bluuebunny/crossref_metadata_2025_split huggingface dataset:
α‐helix to random coil transitions: Determination of peptide concentration from the CD at the isodichroic point
Authors: Holtzer Marilyn Emerson , Holtzer Alfred 
Published: December 2004

AbstractA method is presented for determining the concentrations of peptides and proteins having isodichroic points near 203 nm. The existence of an isodichroic point for a given substance indicates a local two‐state (α‐helix, random coil) population. The mean residue ellipticity at the isodichroic point, [θλi], is, of course, independent of helix content. For a wide variety of synthetic and natural peptides, including both single helices and coiled coils, it is shown that [θλi] is also essentially independent of substance and of whether the transition is induced by temperature, ionic strength, pH, chain length changes, amino acid substitution, or solvent perturbation. Averaging [θλi] values culled from various laboratories gives –151 ± 16 (SD, 7 sources) deg · cm2 · mmol−1. In our laboratory, nonpolymerizable rabbit α‐tropomyosin and two α‐tropomyosin subsequences yield –135 ± 10 (SD, 190 values) deg · cm2 · mmol−1. Thus, given [θλi] for a peptide of known concentration, it is possible to estimate the concentration of any other peptide provided that it has an isodichroic point at which the ellipticity is accurately measurable. It is then possible to calculate [θλ] at any other wavelength for which θ is known. It is advisable to determine [θλi] for the best known peptide in one's own laboratory, since it depends on absolute instrument and cell calibrations and an absolute concentration determination. © 1992 John Wiley & Sons, Inc.
How many numbers are required to specify sequence‐dependent properties of polynucleotides?
Authors: Goldstein Robert F. , Benight Albert S. 
Published: December 2004

AbstractThere are 10 unique dinucleotides of double‐stranded DNA, but only 8 independent nearest‐neighbor energies that occur in circular DNA, as shown by D. M. Gray and I. Tinoco [(1970) Biopolymers 9, 223–244]. We extend that analysis to include end effects, and show that the number of unique dinuoleotide pairs (including ends) is 14. but there are only 12 independent energies. We discuss how these 12 energies (or spectra or any other pairwise additive property) can be measured and displayed, and how they should and should not be compared between experimenters. As an example, we analyzed the recently reported melting curves [M. J. Doktycz et al. (1992) Biopolymers, 32, 849–864] of 16 DNA dumbbells in two different Na+ environments. This analysis reveals a new means for evaluating end effects and the emergence of longer than nearest‐neighbor interactions at low salt concentration. © 1992 John Wiley & Sons, Inc.
Influence of electrostatic interactions on the sugar–phosphate backbone conformation in DNA
Authors: Pechenaya V. I. 
Published: December 2004

AbstractThe influence of sugar ring flexibility in DNA on the mechanism of the B ⇄ A conformational transition is studied. The dipole moment of the deoxyribose as a function of its puckered states is calculated by the quantum‐mechanical method using the MINDO/3 approximation. The interaction of the sugar dipole with the neighbor molecular groups in polynucleotide chains is estimated. The sugar dipole interaction with phosphate groups and counterions is shown to be strong and capable to deform the pseudorotation potential of deoxyribose. The effective pseudorotation potential of sugar ring in the B and A helices is obtained. The results are used to explain the behavior of Raman bands in the region of sugar–phosphate vibrations. The mechanism of the effect of electrostatic forces on the sugar–phosphate backbone conformation, which is essential for the B ⇄ A and other structure transitions, is offered. © 1993 John Wiley & Sons, Inc.
A Monte Carlo method for generating structures of short single‐stranded DNA sequences
Authors: Erie Dorothy A. , Breslauer Kenneth J. , Olson Wilma K. 
Published: December 2004

