bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational studies of an undecapeptide reproducing the consensus sequence around the cleavage site of the RXVRG endoprotease from Xenopus laevis skin
Authors: Baron Daniel , Leseney Anne‐Marie , Chalaoux Francois‐Regis , Riand Jacques 
Published: December 2004

AbstractTwo synthetic fragments, corresponding to the 4–9 and 4–14 sequences of a tetradecapeptide used as a model to test the RXVRG‐endoprotease activity from Xenopus laevis skin, have been studied by two‐dimensional nmr spectroscopies, correlated spectroscopy, and nuclear Overhauser effect (NOE) spectroscopy. Both peptides wore the 5–9 consensus sequence found in several hormonal precursors. The nmr data for the 4–9 hexapeptide did not indicate any particular organization, either in water or in dimethylsulfoxide (DMSO), whereas, the 4–14 undecapeptide, a substrate for the RXVRG endoprotease, showed, in DMSO solution, significant trends of structural organization involving the amino acids pertaining to the consensus domain.From variations of integrated NOE peaks with temperature, the appearent interproton correlation times τc were estimated and the maxima observed with Va17, the central residue in the consensus sequence. A defined tertiary structure in that domain was also supported by medium‐and long‐range NOEs between As6 and Arg8, Glu4 and Gly9, and by the likely involvement of Arg8 and Gly9 NHs in intramolecular hydrogen bonds. Most of these observations could be rationalized by an equilibrium between a 5–3 β‐turn and a 9 → 4 H‐bonded loop.The predominance of one rotamer for the Cα‐Cβ bond was established in four residues. Finally, the average ϕ and ψ angles were derived from two models taking, or not, into account variations in the correlation times along the sequence. This allowed us to discuss the artifacts generated by using an average correlation time through the whole molecule. © 1994 John Wiley & Sons, Inc.
Conformation of retro‐bombolitin I in aqueous solution containing surfactant micelles
Authors: Battistutta Roberto , Bisello Alessandro , Mammi Stefano , Peggion Evaristo 
Published: December 2004

AbstractBombolitins are five naturally occurring heptadecapeptides acting at the membrane level and able to increase the activity of phospholipase A2. As for other peptides with similar function, the biological activity of bombolitins seems to be mainly due to their ability to form amphipathic helical structures. We synthesized and tested the retro sequence of bom‐bolitin I (retro‐bombolitin I). This peptide showed an activity similar to that of the natural sequence and was able to adopt a helical structure in the presence of an amphipathic environment consisting of SDS micelles. The secondary structure of this peptide was fully characterized by CD and nmr spectroscopy. © 1994 John Wiley & Sons, Inc.
Electronic and optical properties of wet‐spun films of Li‐ and Na‐hyaluronate
Authors: Lee S. A. , Vansteenberg M. L. , Lavalle N. , Rupprecht A. , Song Z. 
Published: December 2004

AbstractThe uv absorption of Na‐hyaluronate (NaHA) films and the refractive indices, water content, and swelling of LiHA films have been measured as a function of relative humidity. Three peaks are observed in the uv absorption of NaHA (at about 250, 310, and 330 nm) for water content above 10 water molecules per disaccharide. The absorptivity of the 250, 310, and 330 nm peaks increase as the water content increases, indicating a change in the electronic properties of the HA molecule. The refractive indices, water content, and swelling of LiHA films are used to determine the optical polarizability via the Lorentz–Lorenz relation. The polarizability of LiHA is found to have a similar dependence on water content as NaHA, though the changes observed are larger in magnitude. © 1994 John Wiley & Sons, Inc.
Direct observation of cell wall glucans in whole cells of Saccharomyces cerevisiae by magic‐angle spinning 13C‐nmr
Authors: Krainer Eduardo , Stark Ruth E. , Naider Fred , Alagramam Kumar , Becker Jeffrey M. 
Published: December 2004

AbstractIntact cells of Saccharomyces cerevisiae were examined as an aqueous paste by 13C‐nmr spectroscopy with direct polarization and magic‐angle spinning. The spectra obtained were highly resolved, showing numerous resonances in the 60‐105 ppm range that were assigned to carbons of a liquid‐like domain of the cell wall glucan. Assignments were confirmed by running the spectrum of S. cerevisiae in which the cell wall glucans were labeled with [13C] by feeding the cell [13C ] galactose. The spectra indicate that the glucan in the cell wall of intact S. cerevisiae assumes a helical conformation and suggest that strain 17A fed with galactose preferentially incorporates the resulting glucose into β(1 → 3)‐linkages. © 1994 John Wiley & Sons, Inc.
β‐Turn conformations in crystal structures of model peptides containing α,α‐Di‐n‐propylglycine and α,α‐Di‐n‐butylglycine
Authors: Crisma M. , Valle G. , Toniolo C. , Prasad Sudhanand , Rao R. Balaji , Balaram P. 
Published: December 2004

