bluuebunny/crossref_metadata_2025_split huggingface dataset:
Formation of ψ(+) and ψ(−) DNA
Authors: Shin Y. A. , Eichhorn G. L. 
Published: December 2004

AbstractDNA molecules can be organized into ordered aggregates of opposite handedness by complexation with polylysine and other polypeptides; we have investigated the conditions under which ψ(+) and ψ(−) structures are produced with double‐helical synthetic polynucleotides. Both poly(dGdC)·poly(dGdC) and poly(dAdT)·poly(dAdT) readily form ψ(−) structures with polylysine, although the method of preparation can alter the CD spectra. The GC copolymer, which is more susceptible to conversion into A or Z conformers, forms ψ(+) structures with lysine–alanine copolypeptides more readily than the AT copolymer. Nucleotide base modifications that favor the Z structure, such as bromination and methylation, also favor ψ(+) formation, and the Co(NH3)6Cl3 reagent that readily induces the Z structure also leads to ψ(+). Thus, the production of the ψ(+) structure seems to be frequently correlated with susceptibility to A or Z formation, although there are some cases in which the B conformer also leads to ψ(+). Polyethylene glycol generally produces a ψ(−) structure; the differentiation between ψ(+) and ψ(−) structures seems to require electrically charged polymers.
Studies of collagen fold formation in aqueous solutions of α‐gelatin III
Authors: Thorn I. , Eagland D. 
Published: December 2004

AbstractOptical rotation, viscosity, and density studies are reported on solutions of α‐gelatin in solvent mixtures of water and various monohydric alcohols. Reversion to the collagen fold by the protein is shown to be order in all cases, but changes in magnitude as a function of concentration of the particular alcohol are observed. The structuring effects of the alcohol on water are seen to be reflected in the extent of helix regeneration by the protein. Shorter chain alcohols appear to influence the initial rate of reversion by direct interaction with the protein.
Conformation study on heparin by intermediate‐angle X‐ray scattering
Authors: Yamaguchi Saburo , Hayashi Hisao , Hamada Fumiyuki , Nakajima Akio 
Published: December 2004

AbstractThe conformation of heparin in water was investigated by intermediate‐angle x‐ray scattering (IAXS). The theoretical scattering function for the coil conformation was calculated by the Monte Carlo method using the approximation of separable conformation energies and the conformation energies computed for two disaccharide pairs in heparin. From x‐ray scattering in a relatively small‐angle region, the conformation of heparin is not the ordered 21 helix conformation but the coil conformation obtained by the Monte Carlo calculation. It is expected, from x‐ray scattering in a relatively wide‐angel region, that the sulfate groups of heparin maintain about 7 Å between them.
X‐Ray crystallographic analysis of a ternary intercalation complex between proflavine and the dinucleoside monophosphates CpA and UpG
Authors: Aggarwal A. , Islam S. A. , Kuroda R. , Neidle S. 
Published: December 2004

AbstractWe report the crystal‐structure analysis of a complex involving the drug proflavine and the two dinucleoside monophosphates cytidylyl‐3′,5′‐adenosine (CpA) and uridylyl‐3′,5′‐guanosine (UpG). The planar drug molecule is intercalated between C ⃛G and U ⃛A Watson‐Crick base pairs, in a double‐helical fragmentlike arrangement. Sugar conformations at the 3′‐ends of the two strands are dissimilar. The backbone conformations fall within the ranges of values noted previously for dinucleoside intercalation complexes, and some correlations involving these are noted. The separation of the two strands and the basic twist angle of 16°, compared to other reported complexes, are indicative of sequence‐dependent effects of the drug binding.
Quantitative aspects of the development of a hydrophobic binding site on calmodulin by calcium binding
Authors: Steiner Robert F. 
Published: December 2004

AbstractThe interactive binding by calmodulin of Ca2+ and 1‐anilinonaphthalene‐8‐sulfonate (1,8‐ANS) has been examined. In the presence of saturating levels of Ca2+, calmodulin develops one moderately strong binding site for 1,8‐ANS, plus one or more weaker sites. The binding of 1,8‐ANS by unliganded, or singly liganded, calmodulin is slight; the development of a strong binding site, as well as the characteristic fluorescence enhancement and CD spectrum, requires the binding of two Ca2+ ions. Little further change occurs on binding additional Ca2+ ions.
How alike are the shapes of two random chains?
Authors: McLachlan A. D. 
Published: December 2004

