-infrared Fourier transform Raman spectroscopy was used to obtain the lipid structure of membranes in which the lipid composition was determined previously by 31P-NMR. The disorder (fluidity measured structurally) of the epithelium was evaluated to be 80%, whereas that of the lipids from the cortical and nuclear regions was 55%. The large size of the band at 1650 cm-1 arising from sphingolipids supported the compositional studies which indicate that the major component of human lens membranes is a sphingolipid. Sphingolipids probably account for the high degree of lipid order found in lens membranes. Epithelial membranes were found to contain more glycerolipids and less sphingolipids than fiber cell membranes. This compositional difference would be expected to disorder the epithelial membrane.

Spectral characterization of lipid peroxidation in rabbit lens membranes induced by hydrogen peroxide in the presence of Fe2+/Fe3+ cations: a site-specific catalyzed oxidation.

The role of free-radical-induced lipid peroxidation (LPO) in relation to lens opacity is investigated using Fourier transform infrared spectroscopy. Phospholipids extracted from nuclear and cortical regions of the rabbit lens membranes are subjected to oxidative-damage induced by hydrogen peroxide and Fe2+/Fe3+ cations. Vibrational data suggest a homolytic decomposition of the unsaturated membrane hydrocarbon chains at cis-double bonds, as well as structural modifications at the carbonyl and phosphate-oxygen sites of the fiber cell membranes upon metal oxidation. This is also evident from a substantial induction of the carbonyl groups and a significant dephosphorylation of the phosphate groups in lens phospholipids. These covalent modifications and/or alterations of the carbonyl and phosphate groups, and specificity of certain vibrational modes only to iron oxidation, may serve as a diagnostic probe of the metal-catalyzed LPO in lens membranes. Despite covalent modifications of the hydrophilic part of the lens membranes, hydrocarbon chain region remains largely intact at physiological concentrations of hydrogen peroxide. However, at elevated concentrations of hydrogen peroxide, a substantial breakdown of the acyl chains occurs. Striking similarities observed between the spectral features of the oxidized rabbit lens phospholipids and those of the cataractous human lenses suggest that the mechanism and pathways of lipid oxidation in model animal membranes and in human lenses are similar. Differences in the nuclear or cortical regions are also evident upon metal oxidation. Nuclear lipids experience increased effects of the metal oxidation compared to cortical lipids. Both the nuclear or the cortical lipids indicate effective penetration of the bilayer water creating segregated membrane domains, possibly through breakdown of headgroup-specific lipid-water interactions. This could effectively alter the lens membrane permeability and fluidity, rendering it susceptible to a host of toxic oxidants present in the eye. These findings also demonstrate that LPO can lead to acyl chain degradation that may effectively derange the lens membrane function, which could be a contributing factor in cataractogenesis.

Fourier transform infrared study of the rod outer segment disk and plasma membranes of vertebrate retina.

Phospholipid composition and structure of disk and plasma membranes purified from bovine rod outer segments (ROS) are examined using Fourier transform infrared spectroscopy. Vibrational data indicate that both disk and plasma membranes lack sphingophospholipids, in contrast to the lens membranes. The hydrocarbon chains of the disk lipids are unsaturated by a factor of 5 over the acyl chains of the plasma lipids. The plasma lipids with 3-fold higher cholesterol and 5-fold higher saturation melt at a higher temperature (26 degrees C) than the disk lipids which melt at 16 degrees C. The transition temperature decreases by more than 20 degrees C in going from disk lipids to disk membrane, indicating a large drop in the enthalpy of the ROS membrane-matrix, presumably due to enhanced rhodopsin-lipid interaction. The lipid composition predisposes the disk and plasma membranes to be fluid and structurally disordered (about 84%) around physiological temperature. The fluid phospholipid environment of the disk membrane (i.e., just a few degrees above subzero temperatures) is considered to be vital for the ROS photoreceptor function. The amide I band profile of rhodopsin indicates an extensive alpha-helical (53%) peptide chain, with little beta-sheet (21%) and beta-turns (18%) in ROS membranes. This structure and/or conformation is conserved between 0-60 degrees C even though disk and plasma lipids undergo a phase change. The H-D exchange data indicate that as much as 84% of the peptide residues of ROS membranes in partially bleached retinas is accessible to D2O solvent after 1 h.(ABSTRACT TRUNCATED AT 250 WORDS)

Structural characterization of lipid membranes from clear and cataractous human lenses.

