bluuebunny/crossref_metadata_2025_split huggingface dataset:
The thermodynamic parameters of the interaction of concanavalin A with glycosyl‐free liposomes: A microcalorimetric study
Authors: Lüscher‐Mattli Madeleine 
Published: December 2004

AbstractThe nonspecific interaction of the mitogenic lectin Concanavalin A (Con A) with glycosyl‐free liposomes of various composition has been investigated by microcalorimetric titration measurements. The results obtained show the following features of main interest: (1) the affinity constants (Ka) of the interaction of Con A with liposomal bilayers are in the order of magnitude 105–106M−1. The reaction enthalpies (ΔH) are positive, and small (approximately 0.1 KJ mol−1 lipid), compared to the free energy terms (−ΔG = 30–40 KJ mol−1 lipid). All lectin–lipid interactions are strongly entropy‐controlled (ΔH/TΔS < 1.0). These thermodynamic features are characteristic for hydrophobic interaction processes. (2) The liposomal head‐group charge does not significantly affect the lipid‐affinity of Con A. Electrostatic forces thus appear to play a minor role in lectin–lipid interactions. (3) The lipid affinity of Con A is sensitive to the fluidity of the liposomal bilayers, increasing with increasing fluidity. Below the gel to liquid‐crystal phase transition temperature, the lectin binding to liposomal bilayers is inhibited. (4) The binding isotherms, corresponding to the interaction of Con A with liposomes, composed of tightly packed, saturated phospholipids, exhibit pronounced positive cooperativity. This phenomenon is absent in the binding curves, corresponding to the interaction of Con A with more fluid liposomal bilayers. (5) The Con A specific inhibitor α‐D‐methylmannopyranoside (50 mM) drastically increases the molar reaction enthalpy. The Ka term is significantly reduced in presence of the inhibitor sugar. Urea induces analogous changes in the thermodynamic parameters of the lectin–lipid interaction. The effects of α‐D‐methylmannopyranoside are thus not Con A specific, but are attributable to solvent effects. (6) It was shown that the binding of one Con A molecule affects a large number (approximately 1000) of phospholipid molecules in the liposomal bilayer. (7) The affinity constants (Ka) of the interaction of Con A with glycosyl‐free lipids are smaller by a factor of approximately 10, compared to the Ka terms, reported for Con A binding to biological membranes. The presence of glycosidic receptor groups thus controls the specificity of lectin–membrane interactions, whereas the nonspecific lectin–lipid interactions appear to represent the main driving force for the strong attachment of the lectin to membrane surfaces.
β‐Turns in bridged proline‐containing cyclic peptide models
Authors: Hollósi M. , Kövér K. E. , Holly S. , Radics L. , Fasman G. D. 
Published: December 2004

AbstractThe synthesis, CD, ir spectroscopic, and conformational studies of a series of bridged cyclic peptides of the general formula, cyclo[NH‐(CH2)n‐CO‐Gly‐Pro‐Y‐Gly] (2a–d, Y = Gly or Ser(OBut), n = 4 or 2) is reported. As indicated by difference nuclear Overhauser enhancement and Fourier transform ir experiments, the tetrapeptide sequence of cyclo[NH‐(CH2)4‐CO‐Gly‐Pro‐Gly‐Gly] (2a) and cyclo[NH‐(CH2)2‐CO‐Gly‐Pro‐Gly‐Gly] (2b) adopts a 1 ← 4 hydrogenbonded type II β‐turn conformation in solution, while cyclo[NH‐(CH2)4‐CO‐Gly‐Pro‐Ser(OBut) ‐Gly] (2c) features a type I β‐turn, fixed by 1 ← 4 and Oγ … NH intramolecular H bonds. In aqueous solution 2a and 2c show class B and class C CD spectra, respectively. This is the first case reported of a typical class C CD pattern in aqueous solution for a conformationally mobile system having a type I β‐turn. Based on the comparison of the band intensities of the bridged models with those of linear and cyclic model systems reported earlier, a set of subspectra with reduced band intensities is suggested for use in the CD analysis of the conformation of polypeptides in solution.
Proline‐induced constraints in α‐helices
Authors: Piela Lucjan , Némethy George , Scheraga Harold A. 
Published: December 2004

