bluuebunny/crossref_metadata_2025_split huggingface dataset:
The glucan–chitin complex in Saccharomyces cerevisiae. IV. The electron diffraction of crustacean and yeast cell wall chitin
Authors: Gemperle A. , Holan Z. , Pokorný V. 
Published: December 2004

AbstractCrustacean and yeast cell wall chitin were analyzed by means of transmission electron microscopy and selected‐area diffraction. Single fibrils 8–25 nm wide have been observed in the micrographs of crustacean chitin. Analysis of a series of diffraction patterns obtained from thin crustacean chitin platelets yielded results which were in a better agreement with the theoretical structural model than those measured earlier. In this respect electron diffraction is shown to be superior to the more commonly used x‐ray diffraction. Yeast cell wall chitin had a less perfect structure than the crustacean chitin. Single fibrils were not observed on the micrographs and electron diffraction patterns did not show any preferred fiber orientation. The evaluation of electron‐diffraction patterns of both the primary septum and the adjacent circular zone of scar ring led to the conclusion that α‐chitin is present in both these parts of the mother bud scar.
Fluorescent‐labeled crosslinks in collagen: Pyrenebutyrylhydrazine
Authors: Shambaugh Nathaniel , Fujimori Eiji 
Published: December 2004

AbstractThe aldehydes present in acid‐soluble type I collagen react with pyrenebutyrylhydrazine to form various types of complexes under different reaction conditions. These complexes exhibit one or more of three different pyrene fluorescence bands: monomer, excimer, and aggregate fluorescence. Collagen, whose aldehydes have been reduced with NaBH4, does not react with this fluorescent hydrazine, confirming that the hydrazine reacts specifically with aldehyde groups to form hydrazones. The absence of a reaction with pepsin‐treated collagen also shows that the fluorescent labels are primarily in the nonhelical terminal telopeptides. Upon dialysis, the pyrene label bound to a saturated aldehyde in an α‐chain is lost; whereas that bound to an unsaturated aldehyde remains on the protein. The pyrene monomer fluorescence in the β‐chain of old collagen is stronger than that of young collagen. The formation of the pyrene excimer fluorescence implies the proximity of two pyrene molecules, probably attached to two adjacent aldehydes. Upon changing from acidic to neutral pH, both excimer and aggregate fluorescence bands disappear within a few seconds, revealing a very rapid alteration at the telopeptides.
Interactions of DNA with divalent metal ions. I. 31P‐nmr studies
Authors: Granot Joseph , Feigon Juli , Kearns David R. 
Published: December 2004

Abstract31P‐nmr has been used to investigate the specific interaction of three divalent metal ions, Mg2+, Mn2+, and Co+2, with the phosphate groups of DNA. Mg2+ is found to have no significant effect on any of the 31P‐nmr parameters (chemical shift, line‐width, T1, T2, and NOE) over a concentration range extending from 20 to 160 mM. The two paramagnetic ions, Mn2+ and Co2+, on the other hand, significantly change the 31P relaxation rates even at very low levels. From an analysis of the paramagnetic contributions to the spin–lattice and spin–spin relaxation rates, the effective internuclear metal–phosphorus distances are found to be 4.5 ± 0.5 and 4.1 ± 0.5 Å for Mn2+ and Co2+, respectively, corresponding to only 15 ± 5% of the total bound Mn2+ and Co2+ being directly coordinated to the phosphate groups (inner‐sphere complexes). This result is independent of any assumptions regarding the location of the remaining metal ions which may be bound either as outer‐sphere complexes relative to the phosphate groups or elsewhere on the DNA, possibly to the bases. Studies of the temperature effects on the 31P relaxation rates of DNA in the absence and presence of Mn2+ and Co2+ yielded kinetic and thermodynamic parameters which characterize the association and dissociation of the metal ions from the phosphate groups. A two‐step model was used in the analysis of the kinetic data. The lifetimes of the inner‐sphere complexes are 3 × 10−7 and 1.4 × 10−5 s for Mn2+ and Co2+, respectively. The rates of formation of the inner‐sphere complexes with the phosphate are found to be about two orders of magnitude slower than the rate of the exchange of the water of hydration of the metal ions, suggesting that expulsion of water is not the rate‐determining step in the formation of the inner‐sphere complexes. Competition experiments demonstrate that the binding of Mg2+ ions is 3–4 times weaker than the binding of either Mn2+ or Co2+. Since the contribution from direct phosphate coordination to the total binding strength of these metal ion complexes is small (∼15%), the higher binding strength of Mn2+ and Co2+ may be attributed either to base binding or to formation of stronger outer‐sphere metal–phosphate complexes. At high levels of divalent metal ions, and when the metal ion concentration exceeds the DNA–phosphate concentration, the fraction of inner‐sphere phosphate binding increases. In the presence of very high levels of Mg2+ (e.g., 3.1M), the inner‐sphere ⇄ outer‐sphere equilibrium is shifted toward ∼100% inner‐sphere binding. A comparison of our DNA results and previous results obtained with tRNA indicates that tRNA and DNA have very similar divalent metal ion binding properties. A comparison of the present results with the predictions of polyelectrolyte theories is presented.
A swivel‐jointed formalism for segmentally flexible macromolecules and its application to the rotational behavior of myosin
Authors: Wegener William A. 
Published: December 2004

