bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discontinuous volume transitions induced by calcium–sodium ion exchange in anionic gels and their neurobiological implications
Authors: Tasaki I. , Byrne P. M. 
Published: December 2004

AbstractDiscontinuous volume transitions in poly(acrylic acid) gels were studied by determining equilibrium swelling curves of small gel beads immersed in salt solutions containing varying concentrations of Ca2+ and Na+. Reversible contractions of gel membranes associated with Ca2+‐Na+ exchange were examined using both isometric and isotonic recording devices. A discontinuous change in electric conductance was demonstrated in association with Ca2+‐Na+ exchange in gel membranes. These experimental findings provide a sound physicochemical basis for elucidating the mechanism of nerve excitation. © 1994 John Wiley & Sons, Inc.
Condensation of DNA by basic protiens does not depend on protien composition
Authors: Garcia‐Ramírez Marta , Subirana Juan Antonio 
Published: December 2004

AbstractWe have studied by electron microscopy the size and morphology of the complexes obtained with different DNAs (between 500 and 5243 base pairs long) and four different proteins: sea urchin histone H1; sea cucumber histone ϕ0, chicken erythrocyte histone H5, and clupeine. Surprisingly, the type of protein used has only a marginal influence on the complexes formed. The molecular weight and topology of DNA do not show any influence. The size of the complexes depends strongly on the ratio of positive to negative charges and also on the ionic conditions. Our studies have been mainly carried out at a ratio of 0.4. Under these conditions the average thickness of rods and toroids observed varies between 165 Å at 1.5 mM salt to 290 Å at 100 mM salt, with minor variations around these values depending on the type of DNA and protein used. We conclude that the formation of DNA condensates is mainly determined by a balance of electrostatic and intermolecular forces, the influence of specific interactions is only marginal. This conclusion seems to apply not only to the complexes described here, but also to chromatin fibers and to DNA condensed by low molecular weight counterions and other compounds (polyamines, inorganic ions, ethanol, etc.). © 1994 John Wiley & Sons, Inc.
Low‐temperature IR spectroscopy reveals four stages of water loss during lyophilization of hen egg white lysozyme
Authors: Remmele Richard L. , Stushnoff Cecil 
Published: December 2004

AbstractWater loss during lyophilization of a 49.4 mg/mL solution of lysozyme in D2O was studied with ir spectroscopy using a low‐temperature, single reflection, horizontal, attenuated, total reflectance accessory. Four regions of water loss were identified and assignable to different forms of bound water. The amide I band begins to shift to higher frequency while the amide II concurrently shifts to lower frequency and broadens after the first stage of water loss (sublimation) at −10°C. Additionally, the carboxylate band (at 1584 cm−1) shifts slightly to lower frequency. A second stage at 17°C is characterized by continued shifts in the carboxylate and amide II bands to low frequency, further broadening in the amide II and greater shift to high frequency in the amide I (ascribed to the removal of periphery water around the protein). At the third stage of water loss, the carboxylate band decreases substantially in relative absorbance (consistent with the removal of water from the carbonyl backbone). In the fourth and last stage, the carboxylate band nearly disappears and water loss is very slow. Based upon a final level of hydration of 0.037 h, the last stage corresponds to 25% completion of the removal of water associated with ionizable side chains. From start to finish, the amide I shifts 9 cm−1 to higher frequency. © 1994 John Wiley & Sons, Inc.
Filipin and its interaction with cholesterol in aqueous media studied using static and dynamic light scattering
Authors: Castanho Miguel A. R. B. , Brown Wyn , Prieto Manuel J. E. 
Published: December 2004

