bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hetero‐α‐helical, two‐chain coiled‐coils. Clam–worm hybrid paramyosins
Authors: Crimmins Daniel L. , Holtzer Alfred 
Published: December 2004

AbstractThe specificity of the interaction between the α‐helices in two‐chain coiled‐coils is investigated by studying the formation of hybrid molecules in which one α‐helix is a clam paramyosin chain and the other a worm paramyosin chain. Hybrids are formed by mixing, denaturation, and subsequent renaturation. Comparison is made with a blank solution in which renaturation precedes mixing, thus precluding hybridization. Hybrids are detected by a ruse based on the presence of free sulfhydryl functions on calm chains. This allows molecules comprising two clam chains to be covalently crosslinked by oxidation with 5,5′‐dithiobis(2‐nitrobenzoate). Worm paramyosin chains have no sulfhydryl, so molecules comprising two worm chains or hybrid molecules comprising one chain of each type cannot crosslink. When run on sodium dodecyl sulfate polyacrylamide gel electrophoresis, therefore, the protein separates into two well‐resolved regions, one containing one‐chain species and the other two‐chain species. When the gels are scanned and quantitated, the hybrids show up as an increase in the fraction of material in the one‐chain band compared with the fraction in the blank solution. When renaturation is direct, we find that the fraction of renaturated molecules that are hybrids varies from ∼10% at 5°C to ∼5% at 25°C. These are judged to be nonequilibrium (quenched) values. When renaturation is by slow annealing, the equilibrium fraction hybrids are ∼4% and show a modest, but measurable, increase with increasing temperature. These data allow calculation of the equilibrium constant Kh and standard free energy for the hybridization reaction: (1/2)CC + (½)WW = CW, in which C(W) stands for an α‐helical clam (worm) polypeptide chain. The temperature dependence gives the standard enthalpy and entropy of the reaction. We find ΔH ≃ 1800 cal mol−1 and ΔH ≃ 1.4 cal mol−1 K−1, using molarity concentration units and the infinitely dilute solution in NaCl/phosphate buffer as reference state. The possible molecular significance of these values is discussed, and it is concluded that the observed standard entropy arises essentially entirely from the rotational dissymmetry of the hybrids.
Cu(II)–Protamine interaction. I. The formation and structure of Cu(II)–clupeine Z complexes
Authors: Garnier Arlette , Tosi Lucia , Mosoni Lucienne , Toniolo Claudio , Bonora Gian Maria , Paniago Euclear B. 
Published: December 2004

AbstractThe formation and structure of four different Cu(II)–clupeine Z complexes have been studied using potentiometric and spectroscopic (ir and visible absorption, and CD) measurements. The results thus obtained indicate the presence of up to 8 binding sites in the pH range from 6.5 to 10.5. The spectroscopic evidence suggests that the strongest site available contains the α‐amino terminal and the adjacent peptide nitrogen, which bind to copper from pH 5 to 6.5 to form the first complex. The stability constant of this first complex has a value of (9.5 ± 0.9) × 103 mol−1 1. From pH 6.5 to 8.5, two intervening guanidinium nitrogens of arginine residues occupy the two other corners of the coordination square, giving rise to the second complex. The other sites potentially available from pH 6.5 to 10.5 are formed by two amino nitrogens of arginine residues and two contiguous peptide nitrogens. The first intervene up to pH 8.5, forming the third complex, and the latter from this pH to 10.5, forming the fourth complex. Although the ligands intervening at sites 2–8 appear to be the same, the sites are by no means equivalent. The spectroscopic data enable one to distinguish three different types of binding sites.
Conformational studies on polynucleotide chains. V. A comparison between the quantum‐mechanical and the consistent force field approach
Authors: Tosi Camillo , Rasmussen Kjeld 
Published: December 2004

