bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational Studies of β‐glucans
Authors: Sathyanarayana B. K. , Rao V. S. K. 
Published: May 2005

AbstractSteric and energy contour diagrams have been plotted for disaccharide‐like and for helical structures of linear β‐D‐glucans having (1 → 2), (1 → 3) and (1 → 4) linkages. The allowed conformations constitute only about. 4% of the total conformations, indicating that the freedom of rotation of glucose residues is highly restricted in all the three polysaccharides. The additional restrictions of the monomer unit, as one passes from disaccharide to polysaccaride structures, are severe in the case of (1 → 2) and (1 → 3) linked polysaccharides but not in (1 → 4) linked polysaccharide. The difference in the nature of linkages also has shown to affect the energetically preferred conformations: (1 → 2) linkages lead only to left handed helical conformations; (1 → 3) linkages lead to both right and left handed wide and extended helical conformations, (1 → 4) linkages lead to both right and left handed extended helical conformations. The possible hydrogen bonds between adjacent residues are also dependent on the nature of linkage.
The conformation of single‐strand polynucleotides in solution: sedimentation studies of apurinic acid
Authors: Achter Eugene K. , Kelsenfeld Gary 
Published: May 2005

AbstractTo elucidate the role of the bases in single‐strand polynucleolide conformation, we have studied apurinic acid, a single‐strand polydeoxyribonucleotide from which almost half the bases have been removed. The conformation of apurinic acid in aqueous solution near θ condition has been investigated by sedimentation velocity and sedimentation equilibrium measurements. The unperturbed coil dimensions of apurinic acid are essentially identical to those of poly rU of the same degree of polymerization. The dimensions are also similar to those of poly rA at high temperature, where the adenine residues are not stacked upon one another. We conclude that the considerable rigidity of these polynuclotides is conferred not by residual, undetected base stacking, but by restrictions in rotation about the bonds of the backbone. Furthermore, the rigidity of the ribose‐phosphate backbone cannot be attributed to interactions involving the 2'—OH group.
Circular dichroism studies of isoleucine oligopeptides in solution
Authors: Goodman Murray , Naider Fred , Toniolo Claudio 
Published: May 2005

AbstractA conformational analysis was carried out on a series of L‐isoleucine oligomers having the general formula BOC‐(Ileu)n‐OMe (n = 2–8). These oligopeptides were examined in trifluoroethanol, trifluoroethanol‐acid and mixed organic‐water media. The results indicate that these oligomers form β‐conformations beginning at the heptamer. The stability of the β‐conformations was found to be greater than those formed by oligopeptides derived from L‐alanine.
Change in conformation of various DNAs on melting as followed by circular dichroism
Authors: Sprecher Cindy A. , Johnson W. Curtis 
Published: May 2005

AbstractThe intensities of the CD bands at about 275 and 190 nm were monitored for DNAs with different G + C contents as a function of temperature. The 190‐nm bands showed a nearly complete and cooperative collapse on melting of the DNA, demonstrating that the CD arises from base–base interactions. The small cooperative change on melting shown by the 275‐nm bands indicates that base–base interactions do not contribute much CD intensity here. No significant difference in melting temperature was found between the two wavelengths, but the lack of premelting in the 190‐nm bands contrasted with the significant premelting in the 275 nm bands. Since the 190‐nm bands are particularly sensitive to base–base interactions, the relative positions of the bases must not change much during premelting. Still, changes in such interactions would be noticeable on top of the low intensity of the 275‐nm bands. Premelting is discussed in the light of recent studies on DNA conformation.
Theoretical π‐π* absorption and circular dichroic spectra of polypeptide β‐structures
Authors: Applequist Jon 
Published: May 2005

