bluuebunny/crossref_metadata_2025 huggingface dataset:
Measurement of long‐range2 13C‐1H coupling constants of 95% uniformly 13C‐labeled polysaccharide from streptococcus mitis J22
Authors: Gitti Rossitza , Long Guixia , Bush C. Allen
Published: December 2004

The coaggregation of Streptococcus mitis strain J22 in the early stages of dental plaque formation has been shown to result from interaction of cell wall polysaccharides with lectins on the surface of other oral bacterial species. This bacterium was grown in a medium containing 13C as the sole carbon source. We have isolated the lectin receptor polysaccharide from this strain with full enrichment in 13C and have determined a number of two‐bond and three‐bond 13C‐1H coupling constants from measurements of the offsets in two‐dimensional homonuclear nmr spectra [exclusive correlated spectroscopy (E‐COSY) method]. A scheme for reliable extraction of these coupling constants from homonuclear Hartmann‐Hahn and nuclear Overhauser effect spectroscopy spectra is tested in model compounds. We interpret the three‐bond coupling across the glycosidic linkage in terms of dihedral angles in order to provide conformational information to supplement molecular modeling and nuclear Overhauser effect data. We show that the E‐COSY method works well even for coupling constants smaller than the nmr line width and that a number of the 3JCH across the glycosidic linkage are in the range of 1–2 Hz, which is much smaller than many previously reported values. © 1994 John Wiley & Sons, Inc.
The potential energy surface of methyl 2‐O‐(α‐D‐mannopyranosyl)‐α‐D‐mannopyranoside in aqueous solution: Conclusions derived from optical rotation
Authors: Stevens Eugene S.
Published: December 2004

The optical rotation of methyl 2‐O ‐(α‐D‐mannopyranosyl)‐α‐D‐mannopyranoside is calculated semiempirically as a function of the linkage dihedral angles ϕ (H1‐C1‐O1‐C2′) and ψ (C1‐O1‐C2′‐H2′). Although the rotation calculated for the global energy minimum conformation found in several rigid‐residue modeling calculations (ϕ,ψ = −40°,−20°) is in good agreement with the observed solution rotation, the observed rotation is also compatible with the limited flexibility inferred from more recent relaxed residue modeling calculations on a structurally related rhamnose disaccharide © 1994 John Wiley & Sons, Inc.
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

Two 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

Bombolitins 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

The 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

Intact 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

The 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

The 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

Using 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

The 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

The 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

The 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

We 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

The 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

We 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

Interactions 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

A 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

The 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

We 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.
Biopolymer–surfactant interaction. I. Kinetics of binding of cetyltrimethyl ammonium bromide with carboxymethyl cellulose (Na Salt)
Authors: Maulik Sudeshna , Jana Pijush Kanti , Moulik Satya Priya , Chattoraj Dipti Kumar
Published: December 2004

The kinetics of binding of the cationic surfactant cetyltrimethyl ammonium bromide with the Na salt of carboxymethyl cellulose was studied by the electrometric method using cetyltrimetlyl ammonium+ (CTA+) ion‐selective polyvinyl chloride membrane electrode. The binding process followed the first‐order kinetics and occurred in three stages. Its affinity increased with increasing CTA bromide concentration and decreased with ionic strength. The activation process comprised moderate E and ΔH≠ and negative ΔS≠ for all three stages with a ΔH≠ < TδS≠ trend proving it to be entropy controlled. The ΔG≠ values followed the trend ΔG < ΔG < ΔG (in accordance with k1 > k2 > k3). The enthalpies (ΔH≠) and entropies (ΔS≠) of activation followed a systematic and interdependent trend. The multiple‐stage binding kinetics is grossly comparable with the kinetics of binding of proteins to solid surfaces. © 1995 John Wiley & Sons, Inc.
Low‐frequency vibrations in α‐helices: Helicoidal analysis of polyalanine and deoxymyoglobin molecular dynamics trajectories
Authors: Furois‐Corbin S. , Smith J. C. , Lavery R.
Published: December 2004

