bluuebunny/crossref_metadata_2025_split huggingface dataset:
Studies of fibrin film. II. Small‐angle x‐ray scattering
Authors: Roska Fred J. , Ferry John D. , Lin J. S. , Anderegg John W. 
Published: December 2004

AbstractMeasurements of small‐angle x‐ray scattering have been made on bovine fibrin film, prepared by gentle compaction of coarse fibrin clots, containing 12–15% fibrin plasticized with either aqueous buffer or glycerol. Most of the experiments were made with water‐plasticized films because of the better x‐ray contrast. Both unligated and ligated (i.e., with α‐α and λ‐λ ligation by fibrinoligase, factor XIIIa) films were studied. Theoretical angular scattering profiles were calculated for a simplified model of the fibrin protofibril as a function of stretch ratio in uniaxial elongation based on an orientation distribution derived in the preceding paper. Measurements were made on unstretched films both with slit geometry and with pinhole geometry and two‐dimensional position‐sensitive detection. From the former, which had better resolution, the fundamental peak corresponded to a repeat spacing of 230 ± 5 Å, in agreement with early results of Stryer et al. [(1963) Nature 197, 793–794] and electron micrographs of stained fibrin, and with the half‐staggered overlapping model of the protofibril. Measurements were made with pinhole geometry on film stretched up to a stretch ratio λ = 1.59 at different times after imposition of strain and after release and recovery. The changes in meridional and equatorial scattering profiles, including the more prominent appearance of a harmonic in the former, show the orientation of the protofibrils as previously deduced from birefringence and related quantitatively to stretch ratio. In addition, the original repeat spacing is gradually replaced by one of about 290 Å. The “internal” stretch ratio λx, averaging about 1.28, is independent of the macroscopic stretch ratio λ from 1.14 to 1.59. The change, which is more nearly complete for unligated film and is reversible on release and retraction of the stretched strips, is attributed to an internal transition in the fibrin monomer units, probably involving extension of either the helical connectors or the terminal nodules. The results of stress and birefringence relaxation reported in the preceding paper of this series are interpreted on this basis.
Crystal structures of diketopiperazines containing α‐aminoisobutyric acid: Cyclo(Aib‐Aib) and cyclo(Aib‐L‐Ile)
Authors: Suguna K. , Ramakumar S. , Shamala N. , Prasad B. V. Venkataram , Balaram P. 
Published: December 2004

AbstractThe crystal and molecular structures of two α‐aminoisobutyric acid (Aib)‐containing diketopiperazines, cyclo(Aib‐Aib) 1 and cyclo(Aib‐L‐Ile) 2, are reported. Cyclo(Aib‐Aib) crystallizes in the space group P1 with a = 5.649(3), b = 5.865(2), c = 8.363(1), α = 69.89(6), β = 113.04(8), γ = 116.0(3), and Z = 1, while 2 occurs in the space group P212121 with a = 6.177(1), b = 10.791(1), c = 16.676(1), and Z = 4. The structures of 1 and 2 have been refined to final R factors of 0.085 and 0.086, respectively. In both structures the diketopiperazine ring shows small but significant deviation from planarity. A very flat chair conformation is adopted by 1, in which the Cα atoms are displaced by 0.07 Å on each side of the mean plane, passing through the other four atoms of the ring. Cyclo(Aib‐Ile) favors a slight boat conformation, with Aib Cα and Ile Cα atoms displaced by 0.11 and 0.05 Å on the same side of the mean plane formed by the other ring atoms. Structural features in these two molecules are compared with other related diketopiperazines.
Strategy for trapping intermediates in the folding of ribonuclease and for using 1H‐NMR to determine their structures
Authors: Kuwajima Kunihiro , Kim Peter S. , Baldwin Robert L. 
Published: December 2004

AbstractThe major unfolded form of ribonuclease A is known to show well‐populated structural intermediates transiently during folding at 0°–10°C. We describe here how the exchange reaction between D2O and peptide NH protons can be used to trap folding intermediates. The protons protected from exchange during folding can be characterized by 1H‐nmr after folding is complete. The feasibility of using 1H‐nmr to resolve a set of protected peptide protons is demonstrated by using a specially prepared sample of ribonuclease S in D2O in which only the peptide protons of residues 7–14 are in the 1H‐form. All eight of these protected peptide protons are H‐bonded. Resonance assignments made on isolated peptides containing these residues have been used to identify the protected protons. Other sets of protected protons trapped in the 1H‐form can also be isolated by differential exchange, using either ribonuclease A or S. Earlier model compound studies have indicated that H‐bonded folding intermediates should be unstable in water unless stabilized by additional interactions. Nevertheless, peptides derived from ribonuclease A that contain residues 3–13 do show partial helix formation in water at low temperatures. We discuss the possibility that specific interactions between side chains can stabilize short α‐helixes by nucleating the helix, and that specific interactions may also define the helix boundaries at early stages in folding.
Multiphasic conformation transition of globular proteins under denaturating perturbation
Authors: Wada Akiyoshi , Saito Yoshio , Ohogushi Mikio 
Published: December 2004

