bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rheological studies of creep and creep recovery of unligated fibrin clots: Comparison of clots prepared with thrombin and ancrod
Authors: Bale Marsha D. , Müller Michael F. , Ferry John D. 
Published: May 2005

AbstractMechanical creep and creep recovery in small shearing deformations have been studied in unligated clots formed with both thrombin and ancrod. In thrombin clots, both A binding sites (which interact with “a” sites to link monomer units within a protofibril) and B sites (which interact with “b” sites to form links between protofibrils) are exposed to enable formation of linkages; in ancrod clots, only the A sites are exposed. Fine clots (with minimal lateral aggregation of protofibrils), coarse clots (with substantial aggregation of fibril bundles), and clots of intermediate coarseness were compared. Fine thrombin clots showed less creep at short times but more creep at long times than coarse or intermediate clots and had more irrecoverable deformation relative to the initial elastic deformation. Ancrod clots had greater irrecoverable deformation than the corresponding thrombin clots, both fine and coarse. The permanent deformation in fine ancrod clots was enormous, corresponding almost to fluid character; the rate of permanent deformation was larger than that in fine thrombin clots by more than two orders of magnitude. For all types of clots, differential measurements of compliance (or its reciprocal, elastic modulus), as well as the applicability of the Boltzmann superposition principle to calculation of creep recovery, showed that the overall density of structure remained constant throughout the mechanical history; i.e., if structural elements were breaking, they were reforming at the same rate in different configurations. The possibility that the weakness of ancrod clots is attributable to partial degradation of α‐chains rather than absence of Bb linkages was eliminated by comparisons of clots made with thrombin, ancrod, and ancrod plus thrombin; the last two showed identical partial degradation of α‐chains (by gel electrophoresis), but the first and third had essentially identical initial elastic moduli and creep behavior. Two alternative mechanisms for irrecoverable deformation in fine clots are discussed, involving rupture of protofibrils and slippage of twisted segments, respectively.
Role of interstrand loops in the formation of intramolecular cross‐β‐sheets by homopolymino acids
Authors: Mattice Wayne L. , Scheraga Harold A. 
Published: May 2005

AbstractA matrix treatment of the formation of intramolecular anti‐parallel β‐sheets from a statistical coil has been extended to incorporate interstrand loops of arbitrary size. The behavior of the model is compared with a simpler version in which all pairs of contiguous strands were connected by β‐bends. When large interstrand loops are allowed, there are many more types of sheets than is the case when all contiguous strands must be connected by tight or β‐bends. For this reason, the larger interstrand loops make it easier to introduce the initial sheet into a statistical coil, and the sheet content is enhanced in the early stages of stages of sheet formation (i.e., at small values of the growth parameter t). As the transition continues (i.e., as t increases), a stage will be reached where occupancy of the statistical coil state is negligible because nearly all residues are in sheets or interstrand loops. Now, additional sheet formation can be accomplished only at the expense of residues in the interior of interstrand loops. For this reason, the larger interstrand loops make it more difficult to complete the final stages of sheet formation. These effects are especially dramatic in the formation of cross‐β‐sheets.
Crystal structure of dehydromonopetide, (Z)‐N‐acetyl‐α,β‐dehydrophenylalanine methylamide
Authors: Aubry A. , Allier F. , Boussard G. , Marraud M. 
Published: May 2005

AbstractThe crystal structure of (Z)‐acetyl‐α,β‐dehydrophenylalanine methylamide (monoclinic Cc, a = 10.241(1), b = 15.252(1), c = 8.643(1) Å, β = 120.98(1)°, Z = 4) has been solved by x‐ray diffraction to an R‐factor = 0.148, and compared to that of the homologous L‐phenylalanine dervative. Molecules are intermolecularly hydrogen‐bonded to four neighboring molecules in a three‐dimensional network with alternating layers of interacting amide bonds and orthogonally arranged phenyl rings. The existence of the Cα = Cβ double bond results in a phenyl orientation that is forbidden for phenylananine (χ1 = −7,8°), and in shorter Cα − Cβ and Cβ − Cγ distances. The geometrical paramenters of the peptide backbone are not drastically modified by α,β‐unsaturation. However, the N‐Cα‐C′ angle is increased by nearly 5°, and the dimensions, and therefore probably the electronic conjugation, of the N‐terminal amide group to be affected by the occurrence of the vicinal Cα = Cβ double bond.
Conformational properties of gastrin fragments of increasing chain length
Authors: Peggion E. , Foffani M. T. , Wünsch E. , Moroder L. , Borin G. , Goodman M. , Mammi S. 
Published: May 2005

