bluuebunny/crossref_metadata_2025_split huggingface dataset:
Classical potential energy calculations for ApA, CpC, GpG, and UpU. The influence of the bases on RNA subunit conformations
Authors: Broyde Suse B. , Wartell Roger M. , Stellman Steven D. , Hingerty Brian , Langridge Robert 
Published: December 2004

AbstractClassical potential energy calculations have been made for the ribodinucleoside monophosphates ApA, CpC, GpG, and UpU. Van der Waal's, electrostatic, and torsional contributions to the energy were calculated, and the energy was minimized with the seven backbone conformational angles as simultaneously variable parameters. At the global minimum, ApA and CpC have conformations like double helical RNA: the angles ω′ and ω are g−g−, the sugar pucker is C3′‐endo, and the bases are anti. GpG and UpU, on the other hand, have the ω′,ω angle pair g−t at the global minimum, and for GpG the bases are syn. Energy contour maps for ω′ and ω show two broad, low energy regions for ApA, CpC, and UpU: one is g−g−, and the second encompasses g−t and g+g+ within a single lowenergy contour. The two regions are connected by a path at 10–13 kcal./mole. For GpG, with bases syn, however, only a small low‐energy region at g−t is found. The helical ‘A’ RNA conformation is 8.5 kcal/mole higher for this molecule. Thus, the base composition is shown to influence the conformations adopted by dinucleoside phosphates. Comparison of calculations with experimetal data, where available, show good agreement.
Thermodynamic parameters of the helix–coil transition in polypeptide chains. III. Random copolymers of L‐leucine with L‐glutamic acid
Authors: Bychkova V. E. , Gudkov A. T. , Miller W. G. , Mitin Yu. V. , Ptitsyn O. B. , Shpungin I. L. 
Published: December 2004

AbstractConformational transitions induced by pH changes in random copolymers of leucine and glutamic acid have been studied. Significant differences were observed in the potentiometric titration curves of copolymers with small (up to 4%) and large leucine contents. The helical stability of copolymers with small leucine content, determined from titration curves by the Zimm and Rice method, decreases slightly with an increase in the leucine content, whereas the helical stability of copolymers with large leucine content increases sharply with an increase of the leucine content. It is shown that copolymers with large leucine content aggregate in the region of transition into the helical state, but the increase of their helical state stability is not connected with intermolecular aggregation, as it was also observed for a nonaggregating fraction isolated from one of the copolymers by gel chromatography. A conclusion is made that the helix–coil equilibrium constant s for leucine does not itself exceed the s constant for uncharged polyglutamic acid. The stabilization of the helical state in copolymers with large leucine content is due to intramolecular aggregation of helices in these copolymers. The analysis of the leucine residue distribution between helical and nonhelical regions in globular proteins also gives no real arguments to ascribe special helix‐forming properties to leucine.
Conformational studies of poly(L‐tyrosine). A helix–coil transition in dimethyl sulfoxide–dichloroacetic acid mixtures
Authors: Wen Kuo‐Jung , Woody Robert W. 
Published: December 2004

AbstractPoly(L‐tyrosine) is a random coil in dimethyl sulfoxide. Upon addition of dichloroacetic acid, poly(L‐tyrosine) undergoes a conformational transition centered at about 10% dichloroacetic acid. The transition is nearly complete at 20% dichloroacetic acid. Further addition of dichloroacetic acid leads to precipitation of poly(L‐tyrosine). We have characterized this transition by optical rotation, viscosity, circular dichroism, and infrared. The optical rotation at 350 nm and the intrinsic viscosity increase sharply to values that are consistent with a transition to the α‐helix conformation. The circular dichroism of poly(L‐tyrosine) in dimethyl sulfoxide and in dimethyl sulfoxide/dichloroacetic acid (80:20 v/v) agrees with previous reports for random‐coil and α‐helix conformations, respectively. The infrared spectrum of poly(L‐tyrosine) in dimethyl sulfoxide/dichloroacetic acid (80:20 v/v) shows no evidence of β‐structure. We conclude that the transition on going from dimethyl sulfoxide to 20% dichloroacetic acid in dimethyl sulfoxide is a coil → α‐helix transition. The amide‐I band of poly(L‐tyrosine) in dimethyl sulfoxide/dichloroacetic acid (80:20) is found to be at 1662 cm−1. It has been suggested that this high frequency may be indicative of a left‐handed α‐helix. However, this high amide‐I frequency is consistent with conformational energy calculations of Scheraga and co‐workers. The mechanism of the dichloroacetic acid‐induced transition to an α‐helix is discussed. Dichloroacetic acid and dimethyl sulfoxide interact strongly and the transition presumably involves a marked decrease in the ability of dimethyl sulfoxide to solvate the peptide backbone and aromatic side chains upon complex formation with dichloroacetic acid.
Immobilization of polyribonucleotides in agarose gels at high ionic strength
Authors: Petrović S. L. , Novaković Milka B. , Petrović Jelena S. 
Published: December 2004