AbstractA Monte Carlo method has been developed for generating the conformations of short single‐stranded DNAs from arbitrary starting states. The chain conformers are constructed from energetically favorable arrangements of the constituent mononucleotides. Minimum energy states of individual dinucleotide monophosphate molecules are identified using a torsion angle minimizer. The glycosyl and acyclic backbone torsions of the dimers are allowed to vary, while the sugar rings are held fixed in one of the two preferred puckered forms. A total of 108 conformationally distinct states per dimer are considered in this first stage of minimization. The torsion angles within 5 kcal/mole of the global minimum in the resulting optimized states are then allowed to vary by ±10° in an effort to estimate the breadth of the different local minima. The energies of a total of 2187 (37) angle combinations are examined per local conformational minimum. Finally, the energies of all dinucleotide conformers are scaled so that the populations of differently puckered sugar rings in the theoretical sample match those found in nmr solution studies. This last step is necessitated by limitations in the theoretical methods to predict DNA sugar puckering accurately. The conformer populations of the individual acyclic torsion angles in the composite dimer ensembles are found to be in good agreement with the distributions of backbone conformations deduced from nmr coupling constants and the frequencies of glycosyl conformations in x‐ray crystal structures, suggesting that the low energy states are reasonable. The low energy dimer forms (consisting of 150–325 conformational states per dimer step) are next used as variables in a Monte Carlo algorithm, which generates the conformations of single‐stranded d(CXnG) chains, where X = A, T and n = 3, 4, 5. The oligonucleotides are built sequentially from the 5′ end of the chain using random numbers to select the conformations of overlapping dimer units. The simulations are very fast, involving a total of 106 conformations per chain sequence. The potential errors in the buildup procedure are minimized by taking advantage of known rotational interdependences in the sugar–phosphate backbone. The distributions of oligonucleotide conformations are examined in terms of the magnitudes, positions, and orientations of the end‐to‐end vectors of the chains. The differences in overall flexibility and extension of the oligomers are discussed in terms of the conformations of the constituent dinucleotide steps, while the general methodology is discussed and compared with other nucleic acid model building techniques. © 1993 John Wiley & Sons, Inc.
Kinetic analysis of the hydrodynamic transition accompanying protein folding using size exclusion chromatography. 1. Denaturant dependent baseline changes
Authors: Shalongo William , Heid Paul , Stellwagen Earle 
Published: December 2004

AbstractSize exclusion profiles of proteins with persistent conformations exhibit broad asymmetric peaks whose shape and elution times are dependent on denaturant concentration. The collective elution profiles were precisely simulated by an apparent binding model that treats the denaturant dependence in terms of an apparent matrix binding. The model requires three experimentally measurable parameters: the elution time for the unbound protein, an apparent association equilibrium constant for binding, and an apparent exchange time for binding. The denaturant dependence for each of these parameters is related to the accessible surface area of the protein. © 1993 John Wiley & Sons, Inc.
Microwave absorption spectroscopy of DNA
Authors: Bigio Irving J. , Gosnell Timothy R. , Mukherjee Pritish , Saffer Jeffrey D. 
Published: December 2004

AbstractBy utilizing a novel approach to microwave spectrometry, we have measured the absolute absorption spectrum of plasmid DNA (pUC8.c2), in buffered aqueous solution, from 5 to 20 GHz. Our technique does not suffer from the same experimental difficulties that plague other methods. We observe no absorption resonances in this frequency range, but we do see broadband differences, between DNA and pure buffer, that are attributable to changes in the ionic conductivity of the solutions. These results constitute the first verification, by a totally different technique, of the absence of resonances in the microwave absorption spectrum of DNA, and the first data obtained by any technique in the 10–20‐GHz band. © 1993 John Wiley & Sons, Inc.
Helix‐Forming tendencies of amino acids depend on their sequence contexts: Tripeptides AFG and FAG show incipient β‐bulge formation in their crystal structures
Authors: Parthasarathy R. , Go Kuantee , Chaturvedi Sanjeev 
Published: December 2004

