bluuebunny/crossref_metadata_2025 huggingface dataset:
Mechanochemical study of conformational transitions and melting of Li‐, Na‐, K‐, and CsDNA fibers in ethanol–water solutions
Authors: Rupprecht Allan , Piškur Jure , Schultz Johan , Nordenskiöld Lars , Song Zhiyan , Lahajnar Gojmir
Published: December 2004

Highly oriented fibers of Li‐, Na‐, K‐, and CsDNA were prepared with a previously developed wet spinning method. The procedure gave a large number of equivalent fiber bundle samples (reference length, L0, typically = 12–15 cm) for systematic measurements of the fiber length L in ethanol–water solutions, using a simple mechanochemical set up. The decrease in relative length L/L0 with increasing ethanol concentration at room temperature gave evidence for the B‐A transition centered at 76% (v/v) ethanol for NaDNA fibers and at 80 and 84% ethanol for K‐ and CsDNA fibers. A smaller decrease in L/L0 of LiDNA fibers was attributed to the B‐C transition centered at 80% ethanol. In a second type of experiment with DNA fibers in ethanol–water solutions, the heat‐induced helix–coil transition, or melting, revealed itself in a marked contraction of the DNA fibers. The melting temperature Tm, decreased linearly with increasing ethanol concentration for fibers in the B‐DNA ethanol concentration region. In the B‐A transition region, Na‐ and KDNA fibers showed a local maximum in Tm. On further increase of the ethanol concentration, the A‐DXA region followed with an even steeper linear decrease in Tm. The dependence on the identity of the counterion is discussed with reference to the model for groove binding of cations in B‐DNA developed by Skuratovskii and co‐workers and to the results from Raman studies of the interhelical bonds in A‐DNA performed by Lindsay and co‐workers. An attempt to apply the theory of Chogovadze and Frank‐Kamenetskii on DNA melting in the B‐A transition region to the curves failed. However, for Na‐ and KDNA the Tm dependence in and around the A‐B transition region could be expressed as a weighted mean value of Tm of A‐ and B‐DNA. On further increase of the ethanol concentration, above 84% ethanol for LiDNA and above about 90% ethanol for Na‐, K‐, and CsDNA, a drastic change occurred. Tm increased and a few percentages higher ethanol concentrations were found to stabilize the DNA fibers so that they did not melt at all, not even at the upper temperature limit of the experiments (∼ 80°C). This is interpreted as being due to the strong aggregation induced by these high ethanol concentrations and to the formation of P‐DNA. Many features of the results are compatible with the counterion–water affinity model. In another series of measurements, Tm of DNA fibers in 75% ethanol was measured at various salt concentrations. No salt effect was observed (with the exception of LiDNA at low salt concentrations). This result is supported by calculations within the Poisson–Boltzmann cylindrical cell model. © 1994 John Wiley & Sons, Inc.
The thermodynamics of solvent exchange
Authors: Schellman John A.
Published: December 2004

A model for solvation in mixed solvents, which was developed for the free energy and preferential interaction [J. A. Schellman (1987), Biopolymers, Vol. 26, pp. 549–559; (1990), Biophysical Chemistry, Vol. 37, pp. 121–140; (1993), Biophysical Chemistry, Vol. 45, pp. 273–279], is extended in this paper to cover the thermal properties: enthalpy, entropy, and heat capacity. An important result is that the enthalpy of solvation H̄ responds directly to the fraction of site occupation. This differs from the free energy Ḡ and preferential interaction Γ32, which are measures of the excess binding above a random distribution of solvent molecules. In other words, the enthalpy is governed by K while Ḡ and Γ32 are governed by (K − 1) where K is the equilibrium constant on a mole fraction scale [Schellman (1987)].

The solvation heat capacity C̄p consists of two term: (1) the intrinsic heat capacity of species in solution with no change in composition, and (2) a term that accounts for the change in composition that accompanies solvent exchange.

Binding to biological macromolecules is heterogeneous but experiementalists must use binding isotherms that assume the homogeneity of sites. Equations are developed for the interpretation of the experimental parameters (number of sites nexp, equilibrium constant Kexp, and enthalpy, Δhexp), when homogeneous formulas are applied to the heterogeneous case. It is shown that the experimental parameters for the occupation and enthalpy are simple functions of the moments of the distribution of equilibrium constants over the sites. In general, nexp is greater than the true number of sites and Kexp is greater than the average of the equilibrium constants. The free energy and preferential interaction can be fit to a homogenious formula, but the parameters of the curve are not easily represented in terms of the moments of distributions over the sites.

