bluuebunny/crossref_metadata_2025_split huggingface dataset:
CD of gels and suspensions: Apparent CD in the soret region of sickle hemoglobin gels
Authors: Hjelm Rex P. , Thiyagarajan Pappannan , Johnson Michael E. 
Published: December 2004

AbstractCD spectra in the soret region of sickle‐cell deoxyhemoglobin (deoxy‐HbS) fiber gels are radically different from the CD of deoxy‐HbS in solution. An explanation is found using the Stokes–Mueller representation of the interaction of a polarized beam with the instrument optical train and sample to derive expressions for the apparent CD of gels and suspensions of optically active molecules that consist of randomly oriented domains or particles that are linearly dichroic and linearly birefringent. These theoretical considerations show that the apparent CD spectra from such systems have contributions from the LD and birefringence of each domain even if no net linear birefringence and dichroism is apparent in the sample. Thus, the interpretation of the CD from gels and suspensions is problematic, unless it can be demonstrated that each domain or particle has extremely small absorbance or that the LD and birefringence of each is a very small fraction of the total absorbance. As a result, we conclude that the spectra of HbS gels are not due to the CD of the heme per se; rather, they also reflect the randomly oriented domain structure of the gels and the LD and linear birefringence associated with each domain.
Helix breakers in block copolypeptides
Authors: Mattice Wayne L. 
Published: December 2004

AbstractThe ability of residues of type Y to disrupt the helix formed by residues of type X has been studied in X‐Y‐X‐block copolypeptides. The degree of polymerization of each X‐block is so large that it can be considered to be infinite. Matrix methods are used to obtain a general expression for the helix content of the central residue in the Y‐block. The resulting expression is specialized to the case where the statistical‐weight matrix is of dimensions 2 × 2, with elements, 1, 1, σs, and s. The behavior is evaluated for physically realistic values of σ and s. Two useful generalizations emerge: (1) The ability of the Y‐block to disrupt the helix is determined primarily by the value of s for residues of type Y. Helix disruption does not correlate well with the helix content of a Y‐homopolymer of infinite degree of polymerization. (2) In contrast, the ability of the X‐block to resist the influence of the Y‐block is determined primarily by the helix content of the X‐block. It does not correlate well with s for residues of type X. A random‐coil region in a Y‐block that continues into the following X‐block is more stable if residues of type X have a large value of σ because there is helix initiation in the X‐block. It is this influence of σ that prevents a correlation between s and the ability of the X‐block to resist the disruptive influence of the Y‐block.
Nucleic acid–metal interactions: V. The effect of silver(I) on the structures of A‐ and B‐DNA forms
Authors: Nordén Bengt , Matsuoka Yukio , Kurucsev Tomas 
Published: December 2004

AbstractThe interaction of silver(I) with DNA has been studied with uv LD in aqueous solution and in a humid anisotropic poly(vinyl alcohol) host (B‐DNA) and also in 80% ethanolic solution (A‐DNA). Addition of silver ions has a pronounced effect on the dichroic spectra of DNA, indicating that the DNA structure is significantly altered. By correlation with calculated reduced LD spectra, using intensities and moments of the corresponding electronic transitions of the DNA bases, the experimental spectra of DNA at high silver content may be interpreted in terms of tilt and roll angles of the bases in the double helix. In ethanolic A‐DNA solution there is a pronounced decrease in the orientation by flow of DNA, suggesting that the complexation of DNA to silver may be accompanied by the formation of compact tertiary structures.
Chemical synthesis of polysaccharides. 7. Enzymatic hydrolysis of (1 → 6)‐α‐DL‐glucopyranan (DL‐dextran)
Authors: Okada Masahiko , Sumitomo Hiroshi , Hirasawa Takahito 
Published: December 2004

