bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potentiometric titration of poly‐L‐lysine: the coil‐to‐β transition
Authors: Pederson Dennis , Gabriel Don , Hermans Jan 
Published: December 2004

AbstractWe have performed potentiometric titrations of poly‐L‐lysine. From these data we have calculated the free energy and enthalpy changes for the folding of the random coil to the α‐helix in 10% ethanol (−120 and −120 cal/mole) and from the random coil to the β‐structure in water (−140 and 870 cal/mole) and in 10% ethanol (−180 and 980 cal mole). Comparison of these values with each other and with values for the coil → α‐ helix transition in water (−78 and −880 cal/mole) led to the following conclusions. The stabilization by ethanol of ethanol of the α‐helix with respect to the coil is that predicted from the known free energy of transfer of the peptide group from water to 10% ethanol. Similar data to explain the enthalpy difference are not available. The thermodynamic functions for the transition from α‐helix to β‐structure, obtained by subtracting those for the coil → α‐helix and coil → β‐structure transitions, are explained from a consideration of the structural differences: non bonded interactions of the polypeptide backbone are less favorable in the β‐structure than in the α‐helix, causing an increase in the energy, while hydrophobic contacts between side chains raise the entropy of the β‐structure as compared with the α‐helix, so that the free energy difference between the two structures is small, but enthalpy and entropy differences are large. The observation of only small differences in the free energy and enthalpy changes for the transition from coil β‐structure upon going from water to 10% ethanol is expected by considering both the free energy of transfer of the peptide group (as for the α‐helix) and the free energy and enthalpy of transfer of the apolar part of the side chain involved in hydrophobic bond formation.
β‐Carbonylamides in peptide chemistry. I. Optical rotatory properties of N‐acetoacetyl amino acids
Authors: Toniolo Claudio , Filira Fernando , Di Bello Carlo 
Published: December 2004

AbstractThe Cotton effects of N‐acetoacetyl amino acids and derivatives were examined by a circular dichroism technique. A correlation has been established between the sign of the Cotton effect and the absolute configuration of the asymmetric center. The L derivatives show, in dioxane, negative circular dichroism curves, whereas the D antipodes present positive curves. The effect of solvent and pH and influence of alkylation at the amide nitrogen are also discussed.
Stability characteristics of deuterated myoglobin
Authors: Appel Pearl , Brown W. Duane 
Published: December 2004

AbstractPurified sperm whale myoglobin was deuterated by being exposed to pD 3.5 in D2O buffer for 1 hr, then raised to pD 10.6 for an additional hour, and finally brought to neutrality in a D2O environment. Control myoglobin was similarly treated in H2O. The specific rotation at 233 mμ and/or the absorbance in the Soret region were used to follow the helix‐coil transition of myoglobin subjected to denaturation by acid, alkali, urea and guanidine. Deuterated and control myoglobin had similar 50% transition points in the four denaturing media studied (acid: pH 4.4, pD 4.9; alkali: pH 9.4, pD 10.0; urea, 7.2M; guanidine, 2.5M). The shift toward the alkaline side of 0.5 or 0.6 units of the transition induced by either acid or alkaline denaturation reflects only the weakened acidity of ionizable groups in deuterium systems. Deuterated myoglobin in 3.25M guanidine had a 20% faster denaturation rate than that of control. Acid, urea, and guanidine denaturation curves showed fairly steep transitions, taken as indicative of a one‐step process involving only two states (native and denatured molecules). Supporting this conclusion was the fact that plots of absorption and polarimetry measurements of the helix‐coil transition induced by either acid or guanidine could be superimposed.
Angular dependence of scattered light, rotary frictional coefficients, and distribution of sizes of associated oligomers in solutions of bovine liver glutamate dehydrogenase
Authors: Eisenberg Henryk , Reisler Emil 
Published: December 2004