AbstractDenaturation profiles of 17 globular proteins were studied by the spectroscopic and chromatographic methods with high‐data‐point density. The denaturational transitions are broadly classified into three types according to their multiphasic characteristics. In general, more or less complex internal cooperative events seem to take place in the conformation transition of globular proteins.
Sequential individual resonance assignments in the 1H‐NMR spectra of polypeptides and proteins
Authors: Wüthrich Kurt 
Published: December 2004

AbstractRecently, a new procedure for the assignment of protein 1H‐nmr spectra was introduced that relies on stereochemical considerations of proton–proton distances in polypeptides and on the use of two‐dimensional nmr for obtaining 1H‐1H through‐bond and through‐space connectivity maps. In the present paper a particular aspect of this assignment procedure is discussed in more detail, i.e., how to obtain individual resonance assignments from identification of amino acid side‐chain spin systems and identification of neighboring residues in the amino acid sequence.
The key role of residue 5 in angiotensin II
Authors: Fermandjian Serge , Sakarellos Constantin , Piriou Françlois , Juy Michel , Toma Flavio , Thanh Hung Lam , Lintner Karl , Khosla Mahesh C. , Smeby Robert R. , Bumpus F. Merlin 
Published: December 2004

AbstractThe conformation–biological activity relationships in a series of angiotensin II analogs substituted in position 5 were studied. Results indicated that only analogs with β‐branched residue in position 5 possess spectral and biological properties identical to that of parent angiotensin II.
Immunoassays of peptide hormones and their chemical aspects
Authors: Moroder L. , Nyfeler R. , Gemeiner M. , Kalbacher H. , Wüunsch E. 
Published: December 2004

AbstractThe N‐terminal maleoyl‐β‐alanyl derivative of human gastrin‐[2–17] has been synthesized as a model compound to investigate the usefulness of such peptide derivatives for their mild and selective conjugation, via reaction with thiol groups, to high‐molecular‐weight carrier molecules to produce antigens, as well as to radioiodinable or fluorogenic molecules to prepare tracers for immunoassays. In this context the examined enzyme substrate‐gastrin conjugate was found to exhibit the full immunoreactivity of the parent peptide and to be well suited as tracer in a gastrin fluorescence‐immunoassay.
Conformational study of ribonucleotides, 2′‐deoxyribonucleotides, and arabinonucleotides by carbon‐13 nuclear magnetic resonance
Authors: Blonski Wayne J. P. , Hruska Frank E. , Sadana Krishan L. , Loewen Peter C. 
Published: December 2004

AbstractThe geminal and vicinal 13C‐31P coupling constants have been monitored, as a function of pH, for a series of uracil and cytosine 3′‐ and 5′‐nucleotides with a ribose, arabinose, or 2′‐deoxyribose sugar. Data were also obtained for two 3′,5′‐diphosphates in the ribose and arabinose series. The geminal J(C5′‐P5′) and J(C3′‐P3′) couplings show only a small dependence on the ionization state of the phosphate, decreasing by < 0.5 Hz in the pH 5–7 range. For the ribose and arabinose 3′‐nucleotides, the vicinal J(C4′‐P3′) increase (up to 1.5 Hz) on secondary phosphate ionization in the pH 5–7 range, whereas their J(C2′‐P3′) couplings decrease (up to 1.5 Hz) over the same pH range. In contrast for the 2′‐deoxyribose molecules, both couplings decrease (∼0.5 Hz) on phosphate ionization. The titration curves provide information about the influence of the sugar on the conformation about the C3′O3′ bond. Some conformational trends could be rationalized by consideration of the sugar‐puckerdependent contact interactions between the 3′‐phosphate and the substituents on the furanose ring.
Tyrosine optical activity as a probe of the conformation and interactions of fibronectin
Authors: Welsh E. J. , Frangou S. A. , Morris E. R. , Rees D. A. , Chavin S. I. 
Published: December 2004

