bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antigenic reactivity: Molecular delineation of monohaptenic anaphylactogens
Authors: Schneider C. H. , Guenin R. 
Published: December 2004

AbstractAnaphylactogenic, monohaptenic conjugates carrying a 2,4‐dinitro‐5‐carboxyphenyl substituent as haptenic group and either one of two types of auxiliary groups essential for their anaphylactogenicity were studied. The “hydrocarbon auxiliary groups” require the presence of a hydrocarbon structure such as aliphatic chains of discrete length or planar rings such as provided by phenyl‐ or nicotinoyl residues and become particularly effective in conjunction with a carboxylate group. The benzylpenicilloyl group is an effective auxiliary structure, but the thiazolidine ring as such is not. It appears that the distance between haptenic and hydrocarbon auxiliary groups can be quite large. The “carbohydrate auxiliary group” becomes effective via a different mechanism. It requires disaccharide residues or two closely connected monosaccharides. Single monosaccharides are ineffective. A concept of interest with regard to drug allergy is the possibility that attachment of a single haptenic molecule to a glycoprotein constitutes an anaphylactogen.
Controlled release of macromolecules and pharmaceuticals from synthetic polypeptides based on glutamic acid
Authors: Sidman Kenneth R. , Steber William D. , Schwope Arthur D. , Schnaper Gayle R. 
Published: December 2004

AbstractBiocompatible, biodegradable copolymers of glutamic acid and ethyl glutamate were evaluated for their permeability to proteins ranging in molecular weight from 12,300 to 69,000. The results showed that the copolymers were sufficiently permeable that they could be used for the preparation of implantable, controlled‐release systems capable of releasing therapeutic amounts of high‐molecular‐weight drugs.
Crystal structure and conformation of a cyclic tetrapeptide cyclo(L‐Pro‐Sar)2 containing all‐cis peptide units
Authors: Ueno Katsuhiko , Shimizu Toshimi 
Published: December 2004

AbstractThe crystal structure and conformation of the synthetic cyclic tetrapeptide, cyclo(L‐Pro‐Sar)2, was determined by x‐ray analysis. The peptide crystallizes in the orthorhombic space group P212121 with cell parameters a = 9.277(1), b = 12.884(1), and c = 15.581(2) Å. The crystal structure was solved by the symbolic addition procedure for direct phase determination and least‐squares refinement using 1796 reflections, which led to the final R value of 0.043. This structure provides the first example observed in a crystal of a cyclic tetrapeptide in which all four peptide units have been found in the cis conformation with ω angles deviating slightly by 2°–10° from the ideal value of 0°. It was also found that the two Pro Cα‐CO single bonds assumed a trans′ (ψ = 159.6° and 158.4°) conformation. Adjoining average planes of the peptide groups fall at nearly right angles to each other. The pyrrolidine ring conformations of the two prolyl residues are in the envelope form, with Cγ carbon out of the least‐squares planes for the remaining four atoms.
High‐resolution nmr studies of A‐ and G‐containing oligonucleotides
Authors: Shum Betty Wai‐King , Crothers Donald M. 
Published: December 2004

AbstractWe report the temperature dependence of the H2 and H8 purine ring proton resonances of oligoriboadenylates up to chain length 11, with or without a single guanosine residue at the 5′‐end, second position, or 3′‐end. The results suggest the following generalizations: (1) Stacking of the bases in a right‐handed single‐stranded helix is more extensive in the interior of the chain than at the chain ends. (2) The tendency of the terminal base to unstack is greater at the 5′‐end than at the 3′‐terminus. (3) G stacks more weakly than A, as evidenced by weak stacking of 3′‐terminal G. Anomalies were also observed in the unstacking profile of G at the second position in the chain, indicating a conformational anomaly such as looping out of G, thereby allowing adjacent A's to stack together, or adoption by G of some other alternative structure. (4) The results imply that the environment at a given base is influenced by effects of longer range than nearest‐ or next‐nearest‐neighbor. Increasing ion condensation as chain length increases may be responsible for the slow approach of oligomer behavior to the properties of the high polymer.
Improved methods of analysis for CD data applied to single‐strand stacking
Authors: Causley Gary C. , Staskus Paul W. , Johnson W. Curtis 
Published: December 2004

