bluuebunny/crossref_metadata_2025_split huggingface dataset:
Triple helix–coil transition of covalently bridged collagenlike peptides
Authors: Roth Werner , Heidemann Eckhart 
Published: December 2004

AbstractThe thermal triple helix–coil transition of covalently bridged collagenlike peptides with repeating sequences of (Ala‐Gly‐Pro)n, n = 5–15, was studied optically. The peptides were soluble in water/acetic acid (99:1) and were found to form triple‐helical structures in this solvent system beginning with n = 8. The thermodynamic analysis of the transition equilibrium curves for n = 9–13 yielded the parameters ΔH°s = −7.0 kJ per tripeptide unit, ΔS°s = −23.1 J deg−1 mol−1 per tripeptide unit for the coil‐to‐helix transition, and the apparent nucleation parameter σ ≃ 5 × 10−2. It was suggested through double‐jump temperature experiments that the rate‐limiting step during refolding is not only influenced by the difficulties of nucleation, but also by cis–trans isomerization of the Gly‐Pro peptide bond.
Experimental characterization of poly(hydroxyalkyl‐L‐glutamine) conformations in aqueous calcium chloride and sodium perchlorate solutions
Authors: McCord Robert W. , Madison Edwin L. , Mattice Wayne L. 
Published: December 2004

AbstractPoly(hydroxyalkyl‐L‐glutamine) (alkyl = ethyl, propyl, butyl) solutions have been studied by CD as functions of temperature and activity of calcium chloride and sodium perchlorate. Helical content is altered by changes in salt activity and temperature. The helicity of poly(hydroxybutyl‐L‐glutamine) and poly(hydroxypropyl‐L‐glutamine) falls to zero in a monotonic fashion with increasing calcium chloride activity. A nonzero helicity reappears at activities in excess of 5–50 mol kg−1. Poly(hydroxypropyl‐L‐glutamine) is much more sensitive to calcium chloride than is poly(hydroxybutyl‐L‐glutamine), and both polypeptides are more sensitive to calcium chloride than are typical proteins. Markedly different behavior is observed with sodium perchlorate. This salt acts as a helix stabilizer at low activities but becomes a destabilizer at activities higher than 0.3–1.0 mol kg−1. In this respect the effect of sodium perchlorate on nonionic poly(hydroxyalkyl‐L‐glutamines) resembles that seen with cationic poly(L‐lysine) and poly(L‐arginine). Helix stabilization at low sodium perchlorate activity is moderate for poly(hydroxybutyl‐L‐glutamine) and large for poly(hydroxypropyl‐L‐glutamine) and poly(hydroxyethyl‐L‐glutamine).
Influence of uracil photohydrate formation on the conformational properties of heterodinucleoside monophosphates
Authors: Ezra Fouad S. , Maccoss Malcolm , Danyluk Steven S. 
Published: December 2004

AbstractThe structural properties of uracil photohydrates at the monomer and dimer level in aqueous solution have been examined in detail by nmr spectroscopy. Based on such evidence, the absolute configurations of the two possible diastereomers have been assigned, and the conformational perturbations induced by photohydration have been evaluated. In all instances, photohydration shifts the 2E ⇌ 3E puckering equilibrium of the sugar ring of the uridylyl fragment towards 2E (from 12–18%). In addition, for both dimers examined in detail, ho6UpA and Apho6hU, the effect of dimerization on sugar pucker is such that the 3′‐terminal unit shows a clear increase in the percentage of 3E (relative to the appropriate 5′‐mononucleotide), whereas the percentage 3E of the 5′‐terminal unit shows no change. This is contrary to the findings in the normal dinucleoside monophosphates, where an increased preference for 3E pucker occurs in both residues on dimerization and increased base stacking. Significant base–base interactions were observed in both hydrated dimers despite the loss of the planar π‐system in the uracil fragment. In addition, the rate of photohydration for a particular dimer pair (e.g., ApU and UpA or GpU and UpG) is shown to be inversely dependent on the amount of base stacking in the parent dimer. This latter parameter has also been correlated with the ratio of the two possible diastereomers formed in the reaction and is associated with a preferential attack at one face of the pyrimidine base ring. The shift of the sugar puckering equilibrium towards 2E has been compared with similar shifts observed when adenosine and guanosine are methylated at N(1) and N(7), respectively. The possible biological significance of the above‐mentioned conformational aspects is discussed.
A general multistate model for the analysis of hydrogen‐exchange kinetics
Authors: Krishna N. Rama , Goldstein Gideon , Glickson Jerry D. 
Published: December 2004

