bluuebunny/crossref_metadata_2025_split huggingface dataset:
On an exact starting expression for macromolecular hydrodynamic models
Authors: Wegener William A. 
Published: December 2004

AbstractA calculational method developed by G. K. Youngren and A. Acrivos [J. Fluid Mech. 75, 377 (1975)] expresses the fluid forces exerted over the surface of an immersed body in terms of differences between body and fluid motions. As opposed to bead‐model approaches, this method starts from an essentially exact hydrodynamic expression, and therefore should be of particular interest to those workers trying to obtain accurate coefficients needed to characterize the diffusive and viscoelastic behavior of macromolecules with complex shapes. However, Youngren and Acrivos's treatment has not been widely adopted nor even used as a proper starting place for higher order bead‐model methods. This is probably related to the unfamiliar appearance of their exact expression, which involves two surface integral terms as opposed to the single summation involved in bead models. We show that their expression may be rewritten in the expected analogous form involving one surface integral term whenever stick boundary conditions are applied to a rigid body or a flexible body composed of rigid segments. For spherical segments, we obtain Rotne–Prager‐type bead‐model results by following typical assumptions. Extensions to deformable particles are considered, in which internal friction can be represented by an arbitrarily viscous internal fluid.
Sequence‐dependent recognition of DNA duplexes: Netropsin complexation to the TATA site of the d(G‐G‐T‐A‐T‐A‐C‐C) duplex in aqueous solution
Authors: Patel Dinshaw J. , Shapiro Lawrence 
Published: December 2004

AbstractWe have recorded one‐dimensional exchangeable proton and two‐dimensional nonexchangeable proton nmr spectra on the complex of netropsin with the self‐complementary d(G‐G‐T‐A‐T‐A‐C‐C) duplex in aqueous solution between 25° and 35°C. The antibiotic amide, pyrrole, and methylene protons, and the nucleic acid base and sugar H1′, H2′, H2″, and H3′ protons, have been assigned from an analysis of the two‐dimensional nuclear Overhauser effect (NOESY) spectra of the complex. We observe intermolecular NOEs between the antibiotic concave face amide, pyrrole, and CH2 resonances, and the adenosine H2 and sugar H1′ protons of base‐pairs T3·A6 and A4·T5 in the central TATA core of the d(G1‐G2‐T3‐A4‐T5‐A6‐C7‐C8) duplex. We present a molecular model outlining these seven antibiotic‐DNA contacts for the complex in solution. The observed line‐broadening of several base and sugar protons at the TATA minor groove netropsin binding site in the complex at 35°C are interpreted in terms of intermediate exchange between two orientations of bound netropsin on the duplex.
Calorimetric studies of the polynucleotide analog poly(−)2‐[2‐(thymin‐1‐yl) propanamido]propenoic acid
Authors: Zand R. , Jiang Z. Z. , Overberger C. G. 
Published: December 2004

AbstractThe thermally elicited structural and conformational transitions of the polynucleotide analog, poly(‐)‐2‐[2‐(thymin‐1‐yl)propanamido]propenoic acid, P(‐)TDHA, have been studied using differential scanning calorimetry (DSC), differential thermal analysis (DTA), and thermogravmetric analysis (TGA). The differential scanning calorimetry curves obtained on solid P(‐)TDHA samples exhibited five distinct transitions. The transition occurring at 50°C is attributed to a disruption of interactions involving thymine–thymine stacking. In contrast the transition observed at 83°C is attributed to a hydrogen‐bonding interaction involving the thymine residues, whereas the transition occurring at 110°C is assigned to hydrogen bonding of the carboxylic acid side‐chain groups. The transitions observed at 50, 83, and 110°C are reversible if the heated and quenched sample is allowed to equilibrate in an atmosphere of high humidity. The transition occurring at 127°C is viewed as a structural rearrangement of the polymer backbone that does not involve the participation of water molecules. The transition observed at a temperature above 197°C is attributed to a structural modification of the polymer resulting from decomposition. Solutions of P(‐)TDHA in 0.1M phosphate buffer at pH 7.05 showed only a single transition at 50°C, which is in accord with an observed transition in the solid state assigned to the disruption of base‐stacking interactions. The average enthalpy for the transition at 50°C was 0.92 cal/g in the solid state and 1.08 cal/g for the solution, which provides additional support for the assignment.
A comparative study of lysozyme conformation in various reverse micellar systems
Authors: Steinmann Bettina , Jäckle Hans , Luisi Pier Luigi 
Published: December 2004