AbstractThe crystal state conformations of three peptides containing the α,α‐dialkylated residues. α,α‐di‐n‐propylglycine (Dpg) and α,α‐di‐n‐butylglycine (Dbg), have been established by x‐ray diffraction. Boc‐Ala‐Dpg‐Alu‐OMe (I) and Boc‐Ala‐Dbg‐Ala‐OMe (III) adopt distorted type II β‐turn conformations with Ala (1) and Dpg/Dbg (2) as the corner residues. In both peptides the conformational angles at the Dxg residue (I: ϕ = 66.2°, ψ = 19.3°; III: ϕ = 66.5°. ψ = 21.1°) deviate appreciably from ideal values for the i + 2 residue in a type II β‐turn. In both peptides the observed (N…O) distances between the Boc CO and Ala (3) NH groups are far too long (1: 3.44 Å: III: 3.63 Å) for an intramolecular 4 → 1 hydrogen bond. Boc‐Ala‐Dpg‐Ata‐NHMe (II) crystallizes with two independent molecules in the asymmetric unit. Both molecules HA and HB adopt consecutive β‐turn (type III‐III in HA and type III‐I in IIB) or incipient 310‐helical structures, stabilized by two intramolecular 4 → 1 hydrogen bonds. In all four molecules the bond angle N‐Cα‐C′ (τ) at the Dxg residues are ≥ 110°. The observation of conformational angles in the helical region of ϕ,ψ space at these residues is consistent with theoretical predictions. © 1995 John Wiley & Sons, Inc.
Effects of metal cations on coacervation of α‐elastin
Authors: Miyakawa K. , Totoki M. , Kaibara K. 
Published: December 2004

AbstractThe quasi‐elastic light scattering studies were carried out to investigate effects of metal cations such as Ca2+ and Na+ on the early stage of Coacervation process of α‐elastin, a chemical fragmentation product originated from the biological elastomeric protein elastin, in aqueous solutions. In particular, our attention was focused on changes of two types of dynamical behaviors found in the earlier work, which are a remarkable increase and a monotonous decrease in the hydrodynamic radius R of molecules with temperature for critical and off‐critical concentrations of α‐elastin, respectively. For the critical α‐elastin concentration, an addition of Ca2+ was found to exert little effects on the steep temperature profile of R observed in the absence of Ca2+. On the other hand, an addition of a slight amount of Na+ resulted in a monotonous decrease in R, but its further addition restored a remarkable increase in R similar to the critical behaviors in the salt‐free system. In the case of off‐critical sample, the addition of either Ca2+ or Na+ above a certain concentration induced a change in R from a monotonous decrease to a remarkable increase. For both critical and off‐critical concentrations of α‐elastin, Ca2+ and Na+ brought about an elevation and a lowering of the temperature at which the sample started to be turbid, respectively. © 1995 John Wiley & Sons, Inc.
The distribution of water in arterial elastin: Effects of mechanical stress, osmotic pressure, and temperature
Authors: Weinberg Peter D. , Winlove C. Peter , Parker Kim H. 
Published: December 2004

AbstractUsing gravimetric and radiotracer techniques, we investigated the effects of mechanical stress, osmotic pressure, and temperature on the volumes of the intra‐ and extrafibrillar water spaces in arterial elastin. We also investigated the effects of temperature on water flow through elastin membranes and on dynamic mechanical properties of elastin rings. Compression by mechanical or osmotic loading reduced the hydration of the elastin in an identical manner. Two distinct stages were evident; at low loads there was extensive water removal from the extrafibrillar space while high loads were required to remove water from the intrafibrillar space. Conversely, dehydration caused by mechanical extension of the matrix was associated with a much smaller loss from the extrafibrillar compartment and a large fractional decrease in the intrafibrillar space. Contraction of the matrix as a result of increased temperature had similar effects on hydration to those produced by extension. Water flux across elastin membranes, corrected for changes in viscosity, and specific hydraulic conductivity both increased as a result of temperature‐induced contraction. This effect was attributed to increases in both the fractional volume of the extrafibrillar space and the fiber radius. The elastic modulus decreased with increasing temperature, but there was an increase in viscoelasticity. Previous studies have determined that viscoelasticity depends on the rate of redistribution of intrafibrillar water, so this finding provides additional evidence that heating affects primarily the volume of the intrafibrillar space. © 1995 John Wiley & Sons, Inc.
Computer simulation of the directional displacement of rod‐shaped, arc‐shaped, and circular objects in an array of obstacles, representing a simple model for the gel electrophoresis of small DNA
Authors: Wheeler David L. , Chrambach Andreas 
Published: December 2004