Lipid composition related structural changes in human cataractous lenses was explored by characterizing the hydrophobic hydrocarbon chains in lipid membranes corresponding to twelve Indian cataractous lenses and eight American clear lenses of similar age. The nuclear-lipid phase transitions corresponding to the clear lenses exhibited significantly higher average transition temperatures (nucleus 33 degrees C, cortex 26.3 degrees C) and cooperativities, 38.1, as compared to the value of 24.1 for the cortical-lipid phase transitions. At 36 degrees C, the phase transitions corresponding to cortical and nuclear lipids indicate a similar degree of disorder, 63%, in the hydrocarbon chains, i.e., similar relative amounts of gauche and trans rotomers. The twelve cataractous lenses investigated all had nuclear opacities, four were brunescent and four had cortical opacities. No significant differences were observed in the phase transition parameters (temperature, cooperativity, magnitude, enthalpy) evaluated for the nuclear-lipid membranes corresponding to the different types of cataracts. Furthermore, for the cataractous membranes, the phase transition parameters obtained for the nuclear lipids were comparable to those evaluated for the cortical lipid membranes. However, the cortical lipids exhibited the highest order in membranes from nuclear cataracts without cortical opacity. The cortical lipids from clear, non-cataractous lenses had the lowest level of order. At 36 degrees C, the degree of order in the cortical lipid from clear lenses was comparable to that from nuclear cataractous lenses without cortical opacity. The transition temperature, and cooperativity were significantly higher for cortical lipids from cataractous lenses as compared to those from clear lenses. At 36 degrees C, the degree of order in the cortical lipid membranes was lower for all cataract types vs. clear lens fractions. Our results suggest the possibility that lipid-lipid interactions could be different in cataractous lens membranes. Lipid compositional and chemical differences must account for these altered lipid interactions. These studies will provide a basis for studying lipid-protein interactions and structure-function relationships in the lens membrane.

Infrared study of the structure and composition of rabbit lens membranes: a comparative analysis of the lipids of the nucleus, cortex and epithelium.

Infrared spectra of the phospholipids extracted from the nuclear, cortical and epithelial regions of the rabbit lens membrane bilayers are examined for the first time. Major structural, conformational and compositional differences in the lens membrane are correlated at physiological temperature. Vibrational data distinguish two classes of the phospholipids present in the rabbit lens membranes. Sphingolipids with a sphingosine backbone are largely concentrated in the nucleus whereas phospholipids with a glycerol backbone (glycero-lipids) such as phosphatidylcholine and phosphatidylethanolamine are abundant in the cortical region of the lens. Nuclear lipids are more saturated by a factor of four over the lipids of the cortical region. Nuclear lipids also exhibit increased headgroup and interface hydration and stronger hydrogen bonding over cortical lipids which provide them additional structural stability needed for the clarity of the lens. The lipid composition of the epithelial membranes is structurally similar to that of the cortical region but the hydrocarbon chains are more saturated. Epithelial membranes are largely shielded from bilayer water indicating hydrophilic lipid-water interactions are not important for the stability of these membranes. These membranes exhibit much stronger lipid-lipid interactions, vital for many physical properties like membrane fluidity and permeability. The fiber cell membranes are stabilized by hydrogen bonding of the carbonyls of the interface region and by headgroup-specific lipid-water interactions, while epithelial membranes are stabilized primarily through hydrophobic lipid-lipid interactions. Data also exhibit two phase transitions around 16 and 35 degrees C corresponding to the melting of the hydrocarbon chains from two pools of the phospholipids i.e. glycero- and sphingophospholipids, respectively. The first transition is caused by disruption of the carbonyl hydrogen bonding and disordering of the acyl chains of the glycero-lipids, while second transition is driven mainly from the hydrogen bonding effects of the carbonyls of the sphingolipids followed by acyl/sphingosine chain disordering. Upon transition to the liquid-crystalline phase, a sizable amount of the fiber cell membranes are disordered (approximately 33%) due to increased conformational motion of the acyl chains resulting from a loss of extended CH2 trans segments. These chains of the fully hydrated lipids pack in an hexagonal or triclinic unit cell in rabbit lens membranes.

Estimation of the secondary structure and conformation of bovine lens crystallins by infrared spectroscopy: quantitative analysis and resolution by Fourier self-deconvolution and curve fit.

The secondary structure of six bovine lens protein fractions (two alpha, three beta and one gamma-crystallin) are examined in solution and in solid forms for the first time using FTIR spectroscopy. Films of the nuclear and cortical regions of the bovine lens are also examined. The structure is quantitatively estimated from the vibrational analysis of the resolution-enhanced amide-I profile achieved by Fourier self-deconvolution and linear least-squares curve-fit algorithm. All the protein fractions fold predominantly in a beta-pleated sheet structure with little or no alpha-helical domains in solution or in lyophilized solid form. These proteins also retain their predominant beta-sheet conformation in the cellular phospholipid environment of the lens, in conformity with the structure obtained for all the mammalian species examined to date. Despite structural homology, vibrational data indicate subtle structural differences within each class of the crystallins probably due to presence of several minor substructures/subconformations. Substantial high amounts of turns (approx. 40%) observed in the beta-fractions may have a fundamental implication in stabilizing the tertiary structure of the uniquely folded-proteins vital for the transparency of the lens. These proteins in solid KBr-matrix undergo a major structural change, induced primarily by ionic interactions which refold them in a helical conformation. IR spectroscopy together with band-narrowing procedures has proven to be an effective tool to obtain structural information of proteins in solution, as solid substrates or in a complex biological tissue, such as ocular lens.