AbstractConsistent force field (CFF) calculations were performed for the sugar–phosphate–sugar fragment, taken as a model of the polynucleotide backbone. The potential‐energy‐function is the sum of four contributions, accounting for bond and angle deformation, torsional motions, and nonbonded interactions. Both deoxyribose and ribose systems, with either C(2′)‐endo or C(3′)‐endo puckering in the starting geometry of ribose rings, were considered. A fair number of minima of the conformational‐energy hypersurface were found. Although the numerical method employed in the CFF context cannot solve the problem of finding the global minimum in a definite way, one of the final conformations has a total energy much more attractive than the others, and may be regarded as the most stable conformation attainable with our potential‐energy function. The energy‐minimization affects the puckering of the first ribose ring differently from that of the second: in general, for the C(2′)‐endo system the second ring retains its starting conformation (Ψ′ = 152°), while in the first the Ψ′ is modified by up to 70°; the opposite occurs for the C(3′)‐endo system. This is explained by the different positions of the two rings relative to the phosphate group.
X‐Pro peptides: Synthesis and solution conformation of benzyloxycarbonyl‐(Aib‐Pro)4methyl ester. Evidence for a novel helical structure
Authors: Venkatachalapathi Y. V. , Balaram P. 
Published: December 2004

AbstractThe synthesis of the octapeptide, benzyloxycarbonyl‐(α‐aminoisobutyryl‐L‐prolyl)4‐methyl ester [Z‐(Aib‐Pro)4‐OMe] and an analysis of its solution conformation is reported. The octapeptide is shown to possess three strong intramolecular hydrogen bonds on the basis of studies of the solvent and temperature dependence of NH chemical shifts and rates of hydrogen–deuterium exchange. 13C studies are consistent with a structure involving only trans Aib‐Pro bonds, while ir experiments support a hydrogen‐bonded conformation. The Aib 3, 5, and 7 NH groups are shown to participate in hydrogen bonding. A 310 helical conformation compatible with the spectroscopic data is suggested. The proposed conformation consists of three type III β‐turns with Aib and Pro at the corners and stabilized by 4 → 1 intramolecular hydrogen bonds.
Analysis of high‐resolution thermal dispersion profiles of DNA: Treatment as a collection of discrete subtransitions
Authors: Yen W. S. , Blake R. D. 
Published: December 2004

AbstractThe thermal dissociation of DNA by five distinct local processes as outlined by Azbel [(1980) Biopolymers 19, 61–80] is treated as a collection of two‐state substransitions. With the traditional expression for loop entropy and the assumption of a small, positive loop‐initiation enthalpy, explicit relationships between thermodynamic parameters are derived for all five processes. The effect of each process on subtransitional width, unit enthalpy, and melting temperature is estimated; the latter being in excellent agreement with that predicted by Azbel. Criteria proposed for the deconvolution of the oscillatory high‐resolution melting profiles exhibited by short, homogeneous DNAs [Yen & Blake (1980) Biopolymers 19, 681–700] have been applied to profiles of SV40 fragment [Gabbarro‐Arpa et al. (1979) Nature 280, 515–517] and ϕx174‐RF DNA at two ionic strengths [Vizard et al. (1978) 275, 250–251] and indicate that dissociation of the strands proceeds as a series of local two‐state subtransitions of domains 200–300 base pairs in length. Although the obvious overlap of some subtransitions raises questions about resolution, most sections are very well resolved with the minimum number of subtransitions and yield values for the apparent van't Hoff enthalpy in excellent agreement with those expected by calorimetric measurements. The flexibility of such an approach, where the enthalpy is recognized explicitly as an adjustable parameter, is especially suited for the analysis of profiles from unkown DNA sequences, and for the evaluation of extraordinary variations in free energy, such as that associated with loop formation or that resulting from variations in the linear charge density at low ionic strengths.
Solvent and side‐chain contributions to the two‐cis ⇄ all‐trans equilibria of cyclic hexapeptides, cyclo(Xxx‐Pro‐D‐Yyy)2
Authors: Kopple Kenneth D. , Sarkar Susanta K. , Giacometti Giovanni 
Published: December 2004