AbstractPurine polyribonucleotides poly(A), poly(G), and poly(I) associate reversibly with agarose gels at high NaCl molarities over the pH range 6–10, at 20°−40°C. Pyrimidine polyribonucleotides poly (C) and poly(U) could not be immobilized in agarose gels under the above conditions. However, poly(C) could be immobilized in agarose without precipitation between pH 3.2 and 4.0.Association of poly(G) and poly(I) with agarose appears to decrease progressively with deprotonation of their purine residues, and both polymers interact with the gel very weakly above pH 10 regardless of NaCl concentration. The binding to agarose of these polymers at pH 7.5 is also strongly influenced by temperature in the range 20°−40°C. The association of single‐stranded poly(A) is only shifted toward higher NaCl molarities by increased pH; its binding is also little affected by temperature in the above range.At NaCl molarities effecting the saturating retention in agarose and at neutral pH, the immobilization of several polynucleotides could be prevented by urea in a concentration‐dependent manner. The corresponding profiles of urea molarity appear to disclose a number of hydrophobic interactions between polynucleotides and agarose, some of which could be relatively strong, especially in the case of poly(A).
The association reaction of collagen model polypeptides (Pro‐Pro‐Gly)n
Authors: Shaw Barbara Ramsay , Schurr J. Michael 
Published: December 2004

AbstractThe characterization of recently synthesized (Pro‐Pro‐Gly)n, n = 7, 8 is described, along with melting profile studies of its association equilibrium, and thermal quenching studies of the kinetics of its association reaction. The order of the kinetic reaction is about 3, implying that three peptide chains are involved in the activated state of the rate‐limiting step. The reaction rate was found to exhibit a negative temperature coefficient. With the (Pro‐Pro‐Gly)7 peptide, the concentration dependence of the (Pro‐Pro‐Gly)n association equilibrium was observed for the first time.Detailed thermodynamic analysis for these n = 7, 8 data, together with literature data for n = 10, 15, 20 were carried out for both the simple “all‐or‐none” binding model and for a series of complex equilibrium models. For the latter, all of the (Pro‐Pro‐Gly)n data (in 10% acetic acid) are fit best with a maximally cooperative near‐neighbor model with a standard enthalpy change ΔH = −650 cal/mole of residues, and a standard entropy change ΔS = −14.63 −10/n cal/deg‐mole of residues, wherein the −10 eu represents an end‐effect contribution to the binding free energy.With regard to optical rotatory properties and thermodynamic parameters, the data for the new n = 7, 8 peptides match rather well with the literature data for the n = 10, 15, and 20 peptides.The enthalpic stabilization per residue of the triple‐helical form of (Pro‐Pro‐Gly)n was nearly an order of magnitude smaller than the enthalpic stabilization per additional proline obtained from direct calorimetric measurements on native collagens of different (and much lower) proline contents by Privalov and Tiktopulo. [Biopolymers (1970) 9, 127–139.] Possible explanations for this phenomenon are discussed.
Kinetics of proton transfer reactions of lysozyme with p‐nitrophenol near neutral pH—a study of dynamic properties of Glu 35 and His 15
Authors: Segawa Shin‐Ichi , Husimi Yuzuru , Wada Akiyoshi 
Published: December 2004