We present an approach to the analysis of low‐frequency (0‐200 cm−1) α‐helix vibrations in molecular dynamics simulation. The approach employs the P‐Curves algorithm [H. Sklenar, C. Etchebest, and R. Lavery, (1989) Proteins: Structure, Function and Genetics, Vol. 6. pp. 46–60] to determine the helical axis and a set of helicoidal parameters describing the axis curvature and the position of the repealing units with respect to the axis and each other. The vibrations are analyzed in terms of time correlation functions of the fluctuations of P‐Curves parameters and their Fourier transforms. Simulations of polyalanine and myoglobin are analyzed. For polyalanine, global twisting, bending, and stretching vibrations are found at 11, 20, and 40 cm−1, respectively. In myoglobin, the spectra of the global helix vibrations are qualitatively different from those of polyalanine and considerably more complicated. Local vibrations of individual amino acid units in the helix backbones are also analyzed with P‐Curves and compared. © 1995 John Wiley & Sons, Inc.
CD and fluorescence studies of the human granulocyte‐macrophage colony‐stimulating factor and related peptide conformations in aqueous solution
Authors: Casté L. , Zandomeneghi M. , Houben J. L. , Rovero P. , Pegoraro S. , Revoltella P. R. , Brochon J. C.
Published: December 2004

The absorption, CD, and fluorescence emission spectra, and the fluorescence emission and depolarization lifetimes of the human granulocyte‐macrophage colony‐stimulating factor (hGM‐CSF) and related peptides previously tested for their immunological activity, were measured in water at various pHs and temperatures to obtain information on their conformation in solution. The aim was to correlate the amino acid sequences, and the chain conformations and dynamics of the peptides, with their immunological properties

The CD spectrum of hGM‐CSF revealed, as expected, a structure in solution similar to that in the crystalline state, but the fluorescence data suggest that the Trp 122 residue is more accessible to the solvent than the x‐ray data would lead one to expect. They also suggest that some flexibility exists between the protein's two domains, one made up of theα‐helices A and C and the other of the α‐helices B and D plus the two β‐strands. In aqueous solution, none of the tested peptide CD spectra could be linked to a recognizable ordered conformation, i.e., an α‐helix or a β‐sheet. The fluorescence of the peptide 11–24 suggests that the Trp 13 residue may appear in two types of situations: (a) in aqueous solution and (b) within a globular structure. Its CD spectra show that the tryptophan residue exists in both cases in a highly asymmetric environment independent of the pH. © 1995 John Wiley & Sons, Inc.
Design and characterization of a model αβ peptide
Authors: Butcher Daniel J. , Bruch Martha D. , Moe Gregory R.
Published: December 2004

CD and nmr spectroscopy were used to compare the conformational properties of two related peptides. One of the peptides, Model AB, was designed to adopt a helix‐turn‐extended strand (αβ) tertiary structure in water that might be stabilized by hydrophobic interactions between two leucine residues in the amino‐terminal segment and two methionine residues in the carboxyl terminal segment. The other peptide, AB Helix, has the same amino acid sequence as Model AB except that it lacks the‐Pro‐Met‐Thr‐Met‐Thr‐Gly segment at the carboxyl‐terminus. Although the carboxyl‐terminal segment of Model AB was found to be unstructured, its presence increases the number of residues in a helical conformation, shifts the pKas of three ionizable side chains by 1 pH unit or more compared to an unstructured peptide, stabilizes the peptide as a monomer in high concentrations of ammonium sulfate, increases the conformational stability of residues at the terminal ends of the helix, and results in many slowly exchanging amide protons throughout the entire backbone of the peptide. These results suggest that interactions between adjacent segments in a small peptide can have significant structure organizing effects. Similar kinds of interactions may be important in determining the structure of early intermediates in protein folding and may be useful in the de novo design of independently folding peptides. © 1995 John Wiley & Sons, Inc.
Conformational mimicry: Synthesis and solution conformation of a cyclic somatostatin hexapeptide containing a tetrazole cis amide bond surrogate
Authors: Beusen Denise D. , Zabrocki Janusz , Slomczynska Urszula , Head Richard D. , Kao Jeff L.‐F. , Marshall Garland R.
Published: December 2004