AbstractA very intense negative band is observed at ∼ 183 nm in the CD spectrum of fibronectin from bovine plasma. This transition has not previously been reported, probably because it occurs in a spectral region that has not been readily accessible in earlier studies. At longer wavelength, the observed CD is very similar to spectra reported for human and chick material, having positive bands at ∼230 and ∼200 nm, and a negative band at ∼215nm. The low molar ellipticity of the negative band ([θ] ≈ −2.5 × 103 deg cm2 dmol−1) suggests little α‐helix or β‐sheet structure. The new transition, and the two positive bands at higher wavelength, do not correspond to known transitions of the peptide backbone, but all three are present in the CD of N‐acetyltyrosineamide. It is therefore suggested that the observed CD behavior of fibronectin arises predominantly from the optical activity of tyrosine side chains. The contribution of this side‐chain optical activity to the CD of other proteins is discussed.On raising pH to ionize tyrosine residues, the positive CD band at ∼230 nm is lost in both N‐acetyltyrosineamide and in fibronectin. The spectral change is fully reversible in the model compound, but only partially reversible in fibronectin. From this evidence, and the magnitude of the 183‐nm band, it is suggested that some or all of the tyrosine residues in fibronectin may be present within ordered domains. The possible role of SS bonds in maintaining tertiary structure is discussed. The interaction of fibronectin with heparin is accompanied by a large increase in the 183‐nm band and by slight enhancement of the negative band at 215 nm, consistent with some limited formation of β‐sheet.Present results indicate that CD may be of considerable value in characterization of the molecular organization and biologically relevant interactions of fibronectins and of related glycoproteins of the extracellular matrix.
Crystal structure of a tripeptide, L‐alanyl‐glycyl‐glycine and its relevance to the poly(glycine)‐II type of conformation
Authors: Subramanian E. , Lalitha V. 
Published: December 2004

AbstractA tripeptide molecule, L‐alanyl‐glycyl‐glycine, crystallizes in the form of a left‐handed helix with (ϕ,ψ) = −83°, 170°. A pseudohexagonal packing arrangement and interchain hydrogen‐bonded interactions are reminiscent of the model for the structure of poly(glycine)‐II. Observations of certain intermolecular interactions appear to be relevant to the stereochemical assumptions incorporated in the models proposed for poly(glycine)‐II and related polypeptides.
Nmr studies on complex formation of poly(L‐lysine HBr) with carbonate ion in aqueous solution
Authors: Kakiuchi Kinji , Akutsu Hideo 
Published: December 2004

AbstractDiemer formation of poly(L‐lysine HBr) in carbonate buffer at pD 10.5 was reported in our previous paper [Biopolymers(1981) 20, 345–357]. The mechanism of the dimer formation was investigated employing carbon‐13 and proton nmr. pD dependence of the 13C‐nmr spectrum of poly(L‐lysine HBr) in the presence of carbonate ion clearly shows that a complex formation between the CO ion and protonated ε‐amino group is involved in the stabilization of the dimer form. The lifetime of the complex is longer than 10−2 s. A stoichiometric evaluation suggests that CO bridges two lysyl side chains. A molecular model of the dimer form designated as a single antiparallel β‐ribbon was proposed and discussed in the light of hydrodynamic and ir spectroscopic properties reported earlier. Concentration change experiments indicate that CO binds not only to the dimer formation is inferred as stabilization of the single antiparallel β‐ribbon as an intermediate structure in the conversion between the α‐helix and β‐sheet. The α‐CH proton signal of the lysine residue located in the ordered structure (α‐helix and β‐form) was observed to be separate from that in the random‐coil region.
Collapse of DNA caused by trivalent cations: pH and ionic specificity effects
Authors: Thomas T. J. , Bloomfield V. A. 
Published: December 2004

AbstractA comparison of the condensation of T4 phage DNA by spermidine and Co(NH3) at pH values between 5.1 and 10.2 has been made using quasielastic light scattering to determine translational diffusion coefficients and Stokes radii. Co(NH3) is more effective than spermidine in causing condensation at all pH, indicating that the differences observed in previous work were not due to pH effects, as might have been inferred from recent theories of intermolecular forces. The DNA particles collapsed with Co(NH3) are smaller than those obtained with spermidine. The hydrodynamic radius of spermide‐collapsed structures decreases slightly with increasing pH, while the size of the Co(NH3)collapsed structures is almost independent of pH. These results confirm that there are specific ion effects in DNA condensation by oligocations, in addition to the dominant general polyelectrolyte effects.
Mutual diffusion of crystallin proteins at finite concentrations: A light‐scattering study
Authors: Delaye M. , Gromiec A. 
Published: December 2004