AbstractThe angular dependence of scattering in solutions of bovine liver glutamate dehydrogenase was studied in 0.2M Na‐phosphate buffer, pH 7, 10−4M EDTA, and in buffered solutions saturated with either toluene or benzene. Whereas the shape of the scattering curves is in qualitative accord with the previously reported polymerization to rodlike linear structures, quantitative agreement between the calculated and experimental curves is poor when the polydispersity consistent with the association mechanism (derived from molecular weight determinations by light scattering and equilibrium sedimentation) is properly taken into account. The measurement of rotary frictional coefficients of macroscopic models of linearly associated glutamate dehydrogenase oligomers allowed the calculation of intrinsic viscosities of enzyme solutions but did not permit discrimination, by hydrodynamic means, between systems with different distributions of length.
Electro‐optical properties of nucleic acids and nucleoproteins III. Kramers‐Kronig relationships in linear birefringence and dichroism. Application to a DNA–proflavine complex
Authors: Houssier Glaude , Kuball Hans‐G 
Published: December 2004

AbstractThe relation between the birefringence dispersion curve in a dichroic absorption band and the corresponding dichroism spectrum is given, using the Cauchy's theorem. The theory was checked on a DNA–proflavine complex with the aid of electro‐optical measurements. An excellent agreement between the experimental results and the theoretical calculations was found. The birefringence and dichroism of the complex appear to be determined by the orientation of the macromolecule while no evidence for a contribution of the hyperpolarizabilities to the electro‐optical effect is found.The importance of the dichroism correction in the calculation of the birefringence dispersion curve is emphasized.
Oligonucleotide studies: optical rotatory dispersion of normal and 2′‐O‐methylated diribonucleoside monophosphates
Authors: Singh H. , Hillier B. 
Published: December 2004

AbstractThe optical rotatory dispersion (ORD) of several diribonucleoside monophosphates (NpN) and the corresponding 2′‐O‐methyl substituted dinucleoside monophosphates containing 2′‐O‐methyl ribosyl 3′‐nucleotide and a 5′‐nucleoside (NmpN) were measured at pH 1, 7, and 11.2, at 0.1 ionic strength in order to examine the role of the 2′‐hydroxyl group of the ribose in the conformation of the oligoribonucleotides. The optical measurements are reported from 210 to 340 mμ. The pH effect on the ORD spectra of NpN as well as NmpN are large. No dramatic changes are seen in the shapes of the ORD spectra of the NmpN to the corresponding NpN at pH 7. However, a decrease in the amplitude is seen in most of the NmpN over that of the corresponding NpN ranging from 7 percent in the case of UmpG to 46 percent in AmpA. The differences seen in the NpN and the corresponding NmpN ORD results are best explained as a consequence of a change in the ribosyl conformation on 2′‐O‐methylation, rather than the involvement of the 2′‐hydroxyl group in intramolecular hydrogen bonding in the ribo dimmer. The NmpN behave like NpN and not dNpdN, suggesting that the geometry of the stack in NpmN and NpN depends on the oxygen at the 2′‐carbon and not on what is attached to it.
On the conformations of poly‐N‐methyl‐L‐alanine (PNMA) in solution
Authors: Conti F. , De Santis P. 
Published: December 2004

AbstractHigh‐resolution nuclear magnetic resonance spectra at 100 MHz have been obtained on poly‐N‐methyl‐L‐alanine in the chloroform–trifluoroacetic acid system under various conditions of solvent composition. Different spectra are observed for the CH3–Cα, Cα–H, and N–CH3 protons. On the basis of conformational analysis an interpretation of the NMR results was attempted.
An infrared study on the conformation of poly‐L‐proline in concentrated aqueous salt solutions
Authors: Swenson Charles A. 
Published: December 2004