Potent, cyclic hexapeptide analogues of somatostatin are generally believed to adopt some common secondary structural features: a II′ β turn at one end of the cycle, and a type VI turn with a cis amide bond at the other. A proposed cis amide surrogate, the 1,5‐disubstituted tetrazole, has been placed into a cyclic hexapeptide analog of somatostatin in order to constrain the putative cis amide bond. The final cyclization was done by either chemical or enzymatic means. The product, cyclo(Ala6‐Tyr7‐D‐Trp8‐Lys9‐Val10‐Phe11‐Ψ[CN4]), was found to have 83% of the activity of somatostatin. Solution nmr analysis in DMSO/water revealed that the backbone as well as side chain χ1 and χ2 were well ordered. Relaxation matrix methods were used to extract distance restraints from the nuclear Overhauser effect spectroscopy data set, and these were used in a systematic search of torsional space to identify structures consistent with the nmr data. Restrained minimizations of these structures using a number of different force fields produced structures having the expected βII′ turn at D‐Trp8‐Lys9 and αβVIa turn in the Phe11‐Ψ[CN4]‐Ala6 portion of the molecule. The similarity of the minimized structures to those previously reported for cyclic hexapeptide analogues of somatostatin confirms the similarity of the tetrazole geometry to that of the cis amide in solution. © 1995 John Wiley & Sons, Inc.
Conformation of short DNA fragments by modulated fluorescence polarization anisotropy
Authors: Collini Maddalena , Chirico Giuseppe , Baldini Giancarlo , Bianchi Marco E.
Published: December 2004

The technique of fluorescence polarization anisotropy (FPA) decay of intercalated ethidium has been used to study DNA conformation and dynamics, which are being recognized as primary determinants in transcription control and other cellular processes. Frequency modulated FPA when applied to two DNA molecules, a “straight” 50 base‐pairs duplex fragment, and a bent fragment of similar length, has yielded different rotational diffusion coefficients for the two fragments. The data have been processed with an analytical model and with Brownian dynamics simulations, obtaining a good fit and a quantitative agreement between the two models. Both analyses have confirmed that one fragment can be described as a straight cylinder, while the other fragment is bent, with an angle estimated to be 45° ± 3°. FPA has proved to be very powerful in determining simple conformations of short DNA duplexes and also particularly apt to probe the dynamical features of DNA fragments where conventional methods are either too cumbersome or fail to give quantitative results. © 1995 John Wiley & Sons, Inc.
Core directed self‐assemblies in the solid state of retro aib bis‐peptide dicarboxylic acids: A design strategy for control of molecular orientation in peptides
Authors: Karle Isabella L. , Ranganathan Darshan
Published: December 2004

Self‐assembly patterns as a function of the central core insert in the retro bis‐peptide dicarboxylic acids HOAibXAibOH, containing oxalyl (‐COCO1), fumaryl ( OCHCH CO ;2), and adipoyl [ CO(CH2)4 CO3], have been characterized by single crystal x‐ray diffraction analyses. Extensive hydrogen bonding occurs in each crystal but there are no OH…O bonds between acid groups. Only two types of hydrogen bonds occur in all the crystals:NH…O (acid terminal),2.84‐2.98 Åand OH (acidterminal)…O (corecarbonyl),2.55–2.67 Å (exceptfor an additional intramolecular C5 type bond in the oxalyl moiety in 1). The self‐assembly patterns are a β‐network in1, separate layer assemblies (β‐networks) for two independent molecules in 2 that combine into a three‐dimensional γnetwork, and separate ribbon assembles (αnetworks) for two independent molecules in 3 that combine into an extended β‐network sheet withhydrophobic faces. © 1995 John Wiley & Sons, Inc.
Homooligopeptides composed of hydrophobic amino acid residues interact in a specific manner by taking α‐helix or β‐structure toward lipid bilayers
Authors: Lee Sannamu , Yoshitomi Hideo , Morikawa Miyuki , Ando Setzuko , Takiguchi Hideo , Inoue Tohru , Sugihar Gohsuke
Published: December 2004

