bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thermal denaturation of Na‐ and Li‐DNA in salt‐free solutions
Authors: Korolev N. I. , Vlasov A. P. , Kuznetsov I. A. 
Published: December 2004

AbstractThermal denaturation of Na‐ and Li‐DNA from chicken erythrocytes was studied by means of scanning microcalorimetry in salt‐free solutions at DNA concentrations (Cp) from 4.5 · 10−2 to 1 · 10−3 moles of nucleotides/liter (M). Linear dependencies of DNA melting temperature (Tm) vs lgCp were obtained:

for Na‐ and Li‐DNA, respectively. Microcalorimetry data were compared with the results of spectrophotometric studies at 260 nm of DNA thermal denaturation in Me‐DNA + MeCl solutions at Cp ≃ (6–8) · 10−5 M and Cs = 0–40 mM (Me is Na or Li, Cs is salt concentration). It was found that Eqs. (1) and (2) are valid in DNA salt‐free solutions over the Cp range 6 · 10−5−4.5 · 10−2M. Protonation of DNA bases due to the absorption of CO2 from air in Na‐DNA + NaCl solutions affects DNA melting parameters at Cs < 4 mM. Linear dependence of Tm on lga+ is found in Na‐DNA + NaCl at Cs > 0.4 mMin the absence of contact of solutions with CO2 from air (a+ is cation activity). A dependence of [dTm/dlga+] on Li+ activity was observed in Li‐DNA + LiCl solutions at Cs < 10 mM: [dTm/dlga+] increases from 17°–18° at Cs > 10 mM to 28°–30° at Cs ≃ 0.2–0.4 mM. Spectrophotometric measurements at 282 nm show that this effect was caused by protonation of bases in fragments of denatured DNA in neutral solutions. The Poisson–Boltzmann (PB) equation was solved for salt‐free DNA at the melting point. The linear dependence of Tm vs lgCp was interpreted in terms of Manning's condensation theory. PB and Manning's theories fit the experimental data if charge density parameter (ξ) of denatured DNA is in the range 1.8–2.1 (assuming for native DNA ξ = 4.2). Specificity of Li ions in interactions with DNA is discussed. © 1994 John Wiley & Sons, Inc.
Dynamics and thermomechanical stability of DNA in solution
Authors: Odell J. A. , Taylor M. A. 
Published: December 2004

AbstractWe present an analysis of the response of native DNA solutions to well‐defined elongational flow fields. At low strain rates the DNA duplex behaves as an expanded coil. It shows a noncritical coil‐stretch transition, suggesting relatively little hysteresis of the relaxation time. On the other hand, the relaxation time is consistent with a nonfree draining coil. At higher strain rates we observe midpoint scission. This has been modeled very successfully as a thermomechanically activated process. Scission occurs at hydrolyzable weak linkages along the constituent strands. Complete scission of the DNA helix is, however, considerably less prevalent than would be expected given the low stability of the constituent strands. We speculate upon the molecular origin and biological consequences of this enhanced stability. © 1994 John Wiley & Sons, Inc.
Measurement of grain growth in the recrystallization of rapidly frozen solutions of antifreeze glycoproteins
Authors: Yeh Y. , Feeney R. E. , McKown R. L. , Warren C. J. 
Published: December 2004

AbstractA quantitative estimate of the activation energy for grain growth has been obtained by analyzing ice recrystallization experiments from water and from solutions with small amounts (< 1.0 μg/mL) of antifreeze glycoprotein (AFGP). Rates of grain growth are measured as changes of grain diameter in time, with the supercooled holding temperature aVid glycoprotein concentration as parameters. Arrhenius plots of these rates vs (1/T) yielded slopes proportional to the activation energies for the particular species. The values of activation energy are almost independent of solution concentration or the species of AFGP. Averaged activation energy value for the AFGP‐4 species is Qg = (6.61 ± 1.02) × 105 J/mole. The “less active” AFGP‐8 yielded an average Qg = (5.71 ± 2.39) × 105 J/mole, quite similar to the AFGP‐4 species. The activation energy for recrystallization in a pure ice‐water system was estimated from two temperature points, T = −5.4 and −7.5°C. The best value is 2.39 × 105 J/mole, nearly twice that obtained by M. N. Martino and N. E. Zaritsky [(1989) Cryobiology, Vol. 26, p. 138] in a recrystallization experiment using salt solution, but much smaller than the values derived from the AFGP solutions. Results further show that activation entropy is at least a factor of 2 larger for the AFGP species than that of pure ice‐water system under the same growth conditions. These results suggest significant roles, both energetically and entropically, for AFGP molecules in their ability to inhibit grain growth of ice. © 1994 John Wiley & Sons, Inc.
DNA binding of a spermine derivative: Spectroscopic study of anthracene‐9‐carbonyl‐n1‐spermine with poly[d(G‐C)·(d(G‐C))] and poly[d(A‐T) · d(A‐T)]
Authors: Rodger Alison , Blagbrough Ian S. , Adlam Gareth , Carpenter Mark L. 
Published: December 2004