AbstractThe disrupting effect of a prolyl residue on an α‐helix has been analyzed by means of conformational energy computations. In the preferred, nearly α‐helical conformations of Ac‐Ala4‐Pro‐NHMe and of Ac‐Ala7‐Pro‐Ala7‐NHMe, only the residue preceding Pro is not α‐helical, while all other residues can occur in the α‐helical A conformation; i.e., it is sufficient to introduce a conformational change of only one residue in order to accommodate proline in a distorted α‐helix. Other low‐energy conformations exist in which the conformational state of three residues preceding proline is altered considerably; on the other hand, another conformation in which these three residues retain the near‐α‐helical A‐conformational state (with up to 26° changes of their dihedral angles ϕ and ψ, and a 48° change in one ω from those of the ideal α‐helix) has a considerably higher energy. These conclusions are not altered by the substitution of other residues in the place of the Ala preceding Pro. The conformations of the peptide chain next to prolyl residues in or near an α‐helix have been analyzed in 58 proteins of known structure, based on published atomic coordinates. Of 331 α‐helices, 61 have a Pro at or next to their N‐terminus, 21 have a Pro next to their C‐terminus, and 30 contain a Pro inside the helix. Of the latter, 16 correspond to a break in the helix, 9 are located inside distorted first turns of the helix, and 5 are parts of irregular helices. Thus, the reported occurrence of prolyl residues next to or inside observed α‐helices in proteins is consistent with the computed steric and energetic requirements of prolyl peptides.
Dynamic light‐scattering study of semiflexible polymers: Collagen
Authors: Kubota Kenji , Tominaga Yasunori , Fujime Satoru 
Published: December 2004

AbstractDynamic light‐scattering measurements were carried out for collagen in acetate buffer (pH 4.8) extracted from lathyritic ratskin. The correlation functions were analyzed in terms of the semiflexibility of collagen molecules. The experimental Γ/K2 vs K2 relationship was compared with the theoretical one based on formulation including anisotropy in translational diffusion, chain flexibility, and the hydrodynamic interaction; Γ is the average decay rate and K is the magnitude of the momentum transfer vector. By using the model parameters evaluated from the Γ/K2 vs K2 relationship, a good agreement was obtained between profiles of theoretical and experimental correlation functions over the entire delay times. Detailed examinations of the dynamic light‐scattering spectrum permitted us to conclude that a set of the contour length L of 300 nm and the Kuhn length γ−1 of 340 nm are much more probable than other sets of L and γ−1 that equally explain static quantities such as the radius of gyration. The results show that collagen molecules are well characterized by a wormlike chain model.
Simulation of the diffusion‐controlled reaction between superoxide and superoxide dismutase. II. Detailed models
Authors: Allison S. A. , Bacquet R. J. , McCammon J. A. 
Published: December 2004

AbstractA two‐stage Brownian dynamics simulation method is used to study the diffusion‐influenced bimolecular reaction between superoxide and superoxide dismutase (SOD). The crystal structure of the dimeric enzyme is used in constructing detailed topographical and electrostatic models. Several electrostatic models are considered. In the most realistic, the excluded volume of the protein, which is impermeable to penetration by mobile ions, is assigned a dielectric constant of 2 and the surrounding “solvent” is assigned a value of 78. A finite difference method is used to solve the linearized Poisson–Boltzmann equation. For native SOD, the simulations reproduce the pronounced salt dependence of the rate constant observed experimentally. This salt dependence is attributed to electrostatic interactions between enzyme and substrate that are inherently attractive and amplified by the low dielectric constant of the protein interior. The simulation method is also applied to a modified enzyme, acylated SOD.
The role of hydroxyproline in collagen folding: Conformational energy calculations on oligopeptides containing proline and hydroxyproline
Authors: Bansal M. , Ananthanarayanan V. S. 
Published: December 2004

