Vibrational dynamics and heat capacity of polyglycine I

Earlier works on polyglycine I suffer from several infirmities, such as the dynamic methylene group being replaced by a mass unit and the use of poorly resolved inelastic neutron spectra, which have resulted in wrong assignments and imprecise profile of dispersion curves. In addition, the density-of-states and heat capacity variation as a function of temperature are being reported for the first time. The heat capacity is in good agreement with the measurements reported earlier by Roles and Wunderlich within a certain range (230-350 K). Deviations set in beyond this could be due to the presence of two crystalline states (I and II) in the sample used for the heat capacity measurements.     

Phonon dispersion in polyinosinic acid

A study of the normal modes of vibration and their dispersion in polyinosinic acid [poly (I)] along the helix axis based on Urey-Bradley force field is reported. It leads to a better interpretation of Raman and FTIR spectra. A comparison of dispersion curves of poly (I) with poly (G) has been made. Characteristic features of dispersion curves, such as regions of high density-of-states, repulsion and character mixing are discussed. Predictive value of heat capacity as a function of temperature is reported.     

Infrared and Raman spectroscopy of carbohydrates. Part VI: Normal coordinate analysis of V-amylose

A normal coordinate analysis of V-amylose has been performed for an isolated 6₁ helical chain. Negligible splitting from interactions of vibrations of successive residues is expected between A and E vibrational species due to the large size of the monomer unit. As a result, calculation of only the totally symmetric A modes represents an adequate approximation to the vibrational spectrum of helical polysaccharides. Using this method together with a valence force field we have obtained good agreement between the observed and calculated frequencies. In addition, the computed potential energy distribution and Cartesian displacement coordinates match previous experimental assignments, based on deuterium exchange. The analysis also supports the proposed mechanism for conversion of V-amylose to the more extended B-form. This conversion results in an observed frequency shift for the Raman line at 946 cm^?1 which is predicted by the calculations.     

Vibrational analysis of nucleic acids. I. The phosphodiester group in dimethyl phosphate model compounds: (CH3O)2PO2-, (CD3O)2PO2-, and (13CH3O)2PO2-.

Normal coordinate analyses and vibrational assignments are presented for the dimethyl phosphate anion [(CH3O)2PO2-] and its deuteriomethyl [(CD3O)2PO2-] and carbon-13 [(13CH3O)2PO2-] derivatives in the gauche-gauche conformation. The dimethyl phosphate anion, which is the simplest model for the nucleic acid phosphodiester moiety, exhibits many of the spectral complexities of DNA and RNA and has previously resisted a complete and consistent vibrational analysis. In the present study we make use of new experimental data on the dimethyl phosphate isotopomers, including Raman depolarization measurements, to develop a consistent valence force field for normal modes of the C--O--P--O--C phosphodiester network and its hydrogenic substituents, as well as for stretching and bending modes of the O--P--O network of the anionic phosphodioxy group (PO2-). The force field established for dimethyl phosphate incorporates one significant nonbonded force constant, introduced from ab initio calculations, to account for interaction between the two ester C--O bonds. This study resolves previous problematic assignments for conformation-sensitive symmetric (in-phase) and asymmetric (out-of-phase) skeletal stretching modes of the ester linkages and demonstrates substantial anharmonicity in the hydrogen-stretching vibrations of the methyl substituents. New assignments are proposed for Raman bands of the phosphodioxy group, which may serve as potential indicators of structure and interaction of the DNA phosphates.     

Lattice vibrational modes of poly(rU) and poly(rA)

A normal coordinate analysis has been performed for the polyribonucleotides poly(rU) and poly(rA). The polymers are assumed to be 11-fold infinite helical structures in the A conformation. The hydrogen atoms have been rigidly attached to the appropriate atoms in order to reduce the dimension of the problem. The potential energy is defined in terms of a valence force field initially and a model for the inclusion of nonbonded interactions has been presented. A method for factoring the secular equation for infinite helical polymers in Cartesian coordinates is presented. All of the general features of polyribonucleotide spectra have been reproduced and, in many cases, good quantitative agreement between observed and calculated frequencies is obtained. More specific assignments are offered for some of the observed lines.     