AbstractThe conformational properties of a series of biologically active gastrin peptides of increasing chain length have been investigated in TEE solution by spectroscopic techniques. It was found that elongation of the glutamic acid sequence from 1 to 5 residues at the N‐terminal portion of the molecules causes a cooperative change of the conformation of the peptide backbone. The environment of the biologically important C‐terminal sequence‐Trp‐Nle‐Asp‐Phe‐NH2 monitored by the near‐uv chiroptical propertical properties is alos affected by chain elongation. However, the change of the structure of the C‐terminal portion does not parallel the conformational change of the peptide backbone. In fact, the final folded structure at the C‐terminus is almost reached in the fragment with a sequence of 4 glutamic acid residues, while an additiona, relevent conformational change of the backbne is observed on further elongation of the chain to minigastrin and little gastrin. The ability of the fragments to fold into an ordered conformation on chain elongation parallels the increase of biolocical potency tested in vivo, reported in the literature, and suggests a correlation between these two facts. Ionization of the carboxyl side chains is without effect on the structure of the fragments with 2, 3, and 4 glutamic acid residues, while an effect is observed in minigastrin and little gastrin. From analysis of the CD properties and from their dependence upon side‐chain ionization a structural model is proposed for the hormones minigastrin and little gastrin. This tentative model includes a β‐bend located in the sequence Ala‐Tyr‐Gly‐Trp‐ and a short helical section at the N‐terminal portion of the hormones.
Dependence of purine 8C‐H exchange on nucleic acid conformation and base‐pairing geometry: A dynamic probe of DNA and RNA secondary structures
Authors: Benevides James M. , Thomas George J. 
Published: May 2005

AbstractLaser Raman spectroscopy is employed as a probe of hydrogen isotope exchange in nucleic acids exhibiting different secondary structures. The rates for deuterium exchange of 8C‐H groups in adenine (A), hypoxanthine (I), and guanine (G) residues of ribo‐ and deoxyribopolynucleotides are compared with corresponding rates of mononucleotides. In general, nucleic acid secondary structure significantly retards the rate of purine 8C‐H exchange. Specifically, the exchange kinetics are strongly dependent on both the kind and amount of secondary structure. The retardation factor (R), defined as the quotient of rate constants for monomer and polymer exchanges, is greatest for the A‐helix (9.5 ± 1), intermediate for the B‐helix (2.8 ± 0.6), and smallest for the Z‐helix (1.5), thus permitting the three authenticated DNA structures to be distinguished from one another using the Raman dynamic probe. Polyribonucleotide complexes of the A‐helix family that contain the same backbone conformation and ribosyl pucker (C3′ ‐ endo/anti) but that differ in the geometry of base pairing or number of helix strands are also clearly distinguished by their different deuterium exchange rates. The extraordinarily large retardation of 8C‐H exchange (R > 200) that occurs in multihelical structures is attributed to hydrogen bonding by the purine 7N acceptor. These results indicate that 8C‐H exchange may be exploited to detect Hoogsteen base pairing and possibly interactions of nucleic acid‐binding proteins that involve the 7N site as hydrogen‐bond acceptor. The feasibility of the method for evaluation of solvent penetration to encapsidated genomes of DNA and RNA viruses is considered. The present results also reveal a number of new vibrational band assignments for identification of DNA and RNA secondary structures from equilibrium Raman spectra.
Kinetics of coil to α‐helix to β‐structure transitions of poly(L‐ornithine) in low concentrations of sodium dodecyl sulfate
Authors: Takeda Kunio 
Published: May 2005