In order to investigate the role of each amino acid residue in determining the secondary structure of the transmembrane segment of membrane proteins in a lipid bilayer, we made a conformational analysis by CD for lipid‐soluble homooligopeptides, benzyloxycarbonyl‐(Z‐) Aaan‐OEt (n = 5‐7), composed of Ala, Leu, Val, and Phe, in three media of trifluoroethanol, sodium dodecyl sulfaie micelle, and phospholipid liposomes. The lipid‐peptide interaction was also studied through the observation of bilayer phase transition by differential scanning cahrimetry (DSC). The CD studies showed that peptides except for Phe oligomers are present as a mainly random structure in trifluoroethanol, as a mixture of α‐helix, β‐sheet, β‐turn, and /or random in micelles above the critical micellization concentration and preferably as an extended structure of α‐helical or β‐structure in dipalmitoyl‐D,L‐α‐phosphatidylcholine (DPPC) liposomes of gel state. That the β‐structure content of Val oligomers in lipid bilayers is much higher than that in micelles and the oligopeptides of Leu (n = 7) and Ala (n = 6) can take an α‐helical structure with one to two turns in lipid bilayers despite their short chain lengths indicates that lipid bilayers can stabilize the extended structure of both α‐helical and β‐structures of the peptides. The DSC study for bilayer phase transition of DPPC / peptide mixtures showed that the Leu oligomer virtually affects neither the temperature nor the enthalpy of the transition, while Val and Ala oligomers slightly reduce the transition enthalpy without altering the transition temperature. In contrast, the Phe oligomer affects the phase transition in much more complicated manner. The decreasing tendency of the transition enthalpy was more pronounced for the Ala oligomer as compared with the Leu and Val oligomers, which means that the isopropyl group of the side chain has a less perturbing effect on the lipid acyl chain than the methyl group of Ala. © 1995 John Wiley & Sons, Inc.
Crystal structure and a twisted β‐sheet conformation of the tripeptide L‐leucyl‐L‐leucyl‐L‐leucine monohydrate trimethanol solvate: Conformation analysis of tripeptides
Authors: Go Kuantee , Parthasarathy R.
Published: December 2004

In order to test the helical preference of short oligo‐L‐leucines, we crystallized the tripeptide L‐leucyl‐L.‐leucyl‐L‐leucine (LLL) and carried out x‐ray diffraction studies of it (L‐leucyl‐L‐leucyl‐Lleucine)2. 3CH3OH. H2O, (C39H84N6O12). Crystallized in the monoclinic system, space group P21, cell parameters: a = 12.031(2), b = 15.578(3), c = 14.087(2) Å, α = 90°, β = 97.29(1)°, γ = 90°, V = 2618.6 Å3. MW = 829.1, Dc = 1.051 gcm−3. R index of 0.057 for 4213 reflections (λcukα = 1.5418 Å) > 2σ. LLL takes tip the β‐sheet rather than a helical conformation in the crystalline stale. The three methanol molecules and the water molecule that constitute the solvent of crystallization form a network of hydrogen bonds to the LLL molecules and to one another. It is rather remarkable that though A and L have stronger helical preferences than G, neither AAA nor LLL form the crystalline helix but GAL does, indicating that the helical preferences depend on the sequence context. The residue L2 in molecule A and the residues L1 and L3 of molecule B do not show the preferred conformation for forming helices. Further, very remarkably. LLL exhibits a unique super secondary feature of the protein folding topology, namely the twisted β‐sheet. Where as most short peptides show only the classical p‐sheet conformation. Thai even the tripeptide LLL is able to exhibit the twisted β‐sheet conformation, and with the correct left‐handed twist this suggests that even very short peptide segments possess the ability to assume several of the characteristic topological features exhibited by proteins. An extensive review of tripeptide conformations has been carried out and some results of this study have been included here. © 1995 John Wiley & Sons, Inc.
Conformational study of linear alternating and mixed D‐ and L‐proline oligomers using electronic and vibrational CD and fourier transform IR
Authors: Mästle Werner , Dukor Rina K. , Yoder Gorm , Keiderling Timothy A.
Published: December 2004