AbstractThe binding of polyamines, including spermidine (1) and spermine (2), to poly[d(G‐C) · d(G‐C) ] was probed using spectroscopic studies of anthracene‐9‐carbonyl‐N1‐spermine (3); data from normal absorption, linear dichroism (LD), and circular dichroism (CD) are reported. Ligand LD and CD for transitions located in the DNA region of the spectrum were used. The data show that 3 binds to DNA in a manner characteristic of both its amine and polycyclic aromatic parts. With poly [(dG‐dC) · (dG‐dC)], binding modes are occupied sequentially and different modes correspond to different structural perturbations of the DNA. The most stable binding mode for 3 with poly[d(G‐C) · d(G‐C)] has a site size of 6 ± 1 bases, and an equilibrium binding constant of (2.2 ± 1.1) × 107 M−1 with the anthracene moiety intercalated. It dominates the spectra from mixing ratios of approximately 133:1 until 6:1 DNA phosphate: 3 is reached. The analogous data for poly [d(A‐T) · d(A‐T)] between mixing ratios 36:1 and 7:1 indicates a site size of 8.3 ± 1.1 bases and an equilibrium binding constant of (6.6 ± 3.3) × 105 M−1. Thus, 3 binds preferentially to poly [d(G‐C) · d(G‐C)] at these concentrations. © 1994 John Wiley & Sons, Inc.
Kinked structures of isolated nicotinic receptor M2 helices: A molecular dynamics study
Authors: Sankararamakrishnan R. , Sansom M. S. P. 
Published: December 2004

AbstractThe pore‐lining M2 helix of the nicotinic acetylcholine receptor exhibits a pronounced kink when the corresponding ion channel is in a closed conformation [N. Unwin (1993) Journal of Molecular Biology, Vol. 229, pp. 1101–1124]. We have performed molecular dynamics simulations of isolated 22‐residue M2 helices in order to identify a possible molecular origin of this kink. In order to sample a wide range of conformational space, a simulated annealing protocol was used to generate five initial M2 helix structures, each of which was subsequently used as the basis of 300 ps MD simulations. Two helix sequences (M2α and M2δ) were studied in this manner, resulting in a total often 300 ps trajectories. Kinked helices present in the trajectories were identified and energy minimized to yield a total of five different stable kinked structures. For comparison, a similar molecular dynamics simulation of a Leu23 helix yielded no stable kinked structures. In four of the five kinked helices, the kink was stabilized by H bonds between the helix backbone and polar side‐chain atoms. Comparison with data from the literature on site‐directed mutagenesis of M2 residues suggests that such polar side‐chain to main‐chain H bonds may also contribute to kinking of M2 helices in the intact channel protein. © 1994 John Wiley & Sons, Inc.
Contrasting solution conformations of peptides containing α,α‐dialkylated residues with linear and cyclic side chains
Authors: Prasad Sudhanand , Rao R. Balaji , Balaram P. 
Published: December 2004

AbstractThe conformational properties of α,α‐dialkylated amino acid residues possessing acyclic (diethylglycine, Deg: di‐n‐propylglycine, Dpg; di‐n‐butylglycine, Dbg) and cyclic (1‐amino‐cycloalkane‐1‐carboxylic acid, Acnc) side chains have been compared in solution. The five peptides studied by nmr and CD spectroscopy are Boc‐Ala‐Xxx‐Ala‐OMe, where Xxx = Deg(I). Dpg (II), Dbg (III), Ac6c (IV), and Ac7c (V). Delineation of solvent‐shielded NH groups have been achieved by solvent and temperature dependence of NH chemical shifts in CDCl3 and (CD3)2SO and by paramagnetic radical induced line broadening in pepiide III. In the Dxg peptides the order of solvent exposure of NH groups is Ala(1) > Ala(3) > Dxg(2), whereas in the Acnc peptides the order of solvent exposure of NH groups is Ala(1) > Acnc(2) > Ala(3). The nmr results suggest that Acnc peptides adopt folded β‐turn conformations with Ala(1) and Acnc(2) occupying i + 1 and i + 2 positions. In contrast, the Dxg peptides favor extended C5 conformations. The conformational differences in the two series are clearly borne out in CD studies. The solution conformations of peptides I‐III are distinctly different from the β‐turn structure observed in crystals. Low temperature nmr spectra recorded immediately after dissolution of crystals of peptide II provide evidence for a structural transition. Introduction of an additional hydrogen‐bonding function in Boc‐Ala‐Dpg‐Ala‐NHMe (VI) results in a stabilization of a consecutive β‐turn or incipient 310‐helix in solution. © 1995 John Wiley & Sons, Inc.
A nonhelical, multiple β‐turn conformation in a glycine‐rich heptapeptide fragment of trichogin A IV containing a single central α‐aminoisobutyric acid residue
Authors: Gurunath R. , Balaram P. 
Published: December 2004