AbstractHydrolysis of (1 → 6)‐α‐DL‐glucopyranan (synthetic DL‐dextran) by an endo‐dextranase from a Penicillium species was examined in an acetate buffer solution (pH 5.3) at 37°C. Three samples of different tacticities (isotactic dyad content, 55, 63, and 72%) were employed with a clinical dextran for comparison. Colorimetric determination of the reducing end units of the saccharides produced during hydrolysis showed that the maximum degrees of hydrolysis based on the D‐glucose units, (D.H.)D, for the DL‐dextrans were 21.4, 27.8, and 33.0% in the order of increasing isotacitic dyad content, whereas the (D.H.)D value for the clinical dextran was 51.9%. A statistical treatment of the enzymatic hydrolysis is proposed to interpret the experimental results.
Molecular orbital calculations on the oligopeptides netropsin, distamycin and related compounds
Authors: Manning Mark C. , Woody Robert W. 
Published: December 2004

AbstractThe electronic structure of the antibiotics netropsin, distamycin A, and related compounds has been examined by various theoretical models. Calculations of both the Pariser‐Parr‐Pople (PPP) and the semiempirical CNDO/S types can account for the absorption spectrum of netropsin and distamycin A. The CD spectrum has been calculated for the conformation of netropsin found in the crystal structure of a netropsin/DNA dodecamer. Not all the CD spectral features can be attributed entirely to the chiral conformation of netropsin, indicating that there are significant interactions between netropsin and DNA. A CD calculation was also performed for distamycin A in a similar conformation. An examination of the charge‐density maps of the excited states suggests that there is substantial charge transfer from the pyrrole ring to either of the adjacent peptide linkages in these systems. At higher energies, even longer distance charge transfer can be observed. Similar behavior was seen in the monomers pyrrole‐2‐carboxamide and 3‐(formylamino)pyrrole.
The role of the solvent on the binding of ethidium bromide to DNA in alcohol–water mixtures
Authors: Baldini Giancarlo , Varani Gabriele 
Published: December 2004

AbstractThe binding of ethidium bromide to calf thymus DNA is investigated over a wide range of temperatures and alcohol concentrations by means of fluorescence techniques. The presence of alcohol is found to lower the association constant, as isopropanol and n‐propanol are more effective than ethanol and methanol. It is also found that the data from different alcohols fall very close on the same straight line when plotted vs the solution dielectric constant ϵ. It is shown that the dependence of the binding constant on ϵ is beyond the prediction of current polyelectrolyte theories; rather, it appears that the binding is greatly controlled by the activity coefficient of the dye. The thermodynamic functions of the reaction have been estimated by means of Van't Hoff analysis: a large, negative enthalpy contributes to the binding, whereas the entropy, also favorable, is only slightly responsible for the overall free energy. Both enthalpy and entropy are strong functions of temperature and alcohol concentration. We show that the dependence of the thermodynamic quantities on the temperature is removed by considering “isodielectric” binding. This can be accomplished by a proper choice of the alcohol concentration, so that the thermal dependence of ϵ is compensated. It is found that the isodielectric free energy, enthalpy, and entropy are the same for different alcohols when plotted vs ϵ. When looking at the isodielectric quantities, it appears that the binding is now opposed by a positive enthalpy, whereas the observed favorable free energy results mainly from a large and positive entropy. The relevance of hydrophobic effects emerges from the behavior of the isodielectric thermodynamic quantities, as well as from the similarities observed when other interacting systems are compared.
Stereochemistry of α‐aminoisobutyric acid peptides in solution: Conformations of decapeptides with a central triplet of contiguous L‐amino acids
Authors: Balaram Hemalatha , Sukumar M. , Balaram P. 
Published: December 2004