AbstractBoth static and quasielastic light‐scattering measurements were performed on solutions of crystallin proteins extracted from calf lens cortex. The concentration range between ideal (c → O) and physiologic solutions (c up to 50%, w/w) was investigated. The intensity data are compatible with a model where the globular crystallins behave as “hard spheres,” the radius of which does not depend on concentration. The correlation function of the scattered intensity is correctly described by a single exponential (mutual diffusion) for 0 < c < 5%. For larger concentrations, a slowly relaxing component, whose amplitude increases with c, appears on top of the rapid component describing the mutual diffusion. Heterodyne detection is used to uncouple these two components. The mutual diffusion coefficient is then found to decrease linearly up to c ≃ 10% and to deviate sharply from linearity at larger concentrations.
Synthesis and conformation of the cyclic octapeptides cyclo(Phe‐Pro)4, cyclo(Leu‐Pro)4, and cyclo[Lys(Z)‐Pro]4
Authors: Kimura Shunsaku , Imanishi Yukio 
Published: December 2004

AbstractCyclic octapeptides, cyclo(X‐Pro)4, where X represents Phe, Leu, or Lys(Z), were synthesized and their conformations investigated. A C2‐symmetric conformer containing two cis peptide bonds was found in all of these cyclic octapeptides. The numbers of available conformations due to the cis–trans isomerization of Pro peptide bonds depended on the nature of the solvent and X residue: they decreased in the following order: cyclo[Lys(Z)‐Pro]4 > cyclo(Leu‐Pro)4 > cyclo(Phe‐Pro)4 in CDCl3. 13C spin‐lattice relaxation times (T1) of these cyclic octapeptides were measured, and the contribution of segmental mobility to T1 was found to vary with the nature of the X residue.
Circular dichroism studies of freeze‐drying‐induced conformational changes in human hemoglobin
Authors: Thirion Christian , Larcher Dominique , Chaillot Bernard , Labrude Pierre , Vigneron Claude 
Published: December 2004

AbstractFreeze‐drying of hemoglobin leads to the formation of a significant amount of methemoglobin. It is possible to decrease this transformation in the presence of protective compounds. The mechanism of action of these protectors is presently unknown. Spectroscopic absorption and CD spectra between 190 and 700 nm are presented for samples of hemoglobin freeze‐dried with or without protection and for control solutions of oxyhemoglobin and methemoglobin. The interpretation of the dichroic spectra allows us to observe the secondary, tertiary, and quaternary structure changes that hemoglobin undergoes with freeze‐drying. The results indicate that the absence of a protector weakly influences the conformation in the vicinity of the heme and increases the helicity of protein chains from 75 to 81%. Furthermore, experimental data, in agreement with electron‐spin resonance measurements, suggest that the protective effect is not the result of a direct bond between the iron and the compound added.
Apparent molar volumes of some amino acids and peptides in aqueous urea solutions
Authors: Mishra A. K. , Prasad K. P. , Ahluwalia J. C. 
Published: December 2004

AbstractDensities of solutions of several α‐amino acids and peptides in 3 and 6m aqueous urea solvents have been determined at 298.15 K. These data have been used to evaluate the infinite‐dilution apparent molar volumes of the solutes and the volume changes due to transfer (V) of the α‐amino acids and peptides at infinite dilution from water to aqueous urea solutions. The sign and magnitude of the V values have been rationalized in the framework of Friedman's cosphere‐overlap model. The V values for the glycyl group (CH2CONH) and alkyl side chains have been estimated.
CNDO/2 quantum‐mechanical calculations of the conformational flexibility of the diketopiperazine skeleton
Authors: Ciarkowski Jerzy 
Published: December 2004

AbstractEight conformers typical of diketopiperazine (DKP) ring folding were chosen for analysis. Conformational energy calculations were carried out using the semiempirical quantummechanical CNDO/2 method. The results obtained confirm considerable flexibility of the DKP skeleton. As the degree of folding increases, twisted boat conformations with the nonplanar peptide bonds tend to be more stable, while more rigid regular boat conformations with planar peptide bonds appear to be less stable than a flat one. The CNDO/2 method was found to be reliable enough for conformational studies of cyclic peptide skeletons with cis‐peptide bonds.
Relaxation kinetics of DNA–ligand binding including direct transfer
Authors: Ryan Dennis P. , Crothers Donald M. 
Published: December 2004