AbstractThe gel electrophoresis of DNA of identical length but various static conformations was simulated using a two‐dimensional model of the movement of rod‐shaped, arc‐shaped, and circular objects through random arrays of disk‐shaped obstacles. At low obstacle density, the displacement rate of these objects decreases from the rod‐shaped to the circular to the arc‐shaped objects. At high obstacle densities, the displacement rate of circular objects approaches zero. The alignment of the arc‐shaped objects along the axis of the directional movement of the objects was less than that achieved by the rod‐shaped objects. Rod‐shaped and arc‐shaped objects were retarded in their movement by collisions with the obstacles; the number of collisions of the former, in view of their greater ability to align, was less than that of the latter. Circular objects were exclusively retarded by collisions, while the arc‐shaped objects exhibited an additional retarding mechanism, viz. the suspension (“hanging”) on the obstacles. When the rigid objects were made flexible, their displacement increased. The increase was most pronounced with the circular objects, allowing them to penetrate at obstacle densities from which the rigid objects were excluded. © 1995 John Wiley & Sons, Inc.
Hydrogen exchange studies of the Arc repressor: Evidence for a monomeric folding intermediate
Authors: Burgering Maurits J. M. , Hald Mogens , Boelens Rolf , Breg Jan N. , Kaptein Robert 
Published: December 2004

AbstractThe hydrogen exchange rates of the backbone amide and labile side‐chain protons of the dimeric Arc repressor have been measured. For the slowly exchanging amides in the α‐helical regions, these rates show a concentration dependence. To account for this dependence, the role of the monomer–dimer equilibrium was considered. Extrapolating the observed exchange rates to zero dimer concentration provides estimates of these rates in the monomer and shows that they are significantly retarded compared to those of an unfolded polypeptide. This suggests that the monomer is in a structured “molten globule” like state. In particular, the two helices of Arc retain a high degree of their secondary structure and it is proposed that the two amphiphilic helices are packed together with their hydrophobic faces. Evidence for a partially folded structure in the Arc monomer was reported earlier in two other studies [J. L. Silva, C. F. Silveira, A. Correia, Jr., and L. Pontes (1992) Journal of Molecular Biology, Vol. 223, pp. 545–555: X. Peng, J. Jonas, and J. L. Silva (1993) Proceedings of the National Academy of Science USA, Vol. 90, pp. 1776–1780]. By combining the results of these studies and ours, a folding pathway of the dimeric Arc repressor involving four different stages is proposed. Due to the low concentration of Arc repressor in the cell, the protein is present either as a free monomer or it is bound to DNA presumably as a tetramer. Therefore the folding pathway can be regarded as an integral part of the overall DNA binding process. © 1995 John Wiley & Sons, Inc.
A small‐angle x‐ray scattering study of alginate solution and its Sol–Gel transition by addition of divalent cations
Authors: Wang Zheng‐Yu , White John W. , Konno Mikio , Saito Shozaburo , Nozawa Tsunenori 
Published: December 2004

AbstractThe small‐angle x‐ray scattering (SAXS) technique has been applied to investigate solution and gel structures of alginate in the absence and presence of two divalent cations: Ca(II) and Cu(II). We have observed a broad maximum in the scattering curve, a characteristic of polyelectrolyte, for the purified alginate sample. The scattering maximum disappears in excess of added simple salt and shifts toward the higher angle region with increasing alginate concentration. Concentration dependence of the position and intensity of the maximum follows power law relations with exponents close to those predicted by theory. Data analysis shows an increase in correlation length ξ and cross‐sectional diameter d0, of polymer chains upon gelation and suggests that a dimeric structure is adopted in the junction zone, consistent with the “egg‐box” model previously proposed. In the Ca(II)–alginate system, the molecular parameters ξ and d0 are found to have good correlation with the macroscopic properties of gelation, such as gel point determined by viscosity measurements. However, for the Cu(II)–alginate system there is no clearly transitional behavior observed in ξ and d0, implying that the junction zone may be replaced by a more uniformly distributed site binding of Cu(II) ions to the carboxyl groups of both mannuronate and guluronate residues, in confirmation of previous 13C‐nmr results. © 1995 John Wiley & Sons, Inc.
Chain conformation in polyretropeptides: Quantum mechanical and empirical force field calculations on 2,6,8‐trioxo‐3,5,9‐triazadecane, a model compound for poly(retro‐glycine)
Authors: Alemán Carlos , Bella Jordi 
Published: December 2004