AbstractThe conformational properties of the protected seven‐residue C‐terminal fragment the lipopeptaibol antibiotic Trichogin A IV (Boc‐Gly‐Gly‐Leu‐Aib‐Gly‐Ile‐Leu‐OMe) has been examined in CDCl3 and (CD3)2SO by 1H‐nmr. Evidence for a multiple β‐turn conformation [type I′ at Gly(1)‐Gly(2), type II at Leu(3)‐Aib(4), and a type I′ at Aib(4)‐Gly(5)] suggests that Leu(3) has preferred an extended or semiextended conformation over a helical conformation in CDCl3. This structure is thus in contrast to earlier observations of seven‐residue peptides containing a single central Aib preferring helical conformations in both solution and crystalline slates. A structural transition to a frayed right‐handed helix is absented in (CD3)2SO. These results suggest that nonhelical conformations may be important in Gly‐rich peptides containing Aib. Further, the presence of amino acids with contradictory influences on backbone conformational freedom can lead to well‐defined conformational transitions even in small peptides. © 1995 John Wiley & Sons, Inc.
A method for characterizing transition concertedness from polymer dynamics computer simulations
Authors: Brown Michael L. , Venable Richard M. , Pastor Richard W. 
Published: December 2004

AbstractA statistical method based on classifying the transitions among a set of dihedral angles within an “energy transfer window” is developed, and used to analyze Brownian (BD) and molecular dynamics (MD) simulations of the acyl chains in a lipid bilayer, and MD of neat hexadecane. It is shown for the BD simulation that when a transition of the dihedral angle in the center of the chain occurs, a transition of a particular next nearest neighbor (or angle 2‐apart) will follow concertedly with a probability of approximately 0.10 within a lime window of approximately 3 ps. The MD bilayer simulations, which are based on a more flexible model of the hydrocarbon chains, yield corresponding concerted transition probabilities of approximately 0.083 and window sizes of 1–2 ps. An analysis of angles 4‐apart yields concerted transition probabilities of 0.03 and 0.04 for the BD and MD bilayer simulations, respectively, and window sizes close to those of the corresponding 2‐apart cases. Statistical hypothesis testing very strongly rejects the assertion that these follower transitions are occurring at random. Similar analysis reveals marginal or no evidence of concertedness between 1‐apart (nearest neighbor) and between 3‐apart dihedral angle transitions. The pattern of concertedness for hexadecane is qualitatively similar to that of the lipid chains, although concertedness is somewhat stronger for the 3‐apart transitions and somewhat weaker for those 4‐apart. Finally, it is suggested that the diffusion of small solute molecules in membranes is better facilitated by non concerted transitions, which are associated with relatively large displacements of the chains, than by concerted transitions, which do little to change the chain shape. © 1995 John Wiley & Sons, Inc.
Protein dynamics: Rotational diffusion of rigid and fluctuating three dimensional structures
Authors: Perico Angelo , Guenza Marina , Mormino Michele , Fioravanti Roberto 
Published: December 2004

AbstractThe optimized Rouse‐Zimm approximation to the local dynamics (ORZLD theory) is extended to treat three‐dimensional structures. Rigid model chains of different dimensionality are considered. The local dynamics of random peptides are compared to the rotational correlation times of rigid three‐dimensional protein structures. The treatment of these rigid limits is a necessary step in a more advanced ORZLD theory of the dynamics of proteins including fluctuations relative to the three‐dimensional structure. © 1995 John Wiley & Sons, Inc.
The helix‐coil transition in polypeptides: A microscopic approach. II
Authors: Hairyan Sh. A. , Mamasakhlisov E. Sh. , Morozov V. F. 
Published: December 2004