AbstractIn proton nmr, the chemical exchange rates of slowly exchanging labile hydrogens (with lifetimes in the range ∼ 10 msec – ∼ 1 sec) of peptides, proteins, and nucleic acids can be measured in H2O by a combination of two separate experiments: (1) the transfer of solvent saturation and (2) saturation‐recovery experiments. When these molecules exist in a dynamic equilibrium among different conformations, the experiments cannot be analyzed in a straightforward manner to derive the intrinsic exchange rates. In the present study we have derived analytical expressions for the above two experiments on a biomolecule under certain limiting conditions: (1) the extreme low‐motility limit, where each of the conformational transitions is much slower than the corresponding hydrogen exchange rate with the solvent; (2) the high‐motility limit (EX2 mechanism), which is the opposite extreme of the previous limit; and (3) the low‐motility limit (EX1 mechanism), which is a mixture of limits (1) and (2), i.e., for some of the conformations, the exchange rate with the solvent is much faster than their conformational transition rates, while for the remaining conformations the reverse situation is realized. The results may be considered as a generalization to an arbitrary number of states of the two‐state model treated by Hvidt. Equations have also been derived that are applicable to the iostope exchange method of measuring very slow exchange rates (with life‐times of the order of minutes and longer) in biomolecules. The saturation recovery experiments performed in H2O on the active pentapeptide fragment of thymopoietin serve to illustrate the high‐motility limit. The theoretical formulation presented in this study can be easily adapted to other double‐resonance techniques and also to situations where the kinetics of an arbitrary system existing in a multistate equilibrium are of interest.
Study of the influence of NH ⃛S hydrogen bonds on the reduction potential in Clostridium pasteurianum 2(4Fe‐4S) ferredoxin using deuterium exchange
Authors: Sweeney William V. , Magliozzo Richard S. 
Published: December 2004

AbstractThe effect of deuterium substitution of exchangeable hydrogen atoms on the reduction potential of Clostridium pasteurianum 2(4Fe‐4S) ferredoxin has been studied. The studies were conducted to determine if NH ⃛S hydrogen bonds to the iron–sulfur cluster are dominant in the mechanism of influence of the protein on cluster reduction potential, as has been proposed [Carter, C. W. (1977) J. Biol. Chem. 252, 7802–7811]. Deuteration of the slowly exchangeable hydrogen atoms, however, yields essentially no shift in the reduction potential (−0.2 ± 0.8 mV), suggesting that NH ⃛S bonds are not important modifiers of cluster reduction potential in this protein.
Structural and conformational investigation of carrageenans
Authors: Rochas Cyrille , Rinaudo Marguerite , Vincendon Marc 
Published: December 2004

AbstractA detailed assignment of the 13C chemical shifts of κ‐ and ι‐carrageenans in their Na+ and K+ forms in D2O and dimethylsulfoxide is given. Evidence of the conformational transition induced by temperature variation in the absence of any gel formation on κ‐carrageenans is also presented. This evidence is based on 13C‐nmr and optical rotation experiments.
The chiroptical properties of proteins. II. Near‐ultraviolet circular dichroism of lysozyme
Authors: Goux Warren J. , Hooker Thomas M. 
Published: December 2004

AbstractA study of the near‐uv CD spectrum of lysozyme was carried out in the presence and absence of the inhibitor tri‐N‐acetylglucosamine, and theoretical chiroptical calculations based on the tetragonal crystal structure of the enzyme and the enzyme‐inhibitor complex were performed. The results of these calculations indicate that the near‐uv CD spectrum of lysozyme can be adequately explained in terms of negative rotatory strengths arising from the tryptophan 1La (293–300 nm) and the disulfide n‐σ* bands (250 rm), and positive rotatory strength contributions from the tryptophan 1Lb bands (291 nm) and the tyrosine 1Lb bands (275 nm). Contributions to the rotatory strength of each band were approximated in terms of specific interactions between chromophores. It was found that the rotatory strength of most of the near‐uv transitions arises primarily from coupling interactions involving other side‐chain chromophores and amide groups which are in close proximity. Changes which are observed in the lysozyme CD spectrum on binding of tri‐N‐acetylglucosamine may be explained in terms of changes in the rotatory strength which result from interactions of the 1La transitions of the active‐site tryptophans with the acetamide groups of the inhibitor. The reasonable agreement which is found between the experimental and calculated rotatory strengths implies that the crystal conformation of lysozyme must resemble the solution conformation.
Effects of pD on ring‐stacking interactions between dinucleoside phosphates and tryptamine
Authors: Kolodny N. H. , Neville A. C. 
Published: December 2004