AbstractThe decapeptides Boc‐Aib‐L‐Val‐Aib‐Aib‐(L‐Val)3‐Aib‐L‐Val‐Aib‐OMe and Boc‐Aib‐L‐Leu‐Aib‐Aib‐(L‐Leu)3‐Aib‐L‐Leu‐Aib‐OMe have been studied in CDCl3 and (CD3)2SO solutions by 270‐MHz1 H‐nmr. In CDCl3, the presence of eight intramolecularly hydrogen‐bonded NH groups has been established, consistent with a 310‐helical conformation, for both decapeptides. In (CD3)2SO, only seven solvent‐shielded NH groups are observed, supporting either an α‐helical conformation or a partially unfolded 310‐helix. Ir studies provided supporting evidence for intramolecularly hydrogen‐bonded structures in CHCl3, while CD studies suggest helical conformation in both decapeptides in various solvents. CD studies also support helical folding in the C‐terminal hexapeptides. The central triplet of L‐amino acids appears to destabilize 310‐helical conformations in polar solvents like (CD3)2SO.
A Raman spectroscopic study of the interaction between nucleotides and the DNA binding protein gp32 of bacteriophage T4
Authors: Otto C. , De Mul F. F. M. , Greve J. 
Published: December 2004

AbstractRaman spectra of the bacteriophage T4 denaturing protein gp32, its complex with the polynucleotides poly(rA), poly(dA), poly(dT), poly(rU), and poly(rC), and with the oligonucleotides (dA)8 and (dA)2, were recorded and interpreted. According to an analysis of the gp32 spectra with the reference intensity profiles of Alix and co‐workers [M. Berjot, L. Marx, and A. J. P. Alix (1985) J. Ramanspectrosc., submitted; A. J. P. Alix, M. Berjot, and J. Marx (1985) in Spectroscopy of Biological Molecules, A. J. P. Alix, L. Bernard, and M. Manfait, Eds., pp. 149–154], 1 gp32 contains ≈ 45% helix, ≈ 40% β‐sheet, and 15% undefined structure. Aggregation of gp32 at concentrations higher than 40 mg/mL leads to a coordination of the phenolic OH groups of 4–6 tyrosines and of all the sulfhydryl (SH) groups present in the protein with the COO− groups of protein. The latter coordination persists even at concentrations as low as 1 mg/mL. In polynucleotide–protein complexes the nucleotide shields the 4–6 tyrosine residues from coordination by the COO− groups even at high protein concentration. The presence of the nucleotide causes no shielding of the SH groups. With Raman difference spectroscopy it is shown that binding of the protein to a single‐stranded nucleotide involves both tyrosine and trytophan residues. A change in the secondary structure of the protein upon binding is observed. In the complex, gp32 contains more β‐sheet structure than when uncomplexed. A comparison of the spectra of complexed poly(rA) and poly(dA) with the spectra of their solution conformations at 15°C reveals that in both polynucleotides the phosphodiester vibration changes upon complex formation in the same way as upon a transition from a regular to a more disordered conformation. Distortion of the phosphate–sugar–base conformation occurs upon complex formation, so that the spectra of poly(rA) and poly(dA) are more alike in the complex than they are in the free polynucleotides. The decrease in intensity of the Raman bands at 1304 cm−1 in poly(rA), at 1230 cm−1 in poly(rU), and at 1240 and 1378 cm−1 of poly(dT) may be indicative of increased stacking interactions in the complex. No influence of the nucleotide chain length upon the Raman spectrum of gp322 in the complex was detected. Both the nucleotide lines and the protein lines in the spectrum of a complex are identical in poly(dA) and (dA)8.
Conformation‐Determining role for the N‐acetyl group in the O‐glycosidic linkage, α‐GalNAc‐Thr
Authors: Maeji N. J. , Inoue Yoshio , Chûjô Riichirô 
Published: December 2004

