bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intermolecular association of tetra‐(γ‐benzyl‐L‐glutamate)s in ethylene dichloride solutions
Authors: Imae Toyoko , Ikeda Shoichi 
Published: May 2005

AbstractLight scattering from ethylene dichloride solutions of tetra‐(γ‐benzyl‐L‐glutamate)s has been measured and their association in solution is examined. One of the peptides is monodisperse o‐nitrophenylthio‐tetra‐(γ‐benzyl‐L‐glutamate) ethylamide prepared by a stepwise condensation method, and the other is low‐molecular‐weight poly(γ‐benzyl‐L‐glutamate) prepared by the N‐carboxyanhydride method with n‐hexilamine initiation at [A]/[I] = 4 and factionated by dosslution in formic acid. Concentration‐dependent association of both peptides occurs noncooperatively, without giving critical micelle concentrations. The aggregate size is small: about 23 for the former tetrapeptide and about 7 for the latter polypeptide. While angular dissymmetry is close to unity, light scattering shows anomalous angular dependence, the intensity being symmetrically low with respect to the scattering angle of 90°. The observed angular dependence is interpreted in terms of the effect of optical anisotropy of peptide units. Formation of the anisotropic phase in concentrated solutions of these peptides is also examined briefy.
Thermodynamic examination of the ordering of lipid hydrocarbon chains in the presence of protein
Authors: Chen Chang‐Hwei , Guard‐Friar Deborah 
Published: May 2005

AbstractThermodynamic relationships have been derived to describe the change in the entropy (ΔS) of lipid vesicles in the presence of a protein in terms of experimental quantities, the concentration of protein (C), the temperature (tm), and the enthalpy (ΔH) of the main lipid phase transition. Knowledge of the change in ΔS can provide an insight into the effect of a protein on the ordering of the lipid hydrocarbon chains. For a general case, evaluation of the entropy change requires information on the changes of ΔH and tm with respect to C. In a special cae where tm remains inchanged and (ΔH) varies, the change in ΔS can be represented simply as (ΔHc − ΔHo)/Tm, where the subscripts c and o denote the presence and absence of a protein, respectively. Data for 1,2‐dimyristoyl phosphatidylcholone in the presence of lysozyme was used to illustrate a thermodynamic analysis.
Selective fluorescent labeling at the α‐amino group of bovine pancreatic trypsin inhibitor
Authors: Amir Dan , Varshavski Lidya , Haas Elisha 
Published: May 2005

AbstractExperimental investigation of protein structure and dynamics by spectroscopic methods using external probes requires attachment of a probe to a well‐defined site and preparation of pure samples. Measurements of efficiency of nonradiative excitation energy transfer can yield very detailed information about the structure of proteins, provided that two different probes are selectively attached to well‐defined sites. We have used specific protection of ε‐amino groups using tert‐butylazidoformate at high pH for covalent attachment of the fluorescent probe 2‐naphthoxyacetic acid at the α‐amino group of bovine pancreatic trypsin inhibitor (BPTI). The product is a chromatoraphically homogenous protein derivative that contains the probe at a dye to protein ratio of 1:1, specifically located at the N‐terminus, and and that retains its full biological activity. The HPLC tryptic peptide map of BPTI has been analyzed, and all the peptide fragments have been identified. Analysis of tryptic fragments of the labled BPTI derivative showed that it was selectively labeled at the N‐terminal amino acid. The probe absorbs in the 310–325‐nm range, which is spectrally distinct from the absorption of the protein, and has a monoexponetial fluorescence decay. These and other charactristics make this probe a good energy donor in transfer‐efficiency measurements.
Sequence and conformational effects on imino proton exchange in A · T‐ and A · U‐containing DNA and RNA duplexes
Authors: Mirau Peter A. , Kearns David R. 
Published: May 2005

