bluuebunny/crossref_metadata_2025_split huggingface dataset:
Studies on cyclic peptides. III. The specific interaction of cyclic peptides with benzene and an application of the solvent‐induced nmr shift to the conformational analysis of cyclo‐(Pro‐Sar‐Gly)2
Authors: Sugihara Toshiharu , Imanishi Yukio , Higashimura Toshinobu 
Published: December 2004

AbstractThe interaction between cyclic peptides [cyclo‐(Sar4), cyclo‐(Pro‐Sar‐Gly)2, cyclo‐(Sar‐Sar), and cyclo‐(Sar‐Gly)] with benzene has been investigated by nmr spectroscopy. The experiment with cyclo‐(Sar4) showed that benzene interacted preferentially with the trans peptide bond in a similar manner to the dimethylformamide–benzene interaction. The solvent‐induced nmr shift was then applied to the conformational analysis of cyclo‐(Pro‐Sar‐Gly)2 with the aid of the molecular model. The major conformation was proved to possess the C2 symmetry with internally hydrogen‐bonded glycine residues, in which all peptide bonds were trans. The interaction of cyclo‐(Sar‐Sar) and cyclo‐(Sar‐Gly) with benzene was also studied. The association constant was 0.115‐kg solution per mole of cyclo‐(Sar‐Sar) and 0.089‐kg solution per mole of cyclo‐(Sar‐Gly) in chloroform.
The binding of adenosine to polyuridylic acid in which uracil residues are chemically altered
Authors: Burr J. G. , Mcdowell T. L. , Christian S. D. 
Published: December 2004

AbstractThe binding of adenosine‐14C to polyuridylic acid (poly(U)) and several modified poly(U)s has been studied by equilibrium dialysis. The poly(U) was modified by addition of appropriate reagents across the 5,6‐double bond of the uracil ring to form the photohydrate, photodimer, dihydrouracil, the HOBr addition product and the HSO3− addition product. Modification of the uracil rings decreases the amount of adenosine which can be bound to the poly(U); the decrease in binding is a function of the fraction of uracil rings which have been changed. Using the expression S = S0(1 − αr)2 to relate the fraction of uracil rings modified (r) to the number of binding “sites” remaining (S), it is found that α is about 1 for all the modifications except photodimer where it is about 2. These observations are taken to mean that the loss of binding capacity of the poly(U) resulting from modifications of the uracil ring is caused by loss of planarity of the uracil rings caused by the modifications, and consequent loss of double helix structure, but that for all modifications except photodimer there is no disruption of the poly(U) double helix on either side of the leison. There does appear to be local melting on either side of the photodimer lesion. The sigmoidal binding isotherms (Ab versus Ca) of modified and unmodified poly(U) can be approximated closely by the following equation:

(1) where Ab = bound A, Ca = free A, n = minimum number of adjacent A′s in complex, S = concentration of sites on poly(U), and K1 = (Km)1/m for all m ≥ n.The stacking energy of adenosine (w) can be calculated accurately using the following equation, where dθ/d ln Ca is obtained from Eq. (1).

(2) For unmodified poly(U), w is −2.0 kcal/mole and ΔG° (−;RT ln K1) is −3.2 kcal/mole. The difference (−1.2 kcal/mole) is attributed to hydrogen bonding. Heavily photohydrated poly(U) does not bind guanosine or guanosine‐5′‐phosphate.
Static and dynamic quenching of protein fluorescence. II. Lysozyme
Authors: McGuire Robert , Feldman Isaac 
Published: December 2004

