bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differences in circular dichroism and fluorescence between the DNA complexes formed with 3‐amino‐ and 3,8‐ diaminophenanthridinium derivatives
Authors: Kindelis Antonis , Aktipis Stelios 
Published: December 2004

AbstractThe conformation of DNA complexes formed with various 3‐amino‐ and 3,8‐diamino‐phenanthridinium derivatives were examined by CD and fluorescence methods. The CD of these complexes is characterized by major bands in the 300–350‐nm and the 400–550‐nm regions. The CD properties of the complexes formed with diaminophenanthridinium derivatives suggest that the structure of such complexes is well represented by the intercalation complex formed between DNA and ethidium bromide. The substantial and regular increases in ellipticities near 308 nm that occur with increasing DNA‐bound diaminophenanthridinium to DNA phosphate ratios (r) may result from direct interactions between molecules intercalated in neighbouring binding sites. In contrast, the changes in the shape of the CD of DNA complexes of monoaminophenanthridinium derivatives with r and the much lower maximum ellipticities attained suggest that near‐neighbor interactions among intercalated monoaminophenanthridinium derivatives occur much less efficiently than in the corresponding diamino complexes, if at all. Although alternative explanations for the differences in the optical properties between the mono‐ and diaminophenanthridinium complexes of DNA may be offered, such results seem to indicate that complexes formed with monoaminophenanthridinium derivatives are characterized by a conformation which is quite distinct and different from that of the DNA–diaminophenanthridinium complexes. This conclusion is further supported by the considerable increase in fluorescence that accompanies the binding of the diaminophenanthridinium derivatives to DNA as compared to the minor increases, which occur upon the binding of the monoaminophenanthridinium compounds. The importance of conformation as a factor influencing template, function, especially with respect to the RNA polymerase‐catalyzed synthesis of RNA, is now well appreciated. Therefore, methods which could provide information readily about changes in the conformation of a template, i.e., as a result of dye intercalation, are expected to facilitate our understanding of the effects of conformational change on the function and activity of templates.
Thermodynamic characterization of ethidium bromide binding to a unique site on a yeast tRNAPhe
Authors: Sturgill Thomas W. 
Published: December 2004

AbstractA self‐consistent thermodynamic characterization of the binding of ethidium to yeast phenylalanine‐specific tRNA at 25°C, pH 7.0, in 11 nM MgCl2, 375 nM NaCl, and 25 mM sodium phosphate has been obtained. Two ethidium molecules bind per tRNA under these conditions. The stronger site has a dissociation constant equal to 1.9 ± 0.5 μM and ΔHdis°′ = 12 ± 1 Kcal/mol, and the weaker sites has a dissociation constant equal to 24 ± 9 μM and ΔHdis°′ = 8.9 ± 1.5 Kcal/mol. The average calorimetric ΔHdis°′ for the to sites 10.6 ± 0.4 kcal/mol. The thermodynamics of binding to the stranger sites are most probably the thermodynamics of interaction between A·U (6) and A·U (7), the unique site identified by Jones and Kearns. The binding is enthalpically driven and classical hydrophobic interactions do not appear to be important in the binding reaction.
Influence of local interactions on protein structure. III. Conformational energy studies of N‐acety‐N′‐methylamides of Gly‐X and X‐Gly dipeptides
Authors: Zimmerman S. Scott , Scheraga Harold A. 
Published: December 2004

AbstractConformational energy calculations using an empirical conformational energy program for peptides (ECEPP) were carried out on 20 N‐acetyl‐ N′‐methylamides of Gly‐X and X‐Gly depeptides, where X = Ala, Asn, Asp, Gly, Phe, Ser, Thr, Tyr, Val, and Pro, and also of Leu‐Gly. Each depeptde was found to have 25 or more low‐energy minima, except Gly‐Thr, which had only 11 low‐energy minima because of the stable side chian‐backbone hydrogen present in all low‐energy conformation. As a group, the stble chain‐backbone hydrogen bonds present in all low‐energy conformations. As a group, the Gly‐containing dipeptides were calculated in all low‐energy prpensity for formation of bends than the Ala‐containing depeptides. The X‐ Gly dipeptides were calculated to favor bends more than the Gly‐X dipeptides, primarlly because of the high stability of the type II bend in X‐Gly dipeptides. These results are in agreement with obseved occurrences of bends in the x‐ray structures of globular proteins. The calculated conformation properties were found to be in good agreement with experimental results.
Concentration‐dependent isomerization of bacteriophage T2L
Authors: Welch John B. , Bloomfield Victor A. 
Published: December 2004