AbstractCD spectra of ApA, Poly(A), CpC, and poly(C), measured as a function of tempeature, are used to demonstrate improved methods of analysis for this type of data. Each of the four sets of temperature‐dependent CD spectra are decomposed using singular value deocmposition. This method demonstrates that there are only two independnet parameters in each set of data. The two basis curves in the wavelength domain for each set of data are use to average the CD curves even though they are taken at different temperatures. Each of the four sets of temperature‐dependent data, smoothed in this way, is decomposed in the Taylor series to separate degenerate interactions due to stacking from the intrinsic CD of the chromophores and nondegenerate interactions. Such a decomposition allow the comparison of corresponding interactions whose relative magnitudes are not obvious in the data. The CD due to degenrate interactions fits the van't Hoff equation well in all four cases and thermodynamic parameters are determined. A simplex routine is used to search the space before performing the least‐squares fit of the data of the van't Hoff equation. This guarantees a global solution rather than a local solution. The first of the two basis curves in the temperature domain derived by singular value decomposition also fits the van't Hoff equation well and gives comparable thermodynamic parameters, although the basis curves derived in this manner have no a priori physical significance. Rather than comparing room temperature CD curves, we compare CD curves of the various compounds at their melting temperature where the populations of the stacked conformation are equivalent. We use the Cantor‐Tinoco equation, which relates the CD of a polymer to the CD of the corresponding dimer, to show that the secondary structure of ApA is not the same as poly(A), and the secondary structure of CpC is not the same as poly(C). However, the two dimers have similar degenerate stacking interactions as do the two polymers. A sound theoretical basis is provided for the semiempirical Cantor‐Tonoco equation.
Behavior of amphipathic helices on analysis via matrix methods, with application to glucagon, secretin, and vasoactive intestinal peptide
Authors: Hamed Maher M. , Robinson Randall M. , Mattice Wayne L. 
Published: December 2004

AbstractA configuration partition function, which incorporates concepts embodied in the amphipathic helix hypothesis, has been formulated for a polypeptide in the presence of zwitterionic phospholipid. An enhanced probability is assigned to helix formation in any region of the polypeptide chain where side chains bearing charges of opposite sign will be situated on the same side of the α‐helix but displaced from one another by one turn. This situation will arise when residues i − 4 (or i − 3) and i bear charges of opposite sign and residue i − 4 (or i − 3) through i are in a helical state. Illustrative calculations are performed for polypeptide chains in which the generalized nonionic amino acid residue serving as host has Zimm‐Bragg parameters of σ = 10−4, s = 1. These calculations define conditions under which two interacting charged pairs can cooperate in a synergistic helix augmentation even when the two pairs are separated by significantly more than four generalized nonionic amino acid residues. Furthermore, the two interacting charged pairs, as well as the intervening amino acid residues, may become helical as one unit. Significant augmentation in helicity is observed with plausible values for the enhanced probablity assigned to helix formation for an interacting pair. This model predicts correctly that glucagon and secretin, but not vasoactive intestinal peptide, undergo a coil‐to‐helix trnsition in the presence of zwitterionic phospholipid. This prediction is made with plausible values for the parameter used to express the helicity enhancement. The experimental observation with zwitterionic phospholipids is the direct opposite of that seen for these three peptides in the presence of anionic lipids and detergents. In anionic lipids the amount of induced helicity is in the following order: glucagon < secretin < vasoactive intestinal peptide. Results obtained with these three peptides demonstrate that the nature of the head group of the lipid is important for lipid–protein interaction and that the resulting conformational changes can be rationalized by matrix methods.
Nuclear magnetic resonance study of ring conformations of cyclic tetradepsipeptide AM‐toxins and related peptides
Authors: Higashijima Tsutomu , Shimohigashi Yasuyuki , Kato Tetsuo , Izumiya Nobuo , Ueno Tamio , Miyazawa Tatsuo 
Published: December 2004