AbstractWe have observed that the rate of folding of the enzymatically hydroxylated form of poly(Gly‐Pro‐Pro) into the triple‐helical conformation is considerably higher than that of the unhydroxylated polypeptide [R. K. Chopra and V. S. Ananthanarayanan (1982) Proc. Natl. Acad. Sci. USA 79, 7180–7184]. In this study, we examine a plausible kinetic pathway for triple‐helix formation by selecting peptide models for the unhydroxylated collagen molecule, and computing their conformational energies before and after proline hydroxylation. Starting with the available data on the preferred conformations of proline‐ and hydroxyproline‐containing peptide sequences, energy minimization was carried out on the following pairs of peptides: Gly‐Ala‐Pro‐Gly‐Ala and Gly‐Ala‐Hyp‐Gly‐Ala; Gly‐Pro‐Pro‐Gly‐Ala and Gly‐Pro‐Hyp‐Gly‐Ala; Gly‐Ala‐Pro‐Gly‐Ala‐Pro and Gly‐Ala‐Hyp‐Gly‐Ala‐Hyp. It was found that, with each pair of peptides, the energetically most favorable conformation (I) has an extended structure at the Gly‐Ala or Gly‐Pro segment and a β‐bend at the Pro‐Gly or Hyp‐Gly segment. In the Hyp‐containing peptides, this conformation is further stabilized by a (Hypi + 2)OH…OC(Glyi) hydrogen bond. Conformation I is lower in energy by about 6–13 kcal/mol of the peptide than the fully extended conformations that resemble the single collagen polypeptide chain and contain no intramolecular hydrogen bond. In contrast to the proline counterpart, the hydroxyproline‐containing peptides are found capable of adopting a partially extended conformation that does not contain the β‐bend but retains the (Hyp)OH…OC(Gly) hydrogen bond. The energy of this conformation is intermediate between conformation I and the fully extended conformation. The continuation of the β‐bend along the chain is restricted by stereochemical constraints that are more severe in the latter two pairs of peptides than in the first pair. Such a restriction may be considered to trigger the “unbending” of the minimum energy conformation leading to its straightening into the fully extended conformation; the latter, in turn, would lead to triple‐helix formation through favorable interchain interactions. We propose that the partially extended conformation in the Hyp‐containing peptides could serve as a kinetic intermediate on the way to forming the fully extended conformation. Because of the (Hypi + 2)OH…OC(Glyi) hydrogen bond, this conformation would also serve to lock the trans geometry at the Gly‐Ala(Pro) and Ala(Pro)‐Hyp peptide bonds, thereby enhancing the rate of their helix formation. A scheme for collagen folding in proposed on the basis of these results.
Orientation of DNA during gel electrophoresis studied with linear dichroism spectroscopy
Authors: Jonsson Mats , Åkerman Björn , Nordén Bengt 
Published: December 2004

AbstractA method for in situ study of orientation of DNA during gel electrophoresis has been developed. Linear dichroism spectra measured by this phase‐modulation technique can sensitively and selectively detect orientation of DNA during electrophoretic migration in gel. [Measurement of “electrophoretic orientation” was first reported in 1985 by B. Åkerman, M. Jonsson, and B. Nordén (1985) (J. Chem. Soc. Chem. Commun. 422–423)]. Restriction fragments of duplex DNA of lengths in the ranges of 300–2319 base pairs (bp) and 4361–23130 bp have been studied in 5% polyacrylamide and 1% agarose gels, respectively. The fragments become preferentially oriented with the DNA helix axis parallel to the migration direction. In agarose the orientation is found to increase sigmoidally, and in polyacrylamide, linearly, with the electric field strength, within the field ranges accessible to measurement (0–40 and 5–40 V/cm, respectively). In both types of gels a considerable increase in orientation with length of DNA was observed. Compared to dipole orientation in electric fields, the electrophoretic orientation is high: orientation factor S = 0.027 in agarose for 23130 bp at 10 V/cm and S = 0.004 in polyacrylamide for 2319 bp at 10 V/cm. In addition to orientation of DNA, the electrophoresis also leads to orientation effects in the gel structure owing to Joule heating. In agarose there is also an effect that is associated with the migrating DNA zones and that produces different orientations of the gel at the front and rear parts of a zone. Evidence is presented that this effect is due to a DNA‐induced electroosmotic flow causing a contraction of the gel in the front of the zone and an expansion in the rear. The experimental results on DNA orientation are compared with the reptation theories for gel electrophoresis. The theory of Lumpkin et al. [O. J. Lumpkin, P. Dejardin, and B. H. Zimm (1985) Biopolymers 24, 1573–1593] predicts no orientation length dependence, but it does predict a shape of the field dependence that resembles the shape observed in agarose. The theory of Slater and Noolandi [G. W. Slater and J. Noolandi (1986) Biopolymers 25, 431–454] predicts an orientational length dependence that is an order of magnitude less than the experimental one, and a field dependence that agrees neither with the sigmoidal shape observed in agarose nor with the linear dependence in polyacrylamide.
A type II β‐turn in a flexible peptide: Proton assignment and conformational analysis of the α‐factor from saccharomyces cerevisiae in solution
Authors: Jelicks Linda A. , Naider Fred R. , Shenbagamurthi Ponniah , Becker Jeffrey M. , Broido Michelle S. 
Published: December 2004