AbstractWe have studied the concentration and ionic strength dependence of the fiber‐reorientation transition in T2L bacteriophage, using sedimentation velocity and quasielastic light scattering diffusion measurements. High‐salt and low‐phage concentration favor the form with fibers extended. The equilibrium between the two forms is dependent on the phage Concentration. This behavior is unexpected for a reaction that is apparently unimolecular with respect to phage, and attests to the strong increase in excluded volume and other interactions accompanying fiber extension. The fiber‐extended form has anomalously high diffusion coefficient and low molecular weight according to the Svedberg equation.
Conformation of poly(L‐arginine). II. Complexes with polyanions
Authors: Mita Kazuei , Ichimura Sachiko , Zama Mitsuo 
Published: December 2004

AbstractConformaitons of poly(L‐arginine)/polyanion complexes were studies by CD measurements. The polyanions were the homoplolypeptides poly(L‐glutamic acid) and poly(L‐aspartic acid); the synthetic polyelectrolytes and polyethylenesulfonate; and the polynucleotides were native DNA, denatured DNA, and poly(U). It was found that poly(L‐arginine) forms the α‐helical conformation by interacting with the acidic homopolypeptides and the synthetic anionic polyelectrolytes. In each complex, poly(L‐glutamic acid) is in the α‐helical conformation, whereas poly(L‐aspartic acid) is mostly in the random structure. The poly(L‐glutamic acid) complex changed into the β‐sheet structure at the transition temperature about 65°C in 0.01M cacodylate buffer (pH 7). Even in the presence of 5M urea, this complex remained in the α‐helical conformation at room temperature. The existence of the stable complex of α‐helical poly(L‐arginine) and α‐helical poly(L‐glutamic acid) was successfully supported by the model building study of the complex. The α‐helix of poly(L‐arginine) induced by binding with polyacrylate was the most stable of the poly(L‐arginine)‐polyanion complexes examined as evidenced by thermal and urea effects. The lower helical content of the polyethylenesulfonate‐complexed poly(L‐aginine) was explained in terms of the higher charge density of the polyanion. On the other hand, native DNA, denatured DNA, and poly(U) were not effective in stabilizing the helical structure of poly(L‐arginine). This may be due to the rigidity of polyanions and to the steric hindrance of bases. Furthermore, the distinitive structual behavior of poly(L‐arginine) and poly(L‐lysine) regarding polyanion interaction has been noticed throughout the study.
Fluorescence anisotropy decay studies upon hemoglobin A and its subunits
Authors: Bucci E. , Fronticelli C. , Flanigan K. , Perlman J. , Steiner R. F. 
Published: December 2004

AbstractFluorescent conjugates of hemoglobin A, its isolated β‐chain, and the apo‐derivative of the β‐chain have been prepared in which the β‐93 sulfhydryl was conjugated with 1,5‐AEDANS. Radiationless enery transfer to the heme group results in a major decrease in fluorescence intensity and decay time. Measurements of the time decay of fluorescence anisotropy, employing single‐photon counting, indicate that the apparent rotational correlation time is, in each case, substantially reduced from the value expected for a rigid molecule of the same molecular weight. This observation raises the possibility that internal degrees of rotational freedom exist.
Solvent accessibility study on tRNAPhe
Authors: Thiyagarajan P. , Ponnuswamy P. K. 
Published: December 2004

AbstractIn order to assess the solvent–solute association in the tRNAPhe molecule, solvent accessibility calculations were carried out for its crystalline and completely extended states following the method of Lee and Richards. To do this, results from the calculations on model trinucleotide systems pApXpA with different bases at position X were used. In the folded form of the molecule, it was found that the oxygen atoms O(I) and O(II) of almost all the phosphate groups and the O(2′) atoms of the sugar rings situated throughout the backbone were highly exposed to the solvent. The amount of reduction found in the solvent accessibilities of the various atoms in going from the extended state to the folded state of the molecule indicates the kind of compactness of the tertiary structure in tRNAPhe. The results give quantitative support to many characteristics of the tRNA molecule, such as loop sections, buried/exposed residues, hydrophobic interactions, etc., which were thought to be due to other factors.
Formation of ternary complexes involving zinc or copper ions, polynucleotides, and polypeptides containing glutamic acid and tyrosine residues
Authors: Bere Augustin , Helene Claude 
Published: December 2004