AbstractThe activity and conformation of lysozyme solubilized in apolar solvents via reverse micelles was investigated. The systems used were sodium di‐2‐ethylhexylsulfosuccinate (AOT)/isooctane/H2O, cetyltrioctylammoniumbromide (CTAB)/CHCl3, isooctane/H2O; tetraethyleneglycoldodecylether (EO4C12)/isooctane/H2O, and bulk water. CD spectra of lysozyme in reverse micellar solutions were investigated as a function of w0 (= [H2O]/[AOT]) and were compared to the spectra in aqueous solutions. No marked changes were found in the EO4C12 or in the CTAB systems with respect to water, which indicates that no sizeable conformational changes of the enzyme occurred upon solubilization in the reverse micellar systems. In agreement with previous studies [C. Grandi, R. E. Smith, and P. L. Luisi (1981) J. Biol. Chem. 256, 837–843] dramatic conformational changes can be inferred in the AOT system on the basis of CD studies. This is taken as an indication that the enzyme denatures in this micellar system. This is particularly striking because the enzyme is fully active in AOT reverse micelles. The apparent paradox is solved by the observation that the native CD spectrum (and by inference, the native conformation) is maintained when lysozyme is bound to NAG or NAG3, and by inference, when the substrate is bound, e.g., during enzyme turnover. However, in the absence of added NAG, NAG3, or substrate, the enzyme in the AOT reverse micellar system rapidly denatures. Together with CD studies, fluorescence and nmr data confirm the hypothesis of an irreversible denaturation of lysozyme in the AOT system, the denaturation being slowed down when the substrate is present. The activity of the enzyme has been studied as a function of pH and w0 using the chromophoric substrate 3,4‐dinitrophenyl‐tetra‐N‐acetyl‐β‐D‐chitotetraoside (3,4‐DNP‐NAG4). Generally speaking, the kinetic parameters are comparable to those found in bulk water solution. More detailed, in the CTAB system, kcat tends to be smaller than in aqueous solution (with quite similar KM), whereas in the EO4C12 system (at pH 7.0) the turnover number is larger and KM is smaller than in water. In the AOT system, the kinetic parameters at pH 7.0 are also quite comparable to those found in water.
Prediction of the native conformation of a polypeptide by a statistical‐mechanical procedure. II. average backbone structure of enkephalin
Authors: Paine Gregory H. , Scheraga Harold A. 
Published: December 2004

AbstractThe average conformation of Met‐enkephalin was determined by using an adaptive, importance‐sampling Monte Carlo algorithm (SMAPPS—Statistical Mechanical Algorithm for Predicting Protein Structure). In the calculation, only the backbone dihedral angles (ϕ and ψ) were allowed to vary; i.e., all side‐chain (χ) and peptide‐bond (ω) dihedral angles were kept fixed at the values corresponding to a low‐energy structure of the pentapeptide. The total conformational energy for each randomly generated structure of the polypeptide was obtained by summing over the interaction energies of all pairs of nonbonded atoms of the whole molecule. The interaction energies were computed by the program ECEPP/2 (Empirical Conformational Energy Program for Peptides). Solvent effects were not included in the computation. The calculation was repeated until a total of 10 independent average conformations were established. The regions of conformational space occupied by the average structures were compared with the regions of low conditional free energy obtained by SMAPPS in the first paper of this series. Such a comparison provides an analysis of the capacity of SMAPPS to adjust the Monte Carlo search to regions of highest probability. The results demonstrate that the ability of SMAPPS to focus the Monte Carlo search is excellent. Finally, the 10 independent average conformations and the mean of the 10 average structures were utilized as the initial conformations for a direct energy minimization of the pentapeptide. Of the 11 final energy‐minimized structures, three of the conformations were found to be equivalent to the conformation of lowest energy determined previously. In addition, all but two of the remaining energy‐minimized structures were found to correspond to one of the two other conformations of high probability obtained in the first paper of this series. These results indicate that a set of independent average conformations can provide a rational, unbiased choice for the initial conformation, to be used in a direct energy minimization of a polypeptide. The final energy‐minimized structures consequently constitute a set of low‐energy conformations, which include the global energy minimum.
Computer simulation of the folding–unfolding transition of island‐model proteins—folding pathway, transition process, and fluctuations
Authors: Segawa Shin‐Ichi , Kawai Toshikazu 
Published: December 2004