AbstractKinetics of proton transfer between lysozyme and a pH indicator p‐nitrophenol (p‐Np) were measured by the temperature‐jump method in a pH range of 6.0–7.0. Two well‐defined relaxation processes were observed. The fast process (τ ≃ 15 μsec) was also observed for a lysozyme derivative succinylated at the terminal α‐amino group of Lys 1. Therefore, the fast process was found to be attributable to the proton transfer reaction of His 15 with p‐Np. The slow process (τ ≃ 50 μsec) was found to be characteristic of the proton transfer reaction of Glu 35, because it disappeared completely in solution containing a lysozyme derivative having an ester crosslink between the carboxyl group of Glu 35 and indol C‐2 of Trp 108. The rate constants for proton transfer from Glu 35 and His 15 to p‐Np were found to be 9 × 106/sec/M (±65%, 23°C) and 3 × 108/sec/M (±20%, 25°C), respectively. These data indicate that the proton of the carboxyl group of Glu 35 is kinetically stabilized in lysozyme.
Studies on cytochrome c. X. Synthesis of Nα‐benzyloxycarbonyl‐[Thr107]‐dotetracontapeptide (sequence 67–108) of baker's yeast iso‐1‐cytochrome c
Authors: Moroder Luis , Filippi Bruno , Borin Gianfranco , Marchiori Fernando 
Published: December 2004

AbstractSynthesis of nonapeptide hydrazide (sequence 93–101), [Thr107]‐decapeptide (sequence 99–108), [Thr107]‐tridecapeptide (sequence 96–108), [Thr107]‐hexadecapeptide (sequence 93–108), [Thr107]‐heptacosapeptide (sequence 82–108), and Nα‐benzyloxycarbonyl‐[Thr107]‐dotetracontapeptide (sequence 67–108) of the proposed primary structure of baker's yeast iso‐1‐cytochrome c are described. Evidence is presented to indicate that these materials are sequentially homogeneous.
Studies on cytochrome c. XI. Circular dichroism studies on synthetic peptides related to the C‐terminal region of baker's yeast iso‐1‐cytochrome c
Authors: Moroder Luis , Filippi Bruno , Borin Gianfranco , Marchiori Fernando 
Published: December 2004

AbstractCircular dichroism studies on synthetic peptides related to the C‐terminal region of yeast iso‐1‐cytochrome c were carried out and compared with conformational studies on horse cytochrome c fragments. Evidence is presented for a weaker predisposition for ordered structure in the former peptides when compared with the corresponding region in horse cytochrome c. These findings agree with theoretical predictions and with observations that yeast and other mammalian type cytochromes c differ in several minor respects.
Raman spectroscopic study of poly (β‐benzyl‐L‐aspartate) and sequential polypeptides
Authors: Frushour B. G. , Koenig J. L. 
Published: December 2004

AbstractPoly‐β‐benzyl‐L‐aspartate (poly[Asp(OBzl)]) forms either a lefthanded α‐helix, β‐sheet, ω‐helix, or random coil under appropriate conditions. In this paper the Raman spectra of the above poly[Asp(OBzl)] conformations are compared. The Raman active amide I line shifts from 1663 cm−1 to 1679 cm−1 upon thermal conversion of poly[Asp(OBzl)] from the α‐helical to β‐sheet conformation while an intense line appearing at 890 cm−1 in the spectrum of the α‐helix decreases in intensity. The 890 cm−1 line also displays weak intensity when the polymer is dissolved in chloroform–dichloroacetic acid solution and therefore is converted to the random coil. This line probably arises from a skeletal vibration and is expected to be conformationally sensitive. Similar behavior in the intensity of skeletal vibrations is discussed for other polypeptides undergoing conformational transitions.The Raman spectra of two cross‐β‐sheet copolypeptides, poly(Ala‐Gly) and poly(Ser‐Gly), are examined. These sequential polypeptides are model compounds for the crystalline regions of Bombyx mori silk fibroin which forms an extensive β‐sheet structure. The amide I, III, and skeletal vibrations appeared in the Raman spectra of these polypeptides at the frequencies and intensities associated with β‐sheet homopolypeptides. Since the sequential copolypeptides are intermediate in complexity between the homopolypeptides and the proteins, these results indicate that Raman structure–frequency correlations obtained from homopolypeptide studies can now be applied to protein spectra with greater confidence.The perturbation scheme developed by Krimm and Abe for explaining the frequency splitting of the amide I vibrations in β‐sheet polyglycine is applied to poly(L‐valine), poly‐(Ala‐Gly), poly(Ser‐Gly), and poly[Asp(OBzl)]. The value of the “unperturbed” frequency, V0, for poly[Asp(OBzl)] was significantly greater than the corresponding values for the other polypeptides. A structural origin for this difference may be displacement of adjacent hydrogen‐bonded chains relative to the standard β‐sheet conformation.
Stability of proteins in guanidine·HCl solutions
Authors: Bull Henry B. , Breese Keith 
Published: December 2004

