bluuebunny/crossref_metadata_2025_split huggingface dataset:
An X‐ray study of poly(L‐prolyl‐L‐α‐phenylglycyl‐L‐proline)
Authors: Pra A. Del , Palumbo M. , Goodman M. 
Published: December 2004

AbstractX‐ray diffraction studies have been made on the polytripeptide poly(L‐prolyl‐L‐α‐phenylglycyl‐L‐proline). Its structure has been found to be helical, with a poly(L‐proline) II conformation, packed in an orthorhombic lattice, space group P21212, with a = 14.3 Å, b = 13.5 Å, and c = 9.4 Å.
Models for depolymerizing enzymes. Application to α‐amylases
Authors: Thoma John A. 
Published: December 2004

AbstractSeveral research groups have explored the action pattern of depolymerizing enzymes by examining the distribution of products during the early stages of digestion. Mathematical models for the various mechanisms that have been proposed for the behaviour of depolymerizing enzymes are developed in this paper. Published data for several amylases are reexamined in light of this theoretical analysis. It is concluded that following an initial random attack on a long polymer substrate, the enzyme frequently releases only one of the substrate fragments. The retained fragment may be repetitively hydrolyzed near one end to release a series of oligosaccharides before the enzyme substrate–fragment complex finally dissociates. Near optimum conditions Bacillus subtilis (var. amyloliquefaciens) amylase is unique among the enzymes tested because it does not repetitively attack substrate fragments.
Cooperative disordering of single‐stranded polynucleotides through copper crosslinking
Authors: Rifkind Joseph M. , Shin Yong A. , Heim Jane M. , Eichhorn Gunther L. 
Published: December 2004

AbstractThe thermal transitions of single‐stranded polynucleotides are noncooperative. In contrast, Cu(II) cooperatively disorders the single‐stranded helical structures of poly(A) and poly(C), as demonstrated by ORD and UV spectral changes as a function of the Cu2+ activity, and by a dramatic chain‐length dependence of the spectral changes. Equilibrium dialysis binding studies indicate that the cooperative disordering is paralleled by a somewhat less cooperative binding process.The difference between the thermal‐ and Cu(II)‐induced transition is explained by the following mechanism. (1) Cu(II) initially binds in a noncooperative fashion to phosphate. (2) The Cu(II) so bound forms a second bond to a nonadjacent base site on the same polymer strand or another strand. These intramolecular and intermolecular crosslinks to the bases are responsible for the disordering. (3) The initial crosslinks formed provide nuclei for the cooperative formation of additional crosslinks, producing cooperative spectral changes paralleled by cooperative binding.A comparison of the spectral and binding transitions indicates that there is appreciable noncooperative binding of copper to phosphate, which produces no spectral changes in the presence of added electrolyte. This comparison also indicates that each copper crosslink disorders several bases. The formation of intermolecular crosslinks is demonstrated by a polymer concentration dependence of the disordering. The formation of intramolecular crosslinks can be deduced from the fact that the “cooperative unit” required to explain the differences between the hexamer, which does not readily form intramolecular crosslinks, and the polymer is considerably larger than the cooperative unit determined from the polymer results.The poly(A) disordering transition is less symmetrical than that of poly(C), particularly at low polymer concentrations. These results, together with other phenomena, are explained by a greater flexibility of poly(A), which favors the formation of small intramolecular loops.
The X‐Pro peptide bond as an nmr probe for conformational studies of flexible linear peptides
Authors: Grathwohl Christoph , Wüthrich Kurt 
Published: December 2004

AbstractThe equilibrium between the cis and trans forms of X‐Pro peptide bonds can readily be measured in the 13C nmr spectra. In the present paper we investigate how observation of this equilibrium could be used as an nmr probe for conformational studies of flexible polypeptide chains. The experiments include studies by 13C nmr of a series of linear oligopeptides containing different X‐L‐Pro peptide bonds, with X = Gly, L‐Ala, L‐Leu, L‐Phe, D‐Ala, D‐Leu, and D‐Phe. Overall the study confirms that X‐Pro peptide bonds can generally be useful as 13C nmr probes reporting the formation of nonrandom conformation in flexible polypeptide chains. It was found that the cis–trans equilibrium of X‐Pro is greatly affected by the side chain of X and the configuration of the α‐carbon atom of X. On the basis of these observations some general rules are suggested for a practical applications of the X‐Pro nmr probes in conformational studies of polypeptide chains.
Nmr studies of the molecular conformations in the linear oligopeptides H‐(L‐Ala)n‐L‐Pro‐OH
Authors: Grathwohl Christoph , Wüthrich Kurt 
Published: December 2004