The strengths and deficiencies of this type of thermodynamic model are discussed. © 1994 John Wiley & Sons, Inc.
Morphology and primary crystal structure of a silk‐like protein polymer synthesized by genetically engineered Escherichia coli bacteria
Authors: Anderson J. Philip , Cappello Joseph , Martin David C.
Published: December 2004

The morphology and primary crystal structure of SLPF, a protein polymer produced by genetically engineered Escherichia coli bacteria, were characterized. SLPF is a segmented copolymer consisting of amino acid sequence blocks modeled on the crystalline segments of silk fibroin and the cell attachment domain of human fibronectin. Wide angle x‐ray scattering (WAXS), transmission electron microscopy (TEM), selected area electron diffraction (SAED), and molecular simulations were used to analyze the primary crystal structure of SLPF. TEM experiments conducted on SLPF droplets cast from formic acid on amorphous carbon film demonstrated that these protein films have a microstructure formed of woven sheaves. The sheaves are composed of well‐defined whisker crystallites. The width of the whiskers, 11.8 ± 2.2 nm, may be correlated to the length of the silk‐like segment in SLPF as predicted by molecular simulations. WAXS data, TEM images, SAED, patterns, molecular simulations, and theoretical diffraction patterns all were consistent with the crankshaft model proposed for Silk I by Lotz and Keith. © 1994 John Wiley & Sons, Inc.
Conformational study of sequential Lys and Leu based polymers and oligomers using vibrational and electronic CD spectra
Authors: Baumruk Vladimir , Huo Dongfang , Dukor Rina K. , Keiderling Timothy A. , Lelievre Dominique , Brack André
Published: December 2004

Vibrational CD (VCD) and electronic CD (ECD) spectra of some sequential Lys and Leu based oligo‐ and polypeptides were studied as a function of added salt and (for ECD) as a function of concentration in aqueous solution. For these samples, the VCD spectra can only be measured at relatively high concentrations under which the well‐known salt‐induced transition to a β‐sheet form can be observed for the KL based species, but only the end‐state α‐helical conformation is obvious for the LKKL based samples. ECD concentration dependence demonstrates that, at high concentration with no added or with added salt, LKKL based oligomers and polymers give α‐helical spectra. These data provide evidence of aggregation induced secondary structure formation in an exceptionally simple peptide system. Similarly, the KL based oligomers and polymers give β‐sheet like spectra at high concentration or at high salt. These systems further provide model systems under “normal” aqueous conditions that yield VCD band shapes that correlate to the major secondary structural types of polypeptides. They are in substantial agreement with those spectra obtained on homopolypeptides and on proteins, confirming the relative independence of the VCD technique from side‐chain and solvent effects. © 1994 John Wiley & Sons, Inc.
Thermal denaturation of Na‐ and Li‐DNA in salt‐free solutions
Authors: Korolev N. I. , Vlasov A. P. , Kuznetsov I. A.
Published: December 2004

Thermal 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

We 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

A 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

The 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

The 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

The 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

The 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

A 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

The 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

In 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

Fluorescence 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

In 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

Methodology 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

The 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

Cyclophilin 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.
Small‐angle x‐ray scattering of κ‐carrageenan based systems: Sols, gels, and blends with carob galactomannan
Authors: Turquois Tristan , Rochas Cyrille , Taravel Francois‐R , Doublier Jean Louis , Axelos Monique‐A‐V.
Published: December 2004

Small‐angle x‐ray scattering using a synchroton x‐ray monochromatic radiation was carried out to investigate the structure of different polysaccharides in aqueous medium: carob galactomannan, κ‐carrageenan in the sol and in the gel states, and κ‐carrageenan‐carob galactomannan mixed systems. Experiments performed on a 0.2% carob galactomannan solutions confirmed that this polysaccharide behaved as a neutral polymer in a good solvent. For K‐carrageenan in the / state, either in the sodium form or in the cesium form, a maximum in the scattering curve was evidenced. Position and height of this maximum changed with K‐carrageenan concentration in close agreement with what is expected for wormlike polyelectrolyte in semidilute solution. In the case of k‐carrageenan in the gel state, in the cesium form, scattering curves also exhibited a maximum at an intermediate Q value. The position of this correlation peak did not change with concentration while its intensity increased. This effect was ascribed to a packing of rodlike structures by analogy with a suspension of colloidal elongated particles. This local structure could be viewed as bundles of parallel double helices. Addition of carobgalactomannan in κ‐carrageenan gels induced dramatic structural changes. As the galactomannan concentration increased, the correlation peak tended to vanish. In contrast, no change in the cross‐sectional radius of gyration was noticed. This phenomenon suggested a screening effect of the galactomannan, resulting in a loss of the correlation between the κ‐carrageenan double helices. © 1995 John Wiley & Sons, Inc.
Slow conformational exchange in DNA minihairpin loops: A conformationalstudy 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 , Altona Cornelis
Published: December 2004