Abstract1H‐nmr relaxation has been used to study the effect of sequence and conformation on imino proton exchange in adenine–thymine (A · T) and adenine–uracil (A · U) containing DNA and RNA duplexes. At low temperature, relaxation is caused by dipolar interactions between the imino and the adenine amino and AH2 protons, and at higher temperature, by exchange with the solvent protons. Although room temperature exchange rates vary between 3 and 12s−1, the exchange activation energies (Eα) are insensitive to changes in the duplex sequence (alternating vs homopolymer duplexes), the conformation (B‐form DNA vs A‐form RNA), and the identity of the pyrimidine base (thymine vs uracil). The average value of the activation energy for the five duplexes studied, poly[d(A‐T)], poly[d(A) · d(T)], poly[d(A‐U)], Poly[d(A) · d(U)], and poly[r(A) · r(U)], was 16.8 ± 1.3 kcal/mol. In addition, we find that the average Eα for the A.T base pairs in a 43‐base‐pair restriction fragment is 16.4 ± 1.0 kcal/mol. This result is to be contrasted with the observation that the Eα of cytosine‐containing duplexes depends on the sequence, conformation, and substituent groups on the purine and pyrimidine bases. Taken together, the data indicate that there is a common low‐energy pathway for the escape of the thymine (uracil) imino protons from the double helix. The absolute values of the exchange rates in the simple sequence polymers are typically 3–10 times faster than in DNAs containing both A · T and G · C base pairs.
Model computations on the differential scattering of circularly polarized light (CIDS) by dense macromolecular particles
Authors: Keller David , Bustamante Carlos , Maestre Marcos F. , Tinoco Ignacio 
Published: May 2005

AbstractCircular intensity differential scattering (CIDS) patterns have been calculated for two general types of chiral arrangements. The calculations were done using the second Born approximation. The geometries considered are (a) a linear array of anisotropic scattering groups with a spiraling orientation (a twisted ladder) and (b) a helical array of scattering groups with arbitrary anisotropy and orientation. The CIDS expressions for the first of these models (twisted ladder) reduces to a simple analytical form and clearly illustrates many properties of CIDS patterns. The second geometry (helix) is more general. Calculations were done for oriented scatterers and for rotationally averaged scatterers as would be found in solution.
Vibrational circular dichroism in amino acids and peptides. 10. Fourier transform VCD and Fourier self‐deconvolution of the amide I region of poly(γ‐benzyl‐L‐glutamate)
Authors: Lipp Elmer D. , Nafie Laurence A. 
Published: May 2005

AbstractVibrational CD (VCD) spectra have been obtained in the amide I region of poly(γ‐benzyl‐L‐glutamate), using a Fourier transform ir VCD spectrometer operating at 4‐cm−1 resolution. These results reveal a new negative VCD band at 1650 cm−1 in addition to the previously observed negative positive VCD couplet centered at 1660 cm−1. Fourier self‐deconvolution (FSD) of the VCD spectrum reveals three strong VCD component bands, rather than just two, as originally supposed. FSD also resolves the absorbance spectrum into two components corresponding to the parallel polarized A mode at lower frequency, and an unresolved perpendicular polarized E1 mode at higher frequency. The VCD spectrum is reassigned on the basis of this new spectral data and the FSD‐VCD results are analyzed for the Moffitt contribution and the so‐called helical contribution. Comparison with theory shows the VCD to be more intense than expected, particularly for the helical term. Charge flow between subunits is suggested as an additional source of VCD intensity that is presently not included in theoretical exciton descriptions. The splitting of the E1 mode and the large VCD contribution attributed to the helical term implies a deviation of the polypeptide structure from perfect helical symmetry and, as a result, a mixing of the A and E1 vibrational modes.
Active site dynamics in protein molecules: A stochastic boundary molecular‐dynamics approach
Authors: Brooks C. L. , Brünger Axel , Karplus M. 
Published: May 2005

AbstractThe stochastic boundary molecular‐dynamics approach for studying chemical events in liquids is extended to proteins. A method for simulating the localized dynamics of a portion of a protein is developed and illustrated by an application to the bovine pancreatic trypsin inhibitor (BPTI). The dynamics of the aromatic ring atoms of Tyr 21 of BPTI are targeted as the “active site,” and the results from several different localized models are compared with those from a simulation of the entire molecule. The most consistent results are obtained with a model that consists of a buffer region composed of harmonically constrained Langevin atoms surrounding the active site region whose atoms are treated by molecular dynamics. Possible applications of the model are discussed.
Thermotropic behavior of dimyristoylphosphatidylcholine in the presence of cytochrome c oxidase
Authors: Chen Chang‐Hwei , Guard‐Friar Deborah , Yu Chang‐An 
Published: May 2005