AbstractMetal ions such as Zn2+ and Cu2+ can mediate interactions between copolypeptides (Glux, Tyry)n and polynucleotides. CD data show that these ternary complexes are characterized by an unstacking of nucleic acid bases, while the polypeptide adopts an α‐helical conformation as observed in the two binary complexes polynucleotide–cation and polypeptide–cation. Fluorescence studies demonstrate that tyrosyl side chains interact with nucleic acid bases in the ternary complexes, leading to a quenching of tyrosine fluorescence.
Characterization of molecular motions in 13C‐labeled aortic elastin by 13C‐1H magnetic double resonance
Authors: Fleming W. W. , Sullivan C. E. , Torchia D. A. 
Published: December 2004

AbstractPurified insoluble elastin samples labeled with [1‐13C]valine, [1‐13C]alanine, and [1‐13C]‐lysine were prepared from chick aorta in culture. The molecular mobility at the labeled sites was investigated using 13C‐1H magnetic double‐resonance spectroscopy. Linewidths, T1, and nuclear Overhauser effect (NOE) values of the labeled carbons alone were obtained from dipolar decoupled difference spectra. Analysis of these parameters together with signal intensity measurements showed that essentially all the valyl residues, ca. 75% of the alanyl residues, and ca. 60% of the lysyl residues were characterized by rapid backbone motions having τ = 65 nsec. Resonances due to the remaining alanyl and lysyl residues were detected in cross‐polarization experiments, which enhance the signals of motionally restricted carbons. Since lysyl and alanyl residues are found in the crosslink regions of elastin, whereas valyl residues are not, we conclude that crosslinks rather than secondary structures in the extensible region of the protein are the main source of motional restrictions in the protein. Elastin chain mobility was monitored by linewidth measurements over the range −90 to +70°C. When the swelling solvent (0.15M NaCl) was fixed at 0.6 g/g of elastin, a rapid monotonic reduction in chain mobility was observed as the temperature was lowered from 50 to 5°C. Liquidlike mobility was completely lost at 5°C. In contrast, the same sample in contact with excess solvent retained its liquidlike molecular mobility until −13°C, where it abruptly became rigid. The molecular mobility of this sample was temperature insensitive in the physiologically interesting range, 20–40°C, as a consequence of the opposing influences of temperature and swelling. Taken together these nmr data indicate that under physiological conditions, elastin is a network of mobile chains whose motions are strongly influenced by protein–solvent interactions.
Neutron‐scattering studies of the structure of chromatin core particles in solution
Authors: Braddock Gordon W. , Baldwin John P. , Bradbury E. Morton 
Published: December 2004

AbstractThe structure of the nucleosome core particle in solution has been studied by neutron scattering using the full‐contrast variation technique, which reduces the experimental spectra to three fundamental scatter functions holding information on shape and structure. Systematic calculations of the fundamental scatter functions expected from proposed core‐particle models have been compared with the observed functions and show that the neutron‐scattering criteria severely restrict the number of models which can be valid for the structure in solution. The best model for the core particle in solution has a hydrophobic histone core about which 1.7 ± 0.1 turns of DNA are wrapped at a pitch between 3.0 and 3.5 nm. This core contains most of the histone and has an average thickness of 4 nm and diameter 6.4–7.5 nm. While solution scattering is not able to specify uniquely the actual shape of the core to high resolution, all models which are possible for the shape of the core to a resolution justified by the data have been considered. It is clear that cylindrical or wedge shapes compatible with the above dimensions are valid structures. A hole probably penetrates the histone core, but the data do not allow a diameter greater than 1 nm. Available evidence suggests that about a quarter of the total histone is outside the core.
Interactions between polyelectrolytes. DEAE‐sephadex–polymethacrylic acid
Authors: Feitelson J. , Josephs R. 
Published: December 2004

AbstractThe interaction between a highly swollen polyelectrolyte and a polymer coil‐of low charge density was investigated. Diethylaminoethyl dextran (DEAE) and polymethacrylic acid (PMA) at low pH served as a model system. Distribution measurements of PMA between a DEAE resin and ambient solution showed that the interaction increased with pH (number of charges per PMA molecule), temperature, and molecular weight of PMA. Since the absorption of PMA in the polyelectrolyte phase is an endothermic process it must be accompanied by a large positive entropy increase. The latter was sought in the structural changes of water which occur in the vicinity of the interacting polymers. The magnitude of the enthalpy changes for two PMA fractions indicate that not only interactions between ionized groups but also nonpolar and even purely polymer effects should be considered in this system.
Model connective tissue systems. A physical study of gelatin gels containing proteoglycans
Authors: Meyer F. A. , Comper W. D. , Prestox B. N. 
Published: December 2004