AbstractA formalism is presented to represent the hydrodynamic and diffusion behavior of segmentally flexible macromolecules with a high degree of flexibility. The development specifically treats open assemblies of cylindrically symmetric segments joined at their end points by frictionless swivels. Three‐dimensional diffusion and frictional tensors that govern the rotations of each segment and the translations of some chosen swivel are established and related by a Stokes–Einstein relation. The dependence of these tensors on the choice of swivel is examined, and simplified expressions are obtained by omitting hydrodynamic interactions between segments. These simplified expressions are used to analyze the rotational behavior of a Y‐shaped body in detail. If there is complete flexibility, the rotational motions of each segment reduce, for all practical purposes, to those of a cylindrically symmetric rigid body. Estimates are provided to relate segment rotations to internal motions and restrictions on flexibility. A procedural framework for generating rotational diffusion coefficients for segments of more complicated bodies is applied to a four‐segment two‐swivel myosin model. Comparison of calculated and experimental relaxation times for myosin and its fragments indicates the head–tail junction is highly flexible, with at least a ±60° angular extent of free bending between heads allowed, while the tail is neither straight and rigid nor highly flexible.
Proline‐containing β‐turns in peptides and proteins. II. Physicochemical studies on tripeptides with the Pro‐Gly sequence
Authors: Brahmachari Samir K. , Rapaka Rao S. , Bhatnagar Rajendra S. , Ananthanarayanan V. S. 
Published: December 2004

AbstractAmino acids are known to differ in their individual preferences for each of the four positions of the β‐turn conformation formed by tetrapeptide segments. Proline and glycine show relatively high preferences for positions 2 and 3, respectively, of the β‐turn. Using tripeptides of the type N‐acetyl‐Pro‐Gly‐X‐OH, where X = Gly, Ala, Leu, Ile, and Phe, we have sought to study the influence of the 4th residue X on the stability of the β‐turn conformation in these tripeptides. Our nmr and CD results show that the β‐turn stability is quite significantly governed by the nature of the amino acid residue at this position in the following order: Leu > Ala > Ile, Gly > Phe.
Backbone conformations in nucleic acids: The occurrence of g+g+ internucleotide phosphodiester conformation
Authors: Jayaraman S. , Yathindra N. , Sundaralingam M. 
Published: December 2004

AbstractSemiempirical conformational energy calculations have been performed on dinucleoside triphosphate models with and without base interactions to investigate the conformational requirement for the stereochemical and energetic feasibility of (gauche+,gauche+) phosphodiester conformation in a polynucleotide chain. Results show that the trans conformation of the C4′C5′ bond on the 5′‐sugar (either C3′‐endo or C2′‐endo) of a dinucleoside triphosphate renders the g+g+ phosphodiester energetically favorable. The degree of energetic preference shows a dependence on the C3′O3′ bond torsions (ϕ′); higher g+g+ conformation populations are correlated with higher values of ϕ′ ≃ 270° due to increased van der Waals interactions between adjacent sugar residues. For similar reasons, the g+g+ phosphodiester displays an energetic dependence on the nature and sequence of bases and their orientations. Other conformational combinations that also stereochemically permit the g+g+ phosphodiester are discussed along with base effects.
Two classes of β‐pleated sheet conformation in poly(L‐tyrosine): Evidence from solvent perturbation difference spectroscopy
Authors: Auer Henry E. , Miller‐Auer Helene 
Published: December 2004

