bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational studies of the pentapeptides with weak adrenocorticotropin (ACTH) activities by means of nuclear magnetic resonance spectroscopy
Authors: Higuchi Naoki , Kyogoku Yoshimasa , Yajima Haruaki 
Published: December 2004

AbstractThe conformations of a pentapeptide L‐His‐L‐Arg‐L‐Trp‐Gly with weak adrenocorticotropin (ACTH) activity and its analogs, where each L‐amino acid residue is substituted by D‐residue, were investigated by means of proton and carbon‐13 nmr spectroscopy on their DMSO‐d6 solutions. The spectra indicated the presence of slowly exchangeable conformation isomers for D‐Phe and D‐Arg analogs, due to steric hindrance around the arginine residue. The activation energy of the hindered rotation of the arginine side chain was estimated to be more than 19 ∼ 20 kcal/mol. Spin‐lattice relaxation times of carbon‐13 nuclei also indicated slow segmental motion of the arginine side chain of the D analogs. An effect on proton chemical shifts by intermolecular electrostatic interaction between the arginine side chain and the C terminal carboxylic residue was observed. We did not observe, however, a direct correlation between pentapeptide activity and molecular conformation at this stage of the experiments.
Free‐sliding ligands: An alternative model of DNA–protein interactions
Authors: Woodbury Charles P. 
Published: December 2004

AbstractWe present an alternative to the common lattice model for nonspecific DNA–protein interactions by using ligands that translate freely along the polynucleotide instead of binding to distinct lattice sites along the polynucleotide chain. The general model we present corresponds to a one‐dimensional continuum gas and is referred to as the “continuum model” to distinguish it from the general lattice model. Explicit expressions are obtained for the binding isotherm equation for two version of the continuum model, including the effects of binding‐site exclusion and attractions between bound ligands. Theoretical results are compared to those obtained from the McGhee‐von Hippel (1974) analysis of the lattice model with cooperative interactions between ligands occupying more than one lattice site. Practical applications of the continuum model are illustrated by analyzing (i) the noncooperative binding to single‐stranded DNA by RNase (Jensen and von Hippel, 1976), and (ii) the highly cooperative binding to poly(rA) by a proteolyzed fragment of the gene 32 protein of phage T4 (Lonberg et al., 1981).
Analysis of the potentiometric titration of reduced horse heart cytochrome c
Authors: Marini M. A. , Martin C. J. , Forlani L. 
Published: December 2004

AbstractCurve fitting for the ionization constants found in the potentiometric titration curve of reduced horse heart cytochrome c in 0.15M KCl at 20°C yields values which can precisely reconstruct the experimental curve. The parameters were evaluated assuming that there were 13 group sets with individual ionization constants, that these groups were subject to electrostatic interaction (ω), and that both pK′ and (ω) were necessary to describe the curve. On the basis of an analysis of the residuals, both the simple sum of mass‐law expressions and the electrostatic model could be invoked, although the evaluated ω was both positive and negative. When the standard errors of the parameter values are considered, only the model which assumed no electrostatic interaction is acceptable. The experimental curve is completely described by eight group sets and no electrostatic interaction.
Theoretical evidence for the coupling of winding to compression in the solution conformation of duplex DNA
Authors: Manning Gerald S. 
Published: December 2004

AbstractPublished data indicate linear variation of the duplex winding of DNA with logarithm of the ionic strength. We show that this observation is a natural prediction of a current poly‐electrolyte theory if structural coupling between duplex rotation angle (rotation per base pair) and step height (axial translation per base pair) is assumed. We show also that the coupling must then be negative: the positive winding on augmentation of the ionic strength must be accompanied by a decrement of step height, or axial compression. Cation species specificity of winding, CD spectra, and cation binding affinity are discussed in terms of local variation of dielectric shielding, using current accurate data for dielectric constants of aqueous salt solutions. One need not invoke specific complexation of cations, for which there is no present evidence (in aqueous solution), to explain any of these effects. The analysis is limited to low and moderate ionic strengths. Experimental observations at very high ionic strengths are puzzling and possibly conflicting. It is concluded that a need exists for systematic extension of available duplex winding data throughout the region of moderate to very high ionic strengths. It would be useful to extend the region at the low end as well, in order to distinguish clearly the behavior predicted by our model from that predicted by a referee on the basis of an alternate model described herein.
pH‐Dependent Raman spectra and thermal melting profiles for polycytidylic acid
Authors: O'Connor Timothy , Scovell William M. 
Published: December 2004