AbstractCyclic hexapeptides of the type cyclo(L‐Xxx‐L‐Pro‐D‐Yyy)2 or cyclo(L‐Xxx‐L‐Pro‐Gly)2 exist in solution predominantly in two forms of C2 average symmetry, one with all‐trans peptide bonds and generally well‐established conformation, and another with both Xxx‐Pro peptide bonds cis. We have been measuring the thermodynamic parameters of this equilibrium using carbon and proton nmr spectroscopy. Data have been obtained for peptides in which Yyy = Gly, D‐Ala, or D‐Phe, and Xxx = Gly, L‐Ala, L‐Leu, and L‐Val. In a given solvent, stability of the all‐trans form decreases (ΔG0 increases) as Xxx is changed through the series Gly, L‐Ala‐, L‐Leu, and L‐Val, consistent with expected increasing repulsion between the Xxx side chain and the proline δ methylene across the trnas Xxx‐Pro bond. Also, for a given set of side chains, the stability of the all‐trnas form increases as the polarity of the solvent decreases, consistent with models in which all CO and NH groups are accessible for solvation in the two‐cis form, but two CO and two NH groups are somewhat sequestered in the all‐trans form. With the available data it is not possible to identify pure intramolecular (solvent‐independent) or pure peptide‐bond solvation (side chain‐independent) terms in ΔH° or ΔS°, although trends are discernible.
Synthesis and conformational characterization in the solid state of peptides consisting of L‐phenylalanyl‐L‐phenylalanylglycyl and L‐phenylalanyl‐L‐leucylglycyl residues
Authors: Katakai Ryoichi , Nakayama Yoko 
Published: December 2004

AbstractTwo series of peptides containing L‐phenylalanine, Nps‐(L‐Phe‐L‐Phe‐Gly)n‐OEt (n = 1–6) and Nps‐(L‐Phe‐L‐Leu‐Gly)n‐OEt (n = 1–7), were prepared by the fragment‐condensation method using the tripeptide N‐hydroxysuccinimide esters. Conformational characterization of these peptides in the solid state was performed by ir spectroscopy and x‐ray powder diffraction measurement. The peptides Nps‐(L‐Phe‐L‐Phe‐Gly)n‐OEt take the β‐structure, but the pentadecapeptide and higher peptides of Nps‐(L‐Phe‐L‐Leu‐Gly)n‐OEt form the α‐helix, although the lower homologs take the β‐structure.
Quantitative test of Record's theory for proton‐induced lowering of DNA melting temperature
Authors: Mingot Francisco 
Published: December 2004

AbstractThis report presents a quantitative test of the ability of the counterion condensation theory to describe the proton‐induced lowering of DNA melting temperature. From a general approach of Record et al. [Record, M. T., Anderson, C. F. & Lohman, T. H. (1978) Q. Rev. Biophys. 11, 103–178], we have obtained an expression that may be computer‐fitted to the experimental data by numerical minimization of χ2. To do this, in addition to the assumptions made by Record et al., it was necessary to suppose that the interchange between protons and sodium is independent of pH and, due to the absence of data, take the enthalpies of protonation as thermally independent over the experimental temperature range. The dependences of the enthalpy of denaturation at neutral pH on sodium concentration and on G + C content were taken from literature. In the fitting process we have used 250 melting temperatures obtained at different pH and sodium concentrations for various natural DNAs. The theoretical expression gives a good quantitative description of the G + C and sodium concentration influences on the phenomenon but is only qualitative with respect to the dependence of dT/d log[Na+] on the pH. The adjusted pK values for the bases in denatured DNA agree with those for isolated deoxynucleosides. Interchange between sodium and protons is found to be less than 1:1. Calculated protonation enthalpies are ill‐defined because of their low numerical influence. In short, it appears that the theory gives a good description of most of the aspects of the phenomenon even if it has some shortcomings, perhaps due to the great number of assumptions.
Flow dichroism of T7 DNA as a function of salt concentration
Authors: Rizzo Vincenzo , Schellman John 
Published: December 2004

AbstractMeasurements have been made on the flow dichroism of T7 DNA as a function of NaCl concentration. In high salt, our results are compatible with an optical factor of −1.4 and a persistence length of 470 Å. The former is in agreement with expectations from the x‐ray diffraction structure of fibrous B–DNA, and the latter is in the midrange of recent determinations. As salt concentration is decreased, the persistence length increases. The relation of our study to other recent investigations and with current theories of the electrostatic contribution to persistence length is discussed. We note that the separation of the electrostatic expansion factor into long‐ and short‐range effects is somewhat arbitrary and might affect the interpretation of different experimental results in different ways. Finally, our hydrodynamic factors are consistent with a chain which is partially free‐draining. This goes against the traditional interpretation but is in agreement with two recent observations.
Theoretical π‐π* absorption and circular dichroic spectra of helical poly(L‐proline) forms I and II
Authors: Applequist Jon 
Published: December 2004