AbstractAbsorption and circular dichroic (CD) spectra of the π‐π* transition near 200 nm are calculated for poly(Gly), poly(Ala), poly(Abu), and poly(Val) in the βP (paralle) and βA (antiparallel) pleated‐sheet structures using the dipole interaction model and including interactions among all atoms; optical parameters were obtained from previous studies of related molecules. Most of the calculations are for structures with one or three chains of six residues each. The oscillator strength and splitting of the π‐π* modes are found to be affected only to a small extent by variations in side‐chain structure and conformation, whereas the CD spectrum is very sensitive to these variations. Poly(Gly) and poly(Ala) β‐structures in uniform, planar lattices do not show sufficient rotational strength to account for observed CD spectra. Poly(Abu) and poly(Val) β‐structures in uniform, planar lattices show rotational strengths comparable to experiment when χ1 is near −60° for βA‐structures or in a broad range near 140° for βP‐structures. Poly(Ala) in uniformly twisted βA‐ and βP‐structures or in irregular βA‐structures corresponding to regions of the crystal structure of concanavalin A also show enhanced rotational strengths in the principal π‐π* CD band. Absorption and CD spectra calculated for poly(Abu) in uniform βA‐ and βP‐structures are compared with experimental data on poly(Lys) in the β‐form, assuming side‐chain conformations in Abu that maximize the intensity of the principal CD band. The calculations for the βA‐form show the better agreement with experiment for both types of spectra.
Hydrodynamics, size, and shape of bacteriophage T4D tails and baseplates
Authors: Benbasat Julyet A. , Bloomfield Victor A. 
Published: May 2005

AbstractWe have used translational diffusion coefficient measurements and subunit hydrodynamic theory to determine the dimensions and shape of bacterioophage T4D baseplates and tails. The diffusion coefficient of the baseplate, measured by quasielastic laser light scattering (QLS), was determined previously by Wagenknecht and Bloomfield to be D = 8.56 × 10−8 cm2/s. For the tail, we found D = 5.88 × 10−8 cm2/s by QLS, and D = 6.02 × 10−8 cm2/s by combining sedimentation coefficient and molecular weight in the Svedberg equation. These values, which have an uncertainty of ±2.7%, when combined with subunit hydrodynamic theory, enabled us to refine estimates of dimensions obtained by electron microscopy. For the hexagonal baseplate, the vertex‐to‐vertex distance is about 480 Å, the thickness is 160 Å, and there are six extended short fibers 320‐Å long and 40 Å in diameter. When a baseplate of these dimensions is attached to a tail tube‐sheath‐connector complex 1050‐Å long and 240 Å in diameter, the calculated D is 5.93 × 10−8 cm2/s, within 1% of experiment. This combined use of electron microscopy and hydrodynamics, using the former to ascertain shape, and the latter to obtain solution dimensions, is a powerful approach to the structure of biomolecular complexes.
On the interpretation and prediction of X‐ray scattering profiles of biomolecules in solution
Authors: Pickover C. A. , Engelman D. M. 
Published: May 2005

AbstractIf solution scattering curves can be accurately predicted from structural models, measurements can provide useful tests of predictions of secondary and tertiary structure. We have developed a computational technique for the prediction and interpretation of x‐ray scattering profiles of biomolecules in solution. The method employs a Monte Carlo procedure for the generation of length distribution functions and provides predictions to moderate resolution (∼5 Å). In addition to facilitating the assignment and interpretation of features in a solution scattering profile, the method also allows the elucidation of the role of protein motion in shaping the final scattering curve. The effect of protein motion on a scattering profile is investigated by generating scattering curves from several consecutive 0.147 ps atomic coordinate frames from a molecular dynamics simulation of the motion of bovine pancreatic trypsin inhibitor (BPTI) [McCammon, J. A. & Karplus, M. (1980) Annu. Rev. Phys. Chem. 31, 29–45]. The theoretical approach is applied to chicken egg white lysozyme and BPTI, and the overall features in the resulting theoretical scattering profiles match well with the experimental solution scattering curves recorded on film. It is apparent from this study that the scattering profile prediction technique in conjunction with other experimental methods may have value in testing ideas of conformational change based on crystallographic studies; investigations of this type would include a comparison of predicted scattering curves generated from a variety of crystallographic models with an actual scattering profile of the biomolecule in solution.
Fluoroquinacrine binding to nucleic acids: Investigation of the 19F‐nmr, optical, and fluorescence properties in the presence of DNA, poly(A), and tRNA
Authors: Mirau P. A. , Shafer R. H. , James T. L. , Bolton P. H. 
Published: May 2005