AbstractIn the framework of an earlier constructed model [N. S. Ananikyan et al. (1990) Biopolymers, Vol. 30. pp. 357‐367], some analytical estimates for the correlation length and degree of helicity near the transition point were obtained in the case of an arbitrary topology of hydrogen bond closing (Δ). It was shown that the Zimm‐Bragg cooperativity parameter σ is determined by the set of (Δ‐1) amino acid residues and so is nonlocal. An analytic expression for cooperatively parameters in a heteropolypeptide chain was obtained and numerical calculations showed that in case of heteropolypeptide with random primary structure the nonlocality of cooperativity parameter influenced the temperature dependence of helicity degree. © 1995 John Wiley & Sons, Inc.
Fluorescence energy transfer in one dimension: Frequency‐domain fluorescence study of DNA–fluorophore complexes
Authors: Maliwal Badri P. , Kuśba Józef , Lakowicz Joseph R. 
Published: December 2004

AbstractFluorescence resonance energy transfer among linear DNA bound fluorophores was carried out to study the process in one dimension. The donor fluorescence intensity decays in the case of energy transfer in one dimension are stretched exponential and show exp[‐(t/τ)1/6] time dependence, which results in an initial more rapid decay and subsequent slower decay at long times when compared to those in higher dimensions. DNA‐bound 4′,6′‐diamidino‐2‐phenyl indole (DAPI), acridine orange (AO), and ethidium bromide (EB) were used as donors. The acceptors were in the case of DAPI AO and EB; in the case of AO nile blue (NB), methylene blue (MB), and crystal violet (CV); and NB, MB, and oxazine 750 in the case of EB. As expected, the donor intensity decays became highly heterogeneous upon energy transfer and were characterized by the simultaneous presence of both highly and marginally quenched donors. The intensity decays for all three donors in the presence of various acceptors are satisfactorily described by the Förster model of energy transfer in one dimension. The intensity decays also allow for clear rejection of a two‐ or three‐dimensional model. The experimentally recovered critical Förster distances (R0) ranged between 37 Å in the case of DAPI and EB to 70 Å in the case of AO and CV donor‐acceptor pairs. These recovered R0 values compare reasonably with those calculated from spectral properties if we use values of 1.25 for κ2, and 1.5 for the refractive index of DNA. The κ2 value will be even higher, between 1.5 and 2.0, if the consensus DNA refractive index of 1.75 is used. These κ2 values strongly suggest that the dipoles of the acceptor chromophores when bound to DNA are not randomly oriented but are aligned preferentially in plane. © 1995 John Wiley & Sons, Inc.
Two‐dimensional motion of DNA bands during pulsed‐field gel electrophoresis. II. Effect of field angle
Authors: Neitzey Lynn M. , Holzwarth George , Duke Thomas , Viovy Jean‐Louis 
Published: December 2004

AbstractIn pulsed‐field gel electrophoresis, megabase DNAs are well separated if the angle θ between the two electric fields is 120° but not if θ = 90°. To elucidate the molecular basis for this observation, we measured the instantaneous position (x, y) and velocity (vx, vy) of a band of G‐DNA (670 kb) while the field switched direction, for 90° ≤ θ ≤ 102°. For θ = 120° and long pulse period T. The band retraced the last segment of the preceding pulse before moving in‐ the new field direction. The retracing wax done at a velocity much greater than the average forward velocity. For θ = 90°, rather than retrace itself, the path during one pulse appeared to originate from a point beyond that reached in the previous pulse, end the velocity showed only a brief backward spike.A Monte Carlo simulation that included tube‐length fluctuations and hernias was carried out for a model DNA chain moving through a three‐dimensional network of interconnected pores, with parameters corresponding to the DNA size, agarose concentration, and field strength of the experiments, Both the xy path and the instantaneous velocities of the simulation were in excellent agreement with experiment for 90° ≤ θ ≤ 120°. When the field changed direction in the simulation, hernias often advanced from both ends in the new field direction. In the 120° case, those near the erstwhile trailing segments of the chain soon established superiority because chain tension and a component of the new field aided their growth. For θ = 90° and long T, however, segments from the head end were more likely to continue to lead because there was often an excess of relaxed segments there, and no component of the field aided either end. © 1995 John Wiley & Sons, Inc.
An evaluvation of discrete and continuum search techniques for conformational analysis of side chains in proteins
Authors: Vásquez Maximiliano 
Published: December 2004