IR investigation on dehydrophenylalanine containing model peptides in helical conformation deposited on a crystal surface

Fourier transform ir spectra have been recorded for three 3₁₀‐helical and one α‐helical pentapeptides containing dehydrophenylalanine, in a thin solid film, in order to find marker bands for various secondary structures encountered in peptides containing dehydroaminoacids. The peptide solutions were deposited and dried as thin film on zinc selenide crystal surface. This convenient sampling method has provided reliable estimates of peptide secondary structure in solid state. Detailed vibrational assignments in the spectral region between 1200–1700 cm⁻¹ are reported. In this region, peptide amide I, II, and III vibrations occur. Spectra–structure correlation has been presented based on the amide modes. Comparison of the ir spectra with available crystal structure data provides qualitative support for assignments of ir bands to 3₁₀‐helical structure and α‐helical structure in dehydrophenylalanine containing pentapeptides. Band frequency assignments for 3₁₀‐helical conformation are consistent for all three peptides. All the assignments agree closely with the theoretical predictions. The spectral differences between 3₁₀‐helical peptides and the α‐helical peptide have been highlighted. These findings demonstrate that a method based on ir spectroscopy can be developed for a useful approximation of three‐dimensional structure of dehydropeptides in solid state. © 1999 John Wiley & Sons, Inc. Biopoly 50: 595–601, 1999     

Vibrational analysis and dispersion curves of poly-L-hydroxyproline chain

Dispersion curves and frequency distribution for poly-L -hydroxyproline (PLHP) chain were obtained using Wilson's GF matrix method as modified by Higgs. These are compared with those of poly-L -proline II and polyglycine II, which also have three-fold screw symmetry. Ring and skeletal modes characteristic of PLHP are identified and the assignments of observed infrared and Raman frequencies are reported. Urey-Bradley force constants were evaluated.     

Bacterial Cell Wall Synthesis: New Insights from Localization Studies

In order to maintain shape and withstand intracellular pressure, most bacteria are surrounded by a cell wall that consists mainly of the cross-linked polymer peptidoglycan (PG). The importance of PG for the maintenance of bacterial cell shape is underscored by the fact that, for various bacteria, several mutations affecting PG synthesis are associated with cell shape defects. In recent years, the application of fluorescence microscopy to the field of PG synthesis has led to an enormous increase in data on the relationship between cell wall synthesis and bacterial cell shape. First, a novel staining method enabled the visualization of PG precursor incorporation in live cells. Second, penicillin-binding proteins (PBPs), which mediate the final stages of PG synthesis, have been localized in various model organisms by means of immunofluorescence microscopy or green fluorescent protein fusions. In this review, we integrate the knowledge on the last stages of PG synthesis obtained in previous studies with the new data available on localization of PG synthesis and PBPs, in both rod-shaped and coccoid cells. We discuss a model in which, at least for a subset of PBPs, the presence of substrate is a major factor in determining PBP localization.     

Bacterial cell wall synthesis: new insights from localization studies.

In order to maintain shape and withstand intracellular pressure, most bacteria are surrounded by a cell wall that consists mainly of the cross-linked polymer peptidoglycan (PG). The importance of PG for the maintenance of bacterial cell shape is underscored by the fact that, for various bacteria, several mutations affecting PG synthesis are associated with cell shape defects. In recent years, the application of fluorescence microscopy to the field of PG synthesis has led to an enormous increase in data on the relationship between cell wall synthesis and bacterial cell shape. First, a novel staining method enabled the visualization of PG precursor incorporation in live cells. Second, penicillin-binding proteins (PBPs), which mediate the final stages of PG synthesis, have been localized in various model organisms by means of immunofluorescence microscopy or green fluorescent protein fusions. In this review, we integrate the knowledge on the last stages of PG synthesis obtained in previous studies with the new data available on localization of PG synthesis and PBPs, in both rod-shaped and coccoid cells. We discuss a model in which, at least for a subset of PBPs, the presence of substrate is a major factor in determining PBP localization.     

Interpretation of DNA vibration modes: I--The guanosine and cytidine residues involved in poly(dG-dC).poly(dG-dC) and d(CG)3.d(CG)3

A normal coordinate analysis has been carried out on guanosine and cytidine residues appearing in oligo and polynucleotides by using a simplified valence force field that allows the vibrational spectra of 5'-dGMP and 2'-deoxycytidine molecules to be reproduced. The role of both C2'-endo and C3'-endo conformations on sugar pucker, as well as that of glycosidic torsion angle (X), on several characteristic vibration modes of these residues have been studied. The present calculations based on a non-redundant set of internal coordinates preserving the harmonic approximation of the potential field, allows us to explain quite satisfactorily the modifications of the vibrational spectra in the 1550-1250 cm-1 and 785-500 cm-1 regions, when the right----left-handed conformational transition occurs.     

