bluuebunny/crossref_metadata_2025_split huggingface dataset:
The flexible DNA double helix. I. Average dimensions and distribution functions
Authors: Olson Wilma K. 
Published: December 2004

AbstractA scheme has been developed to treat the spatial arrangements and properties of double‐helical DNA in terms of the constituent atoms and bonds of the system. Heretofore the behavior of DNA in solution has been interpreted in terms of various artificial theoretical models. In this work the flexibility of the DNA double helix is taken to arise from minor perturbations of the rotation angles along the polynucleotide backbone. The rotational motions of the chain are limited to conformations within the B‐DNA family of helices that permit base stacking. The disruptions of hydrogen bonding associated with these angular fluctuations are offered as a plausible description of the well‐known breathing of double‐stranded DNA. Radii of gyration 〈s2〉0 computed on the basis of this model are found to agree with experimental measurements on B‐DNA helices spanning a wide range of molecular weights. Moreover, the three‐dimensional spatial distribution functions Wa(ρ) generated by these limited internal rotations are compatible with various macroscopic descriptions (i.e., rigid rod, wormlike coil, ideal Gaussian) previously ascribed to DNA of different chain lengths. It is further evident from the Wa(ρ) that the “rigid” B‐DNA backbone modeled here, if long enough, can bend into compact conformations. Thus it does not appear necessary to invoke the occurrence of sharp bends or links to account for the condensed forms of DNA in naturally occurring systems.
Fluorescent 2‐aza‐ε‐adenosine derivatives of polyadenylic acid, polyuridylic acid, and polyinosinic acid
Authors: Yip K. F. , Tsou K. C. 
Published: December 2004

AbstractA new fluorescent analog of adenosine, 1,N6‐etheno‐2‐aza‐adenosine, has been incorporated into polynucleotides by polynucleotide phosphorylase polymerization of 1,N6‐etheno‐2‐aza‐adenosine‐5′‐diphosphate and adenosine‐5′‐diphosphate, uridine‐5′‐diphosphate, or inosine‐5′‐diphosphate. These new oligonucletides possess high fluorescence when excited at 358 nm and emit at 495 nm. The ratio of the fluorescent and nonfluorescent portions of the copolymer can be controlled by the initial composition of the 2‐aza‐ε‐adenosine‐diphosphate and the corresponding nucleoside diphosphate. Fluorescent copolymers with a ratio varying from 1.6 to 35 have thus been synthesized. The physicochemical study of copolymers containing less than 10% of the 1,N6‐etheno‐2‐aza‐adenosine moiety showed that they are similar to poly(A), poly(U), or poly(I). Therefore, fluorescence and polarization study of the 1,N6‐etheno‐2‐aza‐adenosine residues that have been incorporated into the copolymer provides a sensitive indicator for the structure of the copolymer. Potentially these new copolymers may provide unique roles in probing the structure of poly(C) and poly(A) in cellular mRNA.
Model for the conformational analysis of hydrated peptides. Effect of hydration on the conformational stability of the terminally blocked residues of the 20 naturally occurring amino acids
Authors: Hodes Zachary I. , Némethy George , Scheraga Harold A. 
Published: December 2004

AbstractThe effects of hydration are included in empirical conformational energy computations on oligopeptides by means of a modified hydration‐shell model. Free energy terms are introduced to account for “specific hydration” due to water–solute hydrogen bonding and for “nonspecific hydration” describing the interaction of the solute with water molecules in a first‐neighbor shell. The dielectric constant has been doubled (over the value used for calculations in the absence of water) to take into account the presence of solvent. Computations were carried out for the N‐acetyl‐N′‐methylamides of the 20 naturally occurring amino acids. Conformational energy maps are compared with similar maps calculated in the absence of hydration. Minimum‐energy conformations are located and compared with the corresponding minima for unhydrated peptides in terms of ordering with respect to potential energy, the dihedral angles at the minima, and the presence of intramolecular hydrogen bonds. The Boltzmann factors for various conformational regions are altered significantly on hydration in some cases. These changes can be explained in terms of differences in the hydration free energy terms for various conformations.
Catastrophic variation of twist and writhing of circular DNAs with constraint?
Authors: Le Bret Marc 
Published: December 2004