AbstractA new method has been described for the study of the denaturation of proteins by guanidine·HCl. The pH of an unbuffered solution of protein is monitored as Gu·HCl solution at a constant rate is run into the protein solution. As the protein undergoes the transition from the native to denatured state a significant and fairly abrupt change in the pH is observed. The behaviour of 14 proteins has been explored. Lysozyme, pepsin, α‐lactalbumin, lima bean trypsin inhibtor, and insulin failed to yield satisfactory transitions by this method. The method is entirely satisfactory with the other proteins. The maximum stabilities of the proteins in respect to Gu·HCl concentration and pH, and at zero rate (by extrapolation) of delivery of Gu·HCl have been studied. The relative stabilities of the proteins differ greatly. The stabilities are not related in a simple way to any known parameter.To supplement the pH change method outlined, the viscosities of nine proteins have been studied as a function of Gu·HCl concentration. A useful empirical equation relating the viscosity of a Gu·HCl solution to its molar concentration has been developed. The linear relationship between the relative fluidity and protein concentration has been confirmed and the intrinsic viscosities of the proteins have been calculated. The viscosities of the proteins vary significantly in respect to Gu·HCl concentration. All of the proteins undergo transitions from the native to the denatured state as shown by increases in the viscosities of their solutions. These transitions coincide closely with those found by the pH change method in respect to Gu·HCl concentration and pH. After the initial transition, the proteins continue to expand (viscosity increases) as the Gu·HCl concentration increases, indicating that the denatured state consists of many molecular configurations likely differing little in their energy content. The presence of disulfide bonds tends to limit the expansion of the protein molecules.
Cu(II)–poly(L‐arginine) complexes. Potentiometric and spectral characterization of amine and peptide nitrogen ligands
Authors: Garnier Arlette , Tosi Lucia 
Published: December 2004

AbstractThe study of Cu(II)–poly(L‐arginine) complexes by potentiometric titration, as well as by optical, circular dichroism, and infrared spectra, provides information about the nature of ligands and the coordination sphere around the metal ion. Three different complexes have been identified. The first, which is formed below pH 8, contains two guanidinium nitrogens and two water molecules at the corners of the coordination square. The constant of the overall process as determined by the Gregor method equals 2.0 ± 0.1 × 10−9. The two other complexes form between pH 8 and 10.5 and they contain two guanidinium and two peptide nitrogens as nearest ligands. One of them is a monomer and the other probably a dimer, which differ in the symmetry of the coordination sphere around the cupric ion. The optical spectra of the three complexes show an absorption band at 260 nm that we have assigned to a charge‐transfer transition between a σ metal nitrogen (amine) molecular orbital and a dx2−y2 metal orbital. The spectra of the two complexes containing peptide nitrogens exhibit another absorption band at 320 nm, which we have assigned to a charge transfer from a π orbital of the amide group to the dx2−y2 metal orbital.
Synthesis of protected oligo (γ‐methyl‐L‐glutamates) and study of their conformation in solution and at the air–water interface
Authors: Caspers J. , Hecq W. , Loffet A. 
Published: December 2004

AbstractOligopeptides having the general formula N‐carbobenzoxy(γ‐methyl‐L‐glutamyl)n‐dimethyl‐L‐glutamate (with n = 1, 3, 5, 7, 11) were prepared, using both solid‐phase synthesis and conventional peptide couplings in solution. The appearance of an ordered structure with increasing chain length was studied in organic solvents and at the air–water interface. The results obtained by thin‐layer chromatography were interpreted. All the studies have demonstrated a very similar behaviour of this type of oligopeptide in solution and in monolayers.
Equilibrium mechanisms of length regulation in linear protein aggregates
Authors: Wagenknecht Terence , Bloomfield Victor A. 
Published: December 2004