Engineering Hybrid Guided Modes in Subwavelength Uniaxial Metamaterial Waveguides

We report anomalous dispersion properties of hybrid guided modes (HGMs) and their group velocity in a subwavelength uniaxial metamaterial waveguide with metal cladding. We derive exact dispersion relations and modal fields of HGMs by solving eigenvalue equation based on basic electromagnetic field theory in detail. Numerical results show that two fundamental HGMs and two types of high-order HGMs can be excited, and their exciting conditions are clarified. In addition, such HGMs can be engineered to belong to normal dispersion or anomalous dispersion. Importantly, the HGMs may be controlled to be forward or backward, and their group velocities may be very small in a certain frequency band. These properties make such metamaterial waveguides have many potential applications in integrated optics, information storage and biosensing.     

Purification and characterization of an extracellular polygalacturonase from Lactobacillus plantarum strain BA 11

Lactobacillus plantarum produced extracellular polygalacturonase in a medium containing 1.5% low methyl-pectin (w/v) and 0.5% glucose (w/v) as inducers. The enzyme was purified (approximately 70-fold) by ammonium sulphate fractionation, Sephadex G-100 gel filtration and DEAE-cellulose ion exchange chromatography. Two peaks (PG I and PG II) of enzymic activity were obtained from the DEAE-cellulose column. The molecular mass of PG I was similar to that of PG II (32 000 Da). The K _m values of PG I and PG II for sodium polypectate were calculated to be 1.63 mg/ml and 1.78 mg/ml respectively. Their isoelectric points were about pH 5.5. The pH optimum was 4.5, while the optimum temperature was 35°C for both PG I and PG II. The two purified enzymes had similar endo modes of action on polygalacturonic acid, as determined by comparison of viscosity reduction and reducing group release.     

An Experimental and Theoretical Study on the Novel Tetraphosphorus Triselenide Boron Triiodide (P<Subscript>4</Subscript>Se<Subscript>3</Subscript>)·(BI<Subscript>3</Subscript>) Adduct

Tetraphosphorus triselenide boron triiodide (P₄Se₃)·(BI₃) has been prepared. The product formed has been characterized by Raman and IR spectroscopy. Vibrational assignments for the normal modes of this Lewis acid-base adduct have been made on the basis of comparison between theoretically obtained and experimentally observed Raman and IR data. The geometries of several possible tetraphosphorus triselenide boron triiodide (P₄Se₃)·(BI₃) adducts have been calculated. The bonding and electron transfer from the tetraphosphorus triselenide P₄Se₃ unit to the Lewis acid BI₃ has been investigated by applying NBO analysis.     

Interpretation of DNA vibration modes: IV--A single-helical approach to assign the phosphate-backbone contribution to the vibrational spectra in A and B conformations

A calculated approach based on the Higgs method for assigning the vibration modes of an infinite helicoidal polymeric chain has been performed on the basis of a reliable valence force field. The calculated results allowed the phosphate-backbone marker modes of the A and B forms, to be interpreted. In the dynamic models used, the bases have been omitted and no interchain interaction was considered. The calculation can also interprete quite satisfactorily the characteristic Raman peaks and infrared bands in the 1250-700 cm-1 spectral region arising from the sugar or sugar-phosphate association and reproduce their evolution upon the B----A DNA conformational transition. They clearly show that the phosphate-backbone modes in the above mentioned spectral region constitute the optical branches of the phonon dispersion curves with no detectable variation in the first Brillouin-zone.     

Growth of Escherichia coli: significance of peptidoglycan degradation during elongation and septation

We have found a striking difference between the modes of action of amdinocillin (mecillinam) and compound A22, both of which inhibit cell elongation. This was made possible by employment of a new method using an Escherichia coli peptidoglycan (PG)-recycling mutant, lacking ampD, to analyze PG degradation during cell elongation and septation. Using this method, we have found that A22, which is known to prevent MreB function, strongly inhibited PG synthesis during elongation. In contrast, treatment of elongating cells with amdinocillin, which inhibits penicillin-binding protein 2 (PBP2), allowed PG glycan synthesis to proceed at a nearly normal rate with concomitant rapid degradation of the new glycan strands. By treating cells with A22 to inhibit sidewall synthesis, the method could also be applied to study septum synthesis. To our surprise, over 30% of newly synthesized septal PG was degraded during septation. Thus, excess PG sufficient to form at least one additional pole was being synthesized and rapidly degraded during septation. We propose that during cell division, rapid removal of the excess PG serves to separate the new poles of the daughter cells. We have also employed this new method to demonstrate that PBP2 and RodA are required for the synthesis of glycan strands during elongation and that the periplasmic amidases that aid in cell separation are minor players, cleaving only one-sixth of the PG that is turned over by the lytic transglycosylases.     