AbstractConformational changes of poly(L‐ornithine) [(Orn)n] were studied in a sodium dodecyl sulfate (NaDodSO4) solution by CD. (Orn)n adopted an unstable and a stable helical structure below and above the NaDodSO4 concentration range where β‐structure was favored, respectively. CD stopped‐flow was used to monitor the transitions from coil to the unstable helix, from the helix to β‐structure, and from coil to β‐structure. Only the rate of the helix to β‐structure transition was accelerated by an increase in NaDodSO4 concentration, whereas the rates of the others were independent of NaDodSO4 concentration. The fractions of coil, α‐helix, and β‐structure in each conformation of (Orn)n caused by NaDodSO4 were computed by simulating a mixed spectrum of typical CD spectra for these structures to the experimentally obtained spectrum. The contents of the unstable and stable helical structures were less than 50 and 73%, respectively.
Aqueous solutions containing amino acids and peptides. Part 20. Volumetric behavior of some terminally substituted amino acids and peptides at 298.15 K
Authors: Leslie Tracy E. , Lilley Terence H. 
Published: May 2005

AbstractThe densities at 298.15 K of aqueous solutions containing some terminally substituted amino acids and peptides containing the glycyl, L‐and D‐alanyl, L‐leucyl, sarcosyl, and L‐prolyl residues have been dertermined and standard state partial molar volumes and volumetric pairwise virial coefficients obtained. It is shown that the partial molar volumes can be represented using group volume contributions, but this approach is only approximate, and significant effects of N‐terminal substitution and sequence dependence are observed. The volumetric virial coefficients for the amino acid amides have been expressed using a group‐additivity approach, and the results obtained indicate that the dominant contributions come from peptide group interactions with other peptide groups and with hydrophobic groups. There is also some evidence of both sequence and chiral effects on the volumetric virial coefficients for proline‐containing dipeptides.
Computer simulation of DNA supercoiling in a simple elastomechanical approximation
Authors: Šelepová Pavla , Kypr Jaroslav 
Published: May 2005

AbstractDNA supercoiling is both an interesting problem from the theoretical point of view and an important phenomenon affecting DNA functions in vivo. Experimentally, however, hardly more than the overall hydrodynamic shape, superhelical density, and enzymic or chemical reactivity of the parameters that are in some way related to DNA secondary and tertiary structure in the superhelical state can be determined. Consequently, it is highly desirable to build up models of DNA supercoiling that, on the one hand, match the above type of global data and, on the other, take advantage of the knowledge about DNA structure at lower levels of complexity, i.e., with linear DNA molecules and its synthetic models. One possible approach, presented here, deals with an extension of Fuller's and Benham's general ideas concerning an elastomechanical model of DNA supercoiling. We extend their model with an algorithm suitable for numerical calculations and construct a fast computer program, ROPASE, that displays the rod shapes as dependent on its elastic properties and applied stress. Development of this program made inevitable a detailed analysis of the input parameters found to be degenerate in the sense that not all of them should be considered variable to generate the whole set of possible solutions of the model. Many calculations were performed using ROPASE to test its properties and the properties of the elastomechanical model. Representative DNA shapes are presented.
Conformational properties of Pro–Pro sequences. I. Crystal structures of two dipeptides with L‐Pro‐L‐Pro and L‐Pro‐D‐Pro sequences
Authors: Aubry André , Vitoux Bernard , Marraud Michel 
Published: May 2005

AbstractThe crystal structures of ButCO‐L‐Pro‐L‐Pro‐NHMe, H2O (1: monoclinic; P21; a = 6.662, b = 11.067, c = 12.205 Å; β = 96.28°) and ButCO‐L‐Pro‐D‐Pro‐NHMe (2: monoclinic; P21; a = 10.770, b = 15.039, c = 11.325 Å; β = 110.00°) have been solved by x‐ray diffraction. Structure 1 accommodates an open disposition with intermolecular interactions involving the water molecule, while 2 is βII‐folded by an intramolecular i + 3 → i hydrogen bond. In both derivatives, small thermal parameters are indicative of fairly fixed conformations for the proline rings. Comparison between conformations of either isolated or adjacent L‐Pro residues in the crystal structures of unstrained oligopeptides shows that the conformational properties of L‐Pro‐L‐Pro sequences are probably a simple combination of those found for isolated L‐Pro residues.
Prediction of the native conformation of a polypeptide by a statistical‐mechanical procedure. I. Backbone structure of enkephalin
Authors: Paine Gregory H. , Scheraga Harold A. 
Published: May 2005