AbstractThe molecular conformations of the linear oligopeptides H‐(L‐Ala)n‐L‐Pro‐OH, with n = 1,2 and 3, have been investigated. 13C nmr observation of the equilibrium between the cis and trans forms of the Ala‐Pro peptide bond indicated the occurrence of nonrandom conformations in solutions of these flexible peptides. The formation of the nonrandom species containing the cis form of the Ala‐Pro bond was found to depend on the deprotonation of the carboxylic acid group of proline, the solvent, and the ionic strength in aqueous solution. The influence of intramolecular hydrogen bonding on the relative conformational energies of the species containing the cis and trans Ala‐Pro peptide bond was studied by comparison of the peptides H‐(Ala)n‐Pro‐OH with analogous molecules where hydrogen bond formation was excluded by the covalent structure. In earlier work a hydrogen bond between the protonated terminal carboxylic acid group and the carbonyl oxygen of the penultimate amino acid residue had been suggested to stabilize conformations including trans proline. For the systems described here this hypothesis can be ruled out, since the cis:trans ratio is identical for molecules with methyl ester protected and free protonated terminal carboxylic acid groups of proline. Direct evidence for hydrogen bond formation between the deprotonated terminal carboxylic acid group and the amide proton of the penultimate amino acid residue in the molecular species containing cis proline was obtained from 1H nmr studies. However, the cis:trans ratio of the Ala‐Pro bond was not affected by N‐methylation of the penultimate amino acid residue, which prevents formation of this hydrogen bond. Overall the experimental observations lead to the conclusion that the relative energies of the peptide conformations including cis or trans proline are mainly determined by intramolecular electrostatic interactions, whereas in the molecules considered, intramolecular hydrogen bonding is a consequence of specific peptide backbone conformations rather than a cause for the occurrence of energetically favored species. Independent support for this conclusion was obtained from model consideration which indicated that electrostatic interactions between the terminal carboxylic acid group and the carbonyl oxygen of the penultimate amino acid residue could indeed account for the observed relative conformational energies of the species containing cis and trans proline, respectively.
Packing analysis of carbohydrates and polysaccharides. IV. A new method for detailed crystal structure refinement of polysaccharides and its application to V‐amylose
Authors: Zugenmaier Peter , Sarko Anatole 
Published: December 2004

AbstractA method is described for predicting and solving crystal structures of linear homopolysaccharides. The method is based on the refinement of the structure with respect to either stereochemical constraints or x‐ray diffraction intensities. In the refinement process, all conformational and packing features of the molecule, such as bond lengths, bond angles, conformational angles, nonbonded contacts, hydrogen bonds, etc., can be allowed to vary until the structure reaches both a conformation and crystalline packing that are in minimum disagreement with the stereochemical restraints and the diffraction data. In this fashion, both packing and conformational features of the structure can be simultaneously refined, and not separately as has been the custom in the past. The refinement procedure is based on a method of constrained optimization which possesses improved characteristics of reaching a solution and avoiding false minima, in comparison with least squares methods. The procedure is, in addition, capable of easily finding molecules of solvent of crystallization. The method was applied to further refining the previously solved crystal structure of V‐amylose. The results indicated that contrary to the previously found six‐fold molecular symmetry in the P212121 space group, the V‐amylose molecule exhibits only two‐fold symmetry with the asymmetric unit consisting of three glucose residues in one‐half turn of the helix. The three residues are nonequivalent principally due to unequal rotational positions of the hydroxymethyl groups. The crystal structure of V‐amylose predicted from stereochemical refinement was identical in all details with that obtained from refining against X‐ray data. The excellent agreement with the diffraction data was indicated by the crystallographic disagreement index R = 0.25.
Fluctuations and mechanical strength of α‐helices of polyglycine and poly(L‐alanine)
Authors: Suezaki Yukio , Gō Nobuhiro 
Published: December 2004