AbstractAggregation of filipin in aqueous medium and filipin‐induced changes in cholesterol micelles have been studied using intensity and dynamic light scattering. The dependencies of filipin aggregate dimensions on concentration, solvent, and temperature were studied, and revealed that the aggregates do not have a well‐defined geometry, i.e., a critical micelle concentration cannot be detected and stable structures are not formed. The aggregates are of size Rg ≈ 110 nm and Rh ≈ 63 nm, referring to the radius of gyration and hydrodynamic radius, respectively. In the concentration range studied (1 μM < C < 30 μM), a low molecular weight species (monomer/dimer) is always present together with the aggregates. In ethanol/ water mixtures, large (Rg ≈ 500 nm), narrow distribution aggregates are formed in the water volume fraction range 0.45 < ΦH2O < 0.65. Aggregation also occurs on changing the temperature; In the range 7–37°C, smaller aggregates (10–30 nm) form and the process is only partially reversible.No pronounced effect of filipin on the structure of the cholesterol micelles was observed (a small increase in Rg and Rh is noted). These results rule out any “specificity” for the filipin interactions with cholesterol, which has been considered a key event in the filipin biochemical mode of action. A reevaluatiori Of this question is suggested and some alternatives are advanced. © 1994 John Wiley & Sons, Inc.
α‐Helical assembly of biologically active peptides and designed helix bundle protein
Authors: Morii Hisayuki , Honda Shinya , Ohashi Shinichi , Uedaira Hatsuho 
Published: December 2004

AbstractThe formation of α‐helical assembly by complexing biologically active peptides with de novo designed protein is described. The de novo designed protein described here is a cystinelinked 4‐helix bundle protein constructed with 80 amino acid residues and forms a hydrophobic core region surrounded by 4 helices in an aqueous solution. The biologically active peptides, such as melittin and human growth hormone releasing factor, contain the sequences that are able to form amphiphilic helices. These peptides alone do not form the α‐helix structure in a diluted solution with low ion strength. But on mixing with the designed helix bundle protein, the peptides are strongly bound to the protein with the induction of α‐helical structure in the biologically active peptides. The content of induced α‐helix is in accord with that estimated from the amphiphilic sequence. The results mean that a novel architecture composed of α‐helices is formed. Fluorescent and temperature‐scanning measurement revealed that the α‐helical assembly is constructed with hydrophobic interaction. Also, it is shown by means of fluorescence depolarization that the assembly has a compact globular form corresponding to 1 : 1 complex. © 1994 John Wiley & Sons, Inc.
Magnesium‐DNA interactions from interpretation of 25Mg‐nmr relaxation rates: Field and coion dependence
Authors: Wright Laura A. , Lerner Laura E. 
Published: December 2004

AbstractWe have used 25Mg‐nmr to investigate the binding of magnesium ions to double‐stranded DNA. We have measured line shapes for 25Mg in the presence of monodisperse calf thymus DNA (160 base pairs; b.p.) (magnesium : phosphate = 2.0) at two different field strengths, 11.75 T and 7.05 T, and used the isotropic model of two‐site exchange developed by Westlund and Wennerstrom to simultaneously fit the line shapes at both field strengths. This model does not reproduce the observed field dependence. This is in contrast to a previous study [E. Berggren, L. Nordenskiold, and W. H. Braunlin (1992), Biopolymers, Vol. 32, pp. 1339–1350] in which a similar model of isotropic two‐site exchange qualitatively reproduced the temperature dependence of the line widths.Relaxation rates were also measured as a function of magnesium : phosphate ratio and colon type. These measurements were used to assess the sensitivity of magnesium relaxation measurements to small changes in DNA structure induced by changes in the solvent environment. The temperature dependence of the line shape varies with the type of coion (chloride or sulfate) present. This coion dependence of the line shape is consistent with the coion dependence of the aggregation midpoint temperature reported by Bloomfield and co‐workers [O. A. Knoll, M. G. Fried, and V. A. Bloomfield (1988) in Structure and Expres‐sion, Vol. 2, R. H. Sarma and M. H. Sarma, Eds., Adenine Press, New York] and attributed to a lyotropic effect. These results suggest that even at low magnesium : phosphate ratios, relaxation parameters are specific to each magnesium–coion–DNA system. © 1994 John Wiley & Sons, Inc.
A CD and an nmr study of multiple bradykinin conformations in aqueous trifluoroethanol solutions
Authors: Cann John R. , Liu Xiaohong , Stewart John M. , Gera Lajos , Kotovych George 
Published: December 2004