AbstractThe fluorescence parameters—lifetime, relative quantum yield, wavelength of maximum fluorescence intensity, half‐width, and polarization—of 0.01% lysozyme were measured at 15°C in aqueous solution, in glycerol–water mixtures (0–90% v/v glycerol), in aqueous urea (0–8M) solutions, and in aqueous guanidine hydrochloride (0–6.4M) solutions. The changes in the static and dynamic quenching of lysozyme fluorescence, monitored by the quantum yield and lifetime measurements, were correlated with the other fluorescence parameters and compared with our earlier results with bovine serum albumin.The results were interpreted in terms of induced conformational changes. The various perturbants altered the fluorescence parameters of lysozyme and bovine serum albumin very differently. The differences were shown to be entirely consistent with our earlier conclusion that bovine serum albumin fluorophores are nonsurface residues and with the conclusion of others that lysozyme fluorophores are surface residues. Unlike their effects on bovine serum albumin, urea and guanidine hydrochloride affect lysozyme structure quite differently, both in nature and degree. We have suggested that the affect of urea on lysozyme fluorescence is an indirect result of reduction in the size of the cleft brought about by the structure‐breaking action of urea on water in the cleft. 4M Urea is sufficient for this reaction.Large decreases in the polarization of the fluorescence of lysozyme in the 0.8–1.6M and 3.2–4.8M guanidine hydrochloride ranges demonstrated two guanidine hydrochloride‐induced conformation changes. A red shift of the fluorescence maximum to 354 nm indicated that the second transition completely exposes all fluorescing tryptophan residues of lysozyme to mobile solvent water. However, even 6.4M guanidine hydrochloride did not completely unravel the lysozyme molecule at 15°C, as evidenced by its failure to cause any of the tyrosine residues to become fluorescent.
The magnitude of intramolecular DNA optical absorbance with variation in [Na+] and GC base composition: For special application to DNA reassociation studies
Authors: Marx Kenneth A. 
Published: December 2004

AbstractThe magnitude of intramolecular DNA optical absorbance is presented as a function of [Na+] and GC composition of the DNA. The data are presented as a ratio of absorbances A0/A0 for the DNA at the denaturing temperature (Td) and renaturing temperature (Tr) under the given conditions. All ratios were determined for Tr corresponding to the temperature optimum (Tm − Tr = 25°C) in DNA reassociation rate. This fact, coupled with the convenient A0/A0 ratio representation, permits the quick estimation of the magnitude of this optical effect in DNA reassociation reactions over a wide range of experimental conditions.
A theoretical estimate of the energy barriers between stable conformations of the proline dimer
Authors: Venkatachalam C. M. , Price B. J. , Krimm S. 
Published: December 2004

AbstractSemi‐empirical energy calculations for an internal Pro‐Pro dimer are presented that take into account the nature of the flexibility of the proline ring due to its puckering. Calculations show that three stable conformations are available for the dimer: the cis (ω = 0°, ψ = 160°); the trans (ω = 180°, ψ = 160°, also referred to as trans′); and the cis′ (ω = 180°, ψ = −40°) conformations. The best conformational pathways between these stable conformations are determined. Calculations also show that the barrier for cis′–trans′ conversion is of the same order of magnitude as that for cis–trans conversion.
On the displacement of cooperative transitions of linear biopolymers by an electric field
Authors: Schwarz Gerhard 
Published: December 2004

AbstractA basic theory for equilibrium properties of cooperative transitions (particularly helix–coil transformations) of sufficiently long linear biopolymers under the influence of an electric field is developed. General relations for the calculation of the distribution of uninterrupted sequences of elementary subunit states (e.g., helical fragments) as well as the overall degree of transition θ are given. Strong cooperativity is found to permit simplifications. It is shown that only in this case can a practically significant field effect be expected. Numerical results are presented for a special example of experimental interest.
Circular dichroism of flow‐oriented nucleic acids. II. Comparison between observed and calculated spectra
Authors: Chung Su‐Yun , Holzwarth G. 
Published: December 2004

AbstractThe ultraviolet circular dichroism (CD) of oriented DNA and RNA molecules is calculated by an extension of Johnson and Tinoco's theory [(1969) Biopolymers 7, 727–749] for unoriented molecules. The calculations are carried out for molecular models of A‐DNA, B‐DNA, planar B‐DNA, C‐DNA, and RNA‐11‐α. The calculated curves are compared to measured spectra [(1975) J. Mol. Biol. 92, 449–466] Chung and Holzwarth, for oriented solutions of DNA in buffer, DNA in 6 M LiCl or in ethylene glycol, and double‐stranded viral RNA. The calculation, which considers only base–base interactions, predicts that the CD of B‐DNA, measured with light propagating parallel to the helix axis, should be large and semiconservative, whereas the CD for light propagating perpendicular to the helix axis should be nonconservative. These predictions agree qualitatively with the experimental observations for DNA in buffer; agreement improves if one assumes the bases to be exactly perpendicular to the helix axis. For the other geometries, agreement is less satisfactory, but qualitative agreement with experiment is obtained and the signs of the specific CD spectra are in accord with observations.
A vibrational study of poly (L‐proline) I and II in the far infrared
Authors: Rabolt John F. , Wedding William , Johnson Kenneth W. 
Published: December 2004