AbstractThe thermotropic behavior of lipid vesicles prepared from dimyristoylphosphatidylcholine in the presence of cytochrome c oxidase has been studied by highly sensitive differential scanning microcalorimetry. This protein has a remarkable effect on the gel–liquid crystalline transition of dimyristoylphosphatidylcholine. In the presence of cytochrome c oxidase, the thermogram of the lipid vesicles exhibits a second endothermic peak, which is adjacent to the main lipid phase‐transition peak and appears at a higher temperature. As the concentration of added protein increases, the two endothermic peaks become further separated, and the transition temperatures and the heats of transition corresponding to both endothermic peaks decrease. A greater decrease in the transition temperature at the lower‐temperature peak with added protein suggests that the lower‐temperature peak is more perturbed than the higher‐temperature peak. The higher‐temperature peak is not thermally reversible. Treatment of sample well above the transition temperature results in a reduction of the magnitude of the higher‐temperature peak. The lipid–protein interaction contributing to the higher‐temperature peak is discussed.
Quasielastic light scattering from long rigid rods
Authors: Hallett F. R. , Nickel B. , Craig T. 
Published: May 2005

AbstractThe purpose of this work was to improve our understanding of quasielastic light scattering from long rigid rods (QL >> 1). For these scatterers, only small angular displacements are required to produce dephasing of the scattering light. This plus the fact that only rods lying perpendicular to Q contribute to the scattered light allow one to simplify the intermediate scattering function to an analytic form. This form is shown to be nonexponential, exhibiting (t)−½ behavior at long delay times. This new scattering function can then be fit to experimental functions using standard methods.
Use of buildup and energy‐minimization procedures to compute low‐energy structures of the backbone of enkephalin
Authors: Vásquez Max , Scheraga Harold A. 
Published: May 2005

AbstractA method for the conformational analysis of a polypeptide, using buildup and energy‐minimization procedures, is presented. It has been tested by computing the conformation of the backbone of Met‐enkephalin, a pentapeptide, and comparing the results with those obtained by a Monte Carlo procedure. The agreement between the results of the two different methods indicates that the multiple‐minima problem has been overcome for the enkephalin molecule (with fixed side‐chain conformations). The buildup procedure uses objective criteria, which should be applicable to the conformational analysis of polypeptides much larger than enkephalin. With anticipated advances in supercomputers, the methodology should be applicable to proteins.
Quaternary structure of elastin: Characterization of multichain peptide fragments obtained by elastase digestion
Authors: Serafini‐Fracassini A. , Field J. M. , Campbell A. M. , Hunter J. C. 
Published: May 2005

AbstractEnzyme‐purified elastin from bovine ligamentum nuchae was digested with elastase in the presence of sodium dodecyl sulfate. Chromatographic fractionation of the digest, after removal of the detergent, resulted in the high‐yield isolation of two peptide fractions (F2 and F3) that differed in size and composition. The larger, F2, which accounted for about 55% of the starting material, was subjected to sedimentation‐equilibrium analysis in three chaotropic solvents. Comparison of the distribution of point‐average molecular weights (Mw and Mz) with protein concentration in the three systems lead to the conclusion that significant self‐association of peptides occurred in the absence of 6M guanidinium hydrochloride. In this solvent, the molecular‐weight distribution was between 25,000 and 34,000, a range of values in agreement with an intrinisic viscosity of 13.1 cc g−1 determined in the same solvent. Assessment of chain weight by N‐ and C‐terminal analysis was consistent with F2 being a multichain molecule comprising four polypeptide chains linked by three polyfunctional amino acids. Results are interpreted in terms of an anisotropic ultrastructural model of the protein, in which four polypeptide chains constitute the primary filament visualized by electron microscopy in the intact fiber.
Binding of ethidium to bacteriophage T7 and T7 deletion mutants
Authors: Griess Gary A. , Serwer Philip , Horowitz Paul M. 
Published: May 2005