AbstractThe Raman spectrum of polycytidylic acid was investigated in the pH range of 6.6–4.1. The thermal melting temperatures and the nature of the thermal melting profiles change in this range as monitored by the three Raman band envelopes, which include the 780‐, 805‐cm−1 bands, the 1190‐, 1285‐cm−1 bands, and the 1527‐cm−1 band. By coupling these data with the theory of Raman scattering intensity and quantitative pH profiles for cytidine, it is shown that the band envelopes studied exhibit specific, yet different information regarding the thermal melting process. The band envelopes at 1170–1310 and 1527 cm−1, which are a sensitive function of both the extent of protonation and base stacking (hypochromic), reveal Tm values which agree with values derived from uv melting profiles. The 760–830‐cm−1 envelope, which is not directly sensitive to cytosine residue protonation, but includes information associated with base stacking (the 780‐cm−1 band) and the nature of the phosphodiester backbone (the frequency‐dependent 805‐cm−1 component), exhibits Tm values which deviate from the values obtained from the other bands. The observed differences are pH‐dependent and correlate well with the extent of deprotonation that takes place in the denaturation process. Details of the spectrum of neutral and protonated poly(C) from pH 7 to 4.1 are discussed and related to the nature of the thermal denaturation process.
DNA and RNA oligomer thermodynamics: The effect of mismatched bases on double‐helix stability
Authors: Nelson Jeffrey W. , Martin Francis H. , Tinoco Ignacio 
Published: December 2004

AbstractThe thermodynamic parameters for the double‐strand formation of the molecules rCAmG + rCUnG, m,n = 5–7, and dCAmG + dCTnG, m,n = 5,6, were measured from optical melting curves. Normal helices are formed when m = n. The deoxyoligomers are more stable than the ribo‐oligomers, due to a more favorable enthalpy. Double helices with mismatched bases can be formed by mixing oligomers with m ≠ n. Such helices may form several possible structures. A structure with a dangling base is favored over a structure with a bulged base. The destabilization of the double strands by the formation of a bulged base was determined to be greater than 1.6 kcal/mol at 10°C. The extent of aggregation in the oligomer double strand rCA7G·rCU7G was determined using ultracentrifugation equilibrium. The possible effects of aggregation on the determination of the thermodynamic parameters for double‐strand formation are discussed.
Structure of micelles formed by monodisperse hexa‐(γ‐benzyl‐L‐glutamate) in solution
Authors: Imae Toyoko , Okahashi Kenji , Ikeda Shoichi 
Published: December 2004

AbstractThe angular dependence of light scattering and the concentration dependence of the relative viscosity have been measured in solutions of o‐nitrophenylthio‐hexa‐(γ‐benzyl‐L‐glutamate) ethylamide in ethylene dichloride. Both the reduced intensity of scattered light and the reduced viscosity of the solution suddenly increase above a certain critical concentration, below which both of them remain low and constant. The Debye plot of light scattering indicates that primary micelles having an aggregation number 48 are formed at the critical micelle concentration and that secondary micelles, each consisting of 294 molecules, then appear in increasing amounts with increasing concentration beyond the critical micelle concentration. The secondary micelle is rodlike and has a length of 1170 Å, if it is rigid. An analysis of the reduced viscosity leads to the intrinsic viscosity for the primary micelle, 0.360 dL g−1, and to that of the secondary micelle, 1.28 dL g−1. If the secondary micelle is represented by a prolate ellipsoid, it should have an axial ratio of 47. If the polypeptide chains are extended in the micelle, the observed aggregation number and axial ratio of the secondary micelle can well accommodate the intermolecularly hydrogen‐bonded in‐register β‐structure of anti‐parallel chains. In the primary micelle, some folded polypeptide chains are involved, and an intermolecularly hydrogen‐bonded out‐of‐register structure would form a rather open network.
Nmr studies of the rates of proline cis–trans isomerization in oligopeptides
Authors: Grathwohl Christoph , Wüthrich Kurt 
Published: December 2004