In recent years various examples of highly stable two‐residue hairpin loops (miniloops) in DNA have been encountered. As the detailed structure and stability of miniloops appear to be determined not only by the nature and sequence of the two bases in the loop, but also by the closing base pair, it is desirable to carry out in‐depth studies of especially designed small model DNA compounds. Therefore, a circular DNA dumbbell‐like molecule is tailored to consist of a stem of three Watson–Crick base pairs, flanked on each side by a minihairpin loop. The resulting circular DNA decanter 5′‐d〈pCGC‐ TT‐GCG‐ TT〉 ‐3′ (I) is studied in solution by means of nmr spectroscope. At a temperature of 269 K the molecule occurs in a 50/50 mixture of two dumbbell structures (denoted L2L2 and L2L4). L2L2 contains three Watson–Crick C‐G base pairs and two two‐residue loops (H2‐family type) in opposite parts of the molecule. On raising the temperature from 269 to 314 K. The L2L4 conformer becomes increasingly dominant (95% at 314 K). This conformer has a partially disrupted closing G‐C base pair in the 5′‐GTTC‐3′ loop with only one remaining solvent‐accessible hydrogen bond between NHα of the cytosine C(1) and O6 of the guanine G(8), whereas the opposite 5′‐CTTG‐3′ loop remains stable.

The disruption of the C(1)‐G(8) base pair in the L2L4 form is correlated with the presence of a syn orientation for the C(1) base at the 5′‐3′ loop‐stem junction in the 5′‐GTTC‐3′ loop. The two conformers. L2L2 and L2L4, occur in slow equilibrium (2–20 s−1). Moderate line broadening of specific 1H, 13C, and 31P resonances of residues C(1), G(8), T(9), and T(10) at low temperatures, due to chemical exchange between L2L2 and L2L4, show that the interconversion from an anti to syn conformer in residue C(1) has a small local effect on the structure of the dumbbell. T1 relaxation measurements, chemical‐shift considerations, and complete hand‐shape calculations of the exchange process of the G(8) imino proton reveal a possibility for the existence of multiconformational slates in the anti–syn equilibrium. © 1995 John Wiley & Sons, Inc.
1H‐nmr studies on the structure of a new thionin from barley endosperm
Authors: Bruix M , González C , Santoro J , Soriano F , Rocher A , Méndez E , Rico M
Published: December 2004

A new thionin from barley, ω‐hordothionin, has been shown to exist in aqueous solution as a mixture of two different isoforms in a 3:2 ratio, as revealed by a complete analysis of its two‐dimensional 1H‐nmr spectra. The conformational heterogeneity arises frtm cis–trans isomerism ahout the Phe 12–Pro 13 peptide bond, where the major, form corresponds to the cis conformation. The complete assignment of chemical shifts and nuclear Overhaiiser effects (NOES) of the two isoforms allow a detailed comparative analysis of their conformational properties, even though a complete calculation of their solution structures is not possible because of a somewhat limited number of NOE constraints. Structures for the two isomers could be modeled, however, on the basis of the high structural homology between ω‐hordothionin and related γ‐thionins, and under the conditions of satisfying all observed experimental data. The two isoforms adopt practically identical global folds and the structural changes imposed by cis–trans isomerization are confined to the region proximal to Pro 13. The cis–trans isomerism occurs in a conserved loop connecting the first β‐strand of the triple‐stranded antiparallel β‐sheet and the α‐helix. A comparative analysis of the sequences of this loop in the different thionins suggests that the cis–trans equilibrium about the X‐Pro peptide bond depends on the size of the side chain of X (X = Gly in γ‐thionins and Phe in ω‐thionin). The structural homology of this new thionin with γ‐thionins as well as with some scorpion toxins and insect defensins suggests that these proteins may share a common mode of functional activity. © 1995 John Wiley & Sons, Inc.
Rational design, synthesis, and biological evaluation of novel growth hormone releasing factor analogues
Authors: Campbell Robert M. , Bongers Jacob , Felix Arthur M.
Published: December 2004