AbstractComplex formation between tryptamine and mononucleotides and dinucleoside phosphates containing adenine and/or cytosine has been studied at five pD's ranging from 1.1 to 7.4 by proton magnetic resonance spectroscopy. Chemical shifts of base ring protons and the ribose anomeric proton in the nucleotides and indole ring protons in tryptamine were monitored and their changes with pD and intermolecular interactions interpreted qualitatively. Stacked complexes were found to exist at all pD's in the range studied. Complex geometries differ depending on pD. An electrostatic interaction between the tryptamine amino group and the nucleotide phosphate group contributes to complex formation above pD 4 but is not strong enough to shift the dinucleoside phosphate equilibrium towards the unstacked conformer.
Cation binding cyclic peptides composed of imino acid residues
Authors: Shimizu Toshimi , Fujishige Shoei 
Published: December 2004

AbstractCyclo(L‐Pro‐Sar)n (n = 2–4) with moderate flexibility and hydrophobicity of molecular structure was synthesized, and the characteristics of these cyclic peptides and their metal complexes in acetonitrile were investigated in connection with the residual properties using 13C‐nmr measurements. The cyclic tetrapeptide cyclo(L‐Pro‐Sar)2 showed a sterically hindered phenomenon in acetonitrile in which the amide backbone adopted a cis‐trans‐cis‐trans sequence. The cyclic hexapeptide cyclo(L‐Pro‐Sar)3 existed as a mixture of several conformers whose interconversion is slow on the nmr time scale, including cis‐cis‐trans and/or cis‐trans‐trans arrangement of the Sar‐Pro bond. Finally, it was demonstrated that the cyclic octapeptide cyclo(L‐Pro‐Sar)4 behaved as a mixture of multiple conformers which allowed for cis‐trans isomerism about the Pro‐Sar peptide bond, of which 20–30% had the all‐cis Sar‐Pro bond isomer and the remaining 70–80% had one (or more) cis Sar‐Pro bond isomer. 13C‐nmr spectra also demonstrated that cyclo(L‐Pro‐Sar)n (n = 3,4) formed a 1:1 ion complex whose conformation was characterized by an all‐trans peptide bond in the presence of excess metal salt. Cation binding studies, using CD measurements, established that the ion selectivity of cyclo(L‐Pro‐Sar)4 in acetonitrile decreased in the order, Ba2+ > Ca2+ > Na+ > Mg2+ > Li+.
Kinetic studies of spin interconversion in ferric mixed‐spin derivatives of myoglobin
Authors: Sano Takayuki , Ishibashi Joji , Ikeda Naoki , Yasunaga Tatsuya , Ogawa Satoshi , Morishima Isao 
Published: December 2004

AbstractKinetic studies of spin interconversion in various derivatives of metmyoglobin such as the fluoride, aquo, hydroxide, azide, imidazole, and cyanide were performed by the coaxial‐cable temperature‐jump method. For all these derivatives, except fluoride and aquomyoglobin, a single relaxation was observed around 3 μsec. The rate constants and activation parameters for the spin interconversion were estimated and are discussed in comparison with those reported for the reaction of synthetic iron complex. Other hemoproteins such as cytochrome c and human hemoglobin were also examined, and the results were compared with those for myoglobin. The effect of buffer solution is also discussed.
Conformational studies of peptides: Crystal and molecular structures of L‐3,4‐dehydroproline and its t‐butoxycarbonyl and acetyl amide derivatives
Authors: Benedetti Ettore , Di Blasio Benedetto , Pavone Vincenzo , Pedone Carlo , Felix Arthur , Goodman Murray 
Published: December 2004

AbstractThe crystal structures of L‐3,4‐dehydroproline, t‐butoxycarbonyl‐L‐3,4‐dehydroproline amide, and acetyl‐L‐3,4‐dehydroproline amide have been determined. L‐3,4‐Dehydroproline is orthorhombic with a = 16.756, b = 5.870, c = 5.275 Å, and Z = 4; t‐butoxycarbonyl‐L‐3,4‐dehydroproline amide is orthorhombic with a = 6.448, b = 8.602, c = 21.710 Å, and Z = 4; acetyl‐L‐3,4‐dehydroproline amide is monoclinic with a = 4.788, b = 10.880, c = 7.785 Å, β = 105.25°, and Z = 2. The final R value for the L‐3,4‐dehydroproline is 0.046 based on 529 reflections; for t‐butoxycarbonyl‐L‐3,4‐dehydroproline amide, 0.050 based on 792 reflections; and for acetyl‐L‐3,4‐dehydroproline amide, 0.058 based on 632 reflections. The structures clearly establish that the free amino acid exists in the zwitterionic form in the crystalline state. The molecular conformations of the t‐Boc and acetyl derivatives consist of two planes: one involving the primary amide and the other the remaining atoms of the molecule. The acetyl‐L‐3,4‐dehydroproline amide contains a tertiary amide bond in the cis conformation. To the best of our knowledge, this is the first example of a cis bond in an acetyl derivative of an amino acid or peptide. At variance with the previously reported proline amides, which present ϕ and ψ values corresponding to those of a right‐handed α‐helical conformation (conformation A), the t‐Boc and acetyl derivatives both have ϕ and ψ values corresponding to a collagenlike conformation (conformation F).
Contribution from the chirality of the growing chain to the enantiomer selectivity in activated‐NCA polymerization of α‐amino acid N‐carboxyanhydride
Authors: Hashimoto Yutaka , Imanishi Yukio 
Published: December 2004