AbstractCD and nmr studies have been carried out on aqueous trifluoroethanol (TFE) solutions of bradykinin (BK) and a bradykinin antagonist. The CD results exhibit a striking effect of TFE on the spectra of BK, with sequence Arg‐Pro‐Pro‐Gly‐Phe‐Ser‐Pro‐Phe‐Arg, and the BK antagonist, with sequence D‐Arg‐Arg‐Pro‐Hyp‐Gly‐Thi‐D‐Ser‐D‐Cpg‐Cpg‐Arg [where Hyp is 4‐hydroxy‐L‐proline; Thi refers to β‐(2‐thienyl)‐L‐alanine and Cpg refers to α‐cyclopentylglycine]. The effect of increasing concentration of TFE in water on the difference ellipticity at 222 nm was examined and showed that BK may be a mixture of at least two different conformers, one of which largely forms when the TFE concentration is increased beyond 80%. The linear extrapolation of 100% of the difference ellipticity of BK at low TFE concentrations yields a value in agreement with that shown by the BK antagonist, indicating that the conformation of BK at the lower TFE concentrations is similar to that of the BK antagonist. The conformational analysis was carried out using both one‐dimensional and two‐dimensional 1H‐nmr techniques. The total correlation spectroscopy (TOCSY) spectrum of BK in a 60/40% (v/v) TFE/H2O solution at 10°C and a nuclear Overhauser effect spectroscopy (NOESY) spectrum that shows only sequential Hα(i) – NH(i + 1) or the Hα(i) – Hδδ′(i + 1) NOEs indicate that the majority of the molecules adopt an all‐trans extended conformation. The TOCSY for BK in the 95/5% (v/v) TFE/H2O solution shows that there are two major conformations in the solution with about equal population. The NOESY experiment shows two new important cross peaks for one conformation, namely Pro2(α)‐Pro3 (α) and the Pro2(α)‐Gly4(NH), indicating a cis Pro2‐Pro3 bond and a type VI β‐turn between residues Arg1 and Gly4 involving cis proline at position 3, respectively. The low temperature coefficient of Gly4 for this conformation suggests the presence of an intramolecular hydrogen bond, therefore a type VIa β‐turn is present. The other conformation is all trans and extended.The BK antafonist shows difference CD spectra in TFE solutions referred to H2O that are superficially indicative of a β‐bend. However, nmr speaks against this possibility, as only one set of peaks were observed in the TOCSY and NOESY experiments, indicating an all‐trans extended confirmation over the range of TFE concentrations. The BK‐antagonist CD data suggest that solvent perturbation of the CD of an extended confirmation perturbation of the optical activity of the thienyl moiety of the peptide since the CD spectrum of N‐acetyl‐β‐thienyl‐L‐alanine N‐methylamide is strongly perturbed by TFE. The present results again demonstrate the complementary relationship between CD and nmr. © 1994 John Wiley & Sons, Inc.
Three‐dimensional Hartree–Fock crystal‐orbital calculation on crystalline diprotonated deoxycytidine‐5′‐monophosphate monohydrate: Toward rationalizing nucleic acid semiconductivity
Authors: Starikov E. B. 
Published: December 2004