AbstractThe number of constraint turns is defined as the number of bound unwinding ligands converted in turns necessary to relax the energy stored in a supercoiled DNA. It is equal to the sum of the twist and of the writhing and is interpreted geometrically. The twist is shown to be related to the derivative of the energy of superhelix formation with respect to the constraint turns. This leads to a semiempirical evaluation of the variation of the conformational energy with the writhing and of the writhing number. The bending contribution to the conformational energy is estimated independently using first‐order elasticity. The variation of the twist and of the writhing with the constraint is, in this model, catastrophic. In particular, the writhing number jumps between intervals of allowed values.
Conformational dependence of vicinal 13C′NCαH coupling constants in peptides: A dirac vector model investigation
Authors: Mohanakrishnan P. , Easwaran K. R. K. 
Published: December 2004

AbstractTheoretical calculations of the heteronuclear vicinal coupling constant 3J(13C′NCαH) in peptides have been carried out using the Dirac vector model. The results showed an angular dependence for this coupling constant, which can be expressed in the form 3J(13C′NCαH) = A cos2 θ + B cos θ + C, where A, B, and C are constants and θ is related to the torsional angle ϕ of the peptide backbone. The results of the present calculations are in very good agreement with those obtained using finite perturbation theory at the INDO level of approximation.
Titration and fluorometric studies of the tyrosine side chain of angiotensin II and related peptides
Authors: Juliano Luiz , Laluce Cecilia , Oliveira Maria C. F. , Paiva Antonio C. M. 
Published: December 2004

AbstractThe effect of charged side chains on the ionization and fluorescence of the Tyr4 phenolic group in angiotensin (Asp‐Arg‐Val‐Tyr‐Ile‐His‐Pro‐Phe) was investigated. Several synthetic peptides related to angiotensin were titrated spectrophotometrically and quantum yields of tyrosine fluorescence were also determined. The electrostatic interactions were interpreted according to the Kirkwood‐Tanford theory, and the results were related to a recently proposed model [J. L. De Coen and E. Ralston (1977) Biopolymers 16, 1929] for angiotensin conformation in solution. The titration and fluorescence results are in good agreement with the folded conformations of this model, with the exception that the data indicate a weaker interaction between the histidine side chain and the C‐terminal carboxyl groups than that proposed in the model.
Raman spectra of polypeptides containing L‐histidine residues and tautomerism of imidazole side chain
Authors: Ashikawa Ikuo , Itoh Koichi 
Published: December 2004

AbstractRaman spectra were measured for poly(L‐histidine) in H2O, poly(L‐histidine‐d2 and ‐d3) in D2O, L‐histidine in H2O, L‐histidine‐d3 (and d4) in D2O, and 4‐methylimidazole in H2O with various pH (or pD) values. The Raman scattering peaks observed for these samples were ascribed to the neutral and positively charged imidazole groups on the basis of the spectral changes due to the pH variation and to the deuterium substitution of the imino protons. The vibrational modes of these peaks were deduced from the normal coordinate analysis made on the positively charged and neutral 4‐ethylimidazoles. The Raman scattering peaks from the imidazole groups in the neutral form clearly indicate that these imidazole groups exist in the equilibrium between the two tautomeric forms, the 1‐N protonated from (tautomer I) and the 3‐N protonated one (tautomer II). For example, the breathing vibration of the 1‐N protonated form is observed at 1282 cm−1 for L‐histidine and at 1304 cm−1 for 4‐methylimidazole, while the breathing vibration of the 3‐N protonated form is observed at 1260 cm−1 for L‐histidine and 4‐methylimidazole. From the temperature dependence of the relative intensities of the tautomer I peak to that of the tautomer II, it was concluded that the tautomer I is energetically more stable than the tautomer II, and the ΔH value is 1.0 ± 0.3 kcal/mol for L‐histidine and 0.4 ± 0.1 kcal/mol for 4‐methylimidazole. Poly(L‐histidine) with the neutral imidazole side chains shows the amide I peak at 1672 cm−1, indicating that the sample assumes the antiparallel pleated‐sheet structure. Poly(L‐Ala75L‐His25) and poly(L‐Ala50L‐His50) were found to take the α‐helical and β‐form conformations, respectively.
Affinity of glycogen synthetase to crosslinked glycogen
Authors: Zemek J. , Bauer Š. , Kuniak Ľ. 
Published: December 2004