AbstractBy using the static correlations of fluctuations in the dihedral angles of the α‐helices of polyglycine and poly(L‐alanine) calculated previously, geometrical fluctuations of a section (consisting of up to 18 peptide units) of the α‐helices of infinite length are calculated. These fluctuations are found to differ in some respects (e.g., the dependence of amplitudes on the length of section) from those of a circular rod made of homogeneous continuous material. However, the moduli of the mechanical strengths (tensile Young's modulus, bending Young's modulus, and the shear modulus) of a circular rod are calculated, whose geometrical fluctuations are approximately equal to the fluctuations of a section consisting of 18 peptide units. They are of the order of 1011 dyn/cm2. The tensile rigidity, flexural rigidity, and torsional rigidity are calculated to be 1.20 × 10−3 dyn, 2.46 × 10−19 dyn·cm2 and 1.79 × 10−19 dyn·cm2 for polyglycine, and 1.96 × 10−3 dyn, 4.05 × 10−19 dyn·cm2 and 3.28 × 10−19 dyn·cm2 for poly(L‐alanine), respectively.
Probing DNA quaternary ordering with circular dichroism spectroscopy: Studies of equine sperm chromosomal fibers
Authors: Sipski M. Leonide , Wagner Thomas E. 
Published: December 2004

AbstractStudies are described which strongly support a cholesteric liquid crystal‐like quaternary structure for the DNA molecules of a biologically native chromosomal preparation from equine sperm cells. Discrete chromosomal fibers released from the head pieces of equine spermatozoon cells were prepared intact and probed for liquid crystalline ordering using reflectance and linear dichroism spectroscopy. Assuming cholesteric liquid crystalline order for the DNA molecules within the chromatin fibers, parameters measured experimentally were used to calculate the circular dichroism (CD) of the fibers. The calculated results compare remarkably well with the experimentally measured CD of the sperm chromosomal fibers and suggest a specific cholesteric liquid crystal‐like quanternary structural ordering of DNA molecules in equine sperm chromatin fibers. The potential of CD spectroscopy as a tool for the study of long‐range ordering of macromolecules is discussed.
The triple helix ⇌ coil conversion of collagen‐like polytripeptides in aqueous and nonaqueous solvents. Comparison of the thermodynamic parameters and the binding of water to (L‐Pro‐L‐Pro‐Gly)n and (L‐Pro‐L‐Hyp‐Gly)n
Authors: Engel Jürgen , Chen Han‐Tee , Prockop Darwin J. , Klump Horst 
Published: December 2004

AbstractThe collagen‐like peptides (L‐Pro‐L‐Pro‐Gly)n and (L‐Pro‐L‐Hyp‐Gly)n with n = 5 and 10, were examined in terms of their triple helix ⇌ coil transitions in aqueous and nonaqueous solvents. The peptides were soluble in 1,2‐propanediol containing 3% acetic acid and they were found to form triple‐helical structures in this solvent system. The water content of the solvent system and the amount of water bound to the peptides were assayed by equilibrating the solvent with molecular sieves and carrying out Karl Fischer titrations on the solvent phase. After the solvent was dehydrated, much less than one molecule of water per tripeptide unit was bound to the peptides. Since the peptides remained in a triple‐helical conformation, the results indicated that water was not an essential component of the triple‐helical structure. Comparison of peptides with the same chain length demonstrated that the presence of hydroxyproline increased the thermal stability of the triple helix even under anhydrous conditions. The results, therefore, did not support recent hypotheses that hydroxyproline stabilizes the triple helix of collagen and collagen‐like peptides by a specific interaction with water molecules. Analysis of the thermal transition curves in several solvent systems showed that although the peptides containing hydroxyproline had tm values which were 18.6° to 32.7°C higher, the effect of hydroxyproline on ΔG was only 0.1 to 0.3 kcal per tripeptide unit at 25°C. The results suggested, therefore, that the influence of hydroxyproline on helical stability may be explained by intrinsic effects such as dipole–dipole interactions or by changes in the solvation of the peptides by alcohol, acetic acid, and water. A direct calorimetric measurement of the transition enthalpy for (L‐Pro‐L‐Pro‐Gly)n in 3% or 10% acetic acid gave a value of −1.84 kcal per tripeptide unit for the coil‐to‐helix transition. From the value for enthalpy and from data on the effects of different chain lengths on the thermal transition, it was calculated that the apparent free energy for nucleation was +5 kcal/mol at 25°C (apparent nucleation parameter = 2 × 10−4 M−2). The value was dependent on solvent and on chemical modification of end groups.
Spectroscopic studies on the interaction of Au(III) with nucleosides, nucleotides, and dimethyl phosphate
Authors: Chatterji D. , Nandi U. S. , Podder S. K. 
Published: December 2004

