Biomedical subjects

G J Thomas

Publications and source records attributed to G J Thomas.

At least 37 records · Page 2Linked to original sources

PubMed2001

Structure and organization of bacteriophage Pf3 probed by Raman and ultraviolet resonance Raman spectroscopy.

The Pseudomonas bacteriophage Pf3 is a long and narrow filament consisting of a covalently closed DNA single strand of 5833 bases sheathed by approximately 2500 copies of a 44-residue subunit. Ultraviolet resonance Raman spectra excited at 257, 244, 238, and 229 nm and off-resonance Raman spectra excited at 514.5 nm are reported for Pf3 in both H2O and D2O solutions. The key Raman bands are assigned to specific protein and DNA groups of the native virion assembly. The results are compared with proposed assembly models and Raman spectra recently reported for the isomorphous (class II) Pseudomonas phage Pf1 and the morphologically distinct (class I) coliphage fd [Wen, Z. Q., Overman, S. A., and Thomas, G. J. , Jr. (1997) Biochemistry 36, 7810-7820; Wen, Z. Q., Armstrong, A., and Thomas, G. J., Jr. (1999) Biochemistry 38, 3148-3156]. Surprisingly, deoxynucleosides of the packaged DNA genome of Pf3 adopt the same conformation (C3'-endo/anti) found for DNA packaged in the class I fd virion rather than that (C2'-endo/anti) associated with DNA in the isomorphous Pf1 virion. However, DNA base stacking in Pf3, as judged by Raman hypochromic effects, differs significantly from that occurring in either Pf1 or fd. Thus, the single-stranded DNA genomes of Pf3, Pf1, and fd are all organized differently within their respective capsids, implying that local subunit-DNA interactions may be important in determining the structure specific to each native assembly. The present study confirms a completely alpha-helical secondary structure for the Pf3 subunit and an unusual indolyl ring environment for the subunit tryptophan residue (Trp-38).

Amides↗

PubMed2001

Expression of the alphavbeta6 integrin promotes migration and invasion in squamous carcinoma cells.

The integrin alphavbeta6 is a fibronectin receptor whose expression is not detectable on normal oral epithelium but is increased significantly in healing and in oral epithelial dysplasia and oral squamous cell carcinoma, suggesting it may promote changes associated with tumor development. To study whether alphavbeta6 may drive invasive behavior we have used transfection and retroviral infection to create a panel of epithelial cell lines expressing various levels of alphavbeta6. We report that increased expression of alphavbeta6 in malignant keratinocytes promotes invasion and leads to an increased capacity for migration towards fibronectin. alphavbeta6 expression may have a significant role in contributing to the malignant behavior of epithelial cells.

Antigens, Neoplasm↗

PubMed2001

alpha v beta 6 Integrin upregulates matrix metalloproteinase 9 and promotes migration of normal oral keratinocytes.

The integrin alpha v beta 6 is a fibronectin receptor that is undetectable on normal keratinocytes in situ, but is increased significantly in wound healing and in culture-established keratinocytes, suggesting that it may promote changes associated with cell motility. Using normal human oral keratinocytes we have shown that cultured cells express relatively high levels of alpha v beta 6 and this integrin has a functional role in both cell adhesion and migration towards fibronectin. We provide experimental evidence that the increased expression of alpha v beta 6 by normal human oral keratinocytes results in coordinate changes, which promote a more migratory phenotype. Thus increased expression of alpha v beta 6 results in a fibronectin-dependent increase in pro-matrix metalloproteinase 9, matrix metalloproteinase 9 activity increases normal human oral keratinocyte migration, and this may be further dependent on plasmin activation. The results suggest a key role for alpha v beta 6 in these processes and indicate a coordinated link between alpha v beta 6 expression and upregulation of matrix metalloproteinase 9. It appears that alpha v beta 6 may function in normal human oral keratinocyte migration through matrix-metalloproteinase-9-dependent and -independent mechanisms.