AbstractTwo completely flexible random chains containing N atoms joined by links of length L can be superimposed by rigid‐body motions to match their structures as closely as possible. The statistics of the root‐mean‐square best‐fit distance D are discussed. For long chains, D2 tends of 0.125L2N. Thus, for a protein of 100 residues, where the Cα‐Cα distance is L = 3.8 Å, the expected root‐mean‐square atomic distance is 13.4 Å. This result gives a surprisingly good fit to the observed results for unrelated structures.
Conformation of cyclic analogs of enkephalin. II. Analogs containing a cystine bridge
Authors: Hall David , Pavitt Nicola 
Published: December 2004

AbstractA systematic survey has been made, using molecular mechanics, of the conformation of the ring entity of the enkephalin analogs, [D‐Cys2‐L‐Cys5]‐enkephalinamide and [D‐Cys2‐D‐Cys5]enkephalinamide. These molecules are considerably more flexible than the analog Tyr‐cyclo(Nγ‐D‐A2bu‐Gly‐Phe‐Leu‐), but the favored conformations of all three are very similar. The results of these studies are compatible with a Gly3‐Phe4 type II′ bend in the active conformation of enkephalin.
Precollapse of T7 DNA by spermidine at low ionic strength: A linear dichroism and intrinsic viscosity study
Authors: Baase Walter A. , Staskus Paul W. , Allison Stuart A. 
Published: December 2004

AbstractAt low salt ([Na+] = 10−3M), spermidine is capable of transforming DNA from a highly extended random coil to a compact particle. The transition takes place at a spermidine concentration of around 25 μM and the compact particle has been previously studied in considerable detail for several different DNAs. The objective of the present study is to see what effect, if any, spermidine has on T7 DNA conformation prior to collapse using flow dichroism and intrinsic viscosity. We conclude that increasing the spermidine concentration from 0 to the collapse transition point (above 20 μM) makes DNA increasingly nondraining. Furthermore, the persistence length dropped from 785 (±42) to 560 (±32) to 445 (±26) Å on increasing the ambient spermidine concentration from 0 to 1 to 10 μM. These results are in good agreement with counterion condensation theory and Odijk's theory of the electrostatic contribution to the persistence length of DNA. Nonetheless, it is concluded that counterion condensation is not entirely responsible for DNA collapse and that crosslinking promotes the transition to the compact state.
Anisotropic rotational motions of poly(L‐glutamic acid) in the α‐helix conformation
Authors: Hahn U. , Hanssum H. , Rüterjans H. 
Published: December 2004

AbstractThe anisotropic rotational motion of the backbone and the side chains of poly(L‐glutamic acid) in the α‐helical structure was investigated using the 13C‐T1 and T2 relaxation times of all carbon atoms with directly attached protons, obtained at a 13C‐Larmor frequency of 67.89 MHz. The evaluation of the nmr data was carried out according to the previously derived anisotropic diffusion model, in which the macromolecule is considered a rigid rod. The rotation of the backbone is characterized by two diffusion constants, D1 and D3, describing the rotation perpendicular to and around the symmetry axis. The additional internal motion of the Cβ‐methylene group is described as a jump process with a jump rate, k1, between two allowed rotametric states. Steric considerations indicate that the occupation of the third rotameric position is forbidden. The rotation of the Cγ‐methylene group is decribed as a one‐dimensional diffusion process around the Cβ–Cγ bond. Investigation of the temperature dependence of the relaxation parameters led to the temperature dependence of the dynamic parameters. Activation energies were determined from these data. The dynamic parameters obtained for poly(L‐glutamic acid) at 291 K are compared with the corresponding results of a previous study of poly(L‐lysine).The development of an anisotropic diffusion model for the motions of the rod‐shaped poly(L‐lysine) α‐helix and its application to the interpretation of the 13C‐relaxation data of this molecule have already been published previously. In this model, both the overall molecular tumbling and the various internal motions have been characterized by diffusion constants or jump rates typical for each process. These dynamic parameters can be calculated from the spin–lattice relaxation times, the spin–spin relaxation times and the NOE factors of the Cα, Cβ, and Cγ nuclei of the polypetide.In the present paper, we describe the application of the above‐mentioned dynamic model to the interpretation of 13C‐relaxation studies of a further homopolypeptide, poly(L‐glutamic acid), in the α‐helical structure. Furthermore, we studied the temperature dependence of the relaxation times of this polymer and determined the anisotropic diffusion parameters at each temperature. From their temperature dependence and from comparison of our present results with the data of our previous study of poly(L‐lysine), we were able to derive new insights into the intramolecular diffusion processes and the excitation of various motions.
QELS‐SEF study on poly(lysine) in the extraordinary phase: Effect of electric field strength on the apparent diffusion coefficient
Authors: Schmitz Kenneth S. , Ramsay Donald J. 
Published: December 2004