Abstract1H‐Nmr was used to measure the rate of cis–trans interconversion of X‐Pro bonds in linear and cyclic oligopeptides. k(cis → trans) = 2.5 × 10−3 s−1 at 25°C was found for the zwitterionic form of H‐Ala‐Pro‐OH, in good agreement with earlier measurements. Replacement of Ala by Phe, Tyr, or Trp resulted in a 10‐fold slower interconversion rate, whereas after substitution of Ala by His or Glu, the rate decreased only slightly. Independent of the residues X, the interconversion rate was increased by a factor of ca. 20 when the peptide chain was elongated by addition of Ala to the C‐terminal Pro. An additional increase by a factor of 6 was observed when going from the protected linear peptide CF3CO‐Gly‐Gly‐Pro‐Ala‐OCH3 to the closely related cyclic compound c[‐Gly‐Gly‐Pro‐Gly‐Ala‐]. These data are evaluated with regard to their possible use in future studies on the role of X‐Pro cis–trans isomerization in the kinetics of protein folding.
Free water in hair keratin? a depolarization thermal‐current study
Authors: Leveque J. L. , Garson J. C. , Pissis P. , Boudouris G. 
Published: December 2004

AbstractIn the keratin structure, the presence of water having the usual properties of “bulk water” has been discussed for many years. Results of experiments designed to study this question are conflicting and thus do not allow a precise idea of the state of water molecules in keratin at high hydration. A recent depolarization thermal‐current (DTC) study gave good evidence for the presence of a well‐defined DTC peak in the depolarization spectrum of ice. Initially, we verified the exact characteristics of this particular peak under our own experimental conditions. Subsequently, we looked for and found this ice peak in keratin samples. It appears when the water content is 19% or greater. The meaning of this result is discussed in relation to the other experimental results reported in the literature dealing with this question.
High‐field magnetic birefringence study of the structure of rodlike phages Pf1 and fd in solution
Authors: Torbet J. , Maret G. 
Published: December 2004

AbstractThe magnetic orientation of the rodlike bacterial viruses Pf1 and fd in dilute aqueous solution was detected by high‐resolution birefringence measurements. Partial alignment takes place parallel to the magnetic field chiefly due to the diagmagnetic anisotropy of the highly ordered α‐helices in the coat protein. It follows from the analysis of the experimental diamagnetic anisotropy that in both phages the α‐helices and aromatic amino acids are oriented relatively parallel to the phage axis. In Pf1 these become, on average, more nearly parallel as the temperature is reduced from about 25 to 5°C. These results demonstrate that high‐resolution magnetically induced birefringence measurements can be used to investigate some general structural features of complicated biological particles in solution.
Viscometric and static light scattering studies on an exopolysaccharide produced by Lactobacillus delbrueckii subspecies bulgaricus NCFB 2483
Authors: Goh Kelvin Kim Tha , Hemar Yacine , Singh Harjinder 
Published: December 2004

AbstractThe rheological properties and molecular parameters of a purified exopolysaccharide (EPS) produced by a ropy strain of Lactobacillus delbrueckii subsp. bulgaricus NCFB 2483 were investigated. Using capillary viscometry, an intrinsic viscosity of 2,013 mL/g was obtained. The flow curves were fitted by both the Carreau and the Cross equations for shear‐thinning fluids, with the Carreau equation giving a better fit. The Cross equation fitted fairly well the plot of reduced viscosity as a function of reduced shear rate with an exponent value (1 − n) of ∼ 0.76, typical of random coil polymers. Furthermore, the concentration dependence of the viscosity plot showed a gradient of approximately 1.1 in the dilute regime and 3.3 in the semidilute regime. Molecular parameters were obtained using a multiangle laser light scattering technique. The 2483 EPS molecules had a weight‐average molar mass of approximately 2 × 106 Da and a z‐average root mean square radius (RMS) of approximately 151 nm. From the light scattering data, the bacterial EPS was also found to have a low polydispersity index (∼ 1.15) and adopt a random coil conformation. © 2004 Wiley Periodicals, Inc. Biopolymers, 2005
Engineering disulfide bonds of the novel human β‐defensins hBD‐27 and hBD‐28: Differences in disulfide formation and biological activity among human β‐defensins
Authors: Schulz Axel , Klüver Enno , Schulz‐Maronde Sandra , Adermann Knut 
Published: December 2004