Antigens, Neoplasm↗

PubMed2001

Cell surface heparan sulfate proteoglycans control the response of renal interstitial fibroblasts to fibroblast growth factor-2.

BACKGROUND: While the progression of renal disease to end stage is strongly correlated with tubulointerstitial changes, the control of the fibrotic process within the interstitium is poorly understood. Basic fibroblast growth factor (FGF-2) has been implicated as a major growth factor involved in fibroblast activation and extracellular matrix synthesis. Furthermore, in many cells, the activity of FGF-2 is controlled by a low-affinity but high-capacity interaction with heparan sulfate (HS) proteoglycans (PGs), such as members of the syndecan family. These molecules are likely to be central to the control of interstitial fibrosis, but as yet, there has been no characterization of their synthesis by interstitial cells. METHODS: The expression of HSPG on the surface of NRK 49F fibroblasts was demonstrated by immunohistochemistry and by metabolic labeling with [(35)S]-sulfate. HSs were characterized by specific enzymatic digestion, size exclusion chromatography, and anion exchange chromatography. The mRNA for syndecan 1 through syndecan 4 in the fibroblasts was detected by semiquantitative reverse transcription-polymerase chain reaction. Fibroblast proliferation was measured by the MTT assay. RESULTS: Immunohistochemistry and [(35)S]-sulfate-labeling demonstrated that renal fibroblasts expressed HSPGs on their surface. Furthermore, enzymatic removal of these HS (but not chondroitin sulfate) glycosaminoglycan (GAG) chains, or inhibition of GAG sulfation, abolished the proliferative response of both NRK cells and primary human cortical fibroblasts to FGF-2 but not to platelet-derived growth factor. The addition of conditioned medium, containing HS-GAG fragments, restored the proliferative response to FGF-2, confirming the specificity of the interaction. Finally, the mRNA for all four syndecans was detected in the fibroblasts, and that for syndecan 1 in particular was up-regulated by FGF-2. CONCLUSIONS: The present study demonstrates that the expression of cell surface HSPG was essential for the proliferation of renal fibroblasts in response to FGF-2, and therefore may play a major role in the development and persistence of a proliferating phenotype during interstitial nephritis.

Animals↗

PubMed2001

Cell adhesion molecules and oral cancer.

Cell adhesion molecules (CAMs) are found on the surfaces of all cells, where they bind to extracellular matrix molecules or to receptors on other cells. As well as having a structural role, CAMs function as signaling receptors, transducing signals initiated by cellular interactions which regulate many diverse processes, including cell division, migration, and differentiation. Cell adhesion molecules are essential for maintaining stable tissue structure. However, cell adhesion must be dynamic to facilitate the mobility and turnover of cells. In dynamic situations, cells alter their cell-cell and cell-matrix interactions by virtue of altered expression and function of CAMs. The expression of CAMs is normally tightly regulated, thereby controlling cell proliferation, mobility, differentiation, and survival. Many of these processes are misregulated in malignant tumors, and it has been shown that many of the characteristics of tumor cells are attributable to the aberrant expression or function of CAMs. Integrins and E-cadherin are the most important CAMs expressed by stratified squamous epithelium. Altered expression of these molecules has been found in oral carcinoma, where loss of CAM expression is often seen in poorly differentiated lesions. However, up-regulation of certain integrins, such as alphavbeta6, has consistently been found in oral cancer, suggesting that it may play an active role in disease progression.

Animals↗

PubMed2000

Structural basis of polyamine-DNA recognition: spermidine and spermine interactions with genomic B-DNAs of different GC content probed by Raman spectroscopy.