AbstractThe infrared absorption of poly‐L‐proline in concentrated aqueous salt solutions was measured in the fundamental region. Of primary interest were the carbonyl absorption of the peptide linkage and the methylene C–H bending absorption of the pyrrolidine ring. These spectral regions each show an additional component in the concentrated salt solutions. Using the position of the absorptions of poly‐L‐proline I (cis) and II (trans) as models, we conclude that both cis–trans linkages are present in the peptide in salt solutions. Increasing the temperature shifts the equilibrium slightly in favor of cis.
Side‐chain conformation in poly(γ‐phenethyl‐L‐glutamate)
Authors: Lefelar Judith A. , Knox James R. , Samulski Edward T. 
Published: December 2004

AbstractX‐ray diffraction and energy‐minimization results are reported for poly(γ‐phenethyl‐L‐glutamate). Orthorhombic unit‐cell parameters of drawn fibers are a = 15.4 Å, b = 26.6 Å, c = 54.4 Å. Atomic coordinates are derived for an α‐helix peptide conformation that corresponds to a calculated side‐chain internal energy minimum. The side‐chain conformation correlates well with the electron density projection; the side chains wrap around the α‐helical main chain with the phenethyl ester group directed toward the N‐terminus. The para‐axis of the benzene ring is inclined at an angle nearly nearly normal to the helix axis. The x‐ray structure factors calculated for this model, when compared to the 10 observed structure factors, yield a crystallographic reliability index of R = 0.23.
Conformations of proline residues in membrane environments
Authors: Deber Charles M. , Glibowicka Mira , Woolley G. Andrew 
Published: December 2004

AbstractAlthough noted as hydrophilic residues with helix‐breaking potential, proline residues are observed in putatively α‐helical transmembrane (TM) segments of many channel‐forming integral membrane proteins. In addition to the recognized property of X‐Pro peptide bonds (where X = any amino acid) to occur in cis as well as trans isomeric states, the tertiary amide character of the X‐Pro bond confers increased propensity for involvement of its carbonyl group in specific H‐bonded structures (e.g., β‐ and γ‐turns) and/or liganding interactions with positively charged species. To examine this latter situation in further detail, we identified Leu‐Pro‐Phe as a consensus sequence triad based on actual occurrences of intramembranous Pro residues in transport protein TM segments. Accordingly, we have undertaken the synthesis of hydrophobic peptides with potential membrane affinity, of which t‐butyloxycarbonyl‐L‐Ala‐L‐Ala‐L‐Leu‐L‐Pro‐L‐Phe‐OH (t‐Boc‐AAALPF‐OH) is an initial compound. Partitioning of this peptide into model membrane environments composed of lipid micelles induces specific conformations(s) for the membrane‐bound hexapeptide, as monitored by 75‐MHz 13C‐nmr spectral behavior of 13C‐enriched Leu and Pro carbonyl carbons, and by 300‐MHz 1H‐nmr spectra of peptide α, β, and aromatic protons. Data are interpreted in terms of an intramolecularly H‐bonded inverse γ‐turn conformation in the membrane environment involving the Leu‐Pro‐Phe triad. The inherent structureal instability of a Pro‐containing segment in a TM helix due to the multiplicity of possible local conformations is discussed as a functional aspect of membrane‐buried prolines in transport proteins.
Synthesis, crystal structure, and molecular conformation of N‐Boc‐L‐Phe‐dehydro‐Leu‐L‐Val‐OCH3
Authors: Narula P. , Patel H. C. , Singh T. P. , Chauhan V. S. 
Published: December 2004