AbstractHuman β‐defensins comprise a large number of peptides that play a functional role in the innate and adaptive immune system. Recently, clusters of new β‐defensin genes with predominant expression in testicular tissue have been discovered on different chromosomes by bioinformatics. β‐Defensins share a common pattern of three disulfides that are essential for their biological effects. Here we report for the first time the chemical synthesis of the new fully disulfide‐bonded β‐defensins hBD‐27 and hBD‐28, and compare the results with synthetic procedures to obtain the known hBD‐2 and hBD‐3. While hBD‐27 was readily converted into a product with the desired disulfide pattern by oxidative folding, hBD‐28 required a selective protective group strategy to introduce the three disulfide bonds. The established synthetic processes were applied to the synthesis of hBD‐2, which, like hBD‐27, was accessible by oxidative folding, whereas hBD‐3 required a selective strategy comparable to hBD‐28. Experimental work demonstrated that trityl, acetamidomethyl, and t‐butyl are superior to other protection strategies. However, the suitable pairwise arrangement of the protective groups can be different, as shown here for hBD‐3 and hBD‐28. Determination of the minimum inhibitory concentration against different bacteria revealed that hBD‐27, in contrast to other β‐defensins tested, has virtually no antimicrobial activity. Compared to the other peptides tested, hBD‐27 showed almost no cytotoxic activity, measured by hemoglobin release of erythrocytes. This might be due to the low positive net charge, which is significantly higher for hBD‐2, hBD‐3, and hBD‐28. © 2004 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2005
High molecular weight poly‐L‐proline: Synthesis and physical‐chemical studies
Authors: Fasman G. D. , Blout E. R. 
Published: December 2004

AbstractPoly‐L‐proline in the molecular weight range 50,000–90,000 has been synthesized from L‐proline‐N‐carboxyanhydride. The molecular weight obtained is dependent on the initiator concentration. The rate constants for the polymerization have been determined by measuring the CO2 evolution. By observation of rotation during the polymerization, it is possible to deduce the conformation of the polymer in the polymerization solution. It is concluded that the immediate product of the polymerization is neither pure form I nor pure form II. The differences between form I and form II of poly‐L‐proline have been further characterized by measurements of their ultraviolet rotatory dispersion and their ultraviolet spectra.
Copolymers of L‐proline and sarcosine: Synthesis and physical‐chemical studies
Authors: Fasman G. D. , Blout E. R. 
Published: December 2004

AbstractA series of high molecular weight copolypeptides of L‐proline and sarcosine have been synthesized. Experimental evidence is presented which indicates that the products are true copolymers rather than mixtures of homopolymers. In contrast to poly‐L‐proline I, a copolymer of L‐proline‐sarcosine I containing approximately 50% sarcosine is soluble in water. Two molecular conformations of the copolymers, similar to those found for polyproline, have been characterized by means of infrared spectroscopy and optical rotatory dispersion. The residue rotation of L‐proline has been obtained from the copolymers and is −250°.
Dielectric dispersion of polyglutamic acid solution
Authors: Takashima Shiro 
Published: December 2004

AbstractThe dielectric dispersion of polyglutamic acid (PGA) was studied in the pH range of 4–9.8. Three different dispersion curves were obtained. Above pH 6.0, where PGA has a random coil configuration, the dielectric dispersion is characterized by a large dielectric increment (ca. 450) and a relaxation time of 10–12.7 × 10−6 sec. Between pH 6.0 and 5.0, where PGA is in a transitional state with small viscosity, a dispersion curve with very small dielectric increment and also small relaxation time was observed. Below pH 5.0, where PGA has a helical configuration, the dispersion is characterized by a relaxation time of 10–12 × 10−6 sec. and a dielectric increment of about 120. The dipole moment of coil and helical forms of PGA were calculated by using Allgen's equation, and qualitative discussions of these dielectric properties are presented.
Dilatometric and refractometric studies of the helix—coil transition of poly‐L‐glutamic acid in aqueous solution
Authors: Noguchi Hajime , Yang Jen Tsi 
Published: December 2004

AbstractThe helix—coil transition of poly‐L‐glutamic acid (PGA) in aqueous solutions was followed by volume changes, ΔV, and also differential refractive indices, Δn. The increase in ΔV or decrease in Δn upon mixing the sodium salt of PGA with dilute HCl gave three straight lines between pH 7 and 4, the two breaks corresponding to the transition zone observed by other physical methods. For the reaction: COO− + H+ → CO‐OH, ΔV per mole of H+ bound was 11.4 and 11.1 ml. in 0.01 and 0.2M NaCl solutions, respectively. An additional conformational change of about 0.5–1 ml. per amino acid residue was observed for the reaction: coil → helix, after taking electrostatic interaction into consideration. This was probably due to the release of the water of hydration at the amide linkages when the polypeptide coil is converted into the α‐helix, or even the occurrence of voids in the polypeptide chain as a result of imperfect packing of the atoms, although the origin of this volume change is still not fully understood at the present time. The volume changes as calculated from Δn by assuming a constant polarizability of the polymer was found to be higher for the association reaction than those mentioned above. On the other hand, the calculated ΔV for the transition was in fair agreement with those by direct measurements.
Effect of hydrophobic bonding on the stability of poly‐L‐alanine helices in water
Authors: Bixon Mordechai , Scheraga Harold A. , Lifson Shneior 
Published: December 2004