Four genomic DNAs of differing GC content (Micrococcus luteus, 72% GC; Escherichia coli, 50% GC; calf thymus, 42% GC; Clostridium perfringens, 27% GC) have been employed as targets of interaction by the cationic polyamines spermidine ([H(3)N(CH(2))(3)NH(2)(CH(2))(4)NH(3)](3+)) and spermine ([(CH(2))(4)(NH(2)(CH(2))(3)NH(3))(2)](4+)). In solutions containing 60 mM DNA phosphate (approximately 20 mg DNA/ml) and either 1, 5 or 60 mM polyamine, only Raman bands associated with the phosphates exhibit large spectral changes, demonstrating that B-DNA phosphates are the primary targets of interaction. Phosphate perturbations, which are independent of base composition, are consistent with a model of non-specific cation binding in which delocalized polyamines diffuse along DNA while confined by the strong electrostatic potential gradient perpendicular to the helix axis. This finding provides experimental support for models in which polyamine-induced DNA condensation is driven by non-specific electrostatic binding. The Raman spectra also demonstrate that major groove sites (guanine N7 and thymine C5H(3)) are less affected than phosphates by polyamine-DNA interactions. Modest dependence of polyamine binding on genome base composition suggests that sequence context plays only a secondary role in recognition. Importantly, the results demonstrate that polyamine binding has a negligible effect on the native B-form secondary structure. The capability of spermidine or spermine to bind and condense genomic B-DNA without disrupting the native structure must be taken into account when considering DNA organization within bacterial nucleoids or cell nuclei.

Animals↗

PubMed2000

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.

Alanine↗

PubMed2000

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.

Amino Acid Sequence↗

PubMed2000

Protein-directed DNA structure II. Raman spectroscopy of a leucine zipper bZIP complex.

Mechanisms of transcription may involve protein-directed changes in DNA structure and DNA-directed changes in protein structure. We have employed Raman spectroscopy to characterize vibrational signatures associated with such induced molecular fitting for two classes of transcription factors-the basic leucine-zipper (bZIP) motif and the high-mobility-group (HMG) box-each with a DNA target site. Results for bZIP are described here; findings for the HMG-box are reported in the preceding paper in this issue [Benevides, J. M., Chan, G., Lu, X.-J., Olson, W. K., Weiss, M. A., and Thomas, G. J., Jr. (2000) Biochemistry 39, 537-547]. The yeast activator GCN4 provides a well-studied example of bZIP recognition, wherein B-DNA serves essentially as a template for protein folding. Analysis of Raman spectra of the 57-residue GCN4 bZIP domain, its AP-1 binding site, and their specific complex confirms a DNA-induced increase in alpha-helicity, attributable to folding of GCN4 basic arms with virtually no change in B-DNA structure, consistent with previous X-ray and NMR structure determinations. The absence of DNA perturbations in the bZIP model contrasts sharply with the HMG box, where DNA structure perturbations predominate. The bZIP and HMG-box models represent two opposing extremes in a range of induced fits identifiable by Raman spectroscopy. Previously characterized lambda repressor/operator complexes [Benevides, J. M., Weiss, M. A., and Thomas, G. J. (1994) J. Biol. Chem. 269, 10869-10878] occupy an intermediate position within this range. A comprehensive tabulation of Raman markers proposed as diagnostic of different protein/DNA recognition motifs is presented. The results are analyzed in terms of available DNA crystal structures (Nucleic Acid Database) to identify details of DNA conformation that correlate with specific Raman recognition markers.

Base Sequence↗

PubMed2000

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.

Indoles↗

PubMed2000

Identification of matrix metalloproteinases and their tissue inhibitors type 1 and 2 in human masseter muscle.