AbstractWe had earlier observed that the detailed nature of the β‐structure adopted by poly(L‐tyrosine) depends on molecular weight [Auer, H. E. & McKnight, R. P. (1978) Biochemistry 17, 2798–2805]. It was proposed that shorter molecules form an open, single‐layered sheet (class I) and that longer chains fold over to generate at least two layers (class II). In this work, solvent perturbation difference spectroscopy of the chromophoric side chain was applied to gain additional support for the model. Two sample‐reference pairs of media, sodium acetate vs sodium chloride and urea vs buffer, were studied. Great care was taken to achieve identical conditions in the sample and reference cells. The factors of importance in executing the experiments are the polypeptide concentration, the degree of side‐chain ionization, achievement of the same class of β‐conformation, and the absence of significant aggregation. Difference spectra obtained with both solvent pairs have similar features. Low‐molecular‐weight samples manifest difference bands arising from both ionized and neutral tyrosine side chains, while high‐molecular‐weight samples yield spectra with contributions primarily from ionized residues. The interpretation of these results is that the class I particle has both ionized and neutral residues exposed to the solvent medium, whereas the class II particle is folded, with neutral residues restricted to the interior of the fold and primarily ionized residues on the outer surfaces exposed to the solvent. Our results, therefore, corroborate the original model.
Microdomain dynamics in folding proteins
Authors: Weaver D. L. 
Published: December 2004

AbstractThe basic formulas for the incorporation into the diffusion–collision model of the stabilities of intermediate states on the folding pathway are derived and discussed. A hypothetical two‐step folding pathway is calculated in detail. A model for the production of incorrectly folded intermediates is suggested and some numerical estimates made. Implications and future directions in the evolution of the model are discussed. Three appendices deal with some mathematical aspects of the model.
Microwave absorption by folded DNA chains
Authors: Kohli M. , Van Zandt L. L. 
Published: December 2004

AbstractAbsorption of radiation by DNA polymer is calculated for the case of bent polymer chains. The molecule is assumed to be straight except for localized bends. The region between two bends is studied in particular. The vibrational properties of the bends are parameterized by a transmission and a reflection coefficient. A general Green function expression for absorption is studied for various values of the damping rate, as well as the transmission/reflection coefficients. Curves of absorption vs frequency are shown for a number of cases.
Properties of the complexes formed by 1‐anilinonaphthalene‐8‐sulfonate with phosphorylase kinase and calmodulin
Authors: Steiner R. F. , Sternberg H. 
Published: December 2004

AbstractPhosphorylase kinase contains four approximately equivalent binding sites for 1‐anilinonaphthalene‐8‐sulfonate (1,8‐ANS). Measurements of the time decay of fluorescence anisotropy have failed to give any indication of internal degrees of rotational freedom involving a significant portion of the tertiary structure. In the presence of 1 mM Ca2+, calmodulin binds one molecule of 1,8‐ANS. No binding occurs in the absence of Ca2+. The binding is strongly temperature‐dependent, a decrease in binding occurring with increasing temperature. Determinations of the time decay of fluorescence anisotropy indicate the presence of internal rotations, which become more important with increasing temperature. Complex formation between phosphorylase kinase and calmodulin reduces the binding of 1,8‐ANS.
Proline ring conformations corresponding to a bistable jump model from 13C spin‐lattice relaxation times
Authors: Shekar S. C. , Easwaran K. R. K. 
Published: December 2004

AbstractA formalism for extracting the conformations of a proline ring based on the bistable jump model of R. E. London [(1978) J. Am. Chem. Soc. 100, 2678–2685] from 13C spin‐lattice relaxation times (T1) is given. The method is such that the relaxation data are only partially used to generate the conformations; these conformations are constrained to satisfy the rest of the relaxation data and to yield acceptable ring geometry. An alternate equation for T1 of 13C nuclei to that of London is given. The formalism is illustrated through an example.
Conformational preferences of amino acid side chains in collagen
Authors: Némethy George , Scheraga Harold A. 
Published: December 2004