AbstractThe interaction of fluoroquinacrine, 3‐fluoro‐7‐chloro‐9‐(diethylamino‐1‐methylbutyl‐amino)acridine, with poly(A), DNA, and tRNA has been investigated by monitoring changes in the 19F‐nmr properties, the fluorescence, and the optical absorbance of the drug. The changes in the properties of fluoroquinacrine in the presence of nucleic acids are similar to those observed for quinacrine and suggest that the drugs bind in a similar fashion. The molecular dynamics of fluoroquinacrine bound to nucleic acids were determined by interpreting the data from a number of different nmr relaxation experiments with a two‐correlation‐time model. The two motions are the long‐range bending motion of the drug‐nucleic acid complex and the sliding of the drug between the base pairs. Both dipolar and chemical shift anisotropy contributions to the nmr relaxation parameters were taken into consideration. The binding of fluoroquinacrine to tRNA appears to be different from that observed for binding to DNA. Optical absorbance and 19F‐nmr were also used to examine the helix‐to‐coil transitions of the drug–nucleic acid complexes. In the DNA complex, the 19F chemical shift changes parallel the absorption changes that occur during the transition. 19F‐nmr and absorption show that the drug–tRNA complexes undergo a cooperative helix‐to‐coil transition, with the drug binding sites melting when the tRNA is 70% denatured.
Fluctuational base‐pair opening in DNA at temperatures below the helix–coil transition region
Authors: Wartell Roger M. , Benight Albert S. 
Published: May 2005

AbstractThe probability of DNA base‐pair opening was calculated at temperatures below the denaturation region. The helix–coil transition theory, modified to include different nearest‐neighbor interactions, was employed. Predictions of base‐pair opening employing DNA melting‐curve parameters differed considerably from predictions based on parameters evaluated from synthetic RNA oligomer data of Gralla and Crothers (G‐C) and formaldehyde–DNA binding experiments of McGhee and von Hippel (M‐vH). Calculations based on the latter parameters indicate a base‐pair‐opening probability of 10−2–10−3 at 35°C in 0.1M NaCl. DNA melting‐curve parameters predict values about 103 smaller. At a temperature 10°C below the transition midpoint of a specific DNA sequence, DNA melting parameters predict base‐pair opening of about 10−3, whereas the G‐C and M‐vH parameters predict that ≳0.16 of the DNA is melted. Experiments and theoretical assumptions relevant to the calculations are analyzed. Evidence suggests that DNA melting parameters are valid when the average loop size exceeds some minimum value, whereas the G‐C and M‐vH parameters appear more valid for single base‐pair loops. A reconciliation of the two sets of predictions can be made if interactions extending beyond neighboring base pairs are considered. Such interactions will make the parameters of the nearest‐neighbor model appear to change with the average loop size. Experiments that may provide further measurements of base‐pair opening are discussed.
Normal modes and structure of iodine in the starch–iodine complex
Authors: Kim Hyunyong 
Published: May 2005

AbstractNormal modes of a linear array of iodine atoms with various repeat units, (I), (II), (II), and (I), have been calculated. The four resonance Raman bands (158, 107, 57, and 27 cm−1) observed with the starch–iodine complex can be assigned to the symmetric modes of either the (II)n or (I)n linear chain. However, the nature of the valence force fields of these two structures is very different: the former consists of a weakly coupled linear chain of (I) structure, while the latter, (I)n, is a tightly bound chain approaching equidistant iodine spacings. The nearly equivalent I‐I stretching force constants obtained in the present normal mode analysis of the (I)n structure is supported by the results of previous x‐ray and I‐129 Mössbauer effect measurements. A numerical method of calculating the frequency dispersions of one‐ and two‐dimensional molecular arrays is given.
Calorimetric determination of base‐stacking enthalpies in double‐helical DNA molecules
Authors: Marky Luis A. , Breslauer Kenneth J. 
Published: May 2005

AbstractDifferential scanning calorimetry was used to directly determine the transition enthalpies accompanying the duplex‐to‐single‐strand transition of poly[d(AT)], poly(dA)·poly(dT), poly[d(AC)]·poly[d(TG)], and d(GCGCGC). The calorimetric data allow us to define the following average base‐stacking enthalpies:

Interaction
ΔH (kcal/stack)