Changes in masticatory muscle structure and function are either developmental, as seen in anomalies of facial form, or adaptive, as seen during procedures such as orthognathic surgery and functional-appliance orthodontic therapy. Remodelling of muscle extracellular matrix is pivotal in these processes. This turnover is mediated via members of the family of enzymes known as matrix metalloproteinases (MMP) and inhibited by the tissue inhibitors of metalloproteinases (TIMP). The aim here was to investigate the in vivo pattern of expression and distribution of MMPs and TIMPs in masseter muscle of humans with both normal and abnormal facial forms. Masseter muscle biopsies were taken from 10 patients, four with long-face syndrome and six normal controls as confirmed by cephalometry. Immunohistochemical techniques were used to show the pattern and distribution of MMPs and TIMP proteins in the muscle. Zymography of tissue extracts was used to determine the presence of MMP activity. Reverse transcriptase-polymerase chain reaction (RT-PCR) was used to detect the presence of MMP and TIMP-2 mRNA. MMP-1 was expressed around the individual muscle fibres, especially in those fibre surfaces in contact with the interstices of the connective tissue and around blood vessels. MMP-9 staining was less intense and was expressed in the interstices of the connective tissue and around blood vessels. Zymography of protein extracts confirmed that MMP-9 activity was present. MMP-2 and MMP-3 were not expressed in the samples, although MMP-2 mRNA could be detected by RT-PCR and its activity could be detected by zymography. Intense TIMP-1 staining was present around each muscle fibre, in the interstices of the connective tissue and surrounding blood vessels; TIMP-2 mRNA could be detected in all samples. These staining patterns were seen in all biopsies examined and were irrespective of the facial form of the donor. These findings provide evidence that the mechanisms required for matrix remodelling are present in the human masseter muscle.

Adult↗

PubMed2000

Low-density lipoprotein stimulates mesangial cell proteoglycan and hyaluronan synthesis.

BACKGROUND: Hyperlipidaemia leads to glomerulosclerosis in small mammals and may contribute to progressive renal disease in man. One prominent feature of lipid-induced glomerular injury in animal models is the accumulation of mesangial matrix. These studies were designed to investigate whether low-density lipoprotein (LDL) enhanced mesangial cell (MC) matrix deposition by modulating the production of proteoglycans (PG) and hyaluronan (HA). METHODS: Growth arrested human MC were metabolically labelled with either 50 microCi/ml Na(2)[(35)S]sulphate or 25 microCi/ml [(3)H]glucosamine and stimulated with LDL (10-100 microg/ml). The radiolabelled PG and HA extracted from the cell layer and the culture medium were isolated, quantified and characterized. Comparison of the PG core proteins synthesized by MC was carried out using Western blot analysis. RESULTS: LDL stimulation led to a dose- and time-dependent increase in [(35)S]sulphate incorporation into PG in the culture medium and to a lesser extent in the cell layer. Analysis of the glycosaminoglycan (GAG) chains showed no difference in either their size or charge. Enzyme digestion studies demonstrated that the synthesis of both chondroitin sulphate PG (CSPG) and heparan sulphate PG (HSPG) was enhanced as was the production of the core proteins of versican (a large CSPG), perlecan (a basement membrane HSPG) and to a lesser extent decorin (a small dermatan sulphate PG (DSPG)). An increase in HA synthesis was also demonstrated in [(3)H]glucosamine labelled cells following LDL stimulation. CONCLUSION: LDL selectively enhances the synthesis of specific PG and HA by mesangial cells. Such effects may contribute to the expansion of the mesangial matrix and modify cell-matrix interactions in lipid-induced renal damage.

Blotting, Western↗

PubMed2000

Induction of hyaluronan metabolism after mechanical injury of human peritoneal mesothelial cells in vitro.

BACKGROUND: Hyaluronan (HA) is an important extracellular matrix component that is involved in cell movement and tissue repair. In vertebrates, HA synthase genes (HAS 1, HAS 2, and HAS 3) that control the synthesis of HA have been identified. In this article, we investigated HA synthesis in the response of human peritoneal mesothelial cells (HPMCs) to injury. METHODS: The expression of HAS 1, HAS 2, and HAS 3 mRNA and the synthesis of [(3)H]-labeled HA were examined in an in vitro model of peritoneal mesothelial cell damage. The staining for uridine diphosphoglucose dehydrogenase, a key enzyme in the synthesis of HA, and biotinylated HA-binding protein was used to determine the cellular location of HA synthesis and its site of deposition. RESULTS: Growth-arrested human HPMCs expressed low levels of mRNA for HAS 2 and HAS 3 but not HAS 1. Following injury to the monolayer, HAS 2 was up-regulated by 6 hours, reaching maximal expression between 12 and 24 hours. In contrast, the expression of HAS 3 was down-regulated. During the same time period, synthesis of HA was increased in the injured monolayer. This synthetic activity appeared to be restricted to cells at the edge of the wound and to cells entering the wound. In a separate series of experiments, the addition of HA to the injured monolayer at a concentration range found in peritoneal fluid (50 to 3300 ng/mL) increased the migration of cells into the wound in a dose-dependent manner. CONCLUSIONS: These studies provide evidence that HA is an important component of peritoneal mesothelial cell migration. The results also suggest that in this process, there is differential regulation of HAS gene expression and that the synthesis of HA is limited to cells located at the leading edge of the wound.