AbstractA series of complexes of Au(III) with nucleosides and nucleotides and their methyl derivatives in different stoichiometry have been prepared. Ultraviolet, visible, ir, and nmr studies have been performed to determine the site of binding of these ligands with the metal ion. In (1:4) Au(III): guanosine complex, N7 is the binding site, whereas at 1:1 complex, a bidentate type of chelation through C6O and N7 is observed. C6‐NH2 is favored over N1 as coordinating site at all stoichiometry in the adenosine complex. Inosine binds through N1 at r = 1. In cytidine, N1 is the binding site, whereas thymidine reacts only at high pH. In the case of nucleotides a bidentate type of chelation through the phosphate and the ring nitrogen occurs. The phosphate binding ability of Au(III) was further confirmed by studying the interaction of Au(III) with dimethyl phosphate—a conformational analog of the phosphate backbone in DNA chain.
Infinite‐dilution viscoelastic properties of fibrinogen and intermediate fibrin polymer
Authors: Nemoto Norio , Nestler F. Henry M. , Schrag John L. , Ferry John D. 
Published: December 2004

AbstractThe storage and loss shear moduli, G′ and G″, have been measured for dilute solutions of bovine fibrinogen in 68% aqueous glycerol and of intermediate fibrin polymer in 6M hexamethylene glycol, by the Birnboim‐Schrag multiple‐lumped resonator apparatus with titanium alloy resonators. The frequency range was 100–5800 Hz, the concentration range 1–6 g/l., and the temperatures 10.0 and 25.0°C. The shear moduli G′ and G″ at finite concentration, and the extrapolated instrinsic shear moduli [G′] and [G″], as functions of frequency, were compared with the predictions of various molecular theories. For fibrinogen, the frequency dependence agreed quite well with the calculations of Hassager for a trinodular rod as modified for the presence of small amounts of dimeric and trimeric aggregates which were deduced from parallel measurements of oscillatory flow birefringence. It was not possible, however, to distinguish between a linearly rigid configuration and one which is freely jointed at the central nodule. A model of a soft elastic sphere (simulating the cage model of Köppel) appeared to be very unlikely. The relaxation time for a rigid trinodular rod and the longest relaxation time for a jointed trinodular rod, calculated from molecular dimensions on the basis of electron microscope measurements, are somewhat smaller than the corresponding observed values; the discrepancy suggests that the molecule is swollen in solution. For the intermediate polymer (which was formed under conditions where ligation is expected), the frequency dependence agreed quite well with that predicted either for a prolate ellipsoid (Cerf‐Scheraga‐Saitō) or for a cylindrical rod (Yamakawa). The relaxation time obtained by fitting to theory agrees quite well with that calculated for a cylindrical rod with molecular dimensions based on a degree of polymerization of 20 and lateral binary association with staggered overlapping.
Packing analysis of carbohydrates and polysaccharides. V. Crystal structures of two polymorphs of pachyman triacetate
Authors: Bluhm Terry L. , Sarko Anatole 
Published: December 2004