Interpretation of DNA vibration modes: I-The guanosine and cytidine residues involved in poly(dG-dC)·poly(dG-dC) and d(CG)3·d(CG)3

Abstract

A normal coordinate analysis has been carried out on guanosine and cytidine residues appearing in oligo and polynucleotides by using a simplified valence force field that allows the vibrational spectra of 5′-dGMP and 2′-deoxycytidine molecules to be reproduced. The role of both C2′-endo and C3′-endo conformations on sugar pucker, as well as that of glycosidic torsion angle (χ), on several characteristic vibration modes of these residues have been studied. The present calculations based on a non-redundant set of internal coordinates preserving the harmonic approximation of the potential field, allows us to explain quite satisfactorily the modifications of the vibrational spectra in the 1550-1250 cm^?1 and 785-500 cm^?1 regions, when the right → left-handed conformational transition occurs.     

Vibrational analysis of peptides,polypeptides, and proteins. V. Normal vibrations of β-turns

The normal modes have been calculated for β-turns of types I, II, III, I′, II′, and III′. The complete set of frequencies is given for the first three structures; only the amide I, II, and III modes are given for the latter three structures. Calculations have been done for structures with standard dihedral angles, as well as for structures whose dihedral angles differ from these by amounts found in protein structures. The force field was that refined in our previous work on polypeptides. Transition dipole coupling was included, and is crucial to predicting frequency splittings in the amide I and amide II modes. The results show that in the amide I region, β-turn frequencies can overlap with those of the α-helix and β-sheet structures, and therefore caution must be exercised in the interpretation of protein bands in this region. The amide III modes of β-turns are predicted at significantly higher frequencies than those of α-helix and β-sheet structures, and this region therefore provides the best possibility of identifying β-turn structures. Amide V frequencies of β-turns may also be distinctive for such structures.     

Purification and characterization of tomato polygalacturonase converter

Extracts of ripe tomatoes contain two forms of polygalacturonase (PG I and PG II). A heat-stable component that binds PG II to produce PG I has been isolated from tomato fruit. This component has been named polygalacturonase converter (PG converter). The PG converter has been purified by gel filtration, ion-exchange chromatography and chromatofocusing. It appears to be a protein with a relative molecular mass of 102000. It was readily inactivated by papain and pronase. The converter was labile at alkaline conditions, and treatment of PG I at pH 11 released free PG II. A similar factor with a lower molecular mass was extracted from tomato foliage.     

Vibrational analysis of peptides, polypeptides, and proteins. XVII. Normal modes of crystalline Pro-Leu-Gly-NH2, a type II beta-turn

A normal mode calculation has been done for Pro-Leu-Gly-NH2 in its crystalline type II beta-turn structure, and assignments have been made to infrared and Raman bands of this molecule and its N-deuterated derivative. Observed and calculated frequencies below 1700 cm-1 agree to within about 6 cm-1. This analysis provides a sound basis for studying the conformation dependence of the vibrational spectrum.     

Carbohydrate composition and electrophoretic properties of tomato polygalacturonase isoenzymes

Two polygalacturonase isoenzymes, PG I and PG II, were extracted from Murrieta tomato and purified by gel exclusion and ion-exchange chromatography. The kinetic constants and activation energies of the purified isoenzymes have been determined. Polygalacturonase I has two polypeptide chains (Mr = 47 500 and 41 400) whereas polygalacturonase II is a single polypeptide (Mr = 47 500) as shown by electrophoresis in polyacrylamide gels in the presence of sodium dodecyl sulphate. Both isoenzymes are glycoproteins. Through gas liquid chromatography, polygalacturonase II was shown to contain 4.6% neutral hexoses and 1.5% amino sugars. There are eight D-mannose, two L-fucose, two D-xylose and three N-acetylglucosamine residues per mole of PG II. The carbohydrate portion of PG II was shown to be attached to the protein part through an N-acetylglucosaminylasparaginyl bond.