AbstractThe swelling behavior of gelatin gels containing proteoglycans (sulphated proteoglycans from bovine intervertebral discs and a hyaluronate proteoglycan from bovine synovial fluid) when immersed in osmotically active solutions of dextran have been measured. The presence of the proteoglycans markedly affects the internal osmotic contribution to the swelling pressure of the gel. These internal osmotic pressures are considerably in excess of the sum of the osmotic activities of the individual components. This behavior is understood in terms of an entropic interaction between the gelatin and the proteoglycan molecules. By use of the “dilute solution” treatment of Flory, the osmotic pressure excesses are related to the volumes and hence dimensions of the interact acting species. A comparison of these values with those calculated by other means shows good agreement. The osmotic behavior of the complex gels can be understood on a mechanistic basis, if we regard the gelatin and sulphated proteoglycans as spheres and the hyaluronate proteoglycan as a rod.
Comprehensive conformational analysis of (Gly‐Pro‐Pro)n and (Gly‐Pro‐Hyp)n related to collagen
Authors: Tumanyan Vladimir G. , Esipova Natalia G. 
Published: December 2004

AbstractA complete analysis of all possible conformations with correct hydrogen bonds of the collagen II type was performed on the basis of developed simultaneous equations. Using a unimodal search (by varying Ψ3), the energetically favorable structure was obtained. No other energetically satisfactory structural solutions are possible. The next aim was to obtain a precise model of the molecule. The program used includes a subroutine for continual deformation of the pyrrolidine rings. The set of parameters determining the structure consists of 14 independent variables (8 dihedral and 6 bond angles). As starting points for the energy optimization, conformations produced by scanning and some structures from previous work were used. The final structures (practically the same for both polymers) have helix parameters h = 0.285 nm and t = 52°, which are in excellent agreement with the 7/2 symmetry of diffraction data. The conformations of the pyrrolidine rings are of the B type, i.e., C2‐Cβ‐exo‐Cγ‐endo. For both polypeptides, the conformations of imino acids in position 3 of the triplet are the same; in position 2, however, they are slightly different. The difference in diffraction patterns for the 7/2 and 10/3 helices is discussed.
Sequence‐dependent conformations of DNA duplexes: The TATA segment of the d(G‐G‐T‐A‐T‐A‐C‐C) duplex in aqueous solution
Authors: Patel Dinshaw J. , Shapiro Lawrence , Hare Dennis 
Published: December 2004

AbstractThe base and sugar protons of the d(G‐G‐T‐A‐T‐A‐C‐C) duplex have been assigned from two‐dimensional correlated (COSY) and nuclear Overhauser effect (NOESY) measurements in D2O solution at 25°C. The nucleic acid protons have been assigned from NOEs between protons on adjacent bases on the same and partner strands, as well as from NOEs between the base protons and their own and 5′‐flanking H1′, H2′, H2″, H3′, and H4′ sugar protons. These assignments are confirmed from coupling constant and NOE connectivities within the sugar protons of a given residue. Several of these NOEs exhibit directionality and demonstrate that the d(G‐G‐T‐A‐T‐A‐C‐C) duplex is a right‐handed helix. The relative magnitude of the NOEs between the base protons and the sugar H2′ protons of its own and 5′‐flanking sugar demonstrate that the TATA segment of the d(G‐G‐T‐A‐T‐A‐C‐C) duplex adopts a B‐DNA type helix geometry in solution, in contrast to the previous observation of a A‐type helix for the same octanucleotide duplex in the crystalline state.
Structural investigation of poly‐L,D‐proline, a synthetic ion channel across bilayer membranes: Crystal structure and molecular conformation of two tetra‐D,L‐proline derivatives
Authors: Colapietro M. , De Santis P. , Palleschi A. , Spagna R. 
Published: December 2004

AbstractThe crystal structures and molecular conformations of two tetraproline derivatives with alternating configurations Boc(D‐Pro,L‐Pro)2OH and Boc(D‐Pro,L‐Pro)2OCH3 are investigated in connection with the ability of the homologous polymer to selectively increase (as an ion channel) the ion permeability across bilayer membranes. Both tetramers are characterized by the cis‐trans alternating conformation of the peptide bonds, which formally transforms in a turn of the poly‐D,L‐proline channel after a cis‐trans change of the central peptide residue.
Base tilt of B‐form poly[d(G)]‐poly[d(C)] and the B‐ and Z‐conformations of poly[d(GC)]‐poly[d(GC)] in solution
Authors: Edmondson Stephen P. , Johnson W. Curtis 
Published: December 2004