AbstractThe affinity of yeast glycogen synthetase to glycogen modified by crosslinking has been studied under various experimental conditions. It was found that the higher the degree of crosslinking, the lower the affinity of glycogen synthetase to glycogen. The amount of glycogen synthetase adsorbed from the solution depends on the amount of crosslinked glycogen added and is inversely proportional to the concentration of the soluble glycogen. The stability of the complex formed between yeast glycogen synthetase and the crosslinked glycogen was found to be maximal at neutral pH range. The presence of glucose 6‐phosphate, uridine 5′‐di‐phosphate, and uridine 5′‐diphosphate glucose enhanced the stability of the complex.
Electron diffraction study of single crystals of amylose complexed with n‐butanol
Authors: Booy F. P. , Chanzy H. , Sarko A. 
Published: December 2004

AbstractElectron diffraction patterns obtained from single crystals of amylose complexed with n‐butanol are reported. The crystals were examined in the frozen state, after quench‐freezing in liquid nitrogen in order to maintain the complexed state in the electron microscope. The patterns may be indexed in the base plane with an orthorhombic unit cell of dimensions a = 27.0 ± 0.2 Å and b = 26.4 ± 0.2 Å, and the symmetry of the patterns is consistent with the P212121 space group. The relationship between the orthorhombic patterns and the pseudohexagonal patterns obtained by previous workers from dried crystals is discussed.
Potentiometric Studies on Interactions of α‐L‐glutamic Acid Oligomers with Cu(II) in aqueous Solutions
Authors: Mosoni L. , Petit‐Ramel M. M. , Domard A. , Rinaudo M. 
Published: December 2004

AbstractFour oligomers of α‐L‐glutamic acid with ends blocked by nonionizable protecting groups were studied in 0.1M NaClO4 solution using potentiometric measurements. The titrations were analyzed using a pit‐mapping method. The results are compared with those obtained with the corresponding polymer. The successive dissociation constants of the carboxylic side chains are obtained for oligomers with degrees of polymerization varying from 1 to 6. Then the successive stability constants corresponding to the association Cu2+–oligomer are given, and the MpHqLr distribution is calculated for each oligomer introducing MHqL complexes.
Effects of metal ions on the hydrolysis of p‐nitrophenyl caproate by modified poly(ethylenimine)s
Authors: Takagishi Toru , Klotz Irving M. 
Published: December 2004

AbstractHydrolysis of nitrophenyl caproate by modified poly(ethylenimine)s containing imidazole moieties is markedly enhanced in the presence of divalent metal ions. The order of effectiveness is Cu(II) > Co(II) > Zn(II) > Ni(II) > Mn(II), with Cu increasing the rate about 20‐fold. The acceleration by the metal ion is much greater in the presence of CH3COO− or Cl− as counterions than in the presence of ClO4−. Turnover experiments, in which moles of substrate cleaved were in substantial excess of moles of metal present, established the catalytic nature of the effects of the metals. The extent of binding of Cu(II) by the polymers was measured. Maximum accentuation in rate of hydrolysis of nitrophenyl ester was observed for the imidazole‐containing polymer when the ratio of imidazole:Cu(II) was 2.75. Some possible mechanisms for the rate enhancement by metal ions are described.
Conformational energy studies of linear dipeptides H‐X‐L‐Pro‐OH
Authors: Hetzel Robert , Wüthrich Kurt 
Published: December 2004

AbstractEmpirical conformational energy calculations with the use of ECEPP energy functions have been carried out for linear dipeptides H‐X‐L‐Pro‐OH, with X = Gly, L‐Ala, D‐Ala, L‐Leu, D‐Leu, L‐Phe, and D‐Phe, in different states of protonation of the end groups. The results of these calculations are compared with the previously reported experimental equilibrium populations for the cis and trans isomers of the X‐Pro bond in the different species. For all the protonation states of the seven dipeptides, the calculated nonbonded interactions and the conformational entropy term lead to a preference of the trans forms over the cis isomers by at least 1 kcal/mol. The electrostatic interactions stabilize the cis conformations in all species except the cationic forms of the D,L‐peptides, and it could further be shown that only the carbonyl group of X and the two end groups contribute significantly to the total electrostatic energy. One of the principal results of the experimental studies, i.e., the occurrence of 5–15% cis‐proline in all the peptides with an uncharged C‐terminus, was corroborated by our investigation of the cationic species. A detailed assessment of the electrostatic contribution to the total energy of the different conformations of H‐Gly‐L‐Pro‐OH indicates that the standard ECEPP parameters tend to overestimate the electrostatic interactions in aqueous solutions of the X‐Pro dipeptides.
Effect of O(2′)‐methylation on the stability of polynucleotide helices
Authors: Yathindra N. , Sundaralingam M. 
Published: December 2004