AbstractThe peptide N‐Boc‐L‐Phe‐dehydro‐Leu‐L‐Val‐OCH3was synthesized by the usual workup procedure and finally by coupling the N‐Boc‐L‐Phe‐dehydro‐Leu‐OH to valine methyl ester. It was crystallized from its solution in methanol–water mixture at 4°C. The crystals belong to the triclinic space group P1 witha= 5.972(5) Å,b= 9.455(6) Å,c= 13.101(6) Å, α = 103.00(4)°, β = 97.14(5)°, γ = 102.86(50)°,V= 690.8(8) Å,Z= 1, dm = 1.179(5) Mg m−3and dc = 1.177(5) Mg m−3. The structure was determined by direct methods using SHELXS86. It was refined by block‐diagonal least‐squares procedure to anRvalue of 0.060 for 1674 observed reflections. The C–Cdistance of 1.323(9) Å in dehydro‐Leu is an appropriate double bond length. The bond angle Cα–Cβ–Cγin the dehydro‐Leu residue is 129.4(8)°. The peptide backbone torsion angles are θ1= −168.6(6)°, ω0= 170.0(6)°, ϕ1= −44.5(9)°, ψ1= 134.5(6)°, ω1= 177.3(6)°, ϕ2= 54.5(9)°, ψ2= 31.1(10)°, ω2= 171.7(6)°, ϕ3= 51.9(8)°, ψ= 139.0(6)°, θT= −175.7(6)°. These values show that the backbone adopts a β‐turn II conformation. As a result of β‐turn, an intramolecular hydrogen bond is formed between the oxygen of theith residue and NH of the (i+ 3)th residue at a distance of 3.134(6) Å. The Boc group has atrans–transconformation. The side‐chain torsion angles of the Phe residue are χ1= 171.6(6)°, χ= −102.1(9)°, and χ= 78.6(10)°. The side‐chain conformational angles of dehydro‐Leu residue are χ2= 2.7(13)°, χ= −107.3(11)°, and χ= 131.3(10)°. The torsion angles χand χthat define the conformation of the valyl side chain are −166.16(6)° and 69.1(9)°, respectively. The crystal structure is stabilized by hydrogen bonds along theaandbaxes, while the van der Waals forces are the stabilizing interactions in thecdirection.
Synthetic and conformational studies on dehydroalanine‐containing model peptides
Authors: Gupta Alka , Chauhan V. S. 
Published: December 2004

AbstractThree model dipeptides containing a dehydroalanine residue (ΔAla) at the C‐terminal, Boc‐X‐ΔAla‐NHCH3[X = Ala, Val, and Phe,] have been synthesized and their solution conformations investigated by1H‐NMR, IR, and CD spectroscopy. NMR studies on these peptides in CDCl3clearly indicate that the NH group of dehydroalanine is involved in an intramolecular hydrogen bond. This conclusion is supported by IR studies also. Nuclear Overhauser effect (NOE) studies are also accommodative of an inverse γ‐turn‐type of conformation that is characterised by conformational angles of ϕ ∼ −70° and ψ ∼ +70° around the X residue, and a CH‐Ni+2H interproton distance of 2.5 Å. It appears that unlike dehydrophenylalanine or dehydroleucine, which tend to stabilize β‐turn type of structures occupying thei+ 2 position of the turn, dehydroalanine favors the formation of an inverse γ‐turn, centered at the proceeding L‐residue in such solvents as CDCl3and (CD3)2SO. A comparison of solution conformation of Boc Val‐ΔAla‐NHCH3with the corresponding saturated analogue, Boc‐Val‐Ala‐NHCH3, is also presented and shows that dehydroalanine is responsible for inducing the turn structure. It may be possible to design peptides with different preferred conformations using the suitable dehydroamino acid.
CD and Fourier transform ir spectroscopic studies of peptides. II. Detection of β‐turns in linear peptides
Authors: Hollósi M. , Majer Zs. , Rónai A. Z. , Magyar A. , Medzihradszky K. , Holly S. , Perczel A. , Fasman G. D. 
Published: December 2004