AbstractThe far infrared spectra of poly(L‐proline) I (190–35 cm−1) and II (400–35 cm−1) were obtained in the solid state at both 300° and 110°K. A significant difference in the region below 100 cm−1 was observed. A very intense band located at 60 cm−1 in the infrared spectrum of form II has no counterpart in form I. This indicates the sensitivity of low‐frequency vibrations to the difference in conformation assumed by both forms in the solid state.Additional bands observed in this study are correlated with ir and Raman data previously reported and tentative assignments are made using the results of normal mode calculations (in the single‐chain approximation) which have been reported.
Configuration‐dependent properties of randomly coiling polynucleotide chains. II. The role of the phosphodiester linkage
Authors: Olson Wilma K. 
Published: December 2004

AbstractThe dependence of the unperturbed dimensions of randomly coiling polynucleotides on the rotations about the phosphodiester linkages of the chain has been examined in order to understand the conformational discrepancies, set forth in paper I, regarding these angles (ω′ and ω). Large values of the characteristic ratio 〈r2〉0/nl2, which agree with the experimental behavior of the chain, are obtained only if a sizeable proportion of the polymer residues have trans ω′ values. The asymmetric torsional potential that is believed to arise from gauche effects associated with the P‐O bonds has been approximated using a hard core model. The calculated characteristic ratio exhibits a strong dependence upon the magnitude of this torsional barrier (separating trans and gauche conformations) and shows agreement with experimental values for polyribonucleotides only if this energy difference is 1 kcal/mol or less.
Optical rotatory dispersion and circular dichroism of silver(I):Polyribonucleotide complexes
Authors: Arya S. K. , Yang Jen Tsi 
Published: December 2004

AbstractOptical rotatory dispersion (ORD) and circular dichroism (CD) spectra of single‐ and multistranded polyribonucleotides undergo extensive changes on binding of the silver ion. These changes are consistent with the proposition that Ag(I) binds to the heterocyclic bases and not to the phosphate groups of polynucleotides. ORD and CD of silver complexes of poly(A)·poly(U) and double‐helical rice dwarf viral RNA display negative Cotton effects when there is more than one Ag(I) per two nucleotide residues in solution. These observations suggest a significant distortion of the double‐helical conformation as a result of Ag(I) binding. Silver(I) binding sites of pyrimidine polynucleotides are apparently saturated when there is one Ag(I) per two nucleotide residues and those of purine polynucleotides at one Ag(I) per nucleotide in solution. These data are consistent with the supposition that some Ag(I) binding sites exist on the pyrimidine ring and additional sites on the imidazole ring of polynucleotides. The sedimentation coefficient of poly(A) increases by severalfold when one Ag(I) is present per nucleotide residue. Silver(I) may introduce intra‐ and interstrand cross‐links (through bidentate chelates) in single‐stranded polynucleotides, resulting in structures with high sedimentation coefficients. Among the polynucleotides studied, poly(U) was an exception. Silver(I) did not affect the optical properties (absorbance, ORD, and CD) of poly(U) at neutral pH.
Preparation and characterization of α‐L‐glutamic acid oligomers
Authors: Rinaudo M. , Domard A. 
Published: December 2004

AbstractThe preparation and characterization of α‐L‐glutamic acid oligomers with degree of polymerization (DP) up to 12 are described. The preparation of polymers with low DP corresponding to various A/I ratios (where A and I are monomer and initiator concentrations, respectively) with end groups blocked is given. The conditions of the fractionation, which separates the different oligomers by ion‐exchange chromatography, are discussed. Finally, the isolation from salt solutions of the pure acidic form is given. Each polymer obtained for a given A/I is characterized at the end of the polymerization by its molecular‐weight distribution. The average DP values calculated are compared to the A/I values; agreement is very good. Potentiometric behaviour during neutralization is obtained as a function of the degree of polymerization and the elaboration of the polyelectrolytic phenomenon is discussed.
Investigation of fibrous structures. II. General method for the elucidation of the conformations of the complementary nucleic acids
Authors: Tumanyan V. G. , Esipova Natalia G. 
Published: December 2004