AbstractAn 1H‐nmr study of 2‐acetamido‐2‐deoxy‐3,4,6‐tri‐O‐acetyl‐D‐galactopyranose (AcGalNAc) glycosylated Thr‐containing tripeptides in Me2SO‐d6 solution reveals two mutually exclusive intramolecular hydrogen bonds. In Z‐Thr(AcGalNAc)‐Ala‐Ala‐OMe, there is an intramolecular hydrogen bond between the Thr amide proton and the sugar N‐acetyl carbonyl oxygen. The strength of this hydrogen bond will be dependent on the amino acid residues on the Thr C terminal side to some undetermined distance. In Ac‐Thr(AcGalNAc)‐Ala‐Ala‐OMe, a different intramolecular hydrogen bond between the sugar N‐acetyl amide proton and the Thr carbonyl oxygen exists. The choice of hydrogen bonds seems dependent on the bulkiness of the residues on the Thr N terminal side. The consequence of such strong hydrogen bonds is a clearly defined orientation of the sugar moiety with respect to the peptide backbone. In the former, the plane of the sugar pyranose ring is roughly oriented perpendicularly to the peptide backbone. The latter orientation is where the plane of the sugar ring is roughly in line with the peptide backbone. In both orientations, the sugar moiety can increase the shielding of the neighboring amino acid residues from the solvent. The idea that the amino acid residues near the glycosylated Thr influence orientation of the sugar moiety with respect to the peptide backbone and in turn possibly hinder peptide backbone flexibility has interesting implications in the conformational as well as the biological role of O‐glycoproteins.
A predictive model of enzymatic cleavage of nucleic acids
Authors: Hough Christopher J. 
Published: December 2004

AbstractA new static model of enzymatic cleavage of polymeric substrates such as nucleic acids has been derived. The model is compared to that elaborated by Tanford and to experimental data. In predicting the fragment distribution for a restriction enzyme digestion of a circular substrate, the model is superior to that of Tanford.
Normal‐Mode calculation for methylated Z‐DNA poly(dG‐m5dC) · (dG‐m5dC)
Authors: Hua X. M. , Prohofsky E. W. 
Published: December 2004

AbstractNormal modes of methylated Z‐DNA poly(dG‐m5dC) · (dG‐m5dC) are computed by helix‐lattice dynamics. Good agreement with Raman spectral data is obtained. We discuss improvements in the formulation of the problem that allow us to greatly reduce the size of the matrix used. This leads to greatly reduced calculation times. The improvements come from using knowledge of the C2 and time‐reversal symmetries.
A 2H‐nmr study of the A‐DNA conformation in films of oriented Na‐DNA: Evidence of a disordered B‐DNA contribution
Authors: Brandes Rolf , Vold Regitze R. , Kearns David R. , Rupprecht Allan 
Published: December 2004

AbstractSolid‐state 2H‐nmr spectra have been obtained from folded films of oriented Li‐ and Na‐DNA molecules with the purine bases selectively deuterium labeled at the 8 position. From line shape simulations, we find that the Na‐DNA sample at 75% relative humidity (rh) contains both A‐DNA and surprisingly large amounts of B‐DNAHere, B‐DNA refers to “B‐DNA family” (i.e. B‐ or C‐DNA).
(57%). For the A‐DNA component the average base tilt is 23°, and the total distribution width of tilt angles and helix axis orientations is ∼ 4° (standard deviation). In the B‐DNA component the base tilt is ∼ 0° and the total distribution width is ∼ 20°. In contrast, films of Li‐DNA only exhibit the B‐form line shape, consistent with a base tilt of ∼ 0° and a total distribution width of base tilt angles and helix axis orientations of 9°. The nmr results that demonstrate the presence of large amounts of B‐DNA in the Na‐DNA sample contrast with the x‐ray diffraction measurements that indicated mainly A‐form. The nmr spectra are used to monitor the B‐DNA content in the Na‐films and to evaluate procedures for increasing the A‐DNA fraction.
α‐Helix‐to‐random‐coil transitions of two‐chain coiled coils: Experiments on the thermal denaturation of ββ tropomyosin cross‐linked selectively at C‐190
Authors: Bracken William Clay , Carey John , Holtzer Marilyn Emerson , Holtzer Alfred 
Published: December 2004