Raman structural characterization of clear human lens lipid membranes.

Raman spectroscopy was used for the first time to characterize the structure of lipid membranes prepared from the nuclear and cortical regions of 48 and 69 year old clear human lenses. The interface region carbonyl band appears as a doublet at 1742 and 1728 cm-1. The lower frequency band is characteristic of a hydrogen bonded carbonyl group, perhaps to bilayer water. From the intensity of the curve fit bands, we calculate that 43% of the carbonyl groups are hydrogen bonded. Our data show that the hydrocarbon chains of the nuclear lipids are 1.4 times more saturated than those of the cortical lipids. The molar ratio of phospholipid CH2/= C-H groups was calculated to be 13 and 18 for cortical and nuclear lipids, respectively. Hydrocarbon chain disorder was estimated to be 72 and 58% (+/- 8% disorder) for the cortical and the nuclear lipids, respectively. Raman spectroscopy is sensitive to structural differences in various regions of the lipid bilayer and could be an effective tool to explore lipid and protein interactions in terms of lens region, age and opacity.

The dual effect of oxidation on lipid bilayer structure.

Sphingomyelin membranes were prepared with different levels of oxidative damage caused by tert-butyl hydroperoxide (TBH). Temperature-induced changes in membrane hydrocarbon chain packing (phase transitions) were monitored using infrared spectroscopy. Lipid phase transition characteristics were evaluated from thermodynamic parameters fitted to the experimental transition curve data. At temperatures below the lipid phase transition Tc, hydrocarbon chains pack in an ordered state whereas above the Tc the hydrocarbon chains pack in a disordered state. Compared to the non-oxidized control, the packing of the hydrocarbon chains of mildly oxidized sphingomyelin (less than 10 nmol TBH/mg lipid) was no different at all temperatures below the Tc, and was more ordered above the Tc. The hydrocarbon chains of strongly oxidized sphingomyelin (greater than 10 nmol TBH/mg lipid) were more disordered at temperatures above and below the Tc compared to the control samples. These results suggest that lipid oxidation has a dual effect on lipid order. A more ordered or disordered state may result depending on the degree of oxidation and the state of lipid order prior to oxidation. These results could be important for explaining the structural changes in oxidized membranes high in sphingomyelin such as those found in the ocular lens and liver plasma membranes.

Spectroscopic detection of lipid peroxidation products and structural changes in a sphingomyelin model system.

The peroxidation induced by tert-butyl hydroperoxide in sphingomyelin from bovine brain was investigated in detail. The lipid peroxidation products resulting from oxidation of lipid acyl chains were detected, identified and characterized by optical absorption. Fourier transform infrared, fluorescence and NMR spectroscopies. The extent of hydrocarbon chain degradation in vitro was quantified by measuring the relative change in absorbance of the peak at 241 nm characteristic of conjugated double bond or diene absorption band. FTIR data revealed that the lipid peroxidation of sphingomyelin disrupted the acyl chain and head group regions resulting in derangement of the ordered membrane.

Adenine and guanine 8CH exchange in nucleic acids: resolution and measurement by Raman optical multichannel analysis.

Deuterium exchange of 8C protons of adenine and guanine in nucleic acids is conveniently monitored by laser Raman spectrophotometry, and the average exchange rate so determined [kA + kG] can be exploited as a dynamic probe of the secondary structure of DNA or RNA [J. M. Benevides and G. J. Thomas, Jr. (1985) Biopolymers 24, 667-682]. The present work describes a rapid Raman procedure, based upon optical multichannel analysis, which permits discrimination of the different 8CH exchange rates, kA of adenine and kG of guanine, in a single experimental protocol. For this procedure, simultaneous measurements are made of the intensity decay or frequency shift in separately resolved Raman bands of adenine and guanine, each of which is sensitive only to 8C deuteration of its respective purine. Resolution of the rates kA and kG is demonstrated for the mononucleotide mixtures, 5'-rAMP + 5'-rGMP and 5'-dAMP + 5'-dGMP, for the polynucleotides poly(dA-dT).poly(dA-dT) and poly(dG-dC).poly(dG-dC), for calf thymus DNA, and for the 17 base-pair operator OR3. We show that the different exchange rates of adenine and guanine, in nucleotide mixtures and in DNA, may also be calculated independently from intensity decay of the composite 1481-cm-1 band, comprising overlapped adenine and guanine components, over a time domain that encompasses two distinct regimes: (1) a relatively more rapid exchange of guanine, and (2) a concurrent slower exchange of adenine. Both methods developed here yield consistent results. We find, first, that exchange of guanine is approximately twofold more rapid than that of adenine when both purines are present in the same structure and solvent environment, presumably a consequence of the greater basicity of the 7N site of guanine. Second, we find that adenine suffers greater retardation of exchange than guanine when both purines are incorporated into a "classical" B-DNA secondary structure, such as that of calf thymus DNA. This finding suggests different microenvironments at the 7N-8C loci of adenine and guanine in aqueous B-DNA. We also confirm that adenine residues of B-form poly(dA-dT).poly(dA-dT) exchange much more slowly than those of other B-DNA sequences, implying a secondary structure for the alternating-AT sequence with unusual stereochemistry in the major groove. The greater resistance of adenine than guanine to 8CH exchange in the B-DNA secondary structure is more evident in high molecular weight calf thymus DNA and in the alternating AT and GC copolymer duplexes than in the smaller 17 base-pair operator OR3.(ABSTRACT TRUNCATED AT 400 WORDS)