AbstractThe technique of quasielastic light scattering (QELS) in the presence of a sinusoidal electric field (QELS‐SEF) was used to examine the diffusion of poly(lysine) in the extraordinary phase, which is defined by the anomalously small value in the apparent diffusion coefficient (Dapp, obtained by QELS methods) as the added salt concentration is lowered below 10 mM. Spectra were obtained for high‐molecular‐weight poly(lysine) (800,000) in 0.5 mM KCl, using a driving frequency of 90 Hz. It was observed that the linewidth, hence apparent diffusion coefficient (DSF), increased with electric field strength (E) over the range 6 < E < 30 V/cm. As might be anticipated, the asymptotic limit, DSF(E = 0), was almost numerically equivalent to Dapp at this KCl concentration. As E approached the upper limit value of 31 V/cm, the value of DSF approached the high salt (500 mM KCl) value of Dapp. These observations are discussed in terms of small‐ion dispersion effects.
Adenine residue: A normal‐coordinate analysis of the vibrational spectra
Authors: Majoube Michel 
Published: December 2004

AbstractThe frequencies observed for adenine in the Raman spectra of adenosine monophosphate (AMP) and biopolymers such as poly(A), DNA, and RNA are compared with those calculated for a model compound, 9‐methyladenine, in which the methyl group is taken as a unit mass concentrated on the carbon. The force field used is a Urey‐Bradley field already tested on polycrystalline adenine and its analogs D‐substituted on the nitrogens, on the carbon at position 8, and on both. Assignments for adenine residue Raman bands are proposed and discussed on the basis of observed and calculated D‐shifts. These assignments are examined, in particular, for bands common to both adenine and guanine residues by analysis of their behavior for Raman hypochromism.
Preferred solution and calculated conformations of dermorphin and analysis of structure–conformation–activity relationships in the series [A1an]‐dermorphin
Authors: Toma Flavio , Dive Vincent , Fermandjian Serge , Darlak Krzysztof , Grzonka Zbigniew 
Published: December 2004

AbstractWe describe the solution (1H‐nmr) and calculated conformations of the opiatelike peptide dermorphin and the analysis of structure–conformation–activity relationships in the series [Alan]‐dermorphin. We used 1H‐nmr spectroscopy to study dermorphin and its analogs [Alan]‐dermorphin (with n = 1, 2…7) dissolved in dimethylsufoxide. Conformational energy calculations using semiempirical partitioned energy function methods were then carried out on dermorphin and its [L‐Ala2]‐analog. Agreement between calculation and experiment is satisfying, both suggesting predominance of a type I β‐turn around Pro6‐Ser7 at the C‐terminus and of an extended structure in the central sequence Phe3‐Gly4‐Tyr5. Detailed analysis by step‐by‐step substitutions with Ala indicates that intraresidue interactions dominate over medium‐range interactions (between adjacent residues), although the latter may also have a noticeable influence in shaping conformations. As a general feature, the effects of substitutions on the arrangement of side chains are always larger on the succeeding residue than on the preceding residue. Almost all the variations of activity observed in the analogs can be explained from conformational changes occurring in the aromatic side chains of the biologically important Tyr1, Phe3, and Tyr5 on substitutions effected on adjacent residues (fluctuations via medium‐range interactions).
Specific assignment of resonances in the 1H‐nmr spectrum of the polypeptide toxin I from Anemonia sulcata
Authors: Gooley Paul R. , Norton Raymond S. 
Published: December 2004

AbstractThe assignment of a large number of resonances in the 300‐MHz 1H‐nmr spectrum of the polypeptide neurotoxin Anemonia sulcata toxin I is described. The initial identification of spin systems is made using both one‐ and two‐dimensional nmr spectra. The subsequent assignment of these spin systems to specific residues in the molecule is based largely on the observation in two‐dimensional spectra of through‐space connectivities between Hα and NH resonances from adjacent residues in the amino acid sequence. Using these techniques, the full spin systems of 22 residues are specifically assigned, together with partial assignments for a further 8. Many of the spin systems from the remaining 16 residues have been defined, although not yet specifically assigned. From the pattern of through‐space connectivities between protons from adjacent residues in the sequence, some inferences may be drawn concerning the secondary structure of this polypeptide in aqueous solution.
2′5′‐linked polynucleotides do form a double‐stranded helical structure: A result from the energy minimization study of A2′p5′A
Authors: Anukanth A. , Ponnuswamy P. K. 
Published: December 2004