AbstractCyclic tetradepsipeptides, AM‐toxin I and II, are the host‐specific phytotoxins of Alternaria mali. In order to elucidate conformation‐toxicity relationships, we analyzed the 270‐MHz proton nmr spectra of AM‐toxins and hydrogenated analogs, (D‐Ala2)AM‐toxin I (toxic) and (L‐Ala2)AM‐toxin I (not toxic), in (C2H3)2SO. These cyclic tetradepsipeptides do not contain N‐substituted amino acid residues, and all the peptide and ester groups have been found to be transoid. Two conformers with very unequal populations have been found for AM‐toxin I and II; the CβCαCO conformations of the Dha2 residues are nonplanar S‐trans in the major conformer and nonplanar S‐cis in the minor conformer. Only one ring conformation has been found for each of (L‐Ala2) and (D‐Ala2)AM‐toxin I. (L‐Ala2)AM‐toxin I takes a C4‐type ring conformation; all the CO groups and Cα‐H bonds are oriented to the same side of the ring. (D‐Ala2)AM‐toxin I takes a new ring conformation; the side chain and CO group of the L‐Amp1 residue are oriented to the same side of the ring. This new conformation is also found for the major conformers of AM‐toxin I and II and thus appears to be required for the toxicity. The ring conformations of Tyr(OCH3)1‐bearing analog tetradepsipeptides have been found to be much the same as those of Amp1‐bearing depsipeptides. Furthermore, on the basis of the two distinct conformations of (D‐Ala2) and (L‐Ala2)AM‐toxin I, an empirical rule is proposed for the stable ring conformations of cyclic tetra‐D,L‐peptides, not containing N‐substituted amino acid residues.
Temperature dependence of the dynamic light scattering of linear ϕ29 DNA: Implications for spontaneous opening of the double‐helix
Authors: Wilcoxon Jess , Schurr J. Michael 
Published: December 2004

AbstractThe apparent diffusion coefficient Dapp(K) of a single sample of linear ϕ29 DNA (Mr = 11.5 × 106) has been measured as a function of K2 from 0.21 × 1010 to 20 × 1010 cm−2 at a variety of temperatures from −0.5 to +70°C. Dapp(K) scales closely as T/η at every value of K2. All of these data are simulated by a particular Rouse‐Zimm model comprised of a constant number of subchains with constant rms subchain extension b = 1057 Å and an apparent subchain diffusion coefficient Dplat that scales at T/η from −0.5 to +70°C. It is inferred from these results that any temperature dependence of the flexural and torsional rigidities of DNA must be rather weak. A less firm inference is that these rigidities actually increase slightly with temperature, possibly in proportion to T, which is weak T dependence in this context. These findings eliminate the possibility that spontaneous transient opening of the DNA structure has any significant effect on the flexural and torsional rigidities of the DNA filament. A review of the most pertinent available data from other experiments concerning spontaneous transient opening of the DNA is presented. The formaldehyde kinetics data do not unequivocally implicate an open base‐pair intermediate and provide only an upper limit to the fraction of open base pairs. An alternative nonopening model with a protonated doorway state is proposed to accommodate the hydrogen‐exchange data. It is concluded that there is presently no incontrovertible evidence for a fraction of unstacked open base pairs greater than about 10−4.
Interaction of calcium ions with peptide hormones of the gastrin family
Authors: Peggion E. , Mammi S. , Palumbo M. , Moroder L. , Wünsch E. 
Published: December 2004

AbstractThe interactions of Des‐Trp1‐Nle12‐minigastrin I (Nle11‐HG‐13) and Nle15‐little gastrin I (Nle15‐HG‐17) with calcium ions have been investigated in water and in trifluoroethanol solution using uv and CD absorption techniques. Both hormones strongly interact with Ca2+ in the organic medium. In the case of Nle11‐HG‐13, the near‐uv chiroptical properties (dominated by the transitions of the Trp residue in the C‐terminal tetrapeptide sequence) indicate that three metal ions per mole of hormone are involved in the binding process. From the different response of near‐uv and far‐uv CD properties to the addition of calcium and from the change of the CD spectra in the aromatic absorption region, it is concluded that the biologically important C‐terminal sequence is directly involved in the interaction with calcium. Elongation of the peptide chain from Nle11‐HG‐13 to Nle15‐HG‐17 (Nle15‐little gastrin I) does not provide any additional binding site for calcium ions. The change of the CD properties in the near‐ and far‐uv indicates that three metal ions per mole of hormone are involved in the binding process. The dichroic absorption in the aromatic region indicates that only one of the two Trp residues of the little gastrin analog is sensitive to the presence of calcium. On the assumption that the variation of the CD properties is proportional to the extent of calcium binding, the binding constants K1, K2, and K3 have been estimated roughly. Two similar sets of binding constants have been found, with K1 ≥ 106M−1 and K3 of the order of 105M−1, indicating similar binding sites in the two hormones with high affinity for calcium ions.
Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features
Authors: Kabsch Wolfgang , Sander Christian 
Published: December 2004