AbstractComparative CD and Fourier transform ir (FTIR) spectroscopic data on N‐Boc protected linear peptides with or without the (Pro‐Gly) β‐turn motif (e.g., Boc‐Tyr‐Pro‐Gly‐Phe‐Leu‐OH and Boc‐Tyr‐Gly‐Pro‐Phe‐Leu‐OH) are reported herein. The CD spectra, reflecting both backbone and aromatic contributions, were not found to be characteristic of the presence of β‐turns. In the amide I region of the FTIR spectra, analyzed by self‐deconvolution and curve‐fitting methods, the β‐turn band shewed up between 1639 and 1633 cm−1 in trifluoroethanol (TFE) but only for models containing the (Pro‐Gly) core. This band war‐also present in the spectra in chloroform but absent in dimethylsulfoxide. These findings, in agreement with recent ir data on cyclic models and 310‐helical polypeptides and protein in D2O [see S. J. Prestrelski, D. M. Byler, and M. P. Thompson (1991), International Journal of Peptide and Protein Research, Vol. 37, pp. 508–512; H. H. Mantsch, A. Perczel. M. Hollósi, and G. D. Fasman (1992), FASEB Journal, Vol. 6, p. A341; H. H. Mantsch. A. Perczel, M. Hollósi, and G. Fasman (1992), Biopolymers. Vol. 33, pp. 201–207; S. M. Miick, G. V. Martinez, W. R. Fiori, A. P. Tedd, and G. L. Millhauser (1992). Nature, Vol. 359, pp. 653–655], suggest that the amide I band, with a major contribution from the acceptor C  O of the 1 ← 4 intramolecular H bond of β‐turns, appears near or below 1640 cm−1, rather than above 1660 cm−1. In TFE, bands between 1670 and 1660 cm−1 are mainly due to “free” carbonyls, that is, C  O's of amides that are solvated but not involved in the characteristic H bonds of periodic secondary structures or β‐turns. © 1994 John Wiley & Sons, Inc.
Electrophoretic mobility of DNA in gels. I. New biased reptation theory including fluctuations
Authors: Duke Thomas , Viovy Jean‐Louis , Semenov Alexander N. 
Published: December 2004

AbstractIn weak electric fields, the motion of DNA molecules undergoing gel electrophoresis may be described by biased reptation. We argue that the degree of molecular orientation induced by the field is determined by a competition between longitudinal fluctuations and drift of the molecule along the tube. A self‐consistent calculation shows that the end‐to‐end vector of long molecules varies with the square root of the field strength, and not linearly as previously supposed. This leads to a number of new predictions about the field dependence of the molecular mobility and the size limit of resolution. We present the results of computer simulations that support the predictions of the theory of biased reptation including fluctuations. Finally, we discuss the correspondence with experimental data and the implications of our findings for the optimization of DNA electrophoresis. © 1994 John Wiley & Sons, Inc.
Conformational transitions of a dipeptide in water: Effects of imposed pathways using umbrella sampling techniques
Authors: Fraternali Franca , Van Gunsteren Wilfred F. 
Published: December 2004

AbstractThe free energy difference between two states of a molecular system separated by an energy barrier can generally be computed using the technique of umbrella sampling along a chosen reaction coordinate or pathway. The effect of a particular choice of pathway upon the obtained free energy difference is investigated by molecular dynamics simulation of a model system consisting of a glycine dipeptide in aqueous solution. Two different reaction coordinates connecting the so‐called C5and C7conformations, one involving intramolecular hydrogen bonds and the other involving the peptide ϕ, ψ angles, are considered.The Gibbs free energy differences ΔG(C5– C7) are small in both cases, 1.5 ± 1 kJ mol−1and 2.2 ± 1 kJ mol−1, respectively. The two different reaction coordinates yield free energy differences that are identical to within their statistical error. It is found that the exchange of solute–solute, solute–water, and water–water hydrogen bonds involves free energy changes of less thankBT, which points at the existence of a multitutde of low free energy pathways connecting the C5and C7dipeptide conformations. © 1994 John Wiley & Sons, Inc.
Microwave dielectric study on bound water of globule proteins in aqueous solution
Authors: Miura Nobuhiro , Asaka Nobuyuki , Shinyashiki Naoki , Mashimo Satoru 
Published: December 2004