AbstractThe effect of ribose(O2′)‐methylation on the stability of (O2′)‐methylated polyribonucleotide helices has been studied by conformational energy calculations. The preferred orientation of the methyl group is found to further stabilize the helical phosphodiester conformation (g−,g−) due to the enhanced short‐range interactions arising between the methyl groups and the adjacent ribose moieties. The experimentally observed increase in melting temperature of (O2′)‐alkylated polyribonucleotides is thus attributable to the enhanced stability of the helical backbone conformation.
Energetic and structural aspects of ethidium cation intercalation into DNA minihelices
Authors: Ornstein Rick L. , Rein Robert 
Published: December 2004

AbstractThe enthalpy ΔH for the intercalation of the ethidium cation (EC) into DNA minihelices can be decomposed into (1) an energy of conformational adjustment (i.e., the energy of minihelix extension and unwinding from the B‐form to the intercalated form) and (2) EC minihelix intermolecular interactions. In the present study, we have focused our attention mainly on a decomposition of the energetic factors of the EC minihelix intermolecular interactions, while the essential features of the energy of conformational adjustment have been discussed in detail elsewhere by us. The structural features of the various resulting energy‐minimized EC‐intercalated complexes are compared with each other and the initial x‐ray model structure. ΔH is estimated to be in the range of −12.3 to −24.0 kcal/mol. This theoretical estimate is qualitatively and quantitatively in agreement with a variety of available experimental data.The energy of conformational adjustment is an energetically unfavorable step, while the energetically favorable contribution of the EC minihelix intermolecular interactions is responsible for the overall favorable nature of the intercalation process involving the EC. On the other hand, the observed preference for intercalation into Pyr(3′–5′)Pur DNA sequences over their isomeric Pur(3′–5′)Pyr sequences is controlled by the energy of conformational adjustment and not by the EC minihelix intermolecular interaction contribution. No base‐composition effect is expected at EC concentrations normally found at cellular conditions. Moreover, the structural features of the various EC‐intercalated complexes are very similar regardless of minihelix base sequence or composition. These results compare favorably with available evidence. The nature of biologically preferred sites of EC binding with the minihelices is discussed.
Study of the rotational diffusion properties of peptides in solution
Authors: Bleich H. E. , Glasel J. A. , Latina M. , Visintainer J. 
Published: December 2004

AbstractIn this paper we examine the theory and method for obtaining rotational diffusion coefficients for peptides in dilute solution from 13C‐nmr spin‐lattice relaxation data. We show that even for the case of nearly equal observed relaxation times of chemically and magnetically nonequivalent alpha‐carbons marked rotational anisotropy will be the usual case. We describe two interactive, minicomputer programs which are of general use in this type of work. The implications of this study on spectral density‐based conformational determinations of peptides is discussed.
Structural characterization of ordered domains in a hydrophobic membrane protein
Authors: Macchi E. M. , Barrantes F. J. 
Published: December 2004

AbstractA delipidized proteolipid protein fraction was purified from organic solvent extracts of bovine cerebral cortex and studied by means of diffraction, electron microscopic, and ir techniques. Special use was made of an electron diffraction procedure which minimized the electron damage to the biological specimens. The ir spectroscopy of the apoprotein fraction indicated the presence of polypeptides in extended β‐conformation, possibly in the antiparallel mode of packing. Electron microscopy of the fraction, negatively stained in organic media, made apparent the presence of both ordered and amorphous material. Only the former, characterized by repeating units of about 40–45 Å in diameter and varying length, produced diffraction patterns in the selected area mode exhibiting a highly undistorted lattice. The two‐dimensional cell parameters of the protein fraction were a = 4.79 Å, b = 7.20 Å, and γ = 90°. The plane group symmetry, corresponding to the systematic absences, was p 2gg, consistent with the β‐pleated sheet structure of simple polypeptides.
Physical association of two simple alkylators to some DNA sequences
Authors: Pearlstein R. A. , Tripathy S. K. , Potenzone R. , Malhotra D. , Hopfinger A. J. , Klopman G. , Max N. 
Published: December 2004