AbstractExperimental results on 2′5′‐linked subunit systems of nucleic acids are interpreted to substantiate the view that the 2′5′‐linked polynucleotides cannot form double‐stranded helical structures. In order to look into this aspect of the 2′5′‐linked units, as well as to make a detailed comparison between the conformational characteristics of 3′5′‐ and 2′5′‐linked systems, we carried out an exhaustive theoretical study on A2′p5′A. The method was to compute the various terms of energy contributions to a conformational state and then to minimize the total energy, permitting all the relevant dihedral angles to adjust themselves. Four hundred thirty two probable starting conformations were considered for this treatment, but we found only 10 of them to come under low‐energy states, i.e., within 5 kcal/mol energy difference with reference to the global minimum energy state. The characteristic properties of these 10 conformations were compared in detail with those previously obtained on the corresponding 3′5′‐linked subunit, as well as such units with other base sequences. As a further step, a model‐building study was undertaken. Using the backbone‐course, base‐stacking, and hydrogen‐bonding possibilities of the 10 low‐energy conformations of the dimer A2′p5′A, double‐stranded helical structures were scrutinized for the 2′5′‐linked polynucleotide. Of a few reasonable forms, a right‐handed duplex structure satisfied our requirements. We describe this new duplex, making comparisons with the standard A‐ and B‐form states of DNA. The available experimental and theoretical results on 2′5′‐linked systems are also analyzed.
Conformational properties of poly[d(G‐T)]·poly[d(C‐A)] and poly[d(A‐T)] in low‐ and high‐salt solutions: Nmr and laser Raman analysis
Authors: Jenkins Bruce G. , Wartell Roger M. , Alderfer James L. 
Published: December 2004

Abstract31P‐ and 1H‐nmr and laser Raman spectra have been obtained for poly[d(G‐T)]·[d(C‐A)] and poly[d(A‐T)] as a function of both temperature and salt. The 31P spectrum of poly[d(G‐T)]·[d(C‐A)] appears as a quadruplet whose resonances undergo separation upon addition of CsCl to 5.5M. 1H‐nmr measurements are assigned and reported as a function of temperature and CsCl concentration. One dimensional nuclear Overhauser effect (NOE) difference spectra are also reported for poly[d(G‐T)]·[d(C‐A)] at low salt. NOE enhancements between the H8 protons of the purines and the C5 protons of the pyrimidines, (H and CH3) and between the base and H‐2′,2″ protons indicate a right‐handed B‐DNA conformation for this polymer. The NOE patterns for the TH3 and GH1 protons in H2O indicate a Watson–Crick hydrogen‐bonding scheme. At high CsCl concentrations there are upfield shifts for selected sugar protons and the AH2 proton. In addition, laser Raman spectra for poly[d(A‐T)] and poly[d(G‐T)]·[d(C‐A)] indicate B‐type conformations in low and high CsCl, with predominantly C2′‐endo sugar conformations for both polymers. Also, changes in base‐ring vibrations indicate that Cs+ binds to O2 of thymine and possibly N3 of adenine in poly[d(G‐T)]·[d(C‐A)] but not in poly[d(A‐T)]. Further, 1H measurements are reported for poly[d(A‐T)] as a function of temperature in high CsCl concentrations. On going to high CsCl there are selective upfield shifts, with the most dramatic being observed for TH1′. At high temperature some of the protons undergo severe changes in linewidths. Those protons that undergo the largest upfield shifts also undergo the most dramatic changes in linewidths. In particular TH1′, TCH3, AH1′, AH2, and TH6 all undergo large changes in linewidths, whereas AH8 and all the H‐2′,2″ protons remain essentially constant. The maximum linewidth occurs at the same temperature for all protons (65°C). This transition does not occur for d(G‐T)·d(C‐A) at 65°C or at any other temperature studied. These changes are cooperative in nature and can be rationalized as a temperature‐induced equilibrium between bound and unbound Cs+, with duplex and single‐stranded DNA. NOE measurements for poly[d(A‐T)] indicate that at high Cs+ the polymer is in a right‐handed B‐conformation. Assignments and NOE effects for the low‐salt 1H spectra of poly[d(A‐T)] agree with those of Assa‐Munt and Kearns [(1984) Biochemistry 23, 791–796] and provide a basis for analysis of the high Cs+ spectra. These results indicate that both polymers adopt a B‐type conformation in both low and high salt. However, a significant variation is the ability of the phosphate backbone to adopt a repeat dependent upon the base sequence. This feature is common to poly[d(G‐T)]·[d(C‐A)], poly[d(A‐T)], and some other pyr–pur polymers [J. S. Cohen, J. B. Wouten & C. L Chatterjee (1981) Biochemistry 20, 3049–3055] but not poly[d(G‐C)].
Total optical activity of agarose: Relation to observable transitions in the vacuum ultraviolet
Authors: Morris E. R. , Stevens E. S. , Frangou S. A. , Rees D. A. 
Published: December 2004