AbstractA three‐dimensional Hartree–Fock crystal‐orbital calculation on the crystal of diprotonated deoxycytidine‐5′‐monophosphate monohydrate has been carried out using the CRYSTAL92 routine package. According to the calculation, this crystallohydrate can be considered a quasi one‐dimensional hole semiconductor with the indirect fundamental gap of 1.66 eV and with a possibility for the uv‐excited quasi one‐dimensional electron photoconductivity. The physical source for such properties is the charge transfer from the phosphate to the water molecule and cytosine residue, favored by the strong electrostatic interaction between nucleotide zwitterions and by the formation of the infinite spirals of hydrogen‐bonded zwitterions along one of the crystallographic axes. © 1994 John Wiley & Sons, Inc.
Conformation and sweet tastes of L‐aspartyl dipeptide methyl esters
Authors: Kim Young Ju , Han Seong Jun , Kim Shi Choon , Kang Young Kee 
Published: December 2004

AbstractIn order to investigate the conformational preferences to elicit tastes, conformational free energy calculations using an empirical potential (ECEPP/2) and the hydration shell model were carried out on the L‐aspartyl dipeptide methyl esters, L‐+HAsp−‐L‐Xaa‐OMe, in the hydrated state, where Xaa includes sweet (Phe, Tyr, Met, and Gly), bitter (Ala, Trp, Val, Leu, and Ile), and tasteless (Ser, Thr, and Abu) residues. The refined preferred conformation of the Phe dipeptide (aspartame) with side chain χ conformation g− is g−Fg− in the hydrated state, which is consistent with the structure deduced from 1H‐nmr experiments. Irrespective of the Xaa and taste, all the dipeptides have the same conformation for the Asp residue, which is attributable to the hydrogen bond between protonated amino hydrogen and carboxylate oxygen and the favored hydration of the carboxylate group. This implies that the L‐aspartyl residue is a necessary factor for the dipeptides to be sweet not a sufficient factor. The computed conformational preferences for sweet, bitter, and tasteless dipeptides in the hydrated state indicate to us that the conformation about the NCα bond of the Xaa residue, i.e., the orientation of the hydrophobic moiety with respect to the AH/B functionalities in the aspartyl moiety, seems to be crucial to elicit the tastes. In addition, the hydrophobicity and the size of the Xaa residue are found to play a major role in determining the tastes. These well accord with the related works reported previously. © 1994 John Wiley & Sons, Inc.
Conformational polymorphism in telomeric structures: Loop orientation and interloop pairing in d(G4TnG4)
Authors: Mohanty Debasisa , Bansal Manju 
Published: December 2004

AbstractSequence repeats constituting the telomeric regions of chromosomes are known to adopt a variety of unusual structures, consisting of a G tetraplex stem and short stretches of thymines or thymines and adenines forming loops over the stem. Detailed model building and molecular mechanics studies have been carried out for these telomeric sequences to elucidate different types of loop orientations and possible conformations of thymines in the loop. The model building studies indicate that a minimum of two thymines have to be interspersed between guanine stretches to form folded‐back structures with loops across adjacent strands in a G tetraplex (both over the small as well as large groove), while the minimum number of thymines required to build a loop across the diagonal strands in a G tetraplex is three. For two repeat sequences, these hairpins, resulting from different types of folding, can dimerize in three distinct ways—i.e., with loops across adjacent strands and on same side, with loops across adjacent strands and on opposite sides, and with loops across diagonal strands and on opposite sides—to form hairpin dimer structures. Energy minimization studies indicate that all possible hairpin dimers have very similar total energy values, though different structures are stabilized by different types of interactions. When the two loops are on the same side, in the hairpin dimer structures of d(G4TnG4), the thymines form favorably stacked tetrads in the loop region and there is interloop hydrogen bonding involving two hydrogen bonds for each thymine–thymine pair. Our molecular mechanics calculations on various folded‐back as well as parallel tetraplex structures of these telomeric sequences provide a theoretical rationale for the experimentally observed feature that the presence of intervening thymine stretches stabilizes folded‐back structures, while isolated stretches of guanines adopt a parallel tetraplex structure. © 1994 John Wiley & Sons, Inc.
Dynamic viscoelastic properties of glycinin and β‐conglycinin gels from soybeans
Authors: Nagano Takao , Akasaka Takeshi , Nishinari Katsuyoshi 
Published: December 2004