AbstractEquilibrium binding of ethidium, quantitated by fluorescence enhancement, to DNA packaged in bacteriophage T7 and T7 deletion mutants has been compared with the binding of this dye to DNA released from its capsid (free DNA). During achievement of apparent equilibrium binding, no change in bacteriophage T7 structure occurred, by the criterion of agarose gel electrophoresis. However, excessive incubation with ethidium bromide caused detectable changes in bacteriophage structure, a possible explanation of disagreements in similar studies previously performed with T‐even bacteriophages. Scatchard plots for packaged DNA had a curvature greater than the previously demonstrated [Bresloff, J. L. & Crothers, D. M. (1981) Biochemistry 20, 3547–3553] curvature for free DNA. By treating plots for packaged DNA as though they were biphasic, it was found that binding to most sites occurred with an apparent association constant (Kap) 3.3–4.3 times lower than the Kap of free DNA. The number of these sites increased significantly as the density of packaged DNA was decreased by use of the deletion mutants. Values of ΔH° for these sites were negative and equal to the ΔH° for free DNA; values of ΔS° were positive and about half the ΔS° for free DNA. A second class of sites, roughly 1.2% of the total, had a significantly higher Kap and more negative ΔH° than those of the majority of sites.
The role of hydrophobic bonding in collagen fibril formation: A quantitative model
Authors: Wallace Donald 
Published: May 2005

AbstractA model has been developed for approximating the free energy of collagen fibril formation (ΔFf) and the equilibrium solubility of collagen under physiological conditions. The model utilizes an expression of Flory for rodlike polymers, with the modification that the “pure” anisotropic phase is defined as a collagen fibril containing about 0.3 g water/g collagen. The model also assumes that χ1, the polymer–solvent interaction term, is entirely due to hydrophobic effects. χ1 is estimated from hydrophobic bond energies of amino acid side chains, using the results of Némethy and Scheraga. The temperature dependence of χ1 is utilized to calculate equilibrium solubilities and ΔFf as a function of temperature.
Conformational behavior of α,α‐dialkylated peptides
Authors: Barone Vincenzo , Lelj Francesco , Bavoso Alfonso , Di Blasio Benedetto , Grimaldi Patrizio , Pavone Vincenzo , Pedone Carlo 
Published: May 2005

AbstractThe preferred conformations of N‐acetyl‐N′‐methyl amides of some dialkylglycines have been determined by empirical conformational‐energy calculations; minimum‐energy conformations were located by minimizing the energy with respect to all the dihedral angles of the molecules. The conformational space of these compounds is sterically restricted, and low‐energy conformations are found only in the regions of fully extended and helical structures. Increasing the bulkiness of the substituents on the Cα, the fully extended conformation becomes gradually more stable than the helical structure preferred in the cases of dimethylglycine. This trend is, however, strongly dependent on the bond angles between the substituents on the Cα atom: In particular, helical structures are favored by standard values (111°) of the N‐Cα‐C′ angle, while fully extended conformations are favored by smaller values of the same angle, as experimentally observed, for instance, in the case of α,α‐di‐n‐propylglycine.
Unified representation of helical parameters: Application to polysaccharides
Authors: Perez Serge , Vergelati Caroll 
Published: May 2005

AbstractA unified representation of helical parameters (n,h) based on a polar mapping is proposed. Its application to the case of polysaccharides allows a straightforward comparison of all secondary structures displayed by this class of biopolymers in the solid state. Based on the concept that a disordered state of a polymer may be described by a succession of local helical parameters, the application of this unified representation has been extended to the simulation of chain behavior in solution.
Molecular mechanical calculations on the interaction of ethidium cation with double‐helical DNA
Authors: Lybrand Terry , Kollman Peter 
Published: May 2005

AbstractMolecular mechanical calculations were done on complexes of ethidium cation with various base‐paired deoxydinucleoside monophosphates [(ApT)2, (TpA)2, (A2 · T2), (GpC)2, (CpG)2, and (G2 · C2)] and deoxyhexanucleoside pentaphosphates [(ATATAT)2, (TATATA)2, (A6 · T6), (GCGCGC)2, (CGCGCG)2, and G6 · C6]. Relative binding energies, sequence preferences, and conformational aspects of the intercalation complexes were studied. The most detailed models used (an all‐atom force field) gave results in good agreement with previous calculations and experimental work. Less‐sophisticated models did not perform as well.
Noncooperative temperature melting of a globular protein without specific tertiary structure: Acid form of bovine carbonic anhydrase B
Authors: Brazhnikov E. V. , Chirgadze Yu. N. , Dolgikh D. A. , Ptitsyn O. B. 
Published: May 2005