AbstractTwo‐dimensional 1H‐nmr spectra of the α‐mating factor [in dimethyl sulfoxide‐d6 (DMSO) and in water] and several dodecapeptide analogues (in DMSO) were obtained. Homonuclear correlated spectroscopy resulted in the complete and unequivocal assignment of all backbone and side‐chain resonances of the peptides. The solution conformation of the pheromones was probed using two‐dimensional (2D) nuclear Overhauser effect spectroscopy (NOESY) and rotating frame nuclear Overhauer effect spectroscopy (ROESY). The 2D NOE results, and results of complementary one‐dimensional experiments, suggest that a type II β‐turn is assumed by the central portion of active pheromones in both DMSO and water. Inactive analogues of the α‐factor do not exhibit this structural feature. Except for this one β‐turn, the nmr parameters for α‐factor are indicative of a conformationally flexible molecule in both solvents. This conclusion is in contrast to that of other researchers who have proposed a highly structured conformation of α‐factor in aqueous solution.
Prediction of protein helix content from an autocorrelation analysis of sequence hydrophobicities
Authors: Horne David S. 
Published: December 2004

AbstractIt is demonstrated that protein α‐helix content can be predicted from an autocorrelation analysis of the protein hydrophobicity sequence. The Fourier transform of the autocorrelation function yields the spectral densities or weights of the various frequencies contributing to the autocorrelation function. Using sequence and secondary structure data from more than 160 proteins and domains, a linear relationship was found between spectral density at periodicity 3.7 and protein α‐helix content (r = 0.83). This relation permits prediction of the helix content (x) of proteins of known sequence to within ± 15%, i.e., as (x ± 15)%. Predictions based on the autocorrelation procedure are compared with values obtained by other methods.
Conformations and mitochondrial uncoupling activity of synthetic emerimicin fragments
Authors: Raj P. Antony , Das Manoj K. , Balaram P. 
Published: December 2004

AbstractSeveral amino terminal fragments of the emerimicins (Ac‐Phe1‐Aib2‐Aib3‐Aib4‐Val5‐Gly6‐Leu7‐Aib8‐Aib9‐Hyp10‐Gln11‐D‐Iva12‐Hyp13‐Ala/Aib14‐Phol15) ranging in length from five to ten residues have been synthesized. Nuclear magnetic resonance studies have been carried out on the 1‐5, 6‐10, 1‐6, 1‐7, 1‐8, 1‐9, and 1‐10 fragments. The number of solvent‐shielded NH groups in CDCl3 solutions for 1‐5, 1‐6, 1‐7, 1‐8, 1‐9, and 1‐10 indicate that 310‐helical structures are favored in this solvent. In (CD3)2SO, an additional NH group, assigned to Aib(3) NH is solvent exposed in the fragments longer than six residues, suggesting partial unfolding of the N‐terminal β‐turn or transition to an α‐helical conformation. The data for fragment 6‐10 are consistent with a conformation having a single Leu‐Aib β‐turn. Infrared studies suggest an increase in the number of intramolecular hydrogen bonds with increasing peptide chain length. Appreciable mitochondrial uncoupling activity is observed for peptides with a chain length of at least seven residues. The order of efficiencies of the fragments is 1‐7 < 1‐8 ∼ 1‐10 < 1‐9, with the decapeptide exhibiting anomalously low uncoupling activity.
Vibrational CD of polypeptides. XII. Reevaluation of the fourier transform vibrational CD of poly(γ‐benzyl‐L‐glutamate)
Authors: Malon Petr , Kobrinskaya Rina , Keiderling Timothy A. 
Published: December 2004