AbstractMonte Carlo computer simulations were performed to elucidate the dynamic aspects of the folding and unfolding transitions of island‐model protein. Five different types of model proteins were designed, according to characteristics of backbone structure. The computer simulations clearly show that the unfolding and folding transitions are all‐or‐none processes between the N‐and U‐states. They are typical Poisson processes. From the Arrhenius plots of rate constants, the activation enthalpies of folding and unfolding were determined. In addition, the folding pathways were determined along the reaction coordinate. Formations of several local structures along a polypeptide chain are almost simultaneous, but the most probable time sequence of events exists at the moment of transition. That is the most probable folding pathway. The unfolding pathway was found to be just the reverse process of the most probable folding pathway. The relationship between the fluctuations in each equilibrium state and the transition process was considered. In contrast to the theory of absolute reaction rate, the transient states are widely distributed along the reaction coordinate. From analysis of the “transient process,” we tried to determine the critical states from which the transient process starts. As a result, we found that the unfolding transition occurs at the stage near the N‐state. During the U‐state, large joined blocks rarely appear, but they appear in the transient process towards the N‐state. However, the “branch point” between the N‐ and U‐states lies near the N‐state, and joined blocks tend to unfold prior to passing over the branch point. We concluded that the stability of later folding intermediates is important for selection of the folding pathway, while preferential selection of an early folding intermediate is important in acceleration of the folding rate. The effects of intrachain cross‐linking and peptide fragment binding on the rate constants were examined by using computer simulations of model proteins. In general, a small‐sized loop formed by cross‐linking accelerates the folding rate and a large‐sized loop contributes much to the stabilization of the native conformation. We also found that peptide fragment binding contributes little to the acceleration of the folding rate of the residual protein.
Structure and internal mobility of proteins: A molecular dynamics study of hen egg white lysozyme
Authors: Ichiye T. , Olafson B. D. , Swaminathan S. , Karplus M. 
Published: December 2004

AbstractThe structure and internal motions of the protein hen egg white lysozyme are studied by analysis of simulation and experimental data. A molecular dynamics simulation and an energy minimization of the protein in vacuum have been made and the results compared with high‐resolution structures and temperature factors of hen egg white lysozyme in two different crystal forms and of the homologous protein human lysozyme. The structures obtained from molecular dynamics and energy minimization have root‐mean‐square deviations for backbone atoms of 2.3 Å and 1.1–1.3 Å, respectively, relative to the crystal structures; the different crystal structures have root‐mean‐square deviations of 0.73–0.81 Å for the backbone atoms. In comparing the backbone dihedral angles, the difference between the dynamics and the crystal structure on which it is based is the same as that between any two crystal structures. The internal fluctuations of atomic positions calculated from the molecular dynamics trajectory agree well with the temperature factors from the three structures. Simulation and crystal results both show that there are large motions for residues involved in exposed turns of the backbone chain, relatively smaller motions for residues involved in the middle of helices or β‐sheet structures, and relatively small motions of residues near disulfide bridges. Also, both the simulation and crystal data show that side‐chain atoms have larger fluctuations than main‐chain atoms. Moreover, the regions that have large deviations among the x‐ray crystal structures, which indicates flexibility, are found to have large fluctuations in the simulation.
Rotational diffusion of short DNA fragments in polyacrylamide gels: An electric birefringence study
Authors: Wijmenga Sybren S. , Maxwell Anthony 
Published: December 2004

AbstractUsing electric birefringence we have examined the rotational diffusion of five short DNA fragments (55 to 256 base pairs) both in polyacrylamide gels as a function of gel concentration and in solution. The length dependence of the measured rotational relaxation times in the gels is in good agreement with the prediction from the Odijk theory for the dynamics of slightly flexible rods in a network. The rotational relaxation times were found to depend on the gel concentration, contrary to the prediction from the Odijk theory. Possible reasons for this observation are discussed. The birefringence decay curves for DNA fragments in the gel were single exponential only at small electric field strength.
Raman amide bands of type‐II β‐turns in cyclo‐(VPGVG)3 and poly‐(VPGVG), and implications for protein secondary‐structure analysis
Authors: Thomas George J. , Prescott Betty , Urry Dan W. 
Published: December 2004