AC/TG, TG/AC
5.6

AT/TA, TA/AT
7.1

AA/TT
8.6

GC/CG, CG/GC
11.9

Comparison with published data on the corresponding RNA interactions reveals remarkably good agreement. By assuming transition enthalpies to result from the pairwise disruption of nearest‐neighbor stacking interactions, we used the enthalpy data listed above to predict the transition enthalpies for three oligomeric DNA duplexes. Excellent agreement was found between the predicted and the calorimetrically determined values.
The C‐terminal extrahelical peptide of type I collagen and its role in fibrillogenesis in vitro
Authors: Capaldi Michael J. , Chapman John A. 
Published: May 2005

AbstractThe formation in vitro of fibrils from type I acid‐soluble calf skin collagen has been studied before and after removal of the extrahelical peptides with carboxypeptidase and with pepsin. Turbidimetric studies show that the mechanism of fibril growth in undigested collagen is similar to that in pepsin‐digested collagen; following carboxypeptidase digestion, however, a different growth mechanism was apparent. The two mechanisms have been further characterized by electron microscopy. In the course of formation of fibrils from undigested collagen, “early fibrils” (short D‐periodic fibrils that have both ends visible) occurred in the lag phase under the precipitating conditions employed here. After pepsin or carboxypeptidase digestion of the collagen no “early fibrils” were seen. In carboxypeptidase‐digested collagen, lateral assembly was inhibited; after pepsin digestion, linear assembly was inhibited. Complete removal of the extrahelical peptides prevented fibril formation under the conditions used here. Electron‐optical examination of segment‐long‐spacing (SLS) dimers established a more complete removal of the C‐terminal peptide after carboxypeptidase digestion than after pepsin digestion. Analyses of staining patterns of SLS dimers and fibrils from undigested and digested samples showed that the C‐terminal peptide in SLS crystallites and fibrils formed from undigested collagen is in a condensed conformation. A proposed conformation, in which condensation occurs predominantly in a hydrophobic region at the proximal end of the C‐terminal peptide, is discussed in terms of a dual role for the C‐terminal peptide in fibrillogenesis. One role, shared with the N‐terminal peptide, is to participate in interactions between the 4D‐staggered molecules leading to the formation of linear aggregates; the other is to participate in interactions between these linear aggregates giving rise to D‐periodic aggregates and lateral (as well as linear) growth.
Kinetics of transfer in aqueous solution of ferriprotoporphyrin IX from human serum albumin to sperm whale apomyoglobin
Authors: Blauer G. , Silfen J. 
Published: May 2005

AbstractKinetic aspects of the transfer reaction of ferriprotoporphyrin IX (FP) from its complex with human serum albumin (HSA) to sperm whale apomyoglobin were investigated by spectrophotometry in aqueous solution. At molar ratios of 2:1 of both HSA and apomyoglobin to FP (1 × 10−5M), the initial rate of transfer at pH 7.4 (0.025M Tris buffer) and 25°C was virtually independent of the concentration of apomyoglobin up to a sixfold excess of the latter. The rate‐limiting step in the transfer reaction is considered to be the dissociation of FP from the FP‐HSA complex with an apparent rate constant of the order of 10−3 s−1 under the above conditions. The initial rate decreased with increasing concentrations of HSA, indicating competition between HSA and apomyoglobin for free FP in the recombination reactions. A steady‐state concentration of the order of 10−9M is estimated for free FP under the conditions given. The initial rate of transfer decreased markedly with pH in the range of pH 5–9 and was also dependent on the type and concentration of the buffer used. Also, various electrolytes at different concentrations showed very different and specific effects on the initial rate of reaction. Similarly, various drugs and analogous substances such as penicillins and salicylate affected the rates of dissociation in different concentration ranges. From the temperature dependence of the initial rate at pH 7.4 in the range of 5–25°C, an overall energy of activation of about 8 kcal/mol and an entropy of activation of about −50 e.u. are evaluated, indicating a much higher order of molecular groups around FP or other steric constraints in the transition state. It appears that kinetic parameters of the biopolymer–small molecule system are more sensitive to environmental changes than corresponding equilibrium data as measured by light absorption.
Flexibility of a labeled polymer chain: Time‐resolved fluorescence depolarization measurements and their interpretation by a Hinged‐Dumbbell model
Authors: Ricka J. , Amsler K. , Binkert Th. 
Published: May 2005