AbstractA new methodology for theoretically predicting the native, three‐dimensional structure of a polypeptide is presented. Based on equilibrium statistical mechanics, an algorithm has been designed to determine the probable conformation of a polypeptide by calculating conditional free‐energy maps for each residue of the macromolecule. The conditional free‐energy map of each residue is computed from a set of probability integrals, obtained by summing over the interaction energies of all pairs of nonbonded atoms of the whole molecule. By locating the region(s) of lowest free energy for each map, the probable conformation for each residue can be identified. The native structure of the polypeptide is assumed to be the combination of the probable conformations of the individual residues. All multidimensional probability integrals are evaluated by an adaptive Monte Carlo algorithm (SMAPPS—Statistical‐Mechanical Algorithm for Predicting Protein Structure). The Monte Carlo algorithm searches the entire conformational space, adjusting itself automatically to concentrate its sampling in regions where the magnitude of the integrand is largest (“importance sampling”). No assumptions are made about the native conformation. The only prior knowledge necessary for the prediction of the native conformation is the amino acid sequence of the polypeptide. To test the effectiveness of the algorithm, SMAPPS was applied to the prediction of the native conformation of the backbone of Met‐enkephalin, a pentapeptide. In the calculations, only the backbone dihedral angles (ϕ and ψ) were allowed to vary; all side‐chain (χ) and peptide‐bond (ω) dihedral angles were kept fixed at the values corresponding to the alleged global minimum energy previously determined by direct energy minimization. For each conformation generated randomly by the Monte Carlo algorithm, the total conformational energy of the polypeptide was obtained from established empirical potential energy functions. Solvent effects were not included in the computations. With this initial application of SMAPPS, three distinct low‐free‐energy β‐bend structures of Met‐enkephalin were found. In particular, one of the structures has a conformation remarkably similar to the one associated with the previously alleged global minimum energy. The two additional structures of the pentapeptide have conformational energies lower than the previously computed low‐energy structure. However, the Monte Carlo results are in agreement with an improved energy‐minimization procedure. These initial results on the backbone structure of Met‐enkephalin indicate that an equilibrium statistical‐mechanical procedure, coupled with an adaptive Monte Carlo algorithm, can overcome many of the problems associated with the standard methods of direct energy minimization.
Effect of salt on sodium polystyrene sulfonate measured by light scattering
Authors: Drifford Maurice , Dalbiez Jean‐Pierre 
Published: May 2005

AbstractThe quasielastic light scattering method was used to study the ionic strength dependence of the mutual diffusion coefficient of sodium polystyrene sulfonate (NaPSS) as a function of NaCl and CaCl2 concentrations. The results indicate a splitting in the relaxation times that depends on the ratio Cp/Cs, where Cp and Cs are the polyion and added salt concentrations. A universal relationship taking into account Manning's theory of condensation and the Debye screening due to the added salt is proposed to characterize the fast–slow relaxation time transition.
Theoretical study of the binding of aliphatic diamines to the minor groove of a B‐DNA (dA‐dT)11 oligomer
Authors: Gresh Nohad 
Published: May 2005