AbstractConformational energy computations were carried out on collagenlike triple‐stranded conformations of several poly(tripeptide)s with the general structure CH3CO(GlyXY)3NHCH3. The sequences considered had various amino acid residues in position X or Y of the central tripeptide, with either Pro or Ala as a neighbor, i.e., Gly‐X‐Pro, Gly‐X‐Ala, Gly‐Pro‐Y, and Gly‐Ala‐Y. Minimum‐energy conformations were computed for the side chains, and their distributions were compared for the four sequences. The residues used were Abu (= α‐aminobutyric acid), Leu, Phe, Ser, Asp, Asn, Val, Ile, and Thr. The conformational energy of a Ch2CH3 side chain in Abu was mapped as a function of the dihedral angle χ1. Intrastrand interactions with neighboring residues do not affect the conformations of a side chain in position Y, and they have a minor effect on it in the X‐Ala sequence, but they strongly restrict the conformational freedom of the side chain in the X‐Pro sequence. Conversely, interstrand interactions do not affect side chains in position X, but they strongly restrict the conformational freedom of a side chain in position Y if there is a nearby Pro residue in a neighboring strand. Hydrogen bonds with the backbone can be formed in some conformations of long polar side chains, such as Asp, Asn, or Gln. All amino acid residues can be accommodated in collagen. Because of the interactions mentioned above, steric and energetic constraints can be correlated with observed preferences of certain amino acids for positions X or Y in collagen. Hence, these preferences may be explained, in part, in terms of differences in the conformational freedom of the side chains in the triple‐stranded structure.
Stabilization of collagen structure: Dependence of collagen denaturation enthalpy on the imino acid content
Authors: Burjanadze T. V. 
Published: December 2004

AbstractAn analysis of the available data on the enthalpy (ΔHr) of denaturation (melting) of collagens with different imino acid content in solution and in the aggregated state has shown that ΔHr in solution increases with increasing denaturation temperature, whereas in the aggregated state there is an inverse dependence. ΔHr in solution correlates with the hydroxyproline content but not with that of proline. No correlation between the change of ΔHr and the imino acid content is observed for the aggregated state.
Monte Carlo simulation of photoselective cyclization of azobenzene‐containing oligosarcosines
Authors: Sisido Masahiko , Imanishi Yukio 
Published: December 2004

AbstractConformations of (Sar)nAzo(Sar)n oligomers [Sar = sarcosine (N‐methylglycine) unit. Azo = p‐aminoazobenzene unit] were computer‐simulated for trans and cis states of the azobenzene group. Each part of the oligosarcosine chain was assumed to behave independently and the ring‐closure probability, i.e., the probability that the end‐to‐end distance of the above oligomer is shorter than 4 Å, was evaluated from an overlap integral of the two three‐dimensional distribution functions for the left and right halves of the oligosarcosine chain. The ring‐closure probability for the cis azobenzene unit was larger than that for trans, indicating the preference of cyclization reaction to the corresponding intermolecular reactions. The prediction agrees qualitatively with the experimental observation reported by us in our companion paper, but the calculated ring‐closure probability for the cis state was substantially larger than the experimental value. The difference was explained as a result of intramolecular overlappings of the two halves of the oligosarcosine chain, which is facilitated when the azobenzene group is in the cis state.
Ionization behavior of proteins. II. Chymotrypsinogen and its group‐modified derivatives: Study of their ionization characteristics by potentiometric and calorimetric titration
Authors: Martin C. J. , Marini M. A. 
Published: December 2004