Vibrational CD (VCD) spectra of a series of blocked linear, alternating D‐ and L‐proline containing oligopeptides, dissolved in D2O and in CDCl3. are reported. For the Boc‐LDL‐Pro3 to Boc‐DLDLDLDL‐Pro8 oligomers. The VCD spectra in the amide I band is a positive couplet, opposite in sense to that obtained for (L‐Pro)n oligomers. While this admits the possibility of their favoring a right‐handed helical chain conformation, the amide I ir spectra for these dl oligomers in D2O indicate a mixed, apparently alternate, cis‐trans conformation that prevents a simple conclusion. Their VCD in D2O evidence no narrowing and has a progressive loss in intensity (measured as Δ /A,) with an increase in chain length. In CDCl3a similar pattern of positive VCD couplets decreasing in intensity with length was seen, but their spectra are narrower. Their electronic CD (ECD) in the uv, also indicates a loss in intensity with increasing length. Oligomers with odd or even numbers of Pro residues have different ECD patterns, indicating that those spectra are strongly influenced by local contributions arising in the N‐terminal groups. The VCD arises from dipolar and vibrational coupling of the amides in the helical structure. All the spectra are consistent with the chiral end groups leading to formation of an excess of one helical handedness. With an increase in length, the influence of this selectiveness is less and the overall CD measured decreases. © 1995 John Wiley & Sons, Inc.
Conformational studies of retro–inverso peptides: The crystal and molecular structure of the hydantoin from H‐Ala‐G‐Ala‐mGly‐OBzl
Authors: Benedetti Ettore , Pedone Emilia M , Kawahata Noriyuki H , Goodman Murray
Published: December 2004

The crystal structure of the hydantoin 1‐[(S)‐1′–aminoethylmalonyl benzyl ester]‐(S)‐4‐methylimidazolidin‐2.5‐dione (1) derived from the peptide H‐Ala‐gAla‐mGly‐OBzl, Having the retro‐inverso modification of the Ala‐Gly bond, has been determined by x‐ray diffraction analysis. The crystals are orthorhombic, space group P212121 with a = 6.539. b = 14.721, c = 17.101 Å, z = 4. The structure was solved by direct methods and refined with anisotropic thermal factors to a final R value of 0.067 for the 947 observed reflections.

Reversal of the Ala‐Gly amide bond perturbs the folding tendency of the backbone shown by the parent peptide t‐BuCO‐Ala‐Gly‐NHiPr. The gem‐diamino residue, gAla, and the malonyl moieties are found in the helical and the extended conformations, respectively. Intramolecular hydrogen bonding is not observed. The molecules in the crystal are held together by the formation of two intermolecular hydrogen bonds of the NHOC type with NO distances of 2.86 and 3.17 Å respectively. 1995 John Wiley&Sons. Inc. © 1995 John Wiley & Sons, Inc.
Thermodynamics of melting of the circular dumbbell d〈pCGC‐TT‐GCG‐TT〉
Authors: Ippel Johannes H , Lanzotti Virginia , Galeone Aldo , Mayol Luciano , van den Boogaart Jaquelien E , Pikkemaat Jeroen A , Altonaf Cornelis
Published: December 2004