AbstractMany of the theoretical methods used for predicting the occurrence of α‐helices in peptides are based on the helical preferences of amino acid monomer residues. In order to check whether the helix‐forming tendencies are based on helical preferences of monomers only or also on their sequence contexts, we synthesized permuted sequences of the tripeptides GAP, GAV, and GAL that formed crystalline helices with near α‐helical conformation. The tripeptides AFG and FAG formed good crystals. The x‐ray crystallographic studies of AFG and FAG showed that though they contain the same amino acids as GAF but in different sequences, they do not assume a helical conformation in the solid state. On the other hand, AFG and FAG, which contain the same amino acids but in a different sequence, exhibit nearly the same backbone torsion angles corresponding to an incipient formation of a β‐bulge, and exhibit nearly identical unit cells and crystal structures. Based on these results, it appears that the helix‐forming tendencies of amino acids depend on the sequence context in which it occurs in a polypeptide. The synthetic peptides AFG (L‐Ala‐L‐Phe‐Gly) and FAG (L‐Phe‐L‐Ala‐Gly), C14H19N3O4, crystallize in the orthorhombic space group P212121, with a = 5. 232(1), b = 14. 622(2), c = 19. 157(3) Å, Dx = 1.329 g cm−3, Z = 4, R = 0.041 for 549 reflections for AFG, and with a = 5. 488(2), b = 14.189 (1), c = 18.562(1) Å, Dx = 1.348 g cm−3, Z = 4, R = 0.038 for 919 reflections for FAG. Unlike the other tripeptides GAF, GGV, GAL, and GAI, the crystals of AFG and FAG do not contain water molecule, and the molecules of AFG or FAG do not show the helical conformation. The torsion angles at the backbone of the peptide are ψ1 = 144. 5(5)°; ϕ2, ψ2 = −98.1(6)°, −65.2(6)° ϕ3, ψ13, ψ31 = 154.1(6)°, −173.6(6)°, 6.9(8)° for AFG; and ψ1 = 162.6(3)°; ϕ2, ψ2 = −96.7(4)°, −46.3(4)°; ϕ3, ψ13, ψ31 = 150.1(3)°, −168.7(3)°, 12.2(5)° for FAG. The conformation angles (ϕ ψ) for residues 2 and 3 for both AFG and FAG show incipient formation of an β‐bulge. © 1993 John Wiley & Sons, Inc.
Shape analysis of molecular surfaces
Authors: Duncan Bruce S. , Olson Arthur J. 
Published: December 2004

AbstractThe description of molecular shape is important in the analysis of protein–protein and protein–ligand interactions. We describe volumetric and surface‐based techniques for computing shape properties of molecular surfaces. The surface is defined as an isocontour of an approximate electron density function. Each technique can compute several scalar and vector surface properties such as the Gaussian and mean curvature, principal curvatures, and principal curvature directions. Shape properties are derived from the eigenvalues and eigenvectors of a 3 by 3 matrix for each surface point. In the volumetric approach, the matrix is the second derivative of an approximate electron density function. In the surface‐based approach, the matrix is the approximate gradient of the surface normal. Derivatives 4 are computed by convolving the density or the surface normals with the derivatives of a Gaussian function. The variance of the Gaussian determines the effective length scale at which the surface is analyzed. Scalar surface properties are displayed as colored dots or shaded triangles, and vector properties are displayed as line segments from each surface point. This report describes the implementation of these procedures and their use in computing the shape properties of Cu‐Zu superoxide dismutase. © 1993 John Wiley & Sons, Inc.
Persistence analysis of the static and dynamical helix deformations of DNA oligonucleotides: Application to the crystal structure and molecular dynamics simulation of d(CGCGAATTCGCG)2
Authors: Prévost C. , Louise‐May S. , Ravishanker G. , Beveridge D. L , Lavery R. 
Published: December 2004

AbstractA theory and graphical presentation for the analysis of helix structure and deformations in oligonucleotides is presented. The parameters “persistence” and “flexibility” as defined in the configurational statistics of polymers of infinite length are reformulated at the oligonucleotide level in an extension of J. A. Schellman's method [(1974) Biopolymers, Vol. 17, pp. 217–226], and used as a basis for a systematic “Persistence Analysis” of the helix deformation properties for all possible subsequences in the structure. The basis for the analysis is a set of link vectors referenced to individual base pairs, and is limited to sequences exhibiting only perturbed rod‐like behavior, i.e., below the threshold for supercoiling. The present application of the method is concerned with a physical model for the angular component of bending, so the link vectors are defined as the unit components of a global helix axis obtained by the procedure “Curves” of R. Lavery and H. Sklenar [(1988) J. Biomol. Struct. Dynam., Vol. 6, pp. 63–91; (1989) J. Biomol. Struct. Dynam., Vol. 6, pp. 655–667]. A discussion, of the relationship between global bending and relative orientation of base pairs is provided. Our approach is illustrated by analysis of some model oligonucleotide structures with intrinsic kinks, the crystal structure of the dodecamer d (CGCGAATTCGCG)2, and the results of two molecular dynamics simulations on this dodecamer using two variations of the GROMOS force field. The results indicate that essentially all aspects of curvature in short oligonucleotides can be determined, such as the position and orientation of each bend, the sharpness or smoothness, and the location and linearity of subsequences. In the case of molecular dynamics simulations, where a Boltzmann ensemble of structures is analyzed, the spatial extent of the deformations (flexibility) is also considered. © 1993 John Wiley & Sons, Inc.
A model for the dynemicin‐A cleavage of DNA using molecular dynamics simulation
Authors: Cardozo Mario G. , Hopfinger A. J. 
Published: December 2004