Cell Movement↗

PubMed1999

Resistance of rheumatoid synovial dendritic cells to the immunosuppressive effects of IL-10.

IL-10 down-regulates the APC function of many dendritic cells (DC), including human peripheral blood (PB) DC. In rheumatoid arthritis (RA), synovial fluid (SF) DC express markers of differentiation and are effective APC despite abundant synovial IL-10. The regulation of DC responsiveness to IL-10 was therefore examined by comparing the effect of IL-10 on normal PB and RA SF DC. Whereas IL-10 down-modulated APC function and MHC class II and B7 expression of PB DC, IL-10 had no such effect on SF DC. Since SF DC have differentiated in vivo in the presence of proinflammatory cytokines, PB DC were cocultured in the presence of IL-10 and either GM-CSF, IL-1beta, TNF-alpha, IL-6, or TGF-beta. GM-CSF, IL-1beta, and TNF-alpha were all able to restore APC function. Whereas the effects of IL-10 on PB DC were shown to be mediated by IL-10R1, neither PB nor RA SF DC constitutively expressed IL-10R1 mRNA or detectable surface protein. In contrast, IL-10R1 protein was demonstrated in PB and SF DC whole cell lysates, suggestive of predominant intracellular localization of the receptor. Thus, DC responsiveness to IL-10 may be regulated through modulation of cell surface IL-10R1 expression or signaling.

Antigen Presentation↗

PubMed1999

Assembly dynamics of the nucleocapsid shell subunit (P8) of bacteriophage phi6.

Phi6 is an enveloped dsRNA bacteriophage of Pseudomonas syringae. The viral envelope encloses a nucleocapsid, consisting of an RNA-dependent RNA polymerase complex within an icosahedral shell assembled from approximately 800 copies of a 16 kDa subunit (protein P8, encoded by viral gene 8). During infection, the nucleocapsid penetrates the host plasma membrane and enters the cytosol, whereupon the P8 shell disassembles and the polymerase complex is activated. To understand the molecular mechanisms of shell assembly and disassembly-processes that have counterparts in most viral infections-we have investigated the structure, stability, and dynamics of P8 in different assembly states using time-resolved Raman spectroscopy and hydrogen-isotope exchange. In the presence of Ca(2+), which promotes shell assembly, the highly alpha-helical conformation of the P8 subunit is stabilized by rapid assembly into shell-like structures. However, in the absence of Ca(2+), the P8 subunit is thermolabile and unstable, manifested by a slow alpha-helix --> beta-strand conformational change and the accumulation of aberrant aggregates. In both properly assembled shells and aberrant aggregates, the P8 subunit retains an alpha-helical core that is protected against deuterium exchange of amide NH groups. Surprisingly, no additional protection against amide exchange is conferred by the shell lattice. Time-resolved assembly and disassembly experiments in deuterated buffers indicate that the regions of P8 involved in subunit/subunit interactions in the intact shell undergo rapid exchanges, presumably due to local unfolding events that are characterized by low activation barriers. Such localized dynamics of P8 within the shell lattice may mediate the nucleocapsid/host membrane interactions that are required in the cytosol for particle assembly during maturation and disassembly during infection.

Bacteriophage phi 6↗

PubMed1999

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.

Alanine↗

PubMed1999

Demonstration by ultraviolet resonance Raman spectroscopy of differences in DNA organization and interactions in filamentous viruses Pf1 and fd.