AbstractFor a successful analysis of the relation between amino acid sequence and protein structure, an unambiguous and physically meaningful definition of secondary structure is essential. We have developed a set of simple and physically motivated criteria for secondary structure, programmed as a pattern‐recognition process of hydrogen‐bonded and geometrical features extracted from x‐ray coordinates. Cooperative secondary structure is recognized as repeats of the elementary hydrogen‐bonding patterns “turn” and “bridge.” Repeating turns are “helices,” repeating bridges are “ladders,” connected ladders are “sheets.” Geometric structure is defined in terms of the concepts torsion and curvature of differential geometry. Local chain “chirality” is the torsional handedness of four consecutive Cα positions and is positive for right‐handed helices and negative for ideal twisted β‐sheets. Curved pieces are defined as “bends.” Solvent “exposure” is given as the number of water molecules in possible contact with a residue. The end result is a compilation of the primary structure, including SS bonds, secondary structure, and solvent exposure of 62 different globular proteins. The presentation is in linear form: strip graphs for an overall view and strip tables for the details of each of 10.925 residues. The dictionary is also available in computer‐readable form for protein structure prediction work.
Matrix‐method calculation of linear and circular dichroism spectra of nucleic acids and polynucleotides
Authors: Rizzo Vincenzo , Schellman John A. 
Published: December 2004

AbstractCalculations of the optical properties (absorption, linear dichroism, circular dichroism, and anisotropic components of the CD) are presented for polynucleotides of random or regular sequence within the formalism of the matrix method using a set of parameters that includes only the ππ* transitions of the aromatic bases. Experimental solution spectra agree favorably with calculated CD spectra for A‐RNA, A‐DNA, and B‐DNA, when coordinates derived from x‐ray studies on fibers are used. Excessive hypochromicity is predicted when parameters intended to reproduce the vacuum‐uv absorption of the chromophores are included in the calculations, but total elimination of these parameters leads to an insufficient hypochromicity for the long‐wavelength absorption band. Using alternative conformations for DNA in low‐salt aqueous solution did not improve the agreement between experimental and calculated spectra, but some features of the optical properties predicted for these variant structures suggest that the tilt of the bases with respect to the helical axis may be larger than that of the fiber B‐form.In the case of polynucleotides with regular structure, which have been traditionally less easy to understand in terms of the standard nucleic acid conformations, a series of alternative structures has been examined. Unexpectedly, the calculated spectrum for the Z‐DNA structure compares almost quantitatively with the experimental spectrum of poly(dGC·dGC) in low salt. This result, which confirms a recent report [Vasmel, H. & Greve, J. (1981) Biopolymers 20, 1329–1332], is in contrast with the current identification of Z‐DNA with the high‐salt form of poly(dGC·dGC). Finally, the optical properties of single‐stranded polyribonucleotides appear to be better explained when alternative structures [91‐helix for poly(rA) and 61‐helix for poly(rC)] are introduced instead of the A‐RNA form.
A monte‐carlo estimate of DNA loop formation
Authors: Post Carol Beth 
Published: December 2004

AbstractThe ends of rather short double‐helical DNA segments (approximately two persistence lengths) can be enzymatically joined to form closed circles. Such covalent closure into circles is a measure of the likelihood of the two ends of the DNA coming into close contact. There is a length of DNA for which loop formation is most likely to occur. We have determined the chain‐length dependence of loop formation for stiff chains using computer‐generated chains of cylinders. The distribution from which the values for the angles between cylinders were chosen relates the chain parameters to a given chain persistence. Our results are compared with those of other theories, including a statistical wormlike chain model, and with the experimental measurements for ring closure of DNA restriction fragments.
Mean‐square helical hydrophobic moments in partially ordered proteins
Authors: Hamed Maher M. , Mattice Wayne L. 
Published: December 2004