Since its initial discovery in 1982, growth hormone‐releasing factor (GRF) has been the subject of intense investigation. This interest was prompted by the potential application of GRF for Stimulating growth in dwarf humans and for performance enhancement in livestock. Substantial research has been focused upon the development of potent, long‐acting analogs as therapeutics. Herein is described a summary of the cumulative efforts of various laboratories endeavoring in this quest. The rationale utilized in GRF analog development is discussed: (1) determination of bioactive core. (2) evaluation of secondary structure, and (3) elucidation of degradation pathways (chemical and enzymatic). Using this information, several series of linear (unnatural and natural sequence) and cyclic GRF analogs were designed, synthesized, and evaluated. Stimulated by the constraints of commercial production, innovative, alternative methods of synthesis were explored: solid‐phase, solution‐phase, enzymatic, and recombinant. To date, the most promising candidate for drug development is [His1, Val2, Gln8, Ala15, Leu27]‐hGRF(1‐32)‐OH. This natural sequence analog, consisting of rodent and human sequences, incorporates the bioactive core, preferred secondary structure, resistance to chemical and enzymatic degradation: with the added benefit of amenability to large‐scale recombinant synthesis. © 1994 John Wiley & Sons, Inc.
Bradykinin antagonists: Development and applications
Authors: Stewart John M.
Published: December 2004

Bradykinin (BK) is involved in regulation of every major physiological system and is an initiator or mediator of many pathophysiological conditions. Rapid progress in understanding these aspects of BK biology has come since the discovery of BK antagonists. This article reviews principal points in the history of the kallikrein–kinin field and of kinin biology. The chemistry and development of antagonists for B1 and B2 kinin receptors is discussed. Uses of the antagonists in biomedical research and potential clinical applications are presented. © 1994 John Wiley & Sons, Inc.
A review of the utility of soluble peptide combinatorial libraries
Authors: Pinilla Clemencia , Appel Jon , Blondelle Sylvie , Dooley Colette , Dörner Barbara , Eichler Jutta , Ostresh John , Houghten Richard A.
Published: December 2004

This is paper reviews the preparation and use of soluble synthetic combinatorial libraries (SCLs) made up of millions of peptide and nonpeptide sequences for the identification of highly active individual compounds. First presented in 1991. SCLs have been prepared in a number of different lengths and formats, and are composed entirely of L‐, D‐, and unnatural amino acids. Also, existing peptide libraries have been chemically transformed to yield large diversities of nonpeptidic compounds. This review encompasses the published work from this laboratory using SCLs for the identification of antigenic sequences recognized by monoclonal antibodies, novel peptide agonists and antagonists to opioid receptors, new trypsin inhibitors, novel antibacterials, and compounds that inhibit melittin's hemolytic activity. SCLs offer a fundamental, practical advance in the study of interactions between peptide and nonpeptide sequences and their biochemical or pharmacological targets. © 1994 John Wiley & Sons, Inc.
Vibrational optical activity of oligopeptides
Authors: Freedman Teresa B. , Nafie Laurence A. , Keiderling Timothy A.
Published: December 2004

Vibrational optical activity (VOA) is a relatively newspectroscopic technique, which has two principal manifestations, ir vibrational CD and vibrational Raman optical activity. Progress in the study of oligopeptides using both of these forms of VOA is reviewed from the perspective of theoretical and instrumental techniques, spectral results, and structural interpretations. © 1994 John Wiley & Sons, Inc.
The importance of extended conformations and, in particular, the PII conformation for the molecular recognition of peptides
Authors: Siligardi Giuliano , Drake Alex F.
Published: December 2004

Crystallographic, isotopic labeling nmr and transferred nuclear Overhauser effect studies have highlighted the extended conformation as a very important element of secondary structure at the binding site of many peptide/protein complexes including peptide inhibitors–enzymes, B‐cell epitopes–antibodies, and T‐cell epitopes–major histocompatibility complex (MHC) of class I and II complexes. This paper discusses the peptide ligand conformation consequences of these findings particularly in view of the identification of the PII conformation (left‐handed extended polyproline II) in free solution. © 1994 John Wiley & Sons, Inc.
Protein structural analysis as a tool for protein design
Authors: Leplae Raphael , Lahm Armin , Tramontane Anna
Published: December 2004

The analysis of known protein structures is a very valuable and indispensable tool for deciphering the complex rules relating sequence to structure in proteins. On the other hand, the design of novel proteins is certainly the most severe test of our understanding of such rules. In this report we describe our own attempt to develop appropriate tools for the investigation of known protein structure properties and their applications to the design of a novel, all β protein. The success of the design project is a demonstration of the usefulness of careful analysis of the data base of known protein structures. © 1994 John Wiley & Sons, Inc.
Production of cellulase and protein from barley straw by Trichoderma viride
Authors: Peitersen Nicolai
Published: December 2004