AbstractChymotrypsinogen, nitrated chymotrypsinogen (two of the four tyrosyls nitrated), acetylated chymotrypsinogen (all amino groups blocked), and nitrated‐acetylated chymotrypsinogen were titrated as f(pH) in an isoperibolic calorimeter at 20°C. After appropriate correction and reduction of both the potentiometric and thermal titration data, the parameters N (ionizable groups per group‐set), pK′, and ΔHi (heat of ionization) were evaluated using the iterative curve‐fitting algorithm of the MLAB computer program. The pK′ parameters so obtained for the two normally ionizing tyrosyl groups in chymotrypsinogen and the two nitrated tyrosyl groups in the nitrated proteins essentially agreed with the results of spectral titration. Excellent fits to all data could be obtained using evaluated parameter sets of N and pK′ for the potentiometric titration data (groups vs pH plots) and N, pK′, and ΔHi sets for the calorimetric data (total heat vs pH plots). The invocation of electrostatic interaction effects was not required to explain the data satisfactorily, despite the differences in charge number and type among the four proteins. Rather, the data can be represented by series expressions of the mass‐action law. Using all information, viz., the consequences of functional group modification, the downscale shift in tyrosyl group pK's on nitration, and the numerical values of the evaluated N, pK′, and ΔHi parameter sets for all proteins, the chemical identity of the various classes of group sets can be assigned with reasonable assurance.
Steady‐state and transient electric birefringence of solutions of bent‐rod macromolecules
Authors: Mellado Pelayo , De La Torre José García 
Published: December 2004

AbstractWe first calculate the steady‐state birefringence, expressed in the form of specific Kerr constant, Ksp, of rigid, bent‐rod macromolecules. Equations are derived for Ksp as a function of the geometric and electro‐optical parameters. We also consider flexibly hinged rods and evaluate Ksp for them by averaging over the angle between the two arms, ϕ. Next, we turn to the time decay of the electric birefringence. The decay function for rigid bent rods is a sum of three exponential terms, and a procedure for their calculation is indicated. We observe that single‐exponential decays can be found for ϕ > 90° or ϕ < 60°, in spite of the high electro‐optical and hydrodynamic anisotropy of the macromolecule. Special attention is paid to the case of rods with equal arms.
Interactions between poly(Gly‐Pro‐Pro) triple helices: A model for molecular packing in collagen
Authors: Némethy George 
Published: December 2004

AbstractPotential‐energy calculations are reported on the interaction between two collagenlike triple‐stranded poly(Gly‐L‐Pro‐L‐Pro) helices. Short helices can pack in a variety of orientations, but there is a unique parallel packing arrangement of the two helices for longer polypeptide chains.
Preferred conformations of peptides containing α,α‐disubstituted α‐amino acids
Authors: Toniolo Claudio , Bonora Gian Maria , Bavoso Alfonso , Benedetti Ettore , di Blasio Benedetto , Pavone Vincenzo , Pedone Carlo 
Published: December 2004

AbstractThe conformational preferences of linear peptides containing α,α‐disubstituted α‐amino acids, derived from the crystal structures of 28 compounds, are reviewed. In particular, the sensitivity of peptide conformation to the geometry of these unusual amino acids is underlined. We also consider possible future directions of research, which, we hope, will result in a complete understanding of the structures adopted by peptaibol antibiotics.
Refinement of the structure of bovine seminal ribonuclease
Authors: Capasso Sante , Giordano Federico , Mattia Carlo A. , Mazzarella Lelio , Zagari Adriana 
Published: December 2004

AbstractWe report here the refinement at 2.5‐Å resolution of the x‐ray crystal structure of bovine seminal ribonuclease, a dimeric covalent enzyme. The protein, which crystallizes with one molecule in the asymmetric unit, consists of two subunits of identical chemical sequences, related by an almost exact binary axis. The tertiary structure of the subunits is similar to that of the pancreatic enzyme, which shows similar catalytic properties. The refinement was carried out using the restrained least‐squares procedure both in the reciprocal and real spaces. The assemblage of the subunits in the dimer is described and discussed.
Lateral and rotational diffusion of EGF–receptor complex: Relationship to receptor‐mediated endocytosis
Authors: Schlessinger Joseph 
Published: December 2004

AbstractThe clustering and internalization of epidermal growth factor (EGF)–receptor complexes on human tumor cells are temperature‐sensitive processes that are completely inhibited at 4°C. The rotational diffusion of EGF–receptor is limited by the viscosity of the lipid matrix, while additional constraints limit the lateral diffusion of the receptor molecule. Although the lateral and rotational diffusion of the occupied receptors are temperature sensitive, they do not provide a rate‐determining factor for the clustering and subsequent internalization of the EGF–receptor. Even at 4°C the occupied receptors move quickly enough to allow the formation of EGF–receptor clusters. The lack of internalization at 4°C must be due to the inhibition of interactions other than a temperature effect on receptor mobility. EGF‐induced receptor clustering involves the formation of microclusters composed of 10–50 receptor molecules.