The conformational behavior of DNA minihairpin loops is sensitive to the directionality of the base pair that closes the loop. Especially tailored circular dumbbells, consisting of a stem of three Watson–Crick base pairs capped on each side with a minihairpin loop, serve as excellent model compounds by means of which deeper insight is gained into the relative stability and melting properties of hairpin loops that differ only in directionality of the closing pair: C‐G vs G‐C. For this reason the thermodynamic properties of the circular DNA decamers 5′‐d〈pCGC‐TT‐GCG‐TT〉‐3′(I) and reference compounds 5′‐d〈pGGC‐TT‐GCC‐TT≤‐3′(II) and 5′‐d(GCG‐TC‐CGC)‐3′(III) are studied by means of nmr spectroscopy. MoleculesIandIIadopt dumbbell structures closed on both sides by a two‐membered hairpin hop. At low temperatureIconsists of a mixture of two slowly exchanging forms, denotedL2L2andL2L4. The low‐temperatureL2L2form is the fully intact minihairpin structure with three Watson–Crick C‐G base pairs. The high‐temperature form,L2L4,contains a partially disrupted closing G‐C base pair in the 5′‐GTTC‐3′ loop, with the cytosine base placed in a syn orientation. The opposite 5′‐CTTG‐3′ loop remains stable. A study of the noncircular hairpin structureIIIshows similar conformational behavior for the 5′‐GTTC‐3′ loop as found inIa syn orientation for C(6) and two slowly exchanging imino proton signals for G(3). The melting point Tm of IIwas estimated to lie above 365 K. The Tm value of the duplex stem and the 5′‐CTTG‐3′ loop of theL2L4form ofIis 352 ± 2 K. The ΔH° is calculated as −89 ± 10 kJ/mol. The Tm value determined for the individual residues of the 5′‐GTTC‐3′ loop lies 4°–11° lower. The enthalpy ΔH° of melting the thymine residues in the 5′‐GTTC‐3′ loop is calculated to be ‐61± 7 kJ/mol. Thermodynamic data of the equilibrium between the slowly exchanging two‐ and four‐membered loop conformers of I reveal an upper limit for ΔH° of +30 kJ/mol in going from a two‐memberedto a four‐membered loop, in agreement with the enthalpy difference of +28 k.j/mol between the two loops at the Tm midpoint. For hairpin III the upper limit for ΔH° going from a two‐membered to a four‐membered loop amounts to ±21 kJ/mol. The mutual exchange rate between the L2 and L4 form in III is estimated as 13.6 s−1. Our results clearly suggest that small four‐way DNA junctions(model for immobilized Holliday junctions) can be designed that consist of a single DNA strandthat features ‐CTTG‐caps on three of the four arms of the junction. © 1995 John Wiley & Sons, Inc.
Structure of two microcystins: Refinement with nuclear overhauser effects and ensemble calculations
Authors: Mierke Dale F , Rudolph‐Böhner Sabine , Müller Gerhard , Moroder Luis
Published: December 2004

Ensemble calculations employing restraints developed from 1H‐nmr were used to examine the conformational states of the two microcystins LR and LY. Despite the fast “flip‐flop” dynamics about the N‐methyl‐dehydroalanine residue and adjacent residues, the main conformational characteristics of the cyclic heptapeptides consist of a compact ring formed by five of the seven amino acid residues with expulsion of a dipeptide portion out of the plane and the unnatural C20 β‐amino acid (2S. 3S. 8S, 9S)‐3‐amino‐9‐methoxy‐2, 6, 8‐trimethyl‐10‐phenyldeca‐4. 6‐dienoic acid pointing upward from the ring. This structure of microcystin LR shows high degrees of similarity with the energy‐minimized structure of nodularin, a cyclic pentapeptide of identical inhibitory potency against protein phosphatases 1 and 2A. Comparison of these structures with those of the less toxic LY variant and with the structurally unrelated okadaic acid, known as potent inhibitor of the protein phosphatases 1 and 2A, allowed us to propose a rational binding mode of this structural diverse set of natural inhibitors. © 1995 John Wiley & Sons, Inc.