AbstractA method is described for preparation of a species of β tropomyosin that is sulfhydryl‐blocked at C36 and disulfide‐cross‐linked at C190. Five steps are involved: (1) Rabbit skeletal muscle tropomyosin, comprising αα and αβ species, is oxidized with ferricyanide, disulfide‐cross‐linking both species at C190. (2) The product is treated with iodoacetamide, blocking the only remaining free sulfhydryl, i.e., C36 of the β‐chains. (3) The C36‐blocked, C190‐cross‐linked product is reduced with dithiothreitol (DTT), unfolded in urea, and α and β chains separated by ion‐exchange chromatography. (4) The C36‐blocked β chains are refolded by dialysis. (5) The refolded, C36‐blocked ββ species are cross‐linked at C190 by ferricyanide oxidation. The resulting C36‐blocked, C190‐cross‐linked ββ product is separated from contaminating species—mostly completely blocked β‐chains and multichain cross‐linked molecules—by size‐exclusion chromatography in denaturing (guanidinium chloride) solvent. The five‐step process and the final product were monitored by titration of free sulfhydryls and by NaDodSO4/polyacrylamide gel electrophoresis (PAGE). Thermal unfolding curves from CD are reported for the resulting pure, C36‐blocked, C190‐cross‐linked ββ species and for its DTT‐reduction product, the noncross‐linked C36‐blocked species. The latter shows almost the same thermal unfolding transition as intact, noncross‐linked ββ species. The former shows a pretransition similar to, but larger in extent than, the one well known to occur in the analogous case of C190‐cross‐linked αα tropomyosin. These unfolding transitions are compared with one another and with that previously reported for doubly cross‐linked (at C36 and C190) ββ species. These comparisons are made in the light of current physical models for coiled‐coil unfolding equilibria. It is concluded that although no extent model is demonstrably satisfactory, any successful model must include strain at the cross‐link, loop entropy, and regional nonuniformities as essential parts of the physics.
Microcalorimetric studies of solvent‐induced conformational change of sodium and cesium salts of poly(L‐glutamic acid) in aqueous media
Authors: Daoust Hubert , St‐Cyr Daniel 
Published: December 2004

AbstractOrganic solvent‐induced coil → helix conformational change of poly(sodium) L‐glutamate (NaPLG) and poly(cesium L‐glutamate) (CsPLG) in solution in aqueous mixed solvents have been studied at 25°C. Heats of dilution of NaPLG in the water–dioxane pair have been measured as a function of polymer concentration and solvent composition. The results indicate that the overall chain conformation in the disordered form is not too different from that in the α‐helical form. Heat capacity measurements by flow microcalorimetry have also been done. The apparent monomolar heat capacity at constant pressure of the polymer, Cp, ϕ, decreases with dilution similarly to other strong polyelectrolytes in aqueous media. In the water–dioxane pair, Cp, ϕ increases with the dioxane content due to partial desolvation of ionic species resulting from increasing ionic association. In the case of the water‐2‐chloroethanol (CE) pair, the transition takes place at low CE content and results show a fast decrease in Cp, ϕ when the α‐helical conformation predominates. It is believed carboxylate groups and CE molecules associate themselves into a complex formation responsible for the transition. The size of the cation plays a significant role in the thermodynamic properties of these polyelectrolytes in solution since sodium ions are more strongly bound to the chain than cesium ions.
Helix–coil dynamics of a Z‐helix hairpin
Authors: Antosiewicz J. , German M. W. , Van De Sande J. H. , Porschke D. 
Published: December 2004