AbstractThe changes in optical activity that accompany and characterize the coil‐helix and helix‐coil transitions of agarose in aqueous solutions and gels have been investigated by combined quantitative analysis of data from vacuum ultraviolet circular dichroism (VUCD) and optical rotary dispersion (ORD). VUCD of agarose in the high‐temperature coil state shows a single accessible Gaussian band centered at ∼183 nm. In the helix state this band is blue‐shifted by ∼9 nm, and the intensity is increased by a factor of ∼2.6. Spectra at intermediate temperatures can be fitted to within experimental error by linear combination of coil and helix spectra, the relative proportions required providing an index of the extent of conformational ordering. ORD spectra throughout the conformational transition have a common form and differ only in absolute magnitude. The temperature course of conformational ordering derived from ORD intensity is in close agreement with the values obtained from VUCD. In both the coil and helix states the accessible VUCD band is positive, while the overall ORD is negative, indicating strong negative CD activity at lower wavelength. The ORD contribution corresponding to the positive VUCD band was calculated by Kronig–Kramers transform, and it was subtracted from the total ORD to give the residual ORD from all other optically active transitions of the molecule. In both the coil and helix states, this residual ORD could be fitted to within experimental error by a single Gaussian CD band at ∼149 nm. A negative band at this wavelength has been reported previously for agarose films, but the observed intensity, relative to that of the lower energy positive band, is substantially smaller than the fitted value under hydrated conditions. In both the coil and helix states the total optical activity of agarose, characterized by observed ORD spectra, can be matched to within experimental error by Kronig‐Kramers transform of the 149‐nm negative band and the smaller positive band at higher wavelength, with no necessary involvement of deeper‐lying transitions. The significance of this conclusion for fundamental understanding of carbohydrate optical activity is discussed.
Synthesis of peptide gels for the investigation of oligopeptide–oligonucleotide interactions
Authors: Eckstein Heiner , Hu Zheng , Schott Herbert 
Published: December 2004

AbstractPeptide gels usable as protein model systems have been synthesized by a cross‐linking copolymerization of acryloyl substituted peptides with 1,4‐tetramethylene dimethacrylate. A specially adapted approach to peptide synthesis allows the removal of the amino terminal Cbo group at the end of the peptide synthesis, followed by the introduction of an acryloyl group. The polymerizable peptide monomers obtained can be transferred into insoluble peptide gels by radical copoylmerization with cross‐linking agents. After cleavage of the protecting groups of the side chains, these peptide gels can be used both as protein model systems for investigating peptide–oligonucleotide interaction and as sorbents for affinity chromatography. The preparation and characterization of the peptide gels Ala‐Lys‐Glu‐Lys‐Ala‐OMe (I), Ala‐Arg‐Glu‐Arg‐Ala‐OMe (II), Ala‐Arg‐Glu‐Lys‐Ala‐OMe (III), and Ala‐Arg‐Ala‐Lys‐Ala‐OMe (IV) as well as the conditions for the removal of the protecting groups is presented. Gel III contains the natural peptide sequence Arg‐Glu‐Lys while the other gels are analogs of this sequence.
Chiral discrimination in the energetics of formation of diastereomeric adducts involving polypeptides
Authors: Paradossi G. , Pispisa B. , Rizzo R. , Barteri M. 
Published: December 2004

AbstractChiral discrimination in the energetics of formation of diastereomeric pairs between iron (III)‐complex ions bound to poly(L‐glutamate) or poly (D‐glutamate) and L‐catecholamines was measured by differential microcalorimetry at 25°C. When the association of substrates by Fe–polypeptide systems was virtually complete, diastereomeric discrimination energies of a few hundred calories per mol were observed, while diastereomeric discrimination entropies were found to be negligibly small. These results are consistent with the finding that the overall stereoselectivity in the electron transfer reaction between the optically active catecholamines and enantiomeric iron(III) materials—corresponding to Δ(ΔG≠) values around 900 cal/mol—is largely controlled by transition state effects in the kinetics.