AbstractThe crystal structures of two polymorphic forms of pachyman triacetate, the fully acetylated derivative of a naturally occuring β‐(1 → 3)‐D‐glucan, were determined by a combination of stereochemical and x‐ray diffraction analysis. The two polymorphs could be obtained depending on the temperature and the degree of stretching of film specimens of the substance: polymorph I resulted from stretching 25–50% at 125°C and polymorph II resulted from further stretching to 300% at 215°C. Both polymorphs had previously been shown to have sixfold helical chain conformations, but of unequal pitch. Subsequent detailed structure refinement performed with bond lengths, bond angles, conformational angles, and helix‐packing parameters as refinement variables, and the simultaneous minimization of packing and conformational energy and the crystallographic R‐factor as refinement criteria, resulted in a complete determination of the two crystal structures. Pachyman triacetate I was found to be a right‐handed helix packing with antiparallel polarity and space group P212121 symmetry (unit‐cell parameters a = 11.0, b = 19.0, c (fiber repeat) = 22.38 Å). The acetate groups were nearly planar and the O(2) and O(4) acetates were oriented in such a fashion that the carbonyl double‐bond nearly eclipsed the corresponding C—H bond of the ring. The O(6) was in the tg position and its acetate was oriented in such a fashion that the bond sequence C(6)—O(6)—C(6C)—C(6M) was nearly trans‐planar, with the carbonyl double‐bond bisecting the tetrahedral angle formed by C(6) and its two hydrogens. The final R = 0.221. Pachyman triacetate II was similarly found to be a right‐handed helix, but packing as a 50:50 mixture of parallel and antiparallel polarities (unit‐cell parameters a = 11.49, b = 20.13, c (fiber repeat) = 18.6 Å). The acetate positions in pachyman triacetate II were substantially the same as in pachyman triacetate I. The final R for the 50:50 mixture was 0.234. Probable reasons for the change in packing polarities are discussed, as are the difficulties encountered in the structure refinement of acetate derivatives.
Intrachain reactions of a pair of reactive groups attached to polymer ends. V. Formation of disulfide linkages in the air‐oxidation of sulfhydryl groups attached to ends of polysarcosine chain
Authors: Sisido Masahiko , Tamura Fumihide , Imanishi Yukio , Higashimura Toshinobu 
Published: December 2004

AbstractPolysarcosine having sulfhydryl groups attached to both ends was synthesized by the NCA method and its air‐oxidation was investigated in aqueous solution with cupric‐ion or ferric‐ion catalysts. Air‐oxidation was also conducted for a polysarcosine having one terminal sulfhydryl group. The product of the air‐oxidation was fractionated by gel chromatography. The product analysis of the fully oxidized monofunctional polymer showed that the sulfhydryl groups were converted into disulfide bonds exclusively. There was no evidence for the interchange between two disulfide linkages or between a disulfide linkage and a sulfhydryl group during the air‐oxidation. The analysis of the products from the bifunctional polysarcosine showed that they were composed of a series of cyclic “monomer,” “dimer,” “trimer,” and higher “oligomers.” The cyclic structure was characterized by the larger elution volume in the gel chromatogram than that for a linear homologue having the same molecular weight. The weight fraction of each cyclic oligomer was determined by gel chromatography. The fraction of cyclic monomer F1 decreased monotonously with increasing the chain length. Smaller values of F1 were observed with cupric‐ion catalyst than with ferric‐ion catalyst. The dependence of F1 on the polymer concentration was much smaller than that expected from a simple competition mechanism between intra‐ and intermolecular reactions. These results indicate that the choice between intra‐ and intermolecular reactions is governed by the mode of the coordination of sulfhydryl groups to transition metal ions.
Conformational studies on polynucleotide chains. I. Hartree‐fock energies and description of nonbonded interactions with Lennard‐Jones potentials
Authors: Matsuoka Osamu , Tosi Camillo , Clementi Enrico 
Published: December 2004

AbstractThe sugar–phosphate–sugar complex C10H18O8P, a unit of the polynucleotide chains, was analyzed, making use of 100 conformational energies computed in the Hartree‐Fock approximation with a small basis set of Gaussian type orbitals. The geometry of the conformations [which corresponds to the C(2′)‐endo deoxy system], the basis set, and the computed total energies are reported in this work. In addition, a number of attempts are presented where we searched for a computationally very simple analytical expression apt to fit, with reasonable accuracy, the computed energies. Lennard‐Jones type potential seems to offer an appropriate form capable of reproducing the positions of the maxima and the minima resulting from ab initio computations, but neither the 6‐12 nor other similar forms seem to be able to correctly reproduce the intensity of the barriers. Form a details analysis of the barriers to rotation about the bonds O(5′)—C(5′) and C(5′)—C(4′) in terms of nonboned interactions, we found that a substantial improvement in the fit of analytical to ab initio energies may be obtained by distinguishing between atoms characterized by the same atomic number but having different chemical characteristics, like the oxygen atoms of the phosphate group, on one hand, and the oxygen atoms of the sugar rings and the hydroxyl groups, on the other.