AbstractMolecular dynamics (MD) simulations to model possible reaction pathways of the dynemicin‐A‐DNA cleavage mechanism were performed. Two base‐pairs sequences, ApCpTp‐ApCpTp‐3′/TpGpApTpGpAp‐5′ and CpApCpGpGpGp‐3′/GpTpGpCpCpCp‐5′, were considered in the calculations. A model based on a prior study of intercalation of dynemicin‐A and posterior activation of the drug was assumed in this study. The minimum energy minor groove intercalation complexes for dynemicin‐A were used as starting structures in the MD simulations for the reactive intermediate species involved in the postulated action mechanism. The dynemicin‐A diol derivative product of the opening of the epoxy ring was used as a “steric mimic” ligand for the DNA‐reactive diaryl intermediate. The calculated changes in the geometry of the intercalation complex, due to the opening of the epoxy ring, correspond to the approach of the postulated intermolecular reaction centers in the intercalation states that are responsible for the highest observed DNA cleavage frequency observed. Conversely, unfavorable reaction geometries were found for the intercalation modes corresponding to the lowest observed DNA cutting frequencies. © 1993 John Wiley & Sons, Inc.
Cyanogen as a selective probe for carbonic anhydrase hydrolase activity
Authors: Karagözler A. A. , Ghenbot G. , Day R. A. 
Published: December 2004

AbstractThe salt bridge probe cyanogen (ethanedinitrile, C2N2; NC–‐CN) inhibits the bovine carbonic anhydrase (EC 4.2.1.1.) hydrolase activity toward various types of esters without significant effect on its hydrolyase activity. Two sets of pyridine derivatives that were isosteric substrates for the two activities were differentially affected. Acetazolamide and salamide are reversible inhibitors of the enzyme; only salamide affords protection of the hydrolase activity against the action of C2N2. Since each is known to bind in different positions within the active site, the selective effect of salamide may arise from its position covering one CO2 site as well as a site important for hydrolase activity. The C2N2 concentration dependence of the time course of hydrolase inhibition is consistent with the existence of a high C2N2 affinity site with slow covalent change and a second site with lower C2N2 affinity, but higher rate of covalent modification of the enzyme. © 1993 John Wiley & Sons, Inc.
Lattice vibrations in crystalline L‐alanine
Authors: Durand Dominique , Field Martin J. , Quilichini Marguerite , Smith Jeremy C. 
Published: December 2004

AbstractZwitterionic L‐alanine forms crystals containing strong hydrogen‐bonding and methyl‐methyl interactions. Well‐defined low‐frequency lattice vibrations exist in the crystals involving correlated intermolecular motions on the picosecond timescale. A characterization of these vibrations is expected to provide useful information on the nature of nonbonded interactions in peptides and proteins. We examine some of the vibrations using coherent inelastic neutron scattering and computer simulation techniques. The neutron scattering measurements are used to determine phonon dispersion relations for the acoustic and some low‐frequency optic modes in the crystal. There is evidence for interaction between the two lowest frequency optical phonons and the longitudinal acoustic mode. The velocity of sound is anisotropic and can be correlated with the hydrogen‐bonding arrangement in the crystal. Corresponding phonon dispersion relations are derived from normal mode analyses of the crystal using the program CHARMM. Although some calculated vibrational frequencies are somewhat too high, the form of the calculated dispersion relations are in good agreement with experiment. © 1993 John Wiley & Sons, Inc.
Differences in melting behavior between homopolymers and copolymers of DNA: Role of nonbonded forces for GC and the role of the hydration spine and premelting transition for AT
Authors: Chen Y. Z. , Prohofsky E. W. 
Published: December 2004