AbstractStatistical thermodynamic theories have been developed in order to explore the consequences of two prominent models of length regulation in linear protein aggregates: the length‐determining factor model and the cumulated strain model. In the former, the possibility that the final subunit is bound with extra stability has been incorporated. Calculations explore the dependence of the sharpness of the onset of extensive polymerization, and the breadth, shape, and most probable value of the distribution as functions of concentrations of template and polymerizing subunit, of subunit association constant, of the strain free energy, and of the maximum length and extra stability of the last subunit in the length‐determining factor model. Numerical calculations are made with particular reference to the parameters of bacteriophage T4 tail‐core polymerization. Both models predict suitably narrow length distributions with plausible values of the thermodynamic parameters. The length‐determining factor model may exhibit highly cooperative behaviour, with either fully polymerized or very short aggregates being observed as the product K[C] of association constant and free monomer constant is varied. This cooperativity is accentuated as binding of the final subunit becomes more stable. Species of intermediate length will be observable only if the length‐determining factor is shortened. In the cumulated strain model, if K[C] is lowered at constant strain free energy per subunit, shorter aggregates will be observed; but increasing K[C] will not yield appreciably longer polymers. As [C] is lowered, the distribution will remain narrow.
The structure of fibrin. An electron microscopic investigation
Authors: Conio G. , Dondero G. , Troglia C. , Trefiletti V. , Patrone E. 
Published: December 2004

AbstractAn electron microscopic investigation on the structure of fibrin is reported. Fibrin morphology was investigated in a wide variety of experimental conditions, and by carefully controlled staining procedures. Two main band patterns A (230‐Å‐spaced main dark bands) and B (230‐Å‐spaced main light bands) are observed for stained fibrin; it is shown that the former results from the superimposition of both positive and negative staining, and the latter is given by positive staining. By suitable denaturation experiments, it was found that the fiber is composed of a regular alternation of lose and dense regions along the axis.We have assumed that the monomer of fibrin is described by the three‐nodular model of Hall and Slayter, as supported by recent investigations. The monomers are arrayed according to a head‐to‐tail sequence along the fiber, and to a staggered lateral association. This model accounts for all the experimental observations, and predicts well the high‐resolution band pattern of fibrin. It further agrees with the results of a recent work on the early stages of the fibrinogen‐to‐fibrin conversion.
Acceleration of DNA renaturation rates
Authors: Wetmur James G. 
Published: December 2004

AbstractThe rate of renaturation of DNA may be increased by altering the effective solvent volume available for DNA in solution. Accelerations are demonstrated when neutral and anionic dextran polymers are used to exclude volume in DNA solutions. The logarithm of the DNA renaturation rate constant is shown to be proportional to the concentration of dextran polymer and to be proportional to the intrinsic viscosity of a series of dextran polymers of identical chemical composition. A theory is proposed to account for these results.
The interaction of glutaraldehyde with poly(α,L‐lysine), n‐butylamine, and collagen. II. Hydrodynamic, electron microscopic, and optical investigations on the reaction products
Authors: Swenson M. K. , Meir E. , Yanai P. , Zvilichovsky B. , Blauer G. 
Published: December 2004

AbstractInteractions of glutaraldehyde with either n‐butylamine, poly(α,L‐lysine), or collagen resulted in a fast release of protons in dilute aqueous solutions at various pH values, followed by much slower changes. The latter reactions, which extended over hours and days, were followed spectrophotometrically and revealed the formation of distinct absorption bands in the visible and near‐ultraviolet regions in all the above systems. The visible‐range bands disappeared upon treatment with sodium borohydride. A qualitative relationship between oxygen uptake by the system n‐butylamine–glutaraldehyde and the slow formation of colored products has been established, while the chemical nature of the reaction products has not been determined.Sedimentation velocity, viscosity, and optical rotation measurements on the products of interaction between poly(L‐lysine) and glutaraldehyde in aqueous solution indicated large conformational changes in the polyamino acid present in excess (in residues) over the dialdehyde. In particular, the intrinsic viscosity dropped considerably after interaction, indicating intramolecular crosslinking. At molar ratios of 1:1 between polylsine residues and aldehyde groups, intermolecular crosslinking of polylysine was obtained at pH 8.6.Electron microscopic examinations of collagen samples treated by glutaraldehyde at various pH values indicated changes from unordered to more ordered structures upon treatment with glutaraldehyde, in particular at pH 10.The present structural and optical investigations are considered to be relevant to tanning processes of hides and to fixation procedures.