The cellulase production by two strains of the cellulolytic fungus Trichoderma viride was examined. The fungi were grown on different preparations of barley straw pretreated with NaOH under high pressure. The production of cellulases and microbial protein by the better strain (QM 9123) was investigated in an aerated 5‐liter fermenter under varying stirring rates (200‐350 rpm) and straw concentrations (1–2%). The pH was kept between 3.5 and 4.5. The growth of the fungus was followed by measuring the quantity of CO2 produced and the cell protein. After 2–6 days growth ceased, the lag phases lasting 0–2 days, increasing with increasing straw concentrations. The maximum enzyme yields were reached after 4–10 days. The protein content of the product was 21–26% and up to 70% of the straw was utilized. The yield constants were calculated to be 0.40–0.56; of the same order as those which can be obtained by growing the fungus on glucose.
Electromagnetic induced kinetic effects on charged substrates in localized enzyme systems
Authors: Seto Y. J. , Hsieh S. T.
Published: December 2004

An analytical expression for the rate efficiency factor of planar localized enzyme systems is derived. The derivation takes into account the isothermal kinetic effect under the externally imposed perturbation of combined electrostatic and high frequency time‐varying fields. The contribution of each individual field to the enzyme reaction is examined through the basic mechanism in which charged substrates interact, with the specific perturbing field. The interaction mechanisms for the electrostatic and for the time‐varying fields are found to be different. This difference regulates the different manners in which enzymatic reaction rates are altered. Enzymatic reactions under electrostatic perturbation can be retarded or enhanced depending on the field polarization. At sufficiently high field intensities the reaction rate may approach zero or approach a maximum value equal to the turnover number of the enzyme. Time‐varying field perturbations, on the other hand, always enhance the enzymatic reactions if bunching effects are negligible. At sufficiently high field intensities, the reaction may approach a value equal to that of the free enzyme system. Several typical numerical examples on pure electrostatic field perturbations, pure time‐varying field perturbations, and combined field perturbations are also presented.
Fed batch culture of Saccharomyces cerevisiae: A perspective of computer control to enhance the productivity in baker's yeast cultivation
Authors: Aiba Shuichi , Nagai Shiro , Nishizawa Yoshinori
Published: December 2004

A means to avoid the glucose effect in the production of baker's yeast from glucose and/or molasses in a fed batch culture by controlling the feed rate of fresh medium with an ad hoc measurement of the respiratory quotient, RQ, is presented. The feed rate is changed stepwise here such that the value of RQ ranges from 1.0 to 1.2 throughout the cultivation. Thus far, the specific growth rate based on the total cell mass and the growth yield obtained throughout are 0.24 hr−1 and 0.55 g cell/g glucose.

Prior to the experimental run mentioned above, equations to predetermine the feed rate and concentration of glucose in the feed are derived from the mass balance of limiting substrates (glucose). Since values of either RQ or I (Q x, oxygen consumption rate with respect to the total cell mass in the fermenter) can be measured quite easily and reliably, computer control of the fermentation in light of this information is discussed.
Microbial production of methane from municipal refuse
Authors: Pfeffer John T. , Khan Khalique A.
Published: December 2004

A heat and caustic pretreatment process has been tested to determine the increase in gas yield that can be obtained from fermentation of organic municipal refuse. A treatment temperature of 130°C and a NaOH concentration of 3 g/100 g of dry solids resulted in the highest gas yield for the conditions tested. The probable increase in gas yield was 20% for the best conditions tested. The treatment procedure also substantially increased the rates of gas production. A high conversion efficiency is possible at much shorter reactor retention times with pretreatment than without pretreatment.
Theoretical model for a submerged biological filter
Authors: Jennings P. A. , Snoeyink V. L. , Chian E. S. K.
Published: December 2004

A mathematical model was developed for percent removal of a pure, non‐adsorbable, biodegradable substrate in a submerged biological filter using the nonlinear Monod expression for the substrate utilization rate. Analytical solutions were obtained using zero and first order linearizations of the Monod expression and were compared to the numerical solution of the nonlinear system. The relevant dimensionless parameter groups describing the system were identified and their effects on substrate flux into the biolayer, effectiveness factor, and percent removal were also examined. Criteria were established for determining the relative accuracy of the two biokinetic approximations and for determining values of “limiting” biolayer thickness.

There are two major results of engineering significance. (1) The approximation of the nonlinear Monod expression by a first order rate expression yields accurate results for a much wider range of bulk concentrations than might be expected from inspection of the Monod half‐velocity coefficient for a given substrate. (2) Percent removal of substrate is a weak function of biolayer thickness (and thus total cell mass) when the thickness is greater than a rather small limiting value but is a strong function of particle radius (and thus biolayer surface area) for a wide range of parameter values including those of common interest.