AbstractThe problem of deducing the DNA structure with correct base pairing and specific symmetry is formulated in the form of algebraic equations. In this way the number of independent variables determining double‐helix conformation can be reduced from six to four. The effectiveness of the method is illustrated by the computations for A‐DNA and B‐DNA. The method allows one to predict all possible conformations of the complementary nucleic acids.
Low Values of the Scheraga–Mandelkern β parameter for proteins. An explanation based on porous sphere hydrodynamics
Authors: McCammon J. A. , Deutch J. M. , Bloomfield Victor A. 
Published: December 2004

AbstractSeveral globular proteins have values of the Scheraga–Mandelkern β parameter significantly below the theoretical minimum value, β0 = 2.112 × 106, for an impermeable sphere. Using the Felderhof–Deutch generalization of the Debye–Bueche–Brinkman theory of hydrodynamics of porous spheres, we have shown that values of β slightly below this supposed minimum are theoretically expected. A porous sphere of uniform density has a minimum β of 2.084 × 106 at a Debye shielding ratio of 6.5, corresponding, for example, to a sphere radius of 11 Å and an inverse hydrodynamic shielding length of 0.6 Å−1, values not far from those of small proteins. A two‐layer porous sphere model gives similar results. Although this is the first theoretical explanation of values of β below β0, the theory is incomplete since β values as low as 2.03 × 106 are observed.
Determination of the relaxation time of the helix–coil transition of poly(γ‐benzyl‐L‐glutamate) by the nmr technique
Authors: Nagayama Kuniaki , Wada Akiyoshi 
Published: December 2004

AbstractNMR measurements of poly(γ‐benzyl‐L‐glutamate) are reported in several different strengths of magnetic field to determine the relaxation time of the helix–coil transition. Nmr spectra of various samples had line shapes varying from the double to single, depending on the extent of the polydispersity of the sample. This result indicated that the correct line shape of a polypeptide is obscured in the overlapping of multipeaks, which are due to the heterogeneity of the molecular weight in the sample. Thus, the conventional line‐shape analysis could not be applied to the kinetic study of the helix–coil transition of polypeptides without consideration of this polydispersity effect on the line shape.To overcome this difficulty, we measured linewidths of nmr spectra for fairly monodisperse samples, using various nmr spectrometers, having field strengths from 60 to 220 MHz. The results were analyzed by a quadratic equation, which involves an additional term proportional to the frequency difference of two sites. The equation differs from the conventional quadratic equation, usually utilized in the case of the fast‐exchange limit, only in this additional term. This modification is required to evaluate correctly the unusual broadening of the linewidth resulting from the polydispersity effect and to determine the relaxation time reflected in nmr.Nmr spectra of three samples (DP‐35, 85, and 250) were measured by 220‐, 100‐, and 60‐MHz spectrometers in trifluoroacetic acid/chloroform at 28°C and linewidths were analyzed. Relaxation times of the helix–coil transition obtained at the transition midpoint are 2.5 × 10−4, 7 × 10−4, and 1.1 × 10−3 sec, for DP‐35, 85, and 250, respectively.
Synthesis of N‐protected peptides by the o‐nitrophenylsulfenyl group using o‐nitrophenylsulfenyl N‐carboxy α‐amino acid anhydrides
Authors: Katakai Ryoichi , Oya Masanao 
Published: December 2004

AbstractN‐protected peptides, which are important intermediates as a carboxyl component in the fragment condensation method, have been prepared in high yields by the reaction of o‐nitrophenylsulfenyl (Nps) N‐carboxy α‐amino acid anhydrides with unprotected peptides and amino acids in aqueous organic systems. An Nps hexapeptide ester was prepared by the fragment condensation of an Nps tripeptide with a tripeptide ester. It was demonstrated that the synthesis of unprotected peptides by the NCA method, followed by N‐protection by the Nps‐NCA, is a rapid and very useful method for preparing Nps peptides.
Stability of steady states in nucleic acid poly[d(A‐T)] synthesis and the stirred flow reactor
Authors: Schneider Friedemann W. 
Published: December 2004