AbstractUsing a newly constructed Fourier transform ir (FTIR) based vibrational CD (VCD) instrument, we have found that elimination of the ellipsoidal collection mirror before the detector and its replacement by a lens leads to a significant improvement in the absorption artifact problem often seen previously in FTIR‐VCD. Reduction in artifact level brings the FTIR‐VCD band shape of the amide 1 band in poly(γ‐benzyl‐L‐glutamate) into better agreement with that found with dispersive instruments. These results indicate that the difference between the spectra obtained with the two methods is not primarily a factor of resolution but is more dependent on artifact level. Thus the previously reported deconvolution of the amide I VCD results and their subsequent interpretation in terms of the helical vs. exciton mechanisms overemphasize weak features in the spectrum. Results based on deconvolution of the absorption spectrum remain valid. Further new data on the amide II and several lower energy transitions that encompass the amide III region show broad single‐signed features—but of the opposite sense—in the two regions, implying that their VCD arises through mutual coupling.
On the interaction of chromomycin A3 with calf thymus DNA in the presence of metal cations at different pH values
Authors: Weinberger Sarah , Shafer Richard , Berman Elisha 
Published: December 2004

AbstractThe interactions of the antitumor antibiotics, chromomycin A3, with a variety of metal cations in the pH range of 3.0–8.5 were systematically studied by CD, absorption, and 1H‐nmr spectroscopies. Results were compared with those obtained in the presence of increasing amounts of calf thymus DNA. The negatively charged chromomycin A3, pKa 6.3, forms aggregates that become ordered and smaller in size, in the presence of variety of metal cations. Spectrophotometric titrations have shown that binding of the neutral drug to DNA at pH 4.5 does not require divalent cations, although the strength of the binding is greatly enhanced in their presence. At higher pH values (> 7.0) and low DNA/drug ratio ( > 20), the metal cations are necessary to induce the binding between chromomycin A3 and DNA. At higher DNA/drug ratios (> 100: 1), an appreciable proportion of the drug is bound even in the absence of divalent cations. Its binding affinity to the DNA is enhanced in the presence of these cations and at low pH values. Therefore, we conclude that chromomycin A3 binds in two related modes, in the presence and in the absence of divalent cations. The spectral data accumulated indicate the metal cation is involved in the binding of the drug to the DNA by forming a drug–metal–DNA ternary complex.
The association behavior of β‐lactamases in polyethylene glycol solution
Authors: Murthy N. Sanjeeva , Braswell Emory H. , Knox James R. 
Published: December 2004

AbstractThe β‐lactamases (EC 3.5.2.6) from Bacillus licheniformis 749/C, Enterobacter cloacae P99, and TEM plasmid RP4 are studied in 10–14% (w/v) polyethyleneglycol (PEG) 8000 solutions at pH 6.5 by x‐ray scattering and in 18% PEG by equilibrium sedimentation. Although all three enzymes crystallize with twofold crystal symmetry from PEG 8000, it is not possible in this study to prove that dimerization occurs; however, both techniques give evidence for association above 1% (w/v) protein concentration. For the B. lichen., P99, and TEM enzymes, a dimerization of at most 0, 5, and 10% (v/v), respectively, account for the variation of radii of gyration Rg with concentration, after accounting for the effects of nonideality. Apparent Rg were 3–5% smaller in PEG solution than in PEG‐free solution. Enhanced ordering of the molecules in PEG solution or the presence of a PEG‐depleted hydration shell around the enzymes can account for the observation of reduced Rg values. Accordingly, values of the partial specific volume (defined at constant chemical potential of PEG) indicate considerable PEG exclusion and are consistent with the ability of high Mr PEGs to induce crystallization of these enzymes.
Vasopressin conformational fluctuations: A molecular dynamics study
Authors: Somoza J. R. , Brady J. W. 
Published: December 2004

AbstractMolecular dynamics simulations have been used to study the conformational fluctuations of the oligopeptide hormone vasopressin. Starting coordinates for these simulations were built upon the crystal structure of pressinoic acid, the cyclic ring moiety of vasopressin, recently determined by x‐ray diffraction. Coordinates for the additional tripeptide “tail” of vasopressin were selected by arbitrary positioning of this segment using interactive computer graphics. Two such starting configurations were minimized to relax strains, and long dynamics simulations (20 and 40 ps) in vacuo were then conducted following extensive heating and equilibration sequences (36 ps). In these studies, vasopressin was found to undergo few substantial conformational changes at 300 K on the time scale simulated, in contrast to the results of a shorter previous simulation, but comparable structural transitions were observed during the equilibration periods. The pressinoic acid structure was found to be a reasonably stable possible conformation for vasopressin in vacuum on this time scale.