AbstractA dielectric relaxation peak due to bound water of globule proteins in aqueous solution was observed at first by the use of a time domain reflectometry. This peak locates around 100 MHz as well as that of the aqueous DNA solution and the moist collagen, and has a relaxation strength in proportion to surface of the globule protein except for trypsin and pepsin of hydrolase. It is suggested that this peak is caused by orientation of bound water molecules on the protein surface. The number of bound water molecules estimated is in good agreement with that obtained by other method such as x‐ray analysis. The solution exhibits another peak below 100 MHz, which is caused by the rotation of globule protein supplemented by migration of the counterion. Its relaxation time is completely proportional to the molecular weight of the protein. © 1994 John Wiley & Sons, Inc.
A laser light scattering study of gellan gels
Authors: Burne P. M. , Sellen D. B. 
Published: December 2004

AbstractA study of gellan has been made using the technique of photon correlation spectroscopy. It has been confirmed that gellan gels are largely stationary at a molecular level like other polysaccharide gels and quite unlike the gels of flexible polymers such as polyacrylamide. Solution‐gel transitions of deacetylated gellan in 0.025MNaCl have been studied both as a function of concentration and temperature, and the results compared with those of a parallel investigation of agarose. The interstitial spaces within gellan gels have also been studied by measuring the diffusion coefficients of dextran fractions within the gels. Since all gels are nonergodic systems, the theory of dynamic light scattering from such systems is discussed insofar as it affects the present work.It has been shown that the gellan and agarose aqueous systems are fundamentally different, in that agarose does not from a solution at very low concentrations, but splits up into macroscopic gel particles. At very low concentrations, gellan forms a solution in the presence of both gelleing and nongelling ions, the molecules of which shows little change in hydrodynamic diameter with temperature in the range 20–80°C.At higher concentrations where gels are formed, both gellan and agarose exhibit hystersis in their tempertature transitions from gel to solution and solution to gel, the solution being of large molecular aggregates. The transitions are sharp, but in both cases ther is a continous rearrangement in the structural morphology over the entire temperature range on heating, rendering the system more homogeneous prior to dissociation. In the case of gellan, however, there are two distincit phases in these structural changes—this is not true of agarose. The mean mass per unit length of the gellan fibre in the presence of 0.025M NaCl is 19 k daltons/nm at 0.7% concentration and varies with concentration to the power 0.15. The mass per unit length of the agarose fibre is much larger (ca. 110 k Daltons/nm), this difference being consistent with the difference in properties at very low concentrations. © 1994 John Wiley & Sons, Inc.
Photophysical behavior of poly(L‐lysine) carrying porphyrin and naphthyl chromophores
Authors: Pispisa B. , Venanzi M. , D'alagni M. 
Published: December 2004

AbstractThe photophysical behavior of protoporphyrin IX (P) and 1‐naphthylacetic acid (N), covalently bound to ε‐amino groups of poly (L‐lysine) (PL), was investigated by steady‐state and time‐resolved fluorescence as a function of pH. Within the whole range of pH explored, i.e., 7–11, exciplex emission is minor and nearly pH independent. Fluorescence quantum yields, decay time measurements, and transient absorption spectra suggest that quenching of the excited naphthyl chromophore chiefly occurs by interconversion to the triplet state when the sample is randomly coiled and by intramolecular electron transfer (ET) from ground‐state porphyrin when the polypeptide is in α‐helical conformation. The kinetic law, based on a two‐state model for the polymeric matrix, is presented. The specific rate constant of photoinduced ET is 3.1 · 107 s−1 (25°C), in excellent agreement with that obtained by taking simply into account the lifetimes of naphthalene fluorescence in α‐helical PNPL and NPL (pH 11). The relaxation time of the helix‐coil transition was found to be definitely shorter than 20 ns. © 1994 John Wiley & Sons, Inc.