AbstractHelical hydrophobic moment ratios, 〈h2〉/〈H2〉, have been evaluated for 34 polypeptides under conditions where the helix content is dictated solely by the short‐range interactions operative in aqueous media. The mean‐square helical hydrophobic moment is denoted by 〈h2〉, and 〈H2〉 is the averaged of the squared hydrophobicites. This ratio would be one in absence of any correlation in the hydrophobicities of amino acid residues in helices. The 〈h2〉/〈H2〉 tend to be substantially larger than values of the analogous ratio formulated for the mean‐square dipole moments of typical synthetic polymers. For 24 of the 34 polypeptide chains considered, 〈h2〉/〈H2〉 is found to be greater than one, indicating a tendency to form helices with amphiphilic character. The ratio is exceptionally large in the case of the δ‐hemolysins. It is also large for two other surface‐active peptides, for two of the four apolipoproteins examined, and for myohemerythrin. A much smaller 〈h2〉/〈H2〉 is found for melittins. If melittins is to form helices with large 〈h2〉/〈H2〉, the configurational statistics must be governed by effects in addition to those short‐range interactions that occur when water is the solvent.
Synthesis and properties of L‐cysteinyl‐L‐cysteine disulfides
Authors: Capasso Sante , Mazzarella Lelio , Tancredi Teodorico , Zagari Adriana 
Published: December 2004

AbstractOligomeric cyclic disulfides, obtained by mild oxidation of the fully protected dipeptide L‐cysteinyl‐L‐cysteine, have been isolated by gel and thin‐layer chromatography. Polymeric material was recycled by a thiol–disulfide exchange‐reaction performed at basic pH. Spectroscopic investigations of the monomer and the two dimers indicate that conformers characterized by dihedral angles about the SS bond close to ±90° are preferred. Moreover, chiroptical and 1H‐nmr data for these compounds suggest higher mobility for the two dimers. The antiparallel dimeric disulfide can be considered a model compound for the hinge region formed at the subunit interface of the bovine seminal ribonuclease, a dimeric enzyme showing a complex kinetic behavior.
β‐Bend conformation of CH3CO‐Pro‐Pro‐Gly‐Pro‐NHCH3: Implications for posttranslational proline hydroxylation in collagen
Authors: Lee Eok , Némethy George , Scheraga Harold A. , Ananthanarayanan V. S. 
Published: December 2004

AbstractConformational‐energy computations have been carried out for the N‐acetyl‐N′‐methylamides of the Pro‐Pro, Pro‐Gly, and Gly‐Pro dipeptides and of the Pro‐Pro‐Gly‐Pro tetrapeptide, serving as models for the conformational analysis of single‐stranded poly(Gly‐Pro‐Pro). The probability of β‐bend formation for the Pro‐Gly sequence is very high, viz., 0.72 for the terminally blocked Pro‐Gly dipeptide, and rises to 0.86 in the tetrapeptide. The β‐bend conformations of the Pro‐Gly sequence are of low energy in single‐chain poly(Gly‐Pro‐Pro) as well. The β‐bend structure had been postulated earlier to be a requirement for post‐translational proline hydroxylation during the biosynthesis of collagen. The present results lend strong support to this proposal by demonstrating that the β‐bend structure is energetically favorable and hence can be accommodated easily in single‐stranded poly(Gly‐Pro‐Pro).
Conversion from a virtual‐bond chain to a complete polypeptide backbone chain
Authors: Purisima Enrico O. , Scheraga Harold A. 
Published: December 2004

AbstractA method for generating a complete polypeptide backbone structure from a set of Cα coordinates is presented. Initial trial values of ϕ and ψ for a selected residue are chosen (essentially from an identification of the conformational region of the virtual‐bond backbone, e.g., and α‐helical region), and values of ϕ and ψ for the remaining residues (both towards the N‐ and C‐terminus) are then computed, subject to the constraint that the chain have the same virtual‐bond angles and virtual‐bond dihedral angles as the given set of Cα coordinates. The conversion from Cα coordinates to full backbone dihedral angles (ϕ,ψ) involves the solution of a set of algebraic equations relating the virtual‐bond angles and virtual‐bond dihedral angles to standard peptide geometry and backbone dihedral angles. The procedure has been tested successfully on Cα coordinates taken from standard‐geometry full‐atom structures of bovine pancreatic trypsin inhibitor (BPTI). Some difficulty was encountered with error‐sensitive residues, but on the whole the backbone generation was successful. Application of the method to Cα coordinates for BPTI derived from simplified model calculations (involving nonstandard geometry) showed that such coordinates may be inconsistent with the requirement that ϕPro be near −75°. In such a case, i.e., for residues for which the algebraic method failed, a leastsquares minimizer was then used in conjunction with the algebraic method; the mean‐square deviation of the calculated Cα coordinates from the given ones was minimized by varying the backbone dihedral angles. Thus, these inconsistencies were circumvented and a full backbone structure whose Cα coordinates had an rms deviation of 0.26 Å from the given set of Cα coordinates was obtained.