AbstractWe report here our results on semiempirical AM1 calculations for the conformational preferences of 2,6,8‐trioxo‐3,5,9‐triazadecane, a model compound for polymers made of retropeptide units. We have evaluated the effect of applying symmetry constraints between chemically equivalent torsion angles. These results suggest that preferred conformations around the NHCH2NH group are quite independent from those on the COCH2CO unit, so all possible combinations generate the complete set of energy minima for the model compound.We have analyzed the implications of the different minimum energy conformation in an infinite chain model and we have explored the conformational space of regular polyretropeptides. This shows a close relation to that of regular polypeptides but with significant differences arising from the change of orientation of the peptide units along the polymer molecule. The energy calculations also support previously proposed models for the crystal structure of the simplest polyretropeptide, poly(retro‐glycine). Finally, we discuss the consequences of retropeptide‐peptide copolymerization as well as the expected conformations for regular alternate terpolymers. © 1995 John Wiley & Sons, Inc.
Two‐dimensional motion of DNA bands during 120° pulsed‐field gel electrophoresis. I. Effect of molecular weight
Authors: Hutson M. Shane , Holzwarth George , Duke Thomas , Viovy Jean‐Louis 
Published: December 2004

AbstractThe instantaneous position and velocity of bands of linear, double‐stranded DNA were measured during 120° pulsed‐field electrophoresis in 1% agarose gels, using a video micrometer capable of simultaneous measurements in two dimensions. When the direction of the field was switched, the band initially retraced the last portion of its path during the preceding pulse. The distance the band moved backward increased with DNA length: 48.5 kb (kilobase pair) DNA moved backward only 0.2 μm, but 1110 kb DNA moved backward 24 μm, before setting off in a positive direction. The velocity of the DNA band was particularly rapid during the backward movement: the magnitude of the velocity spike increased with M, reaching 2.4 μm/s for 1110 kb DNN, which was about 5 times the steady‐state velocity. The velocity in the y direction, perpendicular to the mean drift direction, allowed an even larger transient spike, which also increased with M.Simulation of the dynamics of long DNA chins undergoing gel electrophoresis by a dynamic Monte Carlo method gave instantaneous xy position and velocity in excellent agreement with experiment. The simulation included extensional motions of the DNA within the tube of interconnected agarose pores as well as the possibility of loops (hernias) that escape laterally from the tube. © 1995 John Wiley & Sons, Inc.
Effective water model for Monte Carlo simulations of proteins
Authors: Banks Jay , Brower Richard C. , Ma Jianpeng 
Published: December 2004

AbstractWe present an effective theory for water. Our goal is to formulate on accurate model for the effects of solvation on protein dynamics, without incurring the huge computational cost and the slow temporal evolution typical of molecular dynamics simulations of liquids. We replace the individual water molecules in an all‐atom potential with a local dielectric density field, with self interactions given by the Landau‐Ginzburg free energy and external interactions by Lennard‐Jones forces at the surface of the protein atoms. We explore conformational space with finite temperature Monte Carlo dynamics, using parallel Langevin and Fourier acceleration algorithms well suited to data‐parallel computer architectures such as the Connection Machine. To establish the validity of our approximations, we compare our electrostatic contribution to the solvalion energy with the results of Lim, Bashford, and Karplus using a conventional static continuum dielectric cavity model, and the non electrostatic contributions with estimates of hydrophohic surface free energy. Our model can also accommodate ionic charges and temperature fluctuations, We propose future investigations extending our effective theory of solvation to include explicit orientational entropy and hydroxen‐bonding terms. © 1995 John Wiley & Sons, Inc.
Structural modification of DNA by a DNA‐binding motif SPKK: Detection of changes in base‐pair hydrogen bonding and base stacking by uv resonance Raman spectroscopy
Authors: Takeuchi Hideo , Sasamori Jun 
Published: December 2004