AbstractThe cyclopentadecapeptide, c(VPGVG)3, a model structure for protein type‐II β‐turns [W. J. Cook et al. (1980) J. Am. Chem. Soc. 102, 5502–5505], has been investigated by laser Raman spectroscopy. Data obtained from both normal and deuterated crystals identify amide I, III, I′, and III′ bands characteristic of the β(II)turn. The structurally related polypentapeptide poly(VPGVG) in normal and deuterated forms has also been investigated, and exhibits the same Raman amide bands as c(VPGVG)3. The coacervate of poly(VPGVG), obtained by heating the solution to 40°C, likewise exhibits a Raman spectrum very similar to that of the c(VPGVG)3 crystal. Raman spectra thus indicate closely similar secondary structures for crystalline c(VPGVG)3 and aqueous poly(VPGVG), and provide an empirical basis for interpreting the conformation sensitive amide bands of globular proteins in terms of β(II)turn structures that may be present. An important conclusion from the present findings is that the amide I Raman profile of a protein may not be sufficient in general to distinguish turns from helix and sheet secondary structures, since the major amide I peaks of the β(II)turn at 1676 and 1652 cm−1 overlap, respectively, with amide I profiles generated by β‐sheet and α‐helix conformations.
Solvent effect on the stability of mannobiose conformers
Authors: Tvaroska I. , Perez S. , Noble O. , Taravel F. 
Published: December 2004

AbstractThe conformational equilibria of seven methyl β‐D‐mannobioside conformers have been studied theoretically in five solvents. The structure of each individual conformer has been refined by the PCILO quantum‐chemical method from the seven distinct low‐energy regions determined from (Φ, Ψ) maps calculated by a potential function method. The stability of the conformers in dilute solution has been evaluated by using a method that consists of electrostatic, dispersion, and cavity terms. The calculated abundance of conformers depends on the solvent and results indicate that the preponderant conformer in the solution may not be the one adopted by mannobiose in the crystalline form. Based on the determined abundance of conformers, thermodynamically averaged nmr parameters, dipole moment, and linkage rotation have been calculated. The solvation behavior of methyl β‐D‐mannobioside is compared to those previously estimated for cellobiose and maltose.
Conformational studies of diastereomeric cyclic enkephalins by 1H‐NMR and computer simulations
Authors: Mierke Dale F. , Lucietto Pierluigi , Goodman Murray , Schiller Peter W. 
Published: December 2004

AbstractWe report the solid‐phase synthesis and conformational analysis of a 14‐membered, cyclic enkephalin analog, HTyrc[DA2buGlyPheDLeu] (where A2bu represents α,γ‐diaminobutyric acid). The results from the guinea pig ileum (GPI) and mouse vas deferens (MVD) assays show that the analog, though active, has little selectivity for the μ or δ opioid receptors. Conformational analysis is carried out using 1H‐nmr and computer simulations, including molecular dynamics and energy minimizations. The results obtained here are compared with the findings of our studies carried out on the μ‐receptor‐selective diastereomer, HTyrc[DA2buGlyPheLeu] [N. Mammi, M. Hassan, and M. Goodman (1985) J. Am. Chem. Soc. 107, 4008–4013]. This comparison allows for insight into the regiospecificity of these cyclic enkephalin analogs.
Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves
Authors: Marky Luis A. , Breslauer Kenneth J. 
Published: December 2004