AbstractAs a model compound for the growing chain in the activated‐NCA type of polymerization of α‐amino acid N‐carboxyanhydride (NCA), 3‐[ω‐acetylglycyl‐poly(α‐amino acid) acyl]‐α‐amino acid NCA (called the prepolymer) having various degrees of polymerization (DPs) was synthesized by the polymerization of Phe, Val, Glu(OEt), and Asp(OBzl) NCA in the presence of AcGly NCA by the tertiary amine. Activated (S)‐Phe, Val, Glu(OEt), and Asp(OBzl) NCA were added to the terminal cyclic group of the corresponding (S)‐ or (R)‐ prepolymer, and the enantiomer selectivity in the reaction was investigated. With prepolymers having DPs ranging from 1 to 15, the addition reaction always took place preferentially between species having the same configuration, and the degree of the enantiomer selection increased with increasing DP of the prepolymer. With prepolymers having DP = 1 and 2, we found contributions from the chiral terminal unit and the chiral penultimate unit to the enantiomer selection, respectively. Prepolymer having DP = 5 was shown to take a β‐type conformation, which led to higher enantiomer selection; and prepolymers having DP = 10 and 15 were shown to take an α‐helix conformation, which led to much higher enantiomer selection than did the β‐type conformation. In the present investigation the mechanisms of terminal‐unit control, penultimate‐unit control and conformational control of the enantiomer selection in the activated‐NCA type of polymerization were clearly observed.
Intrachain end‐to‐end charge transfer interaction in oligosarcosines
Authors: Sidido Masahiko , Kanazawa Yoshihiro , Imanishi Yukio 
Published: December 2004

AbstractOligosarcosines with two to seven sarcosine units terminated by an electron donor (p‐dimethylaminoanilide group) and an electron acceptor (3,5‐dinitrobenzoyl group) were synthesized by a liquid‐ or solid‐phase method. The oligomers showed a distinct charge‐transfer (CT) absorption in chloroform and ethanol solutions at low enough concentrations to eliminate the contribution of intermolecular CT interaction. Fractions of the oligomers which form the intrachain CT complex were evaluated at infinite dilution and plotted as a function of the number of sarcosine units n. The plot showed an alternating higher and lower tendency with the increase of n from n = 3 to 7; the total maximum was found at n = 4. The maximum reached 0.24 in chloroform, which is higher than that expected for an unperturbed oligosarcosine chain free from the end‐to‐end interaction, by an approximate factor of 50. The alternating chain‐length dependence was found to be governed by an alternating tendency in the conformational enthalpy required for cyclization.
Three‐dimensional structure of actinoxanthin. III. A 4‐Å resolution
Authors: Pletnev V. Z. , Kuzin A. P. , Trakhanov S. D. , Kostetsky P. V. , Popovich V. A. , Tsigannik I. N. 
Published: December 2004

AbstractThe protein actinoxanthin (molecular weight 10,300) crystallizes in space group P212121, with cell dimensions a = 30.9 Å, b = 48.8 Å, c = 64.1 Å, and z = 4. The three‐dimensional structure of actinoxanthin at 4‐Å resolution was determined by x‐ray methods on the basis of experimental data from the native protein and five isomorphous derivatives. At the stage of solving the phase problem, the heavy atoms in the derivatives were located using direct methods. The actinoxanthin molecule can be described as an oblate ellipsoid with approximate dimensions 20 × 30 × 40 Å and consists of two different sizes of folded units separated by a well‐defined cleft. The larger unit, including the N‐ and C‐terminals of the protein chain, is characterized by a significant content of β‐sheet structure. The smaller unit, containing two deca‐ and hexapeptide cycles closed by disulfide bonds, has a mainly irregular structure.
Structural conformations of nucleosomes at low ionic strength from flow birefringence and intrinsic viscosity
Authors: Harrington Rodney E. 
Published: December 2004