AbstractThe effects of heating temperature on gel properties and conformational changes were investigated in glycinin and β‐conglycinin gels using Theological and Fourier transform ir (FTIR) methods. Solutions of 15 wt % glycinin or β‐conglycinin in 35 mM phosphate buffer at pH 7.6 were heated at various temperatures for 30 min and rheological properties were measured at 20°C. The storage modulus G′ as a function of frequency changed from a monotonical decrease with decreasing frequency to a plateau in the range from 0.0018 to 40 Hz by heating at temperatures higher than 80°C for glycinin and 65°C for β‐conglycinin. A band at 1618 cm−1 (associated with the β‐sheet structure) on ir spectra increased with the formation of heat‐induced gels. The value of the storage modulus G′ correlated well with the increase in absorbance at 1618 cm−1. These results suggest that the formation of a β‐sheet structure may be closely related to the value of the storage modulus G′ for heat‐induced gels in soybean proteins and that heat‐induced gels of glycinin and β‐conglycinin are formed by cross‐links with intermolecular β‐sheet structures. © 1994 John Wiley & Sons, Inc.
Phosphophoryn, an “acidic” biomineralization regulatory protein: Conformational folding in the presence of Cd(II)
Authors: Evans John Spencer , Chiu Thomas , Chan Sunney I. 
Published: December 2004

AbstractThe divalent cation‐induced protein folding properties of the template macromolecule, bovine dentine phosphophoryn (BDPP), have been examined by 1H/31P/13C/113Cd‐nmr spectroscopy. Cd(II) was employed, exploiting the sensitivity of 113Cd‐nmr to ligand‐binding interactions and kinetics. Cation binding was studied over the stoichiometric range of 0–50 : 1 Cd(II) : protein (mole ratio), well below the range of Cd(II) concentration required to induce protein precipitation. The stepwise titration of divalent cation‐depleted phosphophoryn at pH 7.2 in H2O/D2O with 113CdCl2 revealed that (PSer)n, (PSerAsp)n, and (Asp)n polyelectrolyte cation‐binding domains undergo two major transitions in their secondary and tertiary structures: the first transition, occurring between 1 : 10 and 1 : 1 Cd(II) : protein stoichiometry, and the second, between 10 : 1 and 50 : 1. By monitoring the amide NH intensities, 31P‐nmr chemical shift, and 13C Asp‐C, resonances, it was concluded that Cd(II) ions exhibit a binding‐site preference for polyelectrolyte cation‐binding domains, in the order

This preference correlates with the degree of negative charge density for each sequence motif. Accompanying the backbone conformational transitions at the polyelectrolyte regions were conformational transitions in the flanking hinge domains, indicating that the hinge domains participate in the folding of the phosphophoryn molecule as divalent cation binding occurs at the polyelectrolyte domains.We were unsuccessful in detecting phosphophoryn‐bound Cd (11) species by 113Cd‐nmr because of chemical exchange modulation. However, using a smaller 21‐residue peptide mimetic of phosphophoryn, we have observed three stoichiometric‐dependent 113Cd resonances that differ in terms of the oxoanion coordination number. Our observation of multiple Cd(II) species in the presence of the peptide supports our contention that Cd(II) has many chemically distinct coordination sites on phosphophoryn, each in multiple equilibria with H2O, Cl−, and side‐chain oxoatoms. © 1994 John Wiley & Sons, Inc.
Nmr and molecular modeling investigations of the neuropeptide substance P in the presence of 15 mM sodium dodecyl sulfate micelles
Authors: Young John K. , Hicks Rickey P. , Anklin Clemens 
Published: December 2004