Low-frequency dynamics and Raman scattering of crystals, of B-, A-, and Z-DNA, and fibers of C-DNA.

Normal modes of vibration of DNA in the low-frequency region (10-300 cm-1 interval) have been identified from Raman spectra of crystals of B-DNA [d(CGCAAATTTGCG)], A-DNA [r(GCG)d(CGC) and d(CCCCGGGG)], and Z-DNA [d(CGCGCG) and d(CGCGTG)]. The lowest vibrational frequencies detected in the canonical DNA structures--at 18 +/- 2 cm-1 in the B-DNA crystal, near 24 +/- 2 cm-1 in A-DNA crystals, and near 30 +/- 2 cm-1 in Z-DNA crystals--are shown to correlate well with the degree of DNA hydration in the crystal structures, as well as with the level of hydration in calf thymus DNA fibers. These findings support the assignment [H. Urabe et al. (1985) J. Chem. Phys. 82, 531-535; C. Demarco et al. (1985) Biopolymers 24, 2035-2040] of the lowest frequency Raman band of each DNA to a helix mode, which is dependent primarily upon the degree of helix hydration, rather than upon the intrahelical conformation. The present results show also that B-, A-, C-, and Z-DNA structures can be distinguished from one another on the basis of their characteristic Raman intensity profiles in the region of 40-140 cm-1, even though all structures display two rather similar and complex bands centered within the intervals of 66-72 and 90-120 cm-1. The similarity of Raman frequencies for B-, A-, C-, and Z-DNA suggests that these modes originate from concerted motions of the bases (librations), which are not strongly dependent upon helix backbone geometry or handedness. Correlation of the Raman frequencies and intensities with the DNA base compositions suggests that the complex band near 90-120 cm-1 in all double-helix structures is due to in-plane librational motions of the bases, which involve stretching of the purine-pyrimidine hydrogen bonds. This would explain the centering of the band at higher frequencies in structures containing G.C pairs (greater than 100 cm-1) than in structures containing A.T pairs (less than 100 cm-1), consistent with the strengths of G.C and A.T hydrogen bonding.

Phage phi X174 probed by laser Raman spectroscopy: evidence for capsid-imposed constraint on DNA secondary structure.

The Raman spectrum of the isometric bacteriophage phi X174 contains a number of well-resolved bands which have been assigned unambiguously to proteins of the capsid or to the single-stranded DNA (ssDNA) genome. Additional Raman bands of protein and DNA, which are partially overlapped in the spectrum of virus, have been resolution enhanced by Fourier deconvolution to permit improved semiquantitative measurement of spectral intensities and frequencies for structural conclusions. Raman conformation markers indicate that the ssDNA molecule within the capsid contains nucleosides of C2'-endo sugar pucker and anti-glycoside bond orientation, but the nucleic acid backbone lacks the geometry characteristic of B-form DNA. The Raman profile of encapsidated phi X DNA indicates a backbone more similar to heat-denatured DNA than to DNA containing hairpinlike secondary structure. This finding suggests limited interbase interactions in the packaged genome, which is presumably the result of constraints imposed by the viral capsid. Thus, the extensive pairing and stacking of bases indicated by Raman profiles from ssRNA viruses are not evident for the phi X174 chromosome. Overall, the proteins of the virion contain extensive beta-sheet and irregular secondary structures. Fourier deconvolution of the Raman amide I band provides an estimate of the percentage of total beta-sheet structure (approximately 60%) in all proteins of the virion. The amide III region of the spectrum confirms that beta-sheet and irregular domains are the predominant protein secondary structures. Samples of phi X174 concentrated for Raman spectroscopy by either ultracentrifugation or ultrafiltration exhibit nearly identical Raman spectra, indicating that either method can be employed to prepare intact virus without significant loss of DNA or protein components.