AbstractTheoretical computations are performed on the binding of aliphatic diamines +H3N‐(CH2)n‐NH (n = 3–7), to the minor groove of a (dA‐dT)11 oligomer held in the B‐DNA conformation. The computations are performed in the framework of an additive procedure elaborated recently in this laboratory by means of which the intermolecular DNA–diamine interaction energies and the intramolecular energy variations of the diamine are computed simultaneously. The results of the computations show that the binding of the diamines occurs in well‐defined configurations in which each cationic extremity interacts with specific sites, O2(T), N3(A), and O1,(S) in the groove, the overall configuration differing according to the length of the diamine. The overall energy balance for complexation is found to depend on the chain length of the diamine, an optimal value for δE being found for 1,6 diaminohexane. This result is discussed in light of available experimental results of the compared affinities of diamines for the double‐stranded polymer dA‐dT.
Conformational analysis of cholecystokinin fragments CCK4, CCK5, and CCK6 by 1H‐nmr spectroscopy and fluorescence‐transfer measurements
Authors: Fournie‐Zaluski M. C. , Durieux C. , Lux B. , Belleney J. , Pham P. , Gerard D. , Roques B. P. 
Published: May 2005

AbstractThe confortmational behavior of the cholecystokinin‐related fragments CCK4, CCK5, and CCK6 as determined by 1H‐nmr spectroscopy in DMSO‐d6 and water and fluorescence‐transfer measurements in aqueous medium are greatly dependent on the ionization states of these peptides. Under netral conditions, the backbones of CCK5 and CCK6 preferentially adopted folded forms with a β‐turn including the four residues Gly‐Trp‐Met‐Asp, probably stabilized by a hydrogen bond between the CO of Gly and the NH of Phe. In these structures, possible induced by an ionic interaction between the carboxylic group of Asp32 and the NH group of the N‐terminal amino acid, the lateral chains of the various residues are quite distant from each other (15–16 Å). Under acidic conditions, extended structures without interactions between side chains predominate for CCK5 and CCK6, while for CCK4, a conformational change drawing the Trp and Phe side chains in close proximity was shown by fluorescence. The conformations observed in aqueous medium at physiological pH are discussed in relation to the biological activity of these peptides.
Flexibility and length of human bronchial mucin studied using low‐shear viscometry, birefringence relaxation analysis, and electron microscopy
Authors: Mikkelsen Arne , Stokke Bjørn Torger , Christensen Bjørn Erik , Elgsaeter Arnljot 
Published: May 2005

AbstractThe glycoprotein mucin was isolated from the sputum of patients with chronic obstructive bronchitis. The fractionation procedure included treatment with 6M urea at pH 12.5 followed by gel filtration in 6M urea at neutral pH. (1) Using a low‐shear Cartesian diver viscometer, we found that the mucin intrinsic viscosity equals (0.32 ± 0.03) L/g in 1000 mM NaCl solution increasing to (12 ± 3) L/g in 0.1 mM NaCl (pH 7 and 20°C). (2) The relaxation of electrically induced birefringence in mucin solutions was measured and the relaxation spectrum calculated using a Fourier‐transform deconvoltion method. We found that the dominant relaxation time increased from 1 to 150 μs when the exitation pulse duration used was increased from 2 to 300 μs. (3) Mucin was vacuum‐dried from glycerol‐containing solutions followed by low‐angle rotary shadowing and electron microscopy. Mucin was found to be unbranched, with contour lengths ranging from 300 to 2500 nm and with an average of 900 nm. Our result indicate that mucin is an extended and flexible molecule with Kuhn length 0.3–0.5% of the contour length.
Solid‐state conformation of some basic sequential polypeptides
Authors: Vives J. , Azorín F. , Subirana J. A. , Brack A. , Mayer R. 
Published: May 2005

AbstractWe have studied the structure of solid films obtained by x‐ray diffraction, from several basic polypeptides with a defined sequence. The alterating polypeptides poly(Ala‐Lys), poly(Leu‐Lys), poly(Val‐Lys), and poly(Arg‐Leu) all show a cross‐β‐structure in which layers of hydrophilic side chains alternate with layers containing hydrophobic side chains. The other polypeptides studied are not in the β‐conformation and appear to be in the α‐helical conformation. The helices obtained from poly(Lys‐Ala‐Ala) and poly(Lys‐Ala‐Ala‐Lys) appear to be packed in an unusual fashion, which favors interaction between alanine side chains. Such behavior is not found in poly(Lys‐Leu‐Ala).