AbstractWe have measured the CD, isotropic absorption, and linear dichroism (LD) in the vacuum‐uv spectral region for the B‐conformations of poly[d(G)]‐poly[d(C)] and poly[d(GC)]‐poly[d(GC)], and for the Z‐conformation of poly[d(GC)]‐poly[d(GC)] formed in 70% trifluoroethanol. The reduced dichroism (LD divided by isotropic absorption) for all conformations varied with wavelength, indicating that the bases are not perpendicular to the helix axis. Since the directions of the transition dipoles are known, the inclinations and axes of inclination of each base can be determined from the wavelength dependence of the reduced dichroism spectra. The results indicate that the base normals of the (G + C) polymers in the B‐ and Z‐conformations are tilted at angles greater than 19° with respect to the helix axis. The guanine and cytosine bases have different inclinations, and the tilt axes are not parallel. Therefore, the bases for all the (G + C) polymer conformations studied are buckled and propeller twisted.
CD of the li‐salt of DNA in ethanol/water mixtures: Evidence for the B‐ to C‐form transition in solution
Authors: Bokma Jos T. , Curtis W. Johnson , Blok Johan 
Published: December 2004

AbstractThe conformational change of Li‐DNA in water/ethanol mixtures is followed by the change in the CD spectrum in solutions containing various percentages of ethanol in the range from 0 to 95%. Two main transitions can be distinguished. The first occurs in the range from 0 to 70% and is represented by a large reduction of the intensity of the positive CD band around 275 nm, which is apparently related to a small change in the number of base pairs per turn. Secondly, at higher percentages of ethanol (> 80%) a conformational change is detected, which is expressed as a reduction of the 245‐nm negative CD intensity. According to x‐ray diffraction experiments of fibers of Li‐DNA, the C‐form is attained in 95% ethanol, while at 70% ethanol a B‐like structure is observed. The CD experiments reported here also show that for DNA in solution the dependence on percentage of ethanol is composed of two main transition regions. The C‐form would then be adopted at high (∼ 95%) ethanol percentage. The 0–70% transition, although strongly expressed in optical CD experiments, has to be related to relatively small structural changes within the B‐family of DNA structures, which probably induce an enhanced contribution of n → π* transitions to the CD spectrum.
Vibrational spectroscopy of L‐valyl‐glycyl‐glycine, a parallel‐chain β‐structure
Authors: Bandekar Jagdeesh , Krimm S. 
Published: December 2004

AbstractBands in the ir and Raman spectra of L‐valyl‐glycyl‐glycine (VGG) and VGG‐ND have been assigned on the basis of a normal mode analysis of the known parallel‐chain β‐structure of this tripeptide. Amide I, II, III, and V mode shifts are obtained by the interactions of dipole derivatives in symmetry coordinates, referred to as dipole derivative coupling. These derivatives, obtained from ab initio studies, are also used to calculate ir intensities of amide I, II, and V modes. The agreement between predicted and observed frequencies and intensities is very good, providing confidence in the application of our force fields to the calculation of the vibrational modes of the general parallel‐chain β‐sheet structure (following paper).
Collective motion in DNA and its role in drug intercalation
Authors: Chou Kuo‐Chen , Mao Boryeu 
Published: December 2004

AbstractThe effects of collective motion in DNA as reflected by resonance coupling among its intact segments have been discussed for both linear and circular DNA molecules. The results indicate that due to the effects of this kind of internal collective motion, the energy will be at times highly concentrated at some spots. As a result of the overfocus of energy, the stress built up along the direction of hydrogen bonds between complementary base pairs will be dramatically increased, rupturing a series of consecutive hydrogen bonds simultaneously and resulting in a suddenly free jerk, such that the DNA molecule will undergo a local “quake.” The “hole” formed by this kind of quake‐like motion will be large enough for bulky drugs to gain entrance and intercalate into DNA. Even for smaller drugs, this local quake‐like motion can also provide a significant mode of entry for intercalation. Energy minimizations carried out for DNA–drug complexes indicate that, for most drugs, a distortion or disruption of 2 to 4 base pairs occurs at the intercalation site in DNA molecules.