AbstractThe relaxation kinetics of binding of ethidium to calf‐thymus DNA as studied previously by the temperature‐jump method with absorption detection [Bresloff, J. & Crothers, D. M. (1975) J. Mol. Biol. 95, 103] is reanalyzed in terms of a series of models for DNA‐ligand interactions that include cases with and without internal and bimolecular direct transfer of ligands between different binding modes or different binding sites. The experimental results are shown to be consistent with two alternative binding mechanisms. Both models include bimolecular “direct transfer” steps and a site size of two base pairs per site. In the first model, there exist two distinct modes of binding to the DNA double helix at each binding site. In the second model, sites containing at least one GC base pair constitute a different and stronger class of binding sites than those containing only AT base pairs. The existence of a direct transfer pathway between two classes of bound ligands is supported by the linear increase of reciprocal relaxation times far beyond the concentration regions, where off‐rates should have become rate limiting. The second model, incorporating the notion of base selectivity, is in quantitative agreement with published work on ethidium binding to DNAs of different base compositions and with nmr measurements of bound ligand lifetimes.
Microwave dielectric absorption of DNA in aqueous solution
Authors: Foster Kenneth R. , Stuchly Maria A. , Kraszewski Andrzej , Stuchly Stanislaw S. 
Published: December 2004

AbstractThe dielectric properties of aqueous solutions of DNA were measured at frequencies ranging from 0.1 to 12 GHz. The results are analyzed using the Maxwell mixture theory and yield a value for the hydration of the DNA of about 0.4 g/g, which is in the range observed in other investigations. No evidence was found for an additional absorption effect at microwave frequencies, which has been predicted to occur in certain DNA analogs due to the vibrational excitation of the double helix by the applied microwave field.
1H‐ and 31P‐nuclear magnetic resonance studies on the conformation of d‐(CpGpCpG)2 and d‐(CpGpCpGpCpG)2 short helices in B‐conformation
Authors: Cheng Doris M. , Kan Lou‐Sing , Frechet Denise , Ts'O Paul O. P. , Uesugi Seiichi , Shida Toshio , Ikehara Morio 
Published: December 2004

AbstractTwo short DNA helices, d‐(CpGpCpG)2 and d‐(CpGpCpGpCpG)2, in dilute salt solutions have been studied thoroughly by 1H‐ and 31P‐nmr spectroscopy as model systems for the calibration of nmr theory in its application to nucleic acids research. All the nonexchangeable proton resonances of these two short helices have been assigned by the “incremental method,” “sequential homodecoupling” of the sugar protons, thermal perturbation, and computer spectral simulation, as well as the NOE technique.The CD and uv data were also obtained at either identical or half concentrations of the oligomer used in the nmr studies in order to have comparable optical data for estimating helical content and for assigning conformation. The precise assignment of the sugar proton resonances and their corresponding coupling‐constant values provide valuable information about the backbone conformation. The sugar conformation was shown to be predominantly in the 2E‐form (>70%). The rotation of the C4′C5′ is in favor of the gg conformation (55–95%), the rotation of the C5′O5′ bond is highly in favor of g′g′ (83–91%), and the rotation of the C3′O3′ bond is restricted to the domain of ϕ′ ≃ 195°.The CD data and the sugar conformational analyses indicate that these CG helices are in the B‐form in dilute salt solutions. The assignment of NHN hydrogen‐bonded resonances of these two helices are based on their thermal stability. The through‐space magnetic field effects on the base protons and the NHN protons in the helices were calculated and compared with the experimental values. This comparison yields two general conclusions: (1) For the base protons, application of both ring‐current effects and local anisotropic effects in the computations are preferred; but for the NHN protons, the application of the ring‐current effect alone is preferred over the application of both ring‐current effects and local anisotropic effects; and (2) while the computed values in the best theoretical treatment cited above did support the conclusion that these CG helices are in the B‐conformation, the differences among the computed values for the three conformations, A, A′, and B, are not very large, at least for the CG sequence. All the 31P resonances of these CG helices are unambiguously assigned through a specific heterodecoupling technique established previously [Cheng et al. (1982) Biopolymers 21, 697–701]. The complete assignment of all proton resonances and 31P resonance of d‐(CpGpCpG)2 and d‐(CpGpCpGpCpG)2 helices in the B‐form establishes these two deoxy CG helices as valuable model systems for the study of the nmr and polymorphism of nucleic acids.