AbstractMelting measurements of the mono‐base‐pair DNA polymers showed that the melting temperature Tm of the B‐DNA homopolymer poly (dA ) · poly (dT) is higher than that of the copolymer poly [d(A‐T)]. On the other hand, the Tmof the B‐DNA homopolymer poly (dG) · poly (dC) is lower than that of the copolymer poly [d (G‐C)]. From a structural point of view, the cross‐strand base‐stacking interaction in a DNA homopolymer is weaker than that in a DNA copolymer with the same base pair. One would then expect that all the DNA homopolymers are less stable than the copolymer with the same base pair. We find that the inversion of the melting order seen in the AT mono‐base‐pair DNA polymers is caused by the enhanced thermal stability of poly (dA) · poly (dT) from a well‐defined spine of hydration attached to its minor groove. In this paper we employ the modified self‐consistent phonon theory to calculate base‐pair opening probabilities of four B‐DNA polymers: poly(dA)‐poly(dT), poly(dG) · poly(dC), poly[d(A‐T)], and poly[d(G‐C)] at temperatures from room temperature through the melting regions. Our calculations show that the spine of hydration can give the inverted melting order of the AT polymers as compared to the GC polymers in fair agreement with experimental measurements. Our calculated hydration spine disruption behavior in poly(dA) · poly(dT) at premelting temperatures is also in agreement with experimentally observed premelting transitions in poly (dA) · poly (dT). The work is in a sense a test of the validity of our models of nonbonded interactions and spine of hydration interactions. We find we have to develop the concept of a strained bond to fit observations in poly (dA) · poly(dT). The strained‐bond concept also explains the otherwise anomalous stability of the hydration chain. © 1993 John Wiley & Sons, Inc.
Conformational difference between diastereomers of Dnp‐Val‐Aib‐Gly‐Leu‐pNA studied by x‐ray crystal analyses
Authors: Yamada Takashi , Nakao Masayuki , Miyazawa Toshifumi , Kuwata Shigeru , Sugiura Makiko , In Yasuko , Ishida Toshimasa 
Published: December 2004

AbstractIn order to investigate the Conformational change of the α‐aminoisobutyric acid (Aib) containing peptide by the D/L replacement of an amino acid residue, single crystals of two diastereomers, Dnp‐L‐Val‐Aib‐Gly‐L‐Leu‐pNA (L‐L isomer) and Dnp‐D‐Val‐Aib‐Gly‐L‐Leu‐pNA (D‐L isomer), were prepared from aqueous methanol solutions as CH3OH and CH3OH · H2O solvates, respectively, and were analyzed by the x‐ray diffraction method. Molecular conformation of L‐L isomer adopts consecutive two different types of β‐turns, a type II′ β‐turn bent at Aib‐Gly, and a type III β‐turn bent at Gly‐Leu, stabilized by two intramolecular (Leu) NH …︁ OC (Val) and (pNA) NH …︁ OC(Aib) hydrogen bonds. In contrast, these two intramolecular hydrogen bonds lead the D‐L isomer to a distorted 310‐helix conformation consisting of consecutive two type‐III β‐turn of Aib‐Gly‐Leu sequence. The most significant structural difference between these diastereomers is the mutual orientation between the Dnp and pNA chromophores. While the extensive stacking of both the chromophores is intramolecularly formed for the folded conformation of L‐L isomer, they are oriented toward an opposite direction in the open conformation of D‐L isomer and are intermolecularly stacked with each other. The large separation between these diastereomers observed in the chromatography is discussed in the relation with their Conformational differences. © 1993 John Wiley & Sons, Inc.
Further characterization of the kinetic folding intermediate of αα‐tropomyosin and of its 142–281 subsequence
Authors: Mo Jianming , Holtzer Marilyn Emerson , Holtzer Alfred 
Published: December 2004

AbstractThe backbone CD spectrum from 250 to 212 nm for the kinetic folding intermediate of αα‐tropomyosin (αα‐Tm) and nonpolymerizable αα‐Tm was obtained. The spectrum shows that the intermediate is indeed α‐helical with about 70% of the equilibrium α‐helix content. Subsequence 142Tm281 of the α‐tropomyosin chain has five tyrosine residues (at positions 162, 214, 221, 261, 267). Stopped flow CD at the negative peak in the tyrosine spectral region (280 nm) shows that any tyrosine residues that contribute to the spectrum in the region have already reached their final state in the fast phase of folding ( < 0.04 s). © 1993 John Wiley & Sons, Inc.