AbstractInteractions of a DNA‐binding motif SPKK with polynuclcotides have been investigated by uv resonance Raman spectroscopy. Analysis of the Raman spectra has shown that the tetrapeptide SPKK weakens the adenine‐thymine base‐pair hydrogen bonding in poly (dA‐dT)·poly (dAdT) and reduces the adenine‐adeninc base stacking interactions in poly (dA)·poly (dT), both effects being indicative of destabilization of the DNA double helical structure. On the other hand, poly(dG‐dC)·poly(dG‐dC) and poly(dG)·poly(dC) do not show any structural change in the presence of SPKK. The present observations confirm that the SPKK motif, which is frequently found in historic H1 proteins, specifically binds to A/T‐rich regions of DNA and loosens the DNA double‐helical structure. One of the roles of the SPKK motifs in histones may be to increase DNA flexibility so that DNA can wrap around core histones and be assembled into chromosomes more easily. © 1995 John Wiley & Sons, Inc.
Electrophoretic mobility of DNA in gels. III. Experimental study on band inversion
Authors: Heller Christoph , Viovy Jean Louis 
Published: December 2004

AbstractA series of experiments has been undertaken to study the phenomenon of band inversion that can occur during the separation of linear double‐stranded DNA in agarose gels under constant electric field. We found that there can be a considerable band inversion when the DNA fragments are moving as a single species. When separating mixtures of fragments, as it is usually done in routine experiments, the band inversion effect is strongly reduced.Our data support the assumption that DNA–DNA interactions can play an important role in electrophoretic separations. © 1995 John Wiley & Sons, Inc.
The effect of HCl on the solution structure of calf thymus DNA: A comparative study of DNA denaturation by proton and metal cations using fourier transform IR difference spectroscopy
Authors: Tajmir‐Riahi H. A. , Ahmad R. , Naoui M. , Diamantoglou S. 
Published: December 2004

AbstractThe interaction of HCl with calf thymus DNA was investigated in aqueous solution at pH 7‐2 with H+/DNA(P)(P:phosphate) molar ratios (r) of 1/80, 1/40, 1/20, 1/10, 1/4, 1/2, and 1, using Fourier Transform (FTIR) difference spectroscopy. Correlations between spectral changes, proton binding mode, DNA denaturation, and conformational variations are established. A comparison was also made between their spectra of denaturated DNA, in the presence of proton and Cu ions with similar cation concentrations.The FTIR difference spectroscopic results have shown that at low proton concentrations of r = 1/80 and 1/40 (pH 7–5), no major spectral changes occur for DNA, and the presence of H+ results in an increased base‐stacking interaction and helical stability. At higher proton concentrations of r > 1/40, the proton binding to the cytosine and adenine bases begins with major destabilization of the helical duplex. As base protonation progresses, a B to C conformational conversion occurs with major DNA spectral changes. Protonation of guanine bases occurs at a high cation concentration r > 1/2 (pH < 3) with a major increase in the intensity of several DNA in‐plane vibrations. Copper ion complexation with DNA exhibits marked similarities with proton at high cation concentrations (r > 1/10), whereas at low metal ion concentrations, copper–PO2 and copper–guanine N‐7 bindings are predominant. No major DNA conformational transition was observed on copper ion complexation. © 1995 John Wiley & Sons, Inc.
Synthesis and characterization of polyamides containing unnatural amino acids
Authors: Guinn R. Mark , Margot Antoine O. , Taylor Jason R. , Schumacher Michael , Clark Douglas S. , Blanch Harvey W. 
Published: December 2004

AbstractWe describe the synthesis of several polyamides that retain the secondary structure of proteins and contain derivatizable side chains. The derivatizable side chain allows for further reaction of the polymer chain (e.g., chain cross‐linking or addition of pendant groups). Polymers of α‐amino acids containing a terminal unsaturated bond on the side chain have been synthesized. Poly‐L‐pentenyl glycine, poly‐L‐propargyl glycine, and poly‐L‐allyl glycine were synthesized chemically via Leuchs' anhydrides and enzymatically using subtilisin Carlsberg. Poly‐L‐propargyl glycine and poly‐D,L‐allyl glycine folded into the β‐sheet configuration whereas poly‐L‐pentenyl glycine assumed a helical conformation. The secondary structure of poly‐L‐allyl glycine and poly‐D,L‐pentenylglycine could not be determined conclusively. Comparison of properties between the polymers obtained chemically and enzymatically is provided. © 1995 John Wiley & Sons, Inc.