Pf1, a class II filamentous virus, has been investigated by ultraviolet resonance Raman (UVRR) spectroscopy with excitation wavelengths of 257, 244, 238, and 229 nm. The 257-nm UVRR spectrum is rich in Raman bands of the packaged single-stranded DNA (ssDNA) genome, despite the low DNA mass (6%) of the virion. Conversely, the 229-nm UVRR spectrum is dominated by tyrosines (Tyr 25 and Tyr 40) of the 46-residue alpha-helical coat subunit. UVRR spectra excited at 244 and 238 nm exhibit Raman bands diagnostic of both viral DNA and coat protein tyrosines. Raman markers of packaged Pf1 DNA contrast sharply with those of the DNA packaged in the class I filamentous virus fd [Wen, Z. Q., Overman, S. A., and Thomas, G. J., Jr. (1997) Biochemistry 36, 7810-7820]. Interestingly, deoxynucleotides of Pf1 DNA exhibit sugars in the C2'-endo/anti conformation and bases that are largely unstacked, compared with C3'-endo/anti conformers and very strong base stacking in fd DNA; hydrogen-bonding interactions of thymine carbonyls are also different in Pf1 and fd. On the other hand, coat protein tyrosines of Pf1 exhibit Raman markers of ring environment identical to those of fd, including an anomalous singlet at 853 cm-1 in lieu of the canonical Fermi doublet (850/830 cm-1) found in globular proteins. The results indicate markedly different modes of organization of ssDNA in Pf1 and fd virions, despite similar environments for coat protein tyrosines, and suggest strong hydrogen-bonding interactions between DNA bases and coat subunits of Pf1 but not between those of fd. We propose that structural relationships between the protein coat and encapsidated ssDNA genome are also fundamentally different in the two assemblies.

Capsid↗

PubMed1999

Molecular mechanism of DNA recognition by the alpha subunit of the Oxytricha telomere binding protein.

Interactions between telomeric DNA and the alpha subunit of the heterodimeric telomere binding protein of Oxytricha nova have been probed by Raman spectroscopy, CD spectroscopy, and nondenaturing gel electrophoresis. Telomeric sequences investigated include the Oxytricha 3' overhang, d(T4G4)2, and the related sequence dT6(T4G4)2, which incorporates a 5'-thymidylate leader. Corresponding nontelomeric isomers, d(TG)8 and dT6(TG)8, have also been investigated. Both d(T4G4)2 and dT6(T4G4)2 form stable hairpins that contain Hoogsteen G.G base pairs [Laporte, L., and Thomas, G. J., Jr. (1998) J. Mol. Biol. 281, 261-270]. The alpha subunit binds specifically and stoichiometrically to the dT6(T4G4)2 hairpin and alters its secondary structure by inducing conformational changes in the 5'-thymidylate leader without extensive disruption of G.G base pairing. Conversely, binding of the alpha subunit to d(T4G4)2 eliminates G.G pairing and unfolds the hairpin. DNA unfolding is accompanied by conformational changes affecting both the backbone and dG residues, as evidenced by Raman and CD spectra. Interestingly, the alpha subunit also forms complexes with the nontelomeric isomers, d(TG)8 and dT6(TG)8, evidenced by altered electrophoretic mobility in nondenaturing gels; however, Raman and CD spectra of complexes of the alpha subunit with nontelomeric DNA suggest no significant changes in backbone or deoxynucleoside conformations. Similarly, the alpha subunit binds to but does not appreciably alter the secondary structure of duplex DNA. The present results show that while the alpha subunit has the capacity to bind to Watson-Crick and different non-Watson-Crick motifs, DNA refolding is specific to the Oxytricha telomeric hairpin and the retention of G.G pairing is specific to the telomeric sequence incorporating the 5' leading sequence. A model is proposed for alpha subunit binding to telomeric DNA, and the physiological role of the alpha subunit in telomere organization is discussed.

Animals↗