AbstractAbsorption and CD spectra of the π‐π* transition near 200 nm are calculated for helical (Pro)n I and II (n = 6, 10) using the dipole interaction model, including interactions among all atoms, with optical parameters obtained from previous studies of related molecules. Calculated spectra for (Ala)n and (Pro)n in the same conformation show marked differences. The spectra for (Pro)n are sensitive to side‐chain structure but are found to agree reasonably well with exeriment for forms I and II when the side‐chain CC bond length is set at 1.54 Å, with structural data otherwise obtained from x‐ray diffraction studies.
A general method for determination of nucleotide sequences in nucleic acids
Authors: Mandeles Stanley , Tinoco Ignacio 
Published: December 2004

AbstractA method is proposed for the determiantion of nucleotide sequences in nucleic acids. Briefly, the procedure involves the formation of derivatives specific for either the 3′ or 5′ end of nucleic acid. This is followed by a partial enzymatic hydrolysis to yield specific fragments. The functions of the chemically modifying derivative are (a) to serve as a reference point which positions each base according to its distance from the modified end, (b) to provide a convenient means of separating oligomers with derivatives from those without derivatives, (c) to permit the use of additional parameters of fractionation of oligomers with derivative ends. The features of this method include: construction of long sequences from shorter fragments, unequivocal positioning of fragments, independence from quantitative procedures, economical use of nucleic acid polymer, determination of sequences from both ends simultaneously, application to DNA and RNA. Data are presented on the action of pancreatic ribonuclease on bis‐2,4 dinitrophenyl hydrazone derivatives of yeast ribonucleic acid and polyuridylic acid.
Effect of a helix‐coil transformation on magnesium binding to α‐poly‐L‐glutamic acid
Authors: Jacobson Ada L. 
Published: December 2004

AbstractThe effect of magnesium ion binding on the dissociation of side chain carboxyl group in α‐poly‐L‐glutamic acid has been measured by a modified titration technique involving pretitration of the polyacid with a strong base of a weakly bound counterion followed by addition of aliquots of the neutral salt of the more strongly bound counterion, magnesium chloride. The changes in the ionization of the carboxylic acid groups in the poly‐L‐glutamic acid side chains have been measured as a function of both the degree of preionization and of the concentration of magnesium chloride added. These changes have been related to changes in the polymer configuration (helix‐coil transition) as a function of degree of pre‐ionization. The effects of ionic strength and of ion binding have been determined by a comparison of tetramethyl ammonium chloride and of magnesium chloride at the same ionic strength. The plot proposed by Wada has been used to determine the pure helical region, the region of helix‐coil transition, and the pure coil region with both magnesium chloride and tetramethyl ammonium chloride as added salts. At the same ionic strength the effects produced by magnesium chloride addition are far greater than for tetramethyl ammonium chloride. Magnesium chloride at an ionic strength of 0.25 × 10−4 produces an effect equivalent to that of tetramethyl ammonium at an ionic strength of 15.0 × 10−4. This effect is also apparent when the concentration of carboxyl groups ionized by magnesium chloride addition is determined. The much larger effects produced by the magnesium ion are attributed to the enhanced binding of this ion. The results reported indicate binding is favored in the helical configuration. The binding in the random coil configuration is similar to that reported previously for other randomly coiled polyelectrolytes.
Some optical properties of poly‐1‐benzyl‐L‐histidine and poly‐L‐histidine
Authors: Norland K. S. , Fasman G. D. , Katchalski E. , Blout E. R. 
Published: December 2004

AbstractOptical rotatory dispersion and infrared studies made on solutions of poly‐1‐benzyl‐L‐histidine (PBLH) in the solvent system chloroform–dichloroacetic acid (CHCl3DCA) indicate that this polymer exists in three different forms depending upon the solvent composition. These forms are reversibly interconvertible. Form I (PBLH‐I) exists in 100% CHCl3, form II (PBLH‐II) in CHCl3 containing one residue equivalent of DCA (the histidyl‐DCA salt) and form III (PBLH‐III) in CHCl3 with a large excess of DCA. It is suggested that PBLH‐I is an unionized random chain, PBLH‐II is an ionized “left‐handed” α‐helix, and PBLH‐III is an ionized random chain. Some optical rotatory dispersion and infrared measurements are reported for poly‐L‐histidine. A marked change in specific rotation of this polypeptide occurs in aqueous solution in the pH range 5–6.
Optical properties of the poly‐L‐proline and collagen helices
Authors: Gratzer W. B. , Rhodes W. , Fasman G. D. 
Published: December 2004