AbstractThe template directed synthesis of poly[d(A‐T)] from the nucleoside triphosphates in the presence of DNA polymerase I is carried out continuously in a stirred flow reactor for the first time. The initial objective is to test the kinetic stability of the established steady states at various flow rates. Graphical analysis predicts instable steady states for certain high flow rates. As a consequence of instabilities multiple steady states and steady‐state hysteresis may occur. Steady‐state hysteresis has now been found experimentally. For a different enzyme fraction of low exonuclease activity we found the steady‐state absorbance at 260 nm to be almost invariant with flow rate at high enzyme concentrations even if the flow rate was increased by a large factor. We call this phenomenon kinetic buffering. Relaxation of a large flow perturbation approaches the steady state in a sigmoidal fashion. Concentration oscillations at 260 nm occurred in one experiment using an enzyme fraction of low exonuclease activity after perturbing the steady state by monomer (dATP). Advantages of the stirred flow reactor method over serial transfer are discussed.
Raman studies of bovine serum albumin
Authors: Lin V. J. C. , Koenig J. L. 
Published: December 2004

AbstractThe Raman Spectra of bovine serum albumin have been obtained in the solute state, in alkaline and acidic solutions, and in the gel. The reversible denaturations of bovine serum albumin solutions by heat, acid's, and alkali were studied and a new mechanism for heat denaturation has been proposed based on a continuous unfolding of the α‐helices.
Low‐frequency Raman spectra of lysozyme
Authors: Genzel L. , Keilmann F. , Martin T. P. , Wintreling G. , Yacoby Y. , Fröhlich H. , Makinen Marvin W. 
Published: December 2004

AbstractNew techniques in laser Raman spectroscopy are used to obtain spectra of aqueous solutions of lysozylme for frequency shifts as small as 5 cm−1. In addition, Raman measurements are made on two crystalline forms of hen egg white lysozyme. The spectra obtained from the solution and from the crystal are found to be similar for frequencies above 100 cm−1. However, a low‐frequency band at 25 cm−1 observed in crystalline lysozyme is not found in the solution, indicating that this band cannot be attributed to an internal molecular vibration.
Molecular forces in ribosomes and polynucleotide complexes
Authors: Bresler S. E. , Saminsky E. M. , Chernajenko V. M. 
Published: December 2004

AbstractThe stability constant of the complex of tRNA with 50S subunits of ribosomes was compared in ordinary and heavy water. A considerable effect (about fourfold) was observed, showing the importance of hydrogen bonds in this interaction. In addition, the isotope effect of complementary polynucleotide interaction was measured for two examples. In the case of the binary complex of heptainosinic acid oligomers with poly(C) in the presence of 10−3 M MgCl2, the transfer from ordinary to heavy water gave an increase of the stability constant of about 5%. But in the case of a ternary complex of hexaadenylic acid with poly(U) under the same conditions, the stability constant in D2O increased threefold. The isotope effect depends strongly on magnesium ion concentration and is possibly due to some specific mechanism of magnesium ion complexing involving water molecules.
Relative stability of the α‐helix of deuterated poly(γ‐benzyl‐L‐glutamate)
Authors: Karasz F. E. , Gajnos G. E. 
Published: December 2004

AbstractThe coil‐to‐helix transition temperatures of hydrogen bearing and deuterated poly(γ‐benzyl‐L‐glutamate) in 1,3‐dichlorotetrafluoroacetone/H2O and/D2O mixtures, respectively, have been determined. Together with previously obtained data for the conformational transition of this polypeptide in normal and deuterated dichloroacetic acid, these results have been used in an analysis of the effect of deuterium substitution on the intrinsic stability of the α‐helical form of poly(γ‐benzyl‐L‐glutamate). The findings, consistent for both solvent systems, showed that the deuterated polypeptide is some 5% more stable than the normal protonated poly(γ‐benzyl‐L‐glutamate), while the polypeptide‐active solvent interaction enthalpy is also slightly increased by deuterium substitution in the respective molecules. A consideration of available data for poly(β‐benzyl‐L‐aspartate) reveals an anomaly with respect to the present analysis.