AbstractThe shape and structure of nucleosomes from chicken erythrocytes as a function of ionic strength in solution using the complementary techniques of streaming birefringence and intrinsic viscosity were studied. As characterized by both rotational diffusion and optical anisotropy, three distinct conformational levels were observed. Above ∼8 mM ionic strength, the particles are oblate ellipsoids or discs with axial ratio of ∼0.5. Below ∼8 mM, two structural variants were observed: a relatively more symmetrical particle which exists between ∼8 and ∼0.5 mM, and a relatively asymmetric structure below ∼0.5 mM. Birefringence data are consistent with an “opened clamshell” type of model for the first of these and with a somewhat compacted form of linear DNA for the latter. The results provide insights into possible conformational states of transcriptionally active chromatin at the nucleosomal level of structure.
Kinetics of activation and desensitization in receptor proteins
Authors: Kanehisa Minoru I. 
Published: December 2004

AbstractReceptors are functional membrane proteins on the cell surface that recognize external signals and trigger biological responses by generating intracellular signals. Due to prolonged exposure to external signals, receptors are often desensitized and no longer produce intracellular signals. This simple control mechanism may work without negative‐feedback regulation from another molecule if the active state of a receptor reflects a transient metastable molecular structure. A theoretical framework is developed to identify a metastable state associated with a conformational transition of protein molecules, in which a transient state can be observed somewhat above the equilibrium transition point. The conducting state of the acetylcholine receptor may thus represent a metastable state associated with a conformational transition from the resting state to the desensitized state. Similarly, the conducting state of the voltage‐sensitive sodium channel may represent a metastable state associated with a conformational transition from the resting state to the refractory state. The rates of appearance and disappearance of the transient state, as well as the equilibrium ratio of the two preexisting states, can be estimated from the free energy of protein structure. The appearance of the transient state is generally a multirelaxation process and may show a time lag, while the disappearance is a slower single‐relaxation process.
Thermodynamic interaction between urea and the peptide group in aqueous solutions at 25°C
Authors: Schönert Hansjürgen , Stroth Leo 
Published: December 2004

AbstractIsopiestic vapor pressure measurements of the ternary systems water + triglycine + urea and water + glycine‐L‐alanine + urea were made and used to calculate the Gibbs free energy of these systems. Together with recently published analogous results on systems, in which the first solute was glycine or alanine or diglycine, and measurements of the excess enthalpy of all these solutions, it is possible to calculate the Gibbs free energy of transfer and the enthalpy of transfer of the peptide group from water to aqueous urea solutions. The transfer can be described as a binding of urea to the peptide group with ΔG = −1.85 kJ mol−1 and ΔH = −18.7 kJ mol−1 at 298.1 K.
Transient‐phase energetics of the oxidative deamination of L‐glutamate by L‐glutamate dehydrogenase and NADP: A reaction with a large negative heat capacity of activation
Authors: Colen Alan H. , Medary Richard T. , Fisher Harvey F. 
Published: December 2004

AbstractA study of the temperature dependence of the initial transient velocities of the oxidative deamination of L‐glutamate by glutamate dehydrogenase and NADP has permitted the determination of the enthalpies, entropies, and heat capacities of the phenomenological parameters for mechanistic steps up to and including the catalytic hydrogen‐transfer step. The most striking feature observed is the extremely large negative heat capacity of activation (−590 ± 150 cal K−1 mol−1) for the catalytic step itself. Possible sources of such heat capacities are considered, with particular focus on the effects of hidden equilibria among multiple thermodynamic states. Heat‐capacity changes of the sort observed here can be produced by shifts of such dynamic equilibria between multiple forms of the free enzyme induced by the formation of the catalytic transition state.
A circular dichroism study of valinomycin barium ion complex
Authors: Devarajan S. , Easwaran K. R. K. 
Published: December 2004

AbstractComplex formation of valinomycin with Ba2+ ions was investigated by circular dichroism spectroscopy. The results indicated that Ba2+ forms entirely different types of complexes when compared with K+. The data with perchlorate salt showed evidence for the formation of less stable V2C (peptide sandwich), VC (1:1), and VC2 (ion sandwich) complexes followed by a stable final complex upon gradual addition of salt (V stands for valinomycin and C for the cation). This final complex possibly has a flat structure with no internal hydrogen bonds, similar to that of valinomycin in highly polar solvents. The possible complexation mechanism and the role played by anions and isopropyl side chains are highlighted.