AbstractTo better understand the structural basis of the biological activity of the neuropeptide substance P SP; (Arg‐Pro‐Lys‐Pro‐Gln‐Gln‐Phe‐Phe‐Gly‐Leu‐Met‐NH2), two‐dimensional nmr spectroscopy experiments and simulated annealing calculations were used to investigate the conformation adopted in the presence of the membrane model system sodium dodecyl sulfate. It was determined that SP in the presence of SDS micelles undergoes a conformational equilibrium between an α‐ and a 310‐helix involving the midregion (Pro4‐Gln5‐Gln6‐Phe7‐Phe8) of the peptide. The C‐terminus adopts an extended conformation while the N‐terminus remains quite flexible. The conformation adopted by SP in the presence of SDS micelles yields a structure that is consistent with the model of a neurokinin‐1 selective ligand proposed by Convert. © 1994 John Wiley & Sons, Inc.
A crystal structure with features of an antiparallel α‐pleated sheet
Authors: Di Blasio Benedetto , Saviano Michele , Fattorusso Roberto , Lombardi Angela , Pedone Carlo , Valle Valentina , Lorenzi Gian P. 
Published: December 2004

AbstractA single‐crystal x‐ray diffraction analysis of Boc‐L‐Ala‐D‐aIle‐L‐Ile‐OMe has been carried out. The analysis has shown (a) that the tripeptide molecules have in part an α‐extended conformation, the torsion angles of the L‐Ala and D‐aIle residues being φ1 = −75.1° and ψ1 = −25.8° and φ2 = 67.3° and ψ2 = 44.1°, respectively, and (b) that the molecules are organized in rippled planes where they occur in relative antiparallel orientation linked together side by side by H bonds. This molecular organization of the tripeptide corresponds closely to that of an antiparallel α‐pleated sheet, and likely constitutes the first example of a structure of this kind for which a characterization at the atomic level has been achieved. A molecular dynamics study has shown that the molecular conformation of the tripeptide in the crystalline state is determined primarily by intermolecular interactions. © 1994 John Wiley & Sons, Inc.
β‐Alanine containing cyclic peptides with predetermined turned structure. V
Authors: Pavone Vincenzo , Lombardi Angelina , Saviano Michele , Di Blasio Benedetto , Nastri Flavia , Fattorusso Roberto , Maglio Ornella , Isernia Carla 
Published: December 2004

AbstractIn the present paper we describe the synthesis, purification, single crystal x‐ray analysis, and solution structural characterization by nmr spectroscopy, combined with restrained molecular dynamic simulations, of the cyclic hexapeptide cyclo‐(Pro‐Phe‐β‐Ala‐Phe‐Phe‐β‐Ala). The peptide was synthesized by classical solution methods and the cyclization of the free hexapeptide was accomplished in good yields in diluted methylenechloride solution using N, N‐dicyclohexyl‐carbodiimide. The compound crystallizes in the monoclinic space group P21 from methanol/ethyl acetate. The molecule adopts in the solid state a conformation characterized by cis β‐Ala6‐Pro1 peptide bond. The α‐amino acid residues are at the corner positions of turned structures. The Pro1‐Phe2 segment is incorporated in a pseudo type I β‐turn, while Phe4‐Phe5 is in a typical type I β‐turn. Assignment of all 1H and 13C resonances was achieved by homo‐ and heteronuclear two‐dimensional techniques in dimethylsulfoxide (DMSO) solutions. The conformational analysis was based on inter‐proton distances derived from rotating frame nuclear Overhauser effect spectroscopy spectra and homonuclear coupling constants. Restrained molecular dynamic simulation in vacuo was also performed to built refined molecular models. The molecule is present in DMSO solution as two slowly interconverting conformers, characterized by a cis‐tran isomerism around the β‐Ala6‐Pro1 peptide bond. This work confirms our expectations on the low propensity of β‐alanyl residues to be positioned at the corners of turned structure. © 1994 John Wiley & Sons, Inc.