AbstractThe Lifson‐Roig theory for the helix‐random coil transition in polyglycine has been modified to take side‐chain interactions into account. The modified theory is developed specifically for poly‐L‐alanine which probably contains a β1‐α4 hydrophobic bond. A conditional probability, expressing the strength of such a hydrophobic bond, is evaluated from the Nemethy‐Scheraga data for the free energy of formation of the bond. This, together with the conditional probabilities for the states of the backbone chain, permit an evaluation of the partition function and properties of the helix‐random coil transition. It is seen that the hydrophobic bond renders the poly‐L‐alanine helix much more stable than the corresponding polyglycine one, in agreement with data obtained by Gratzer and Doty.
β‐Conformation in γ‐globulin
Authors: Imahori Kazutoma 
Published: December 2004

AbstractAn oriented film of γ‐globulin fibrils obtained by precipitating human γ‐globulin with anti‐human γ‐globulin horse serum was examined with polarized infrared light. When the film was examined with light polarized parallel to the fibril axis, the amide I band was observed at 1635 cm.−1, indicating the cross‐β structure in γ‐globulin fibrils. The reasonableness of this structure for γ‐globulin is discussed by comparing its optical rotatory dispersion constants with those of poly‐O‐acetyl‐L‐serine, which had previously been shown to be the intrachain cross‐β structure.
Energy transfer between tryptophans and aromatic ligands in apomyoglobin
Authors: Luk Chun Ka 
Published: December 2004

AbstractThe binding of three aromatic molecules to apomyoglobin has been investigated. In each case equilibrium dialysis studies and tryptophan fluorescence quenching studies indicate that a one to one complex has been formed. The fluorescence quenching studies further suggest that the binding of the aromatic molecules is at the heme site with possible involvement of the arginine CD3. Xenon, which is known to quench the fluorescence of aromatic hydrocarbons, is found to be bound to apomyoglobin‐aromatic molecule complexes and quenches the emission of the aromatic molecule in the complexes. Oxygen quenches pyrene fluorescence in water solution but does not quench the pyrene fluorescence from the apomyoglobin‐pyrene complex. This is explained by a slower rate of diffusion of oxygen to pyrene in the apomyoglobin‐pyrene complex.
Effects of salts on the nonequivalent stability of the α‐helices of isomeric block copolypeptides
Authors: Ihara Shoji , Ooi Tatsuo , Takahashi Sho 
Published: December 2004

AbstractThe stability of the α‐helices of isomeric block copolypeptides is nonequivalent, as reported previously. In order to explore the origin of the nonequivalence, the stability of α‐helix of two block copolypeptides, (L‐Ala)20‐(L‐Glu)20‐(L‐Phe) (designated as AEF) and (L‐Glu)20‐(L‐Ala)20‐(L‐Phe) (EAF), in aqueous solution was investigated as a function of pH, temperature, and salt concentration by the measurement of the α‐helical content using CD at 223 nm. The transition temperature, Tm, as a measure of the stability of the α‐helix, decreased with increasing the salt concentration for EAF, while Tm increased for AEF. The results indicate that electrostatic interactions affect the nonequivalence of such helical stability. Thermodynamic quantities, ΔG, ΔH, and ΔS, of the thermal transition from random coil to α‐helix were obtained by applying the curve‐fitting method to the data. The major contribution to the effects of salts seems to be the entropic term, not the enthalpy term. This is unexpected, since the salt ions would weaken electrostatic interactions between ionized groups and the dipole along the helical axis, which affect the enthalpy term. In addition, the dependence of the electrostatic effect on the salt concentration is different for EAF and AEF. There fore, the nonequivalence cannot be accounted for by only the electrostatic effect, suggesting that it originates from some intrinsic property of the α‐helix.