AbstractThe helix–coil transition of a Z‐helix hairpin formed from d(C‐G)5T4(C‐G)5 has been characterized by equilibrium melting and temperature jump experiments in 5M NaClO4 and 10 mM Na2HPO4, pH 7.0. The melting curve can be represented by a simple all‐or‐none transition with a midpoint at 81.6 ± 0.4°C and an enthalpy change of 287 ± 15 kJ/mole. The temperature jump relaxation can be described by single exponentials at a reasonable accuracy. Amplitudes measured as a function of temperature provide equilibrium parameters consistent with those derived from equilibrium melting curves. The rate constants of Z‐helix formation are found in the range from 1800 s−1 at 70°C to 800 s−1 at 90°C and are associated with an activation enthalpy of −(50 ± 10) kJ/mole, whereas the rate constants of helix dissociation are found in the range from 200 s−1 at 70°C to 4500 s−1 at 90°C with an activation enthalpy +235 kJ/mole. These parameters are consistent with a requirement of 3–4 base pairs for helix nucleation. Apparently nucleation occurs in the Z‐helix conformation, because a separate slow step corresponding to a B to Z transition has not been observed. In summary, the dynamics of the Z‐helix–coil transition is very similar to that of previously investigated right‐handed double helices.
Thermodynamics of the B to Z transition in poly(dGdC)
Authors: Chaires Jonathan B. , Sturtevant Julian M. 
Published: December 2004

AbstractThe thermodynamics of the B to Z transition in poly(dGdC) was examined by differential scanning calorimetry, temperature‐dependent absorbance spectroscopy, and CD spectroscopy. In a buffer containing 1 mM Na cacodylate, 1 mM MgCl2, pH 6.3, the B to Z transition is centered at 76.4°C, and is characterized by ΔHcal = 2.02 kcal (mol base pair)−1 and a cooperative unit of 150 base pairs (bp). The tm of this transition is independent of both polynucleotide and Mg2+ concentrations. A second transition, with ΔHcal = 2.90 cal (mol bp)−1, follows the B to Z conversion, the tm of which is dependent upon both the polynucleotide and the Mg2+ concentrations. Turbidity changes are concomitant with the second transition, indicative of DNA aggregation. CD spectra recorded at a temperature above the second transition are similar to those reported for ψ(–)‐DNA. Both the B to Z transition and the aggregation reaction are fully and rapidly reversible in calorimetric experiments. The helix to coil transition under these solution conditions is centered at 126°C, and is characterized by ΔHcal = 12.4 kcal (mol bp)−1 and a cooperative unit of 290 bp. In 5 mM MgCl2, a single transition is seen centered at 75.5°C, characterized by ΔHcal = 2.82 kcal (mol bp)−1 and a cooperative unit of 430 bp. This transition is not readily reversible in calorimetric experiments. Changes in turbidity are coincident with the transition, and CD spectra at a temperature just above the transition are characteristic of ψ(–)‐DNA. A transition at 124.9°C is seen under these solution conditions, with ΔHcal = 10.0 kcal (mol bp)−1 and which requires a complex three‐step reaction mechanism to approximate the experimental excess heat capacity curve. Our results provide a direct measure of the thermodynamics of the B to Z transition, and indicate that Z‐DNA is an intermediate in the formation of the ψ‐(–) aggregate under these solution conditions.
Pulsed field electrophoresis
Authors: Dee Gregory T. 
Published: December 2004

AbstractPulsed field electrophoresis, or PFE, provides good separation between large molecules that under constant field electrophoresis are hard to isolate. This is due to the weak dependence of the constant field mobility on the molecular weight for these large molecules. If a spectrum of relaxation times exists that describes the recovery of the mobility to its constant field value after a reversal of the field, then we show that molecules with differing molecular weights are separated into two groups. Those with short relaxation times are unaffected by the cycling of the field and those with long relaxation times exhibit reduced mobilities. If the molecules adopt conformations that decrease their mobility initially, after a field reversal we demonstrate that a minimum develops in the mobility as a junction of the relaxation time. Using the model we demonstrate that effects of varying the switching times as a function of time. We predict that exponential rather than linear dependencies of the switching times on time increase the range of molecular weights over which enhanced separation can occur.