AbstractTime‐resolved fluorescence depolarization was applied to investigate the dynamics of low‐molecular‐weight polyethylene glycols (MW 150, 400, 1000, 4000) labeled by fluorescein‐isothiocyanate. The analysis of measurements revealed considerable flexibility of the polymer chain. To interpret the observed dependence of the relaxation time of polarization anisotropy on the molecular weight of the polymer, a simple freely‐hinged dumbbell model was developed. The properties of the model were investigated by computer experiments. The model was found to account well for the measured data.
Secondary structure of peptides. 4: 13C‐Nmr CP/MAS investigation of solid oligo‐ and poly(L‐alanines)
Authors: Kricheldorf Hans R. , Mutter Manfred , Maser Franz , Müller Detlef , Förster Hans 
Published: May 2005

AbstractPrimary and tertiary amine‐initiated polymerizations of L‐alanine‐N‐carboxyanhydride (L‐Ala‐NCA) were conducted at 20 or 100°C in a variety of solvents. The 75.5‐MHz 13C‐nmr CP/MAS spectra of the resulting poly(L‐alanines) revealed that all samples contain both α‐helix and pleated‐sheet structures. Depending on the reaction conditions the α‐helix content varied between ca. 1 and 99%. Reprecipitation from aprotic nonsolvents does not change the α‐helix/β‐sheet ratio, indicating that this ratio is thermodynamically controlled. Since relatively large amounts of oligopeptides of degree of polymerization (DP) 4–6 can be extracted by means of acetic acid, it is concluded that (a) most poly(L‐alanines) possess a bimodal molecular weight distribution, (b) the oligopeptide fraction with DP ⩽ 11 is responsible for the β‐sheet fraction of all samples, and (c) the two‐stage crystal growth proposed by Komoto and Kawai is not correct. Solubilizing initiators such as poly(ethylene oxide) NH2 prevent the precipitation of oligoalanine and, thus, the formation of a β‐sheet structure. 13C‐nmr CP/MAS measurements also show that tri‐ and tetra‐L‐alanines form insoluble β‐sheet structures.
Mobility of oligopeptides on normal‐phase silica: Effect of positional isomerism
Authors: Naider Fred , Huchital Michael , Becker Jeffrey M. 
Published: May 2005

AbstractIsomeric oligopeptides composed of five methionyl residues and one glycyl residue or of five γ‐methyl‐L‐glutamyl residues and one glycyl residue all exhibit marked differences in retention on normal‐phase silica. When the glycyl residue is at internal positions of hexa or heptapeptides, the peptide elutes most rapidly form the μPorasil column. Comparison of the effect of positional isomerism on retention in short oligopeptides with the effect on retention of hexamers and heptamers suggests that a change in peptide conformation may be responsible for the change in oligopeptide mobility.
Influence of base‐pair changes and cooperativity parameters on the melting curves of short DNAs
Authors: Benight Albert S. , Wartell Roger M. 
Published: May 2005

AbstractTheoretical melting curves were calculated for four DNA restriction fragments, 157–257 base pairs (bp), and a series of hypothetical block DNAs with sequences d(C2xAxC2x). d(C2xTxG2x), 5 ⩽ x ⩽ 40. These DNAs provided a mixture of A·T/G·C sequence distributions with which to investigate the effects of parameters and base‐pair changes on the melting of short DNAs. The sensitivity of DNA melting curves to changes in internal loop melting parameters σ and κ was examined. As Expected, theoretical melting curves of short DNAs with a quasirandom base‐pair sequence vary little with changes in internal loop parameters. End melting dominates the transition behaviour of these moleucles. This was also observed for the block DNAs up to x = 22. Beyond this length, melting curves are highly sensitive to the internal loop parameters. Sensitivity is also predicted for a 157‐bp fragment with a block distribution of A·T and G·C pairs. These results indicate that accurate evaluation of internal loop parameters is possible with short DNAs (100–200 bp) containing a G·C/A·T/G·C block distribution with at least 22 bp in each block. Duplex‐to‐single‐strands dissociation parameters were reevaluated form experimental melting curve data of eight DNA fragments using a least squares fit approach. This analysis confirmed parameter values previously found with a simplified dissociation model. A Priori predictions are made on the effects of base‐pair changes on the melting curves of three characterized DNA restriction fragments. Single base‐pair changes are predicted to induce small but measurable changes in the melting curves. The characteristics of the altered melting curves depend on the location of the base‐pair change.