AbstractHeat denaturation of native globular proteins is a cooperative process usually connected with the melting of the main part of their regular secondary structure. In this paper, a noncooperative temperature‐induced melting of the regular secondary structure in the carbonic anhydrase B at pH 2.6 in heavy water is observed by ir spectroscopy. The molecules of carbonic anhydrase B in an acid medium, unlike the native ones, do not have a specific tertiary structure. Nevertheless, the β‐structure content is about the same in both of these states. A temperature‐induced noncooperative melting process takes place from 10 to 67°C with a decrease of the antiparallel β‐form content by about one third. The remaining part of the β‐form melts with a more intensive heat absorption, with a maximum at 87°C. The whole melting process is practically reversible. We assume that the observed noncooperative process displays a general property of a new type of structural state of the globular protein—the “molten globule state.”
Amino acid composition and hydrophobicity patterns of protein domains correlate with their structures
Authors: Sheridan Robert P. , Dixon J. Scott , Venkataraghavan R. , Kuntz I. D. , Scott K. P. 
Published: May 2005

AbstractWe examine the correlation between the sequence and tertiary structure for 212 domains from globular proteins and polypeptides. The sequence of each domain is described as a set of 25 features: the mole percent of 20 amino acids, the number of residues in the domain, and the abundance of four simple patterns in the hydrophobicity profile of the sequence. Each domain, then, is described as a location in 25‐dimensional sequence‐feature space. We use pattern‐recognition methods to find the two axes through the 25‐dimensional sequence‐feature space that best discriminate, respectively, predominantly α‐helix domains from predominantly β‐strand domains (the “secondary structure vector,” SV) and parallel α/β domains from other domains (the “parallel vector,” PV). When we divide the domains into two categories based on whether the cysteine content is above (CYS‐RICH) or below (NORMAL) 4.5%, we find the secondary structure vector for the subset of CYS‐RICH domains points in a significantly different direction than the equivalent vector for the NORMAL domains. Thus, CYS‐RICH and NORMAL, domains are best treated separately. The secondary structure vector and the parallel vector for NORMAL domains describes statistically meaningful information, but the secondary structure vector for CYS‐RICH domains may not be as reliable. We show how the secondary structure content of a NORMAL domain can be predicted by projecting the domain in the feature space onto the secondary structure vector. We subdivide the domains into five structural classes based on whether there is a parallel or mixed β‐sheet in the domain and whether there are more helix or strand residues: NORMAL ALPHA, NORMAL BETA, NORMAL PARALLEL, CYS‐RICH ALPHA, and CYS‐RICH BETA. When we project the NORMAL domains onto the plane containing the origin of the feature space and SV and PV, we see that ALPHA, BETA, and PARALLEL, domains cluster in the plane, with the BETA cluster partially overlapping the PARALLEL cluster. The separations between the clusters are such that, by looking at the location of any given NORMAL domain in the plane, we can correctly predict its structural class with 83% accuracy. CYS‐RICH ALPHA and BETA domains cluster when projected onto the CYS‐RICH SV vector, and the classes can be preducted with 83% accuracy, but this accuracy for CYS‐RICH domains may not be statistically meaningful.
Conformations of dinucleoside monophosphates in relation to duplex DNA structures
Authors: Rao Shashidhar N. , Sasisekharan V. 
Published: May 2005

AbstractMononucleotide conformations are important in understanding the structural aspects of nucleic acids and polynucleotides. In order to study the influence of stacking interactions between adjacent bases in a polynucleotide on the preferred conformations of mononucleotides, conformational energy calculations have been carried out on dinucleoside monophosphate fragments. Four base sequences—d(ApT), d(TpA), d(CpG), and d(GpC)— have been analyzed in the framework of helical structures. Flexibility of the furanose ring has been incorporated in the investigations. Energetically favored conformers of the four compounds correspond to a variety of left‐ and right‐handed uniform helical structures, similar to those of the commonly observed polymorphous forms. Implications of these investigations on the further understanding of double‐helical polynucleotide conformations are briefly discussed.