AbstractMolecular mechanics calculations have been used to determine the preferred physical association sites of the known alkylating agent dimethyl aziridinium ion (Az+) and a CH prototype test probe with B‐form, tetrameric DNA sequences. Electrostatic interactions are most important in determining these preferential physical association sites. In turn, the intermolecular energy minima depend on the charge distribution assigned to the DNA sequence. However, for three reported DNA charge distributions, only two distinct sets of energy minima were obtained for the CH‐like ion interacting with (G‐C)4, (A‐T)4, and [(G‐C)·(A‐T)]2 deoxyribonucleic acids. These minima correspond to physical association geometries in which the CH‐like ion is near known alkylation sites. The results of the Az+ … [(G‐C)·(A‐T)]2 interaction are virtually identical to those found for the CH‐like ion. Aqueous solvation energetics have little effect on the physical association of Az+ with [(G‐C)·(A‐T)]2.
DNA bis‐intercalation: Theoretical calculation of binding curves
Authors: Shafer Richard H. 
Published: December 2004

AbstractA statistical mechanical calculation of the binding properties of DNA bis‐intercalators is presented, based on the sequence‐generating function method of Lifson. The effects of binding by intercalation of one or both chromophores of a bifunctional intercalating agent are examined. The secular equation for a general model that includes the effects of neighbor (nearest and non‐nearest) exclusion and/or cooperativity in the binding of both singly and doubly intercalated ligands is derived. Numerical results for binding curves are presented for a more restricted model in which each type of bound ligand rigorously excludes its nearest neighbor and the total number of sites covered by a doubly intercalated ligand is variable. At low values of free ligand concentration bis‐intercalation dominates the binding process, while at high value of free ligand concentration, intercalation of only one chromophore per ligand becomes significant due to the unavailability of contiguous free sites required for bis‐intercalation. Also, depending on the binding parameters, the free energy of the system can be lowered by a loss of doubly intercalated ligands in favor of singly intercalated ones. Corresponding to this transition in binding mode, the average number of sites occupied by a bound ligand decreases from that characteristic of bis‐intercalation to that characteristic of mono‐intercalation as free ligand concentration increases. An analysis of Scatchard plots describing bis‐intercalation is presented.
Absorption and circular dichroic spectral studies on the self‐association of daunorubicin
Authors: Martin S. R. 
Published: December 2004

AbstractThe self‐association of daunorubicin in aqueous solution has been examined using visible absorption, fluorescence, and CD measurements. Spectral changes in the concentration range 10−6 to 1.5 × 10−3M have been interpreted in terms of a monomer–dimer equilibrium for daunorubicin. The data have been analyzed using a nonlinear curve‐fitting technique. The results obtained in this study differ markedly from previously published results, and possible reasons for this difference are discussed. The effect of solvent, temperature, and ionic strength on the dimerization process is investigated.
Kinetics of macromolecules reacting with ligand
Authors: Phillipson Paul E. , Wyman Jeffries 
Published: December 2004

AbstractIn order to get an idea of the transient and stationary behavior to be looked for in a biological macromolecular system such as an enzyme or respiratory protein in the presence of its ligands, we have studied the coupled kinetic equations applicable to a simple allosteric model, based on the concerted two‐state model of Monod et al. [(1965) J. Mol. Biol. 12, 88–118]. Exact solutions of the equations are given for three special cases, and two complementary methods are developed to generate approximate solutions in the general case, always, however, with the assumption that the equations are linear due to maintenance of ligand activity at a constant level. Subject to this assumption, these approximation methods have applicability to coupled rate equations beyond those considered here. As an illustration of how the results can provide the basis for a detailed analysis of actual kinetic data on working proteins, the formalism is applied to the kinetics of binding of oxygen by hemoglobin. An important result is that although time evolution to the steady state is in principle determined by several relaxation times, the effect of cooperativity for the case considered is to establish the dominance of one of them relative to the others. This suggests that for a macromolecule with a large number of binding sites, only one, or at most a few, of the many possible relaxation times are significant for specification of cooperative kinetics. The methods developed here, which will be applied more extensively elsewhere, provide a systematics for finding these dominant relaxation times.