AbstractPoly‐L‐proline I and II, polyphydroxy‐L‐proline II, polysarcosine, and collagen, as well as two model amides have been examined by far ultraviolet spectrophotometry. Absorption spectral data are presented. Neither in solution nor in oriented films of poly‐L‐proline I and II is there any indication of excition resonance splitting of the peptide absorption band. In collagen there is some, in the poly‐L‐prolines only minimal, hypochromicity. These observations, at least in poly‐L‐proline II, run counter to theory. Optical rotatory dispersion measurements in the ultraviolet indicate simple dispersion in collagen and poly‐L‐proline II down to at least 232 mμ. The Cotton effect (trough at 233 mμ) observed in α‐helical polypeptides and proteins is absent. The implications of these findings are discussed.
Electric properties of macromolecules. VIII. Kerr constants and rotational diffusion of some proteins in water and in glycerol—water solutions
Authors: Krause Sonja , O'Konski Chester T. 
Published: December 2004

AbstractKerr constants and birefringence relaxation times were measured on gamma‐globulin (I) in aqueous solution and on bovine serum albumin (II), beta‐lactoglobulin (III), ovalbumin, (IV), ribonuclease (V), lysozyme (VI), and chymotrypsin (VII) in glycerol–water solutions. Rotational diffusion constants were calculated from the data and were compared with those calculated from the protein dimensions obtained by other methods. The calculated and observed rotational diffusion constants were in excellent agreement for I, IV, V, and VII, and were within a factor of two for III. VI showed evidence of aggregation and II gave a low relaxation time in glycerol–water solution, apparently because of a structural change or a localized solvent viscosity effect. The earlier results for maximum dimensions based upon the dielectric relaxation time method were found to be in agreement with present findings in a number of instances, in spite of the possible complication of the dielectric method by ionic polarization effects.
Electric properties of macromolecules. X. Conduction and the question of ferroelectricity in solid sodium deoxyribonucleate
Authors: O'Konski C. T. , Shirai M. 
Published: December 2004

AbstractData are presented for electric conduction in solid sodium deoxyribonucleate as a function of water content and over a wide range of frequencies. We have also examined the loops seen in a ferroelectric hysteresis bridge. It is proposed that both the conductivity and the loops of samples with high water content are probably due to ion conduction and electrolysis. Dry samples appear to have the characteristics of an inhomogeneous semiconductor. Possible mechanisms of carrier generation are briefly discussed.
NMR study on molecular mobility of DNA molecules in solution
Authors: Lubas Barbara , Wilczok Tadeusz 
Published: December 2004

AbstractThe molecular mobility of calf thymus DNA molecules in solution has been discussed in terms of correlation time τ calculated from measurements of longitudinal T1 and transverse T2 magnetic relaxation times. The influence of DNA concentration and ionic strength of the solution upon freedom of movement of DNA molecules was studied for native and denatured DNA and also during thermal helix‐coil transition. The dependence of τ values on temperature was carried out by comparing the values of correlation times τtat given temperature with the correlation time τ20 at 20°C. The molecular rotation of DNA at 20°C and at higher ionic strength at 0.15 and 1.0.M NaCl is described by τ values of the order of 1.0–1.2 × 10−8 and was reduced slightly with increase of temperature below the helix‐coil transition. The molecular rotation of DNA in 0.02MNaCl was lower at 20°C as compared to DNA in solvents with higher NaCl concentrations and increases rapidly with increase of temperature in the range 20–60°C. The values of correlation time are characterized by fast increase at temperatures above the spectrophotometrically determined beginning of melting curve. The beginning of this increase is observed at about 65, 80, and 85°C for DNA in 0.02, 0.15, and 1.0MNaCl, respectively. Values of correlation time for denatured DNA are in all cases about 1.1–1.4 times that for native DNA. The obtained results are discussed in terms of conformation of DNA molecules in solution as well as in terms of water dipole binding in DNA hydration shells.
Pressure independence of the rotor speed‐induced aggregation of DNA
Authors: Poon Pak H. , Schumaker Verne N. 
Published: December 2004

AbstractThe rotor speed‐dependent aggregation of T4 DNA in the analytical ultracentrifuge is studied in the presence of high pressure generated by compressed nitrogen gas in the cell. The extents of aggregation at various speeds are found to be practically the same in the presence and absence of pressure.