AbstractIn this paper, we derive the general forms of the equations required to extract thermodynamic data from equilibrium transition curves on oligomeric and polymeric nucleic acids of any molecularity. Significantly, since the equations and protocols are general, they also can be used to characterize thermodynamically equilibrium processes in systems other than nucleic acids. We briefly review how the reduced forms of the general equations have been used by many investigators to evaluate mono‐ and bimolecular transitions, and then explain how these equations can be generalized to calculate thermodynamic parameters from common experimental observables for transitions of higher molecularities. We emphasize the strengths and weaknesses of each method of data analysis so that investigators can select the approach most appropriate for their experimental circumstances. We also describe how to analyze calorimetric heat capacity curves and noncalorimetric differentiated melting curves so as to extract both model‐independent and model‐dependent thermodynamic data for transitions of any molecularity. The general equations and methods of analysis described in this paper should be of particular interest to laboratories that currently are investigating association and dissociation processes in nucleic acids that exhibit molecularities greater than two.
Local deformation studies of chain molecules: Differential conditions for changes of dihedral angles
Authors: Braun W. 
Published: December 2004

AbstractNew first and second‐order differential equations for changes of dihedral angles characterizing local deformations of chain molecules with fixed bond lengths and bond angles are derived. Two methods for integrating the differential relations are given. The proposed method is used to generate a path of locally deformed conformations around a β‐turn region of a small protein, bovine pancreatic trypsin inhibitor. The variable regions change their conformations by more than 3 Å root‐mean‐square distance value whereas the fixed regions stay within 0.02 Å. Possible applications of this method are in the field of computer graphics, Monte Carlo simulations, and energy minimization calculations of chain molecules.
Conformational studies of nucleic acids. V. Sequence specificities in the conformational energetics of oligonucleotides: The homo‐tetramers
Authors: Pearlman David A. , Kim Sung‐Hou 
Published: December 2004

AbstractThe conformational energetics of the tetranucleoside triphosphates d(ApApApA), d(GpGpGpG), d(CpCpCpC), d(TpTpTpT), ApApApA, GpGpGpG, CpCpCpC, and UpUpUpU are thoroughly examined using a classical potential energy function. The sugar modeling method and multiple correlation functions derived in previous papers of this series are utilized in these examinations. The data are analyzed and compared in terms of the energy profiles for rotation about the conformation‐determining torsion angles in the tetramers. Overall, the predictions are in reasonable qualitative agreement with the existing experimental data. It is found that the base type does not greatly affect the locations of the important minima in these profiles, but rather exerts a large influence on the relative depths of the minima and the barriers to conversion between them. Conformational sequence dependence is manifest to a greater extent by the DNA tetramers than the RNA tetramers. Of the DNA tetramers, d(CpCpCpC) appears, from the results presented herein, to have the greatest potential for polymorphism. This and other findings are analyzed in terms of the preferences of particular DNA sequences for either the A‐, B‐, or Z‐conformation.
An analysis of the 225–230‐nm CD band of elapid toxins
Authors: Hider R. C. , Drake A. F. , Tamiya N. 
Published: December 2004

AbstractSpectroscopic measurements of three representative elapid toxins are presented. An analysis of the data leads to the conclusion that the 228‐nm CD band in this class of proteins originates largely in the disulfide chromophore. The intensity of this CD band is sensitive to conformational change associated with the disulfide group.
Mobility of enzymes on insoluble substrates: The β‐amylase–starch gel system
Authors: Henis Yoav I. , Yaron Tamar , Lamed Raphael , Rishpon Judith , Sahar Elhanan , Katchalski‐Katzir Ephraim 
Published: December 2004

AbstractThe movement of enzymes along the surfaces of biopolymers containing enzyme‐susceptible sites can be described as a lateral diffusion process characterized by an apparent diffusion coefficient [E. Katchalski‐Katzir, J. Rishpon, E. Sahar, R. Lamed, and Y. I. Henis (1985) Biopolymers 24, 257–277]. Studies on the diffusion of enzymes on biopolymer substrates can therefore provide important information on the mechanism of enzyme–biopolymer interaction. For this reason, the motion of fluorescently labeled β‐amylase [α‐D‐(1 → 4)glucan maltohydrolase; E.C. 3.2.1.2] on the surface of starch gels was studied by fluorescence photobleaching recovery. The results indicate that the motion of β‐amylase on the surface of the gel substrate occurs by both lateral diffusion along the surface (over micron distances) and exchange between bound and free enzyme molecules in the solution covering the gel, and that the two processes occur concomitantly and in a random manner. Surface diffusion also appears an important process with respect to the action of the enzyme on the substrate sites, since this component of the motion disappears upon inactivation of the enzyme, leaving only exchange to contribute to the measured motion.