AbstractMethodology for calculation of side‐chain conformations in proteins is evaluated. The role and impact of corrections to idealized rotameric structures are considered, by incorporating methods for torsional optimization into rotamer‐packing algorithms. Off‐rotamer corrections given by continuum torsional optimization improve, over simpler rotamer‐packing procedures, the accuracy with which the conformations of side chains of buried amino acids can be predicted. The analogy between protein side‐chain calculations and spin systems is explored by adapting spin simulation methods to side‐chain packing algorithms. Implementations of mean‐field and heat‐bath algorithms for side‐chain packing are described and their performance tested. The procedures introduced here address the combinatorial problem in an efficient and reasonably effective manner, as evidenced by analysis of their convergence properties. Application of refined protocols yields overall prediction accuracies of 80% for χ1 and 68percnt; for χ1,2 pairs for a test set of 60 proteins, using a 40° cutoff to define correct placement. For buried amino acids (defined as having less than 30% relative solvent accessibility) the prediction accuracies increase to 88percnt; for χ1 and 79percnt; for χ1,2 pairs. The influence of the form of the potential energy function is studied by comparing results obtained with 12‐6 and 9‐6 potentials. The 9‐6 form leads to more accurate results. Detailed comparison with previous work is presented, and the effect of combinatorial packing steps is shown to be important for all but the smallest proteins. © 1995 John Wiley & Sons, Inc.
Characterization of the binding of YO to [poly(dA‐dT)]2 and [poly(dG‐dC)]2, and of the fluorescent properties of YO and YOYO complexed with the polynucleotides and double‐stranded DNA
Authors: Larsson Anette , Carlsson Christina , Jonsson Mats 
Published: December 2004

AbstractThe interaction between the fluorescent dye YO (oxazole yellow) and the alternating polynucleotides [poly(dA‐dT)]2[the duplex of alternating poly(dA‐dT)]and [poly(dG‐dC)]2[the duplex of alternating poly(dG‐dC)] has been studied with optical spectroscopic techniques including absorbance, flow linear dichroism, CD, and fluorescence measurements. The principal features of the spectra are very similar for the two polynucleotide solutions, showing that YO binds quite similarly to AT and GC base pairs. From a strongly negative reduced linear dichroism (LDr) in the dye absorption band, an induced negative CD, and transfer of energy from the bases to bound YO, we conclude that at low mixing ratios YO is intercalated in both [poly(dA‐dT)]2 and [poly(dG‐dC)]2. At higher mixing ratios an external binding mode starts to contribute, evidenced from the appearance of an exciton CD. The conclusion that YO binds in a similar way to AT and GC base pairs should be valid also for the dimer YOYO since its YO units have been found to bind to double‐stranded (dsDNA) in the same way as the YO monomer.The fluorescence properties of YO and YOYO complexed with DNA or the polynucleotides have been characterized by studying the dependence of fluorescence intensity on temperature, mixing ratio, and ionic strength. The fluorescence intensity and fluorescence lifetime of YO‐DNA decrease strongly with increasing mixing ratio, whereas the fluorescence intensity of YOYO‐DNA shows a weaker dependence, indicating that the quantum yield depends on the distance between the YO chromophores on the DNA chain. Further, the fluorescence intensity of YO depends on the base sequence; the quantum yield and fluorescence lifetime for YO complexed with [poly(dG‐dC)]2 are about twice as large as for YO complexed with [poly(dA‐dT)]2. Measurements of excitation spectra at different mixing ratios and different emission wavelengths indicate that the fluorescence of the externally bound chromophores is negligible compared to the intercalated ones. © 1995 John Wiley & Sons, Inc.
Specific interaction between cyclophilin and cyclic peptides
Authors: Gallo Pasquale , Saviano Michele , Rossi Filomena , Pavone Vincenzo , Pedone Carlo , Ragone Raffaele , Stiuso Paola , Colonna Giovanni 
Published: December 2004

AbstractCyclophilin A, a peptidyl‐prolyl cis–trans isomerase that catalyzes the otherwise slow isomerization of Xaa‐Pro imidic bond, specifically binds the immunosuppressant cyclosporin A. Herein we reportevidence on binding of cyclolinopeptide A and its synthetic analogue, [Aib5,6‐D‐Ala8] cyclolinopeptide, to bovine cyclophilin A. Binding experiments were monitored by fluorescence. CD, and second‐derivative spectroscopies, evidencing no remarkable rearrangement of protein structure organization. The possibility that cyclolinopeptide A could act as a substitute of cyclosporin A in the immunosuppression modulation is also briefly discussed. © 1995 John Wiley & Sons, Inc.