bluuebunny/crossref_metadata_2025_split huggingface dataset:
A study of model energetics and conformational properties of polynucleotide triplexes
Authors: Van Vlijmen Herman W. Th. , Rameé Graciela L. , Pettitt B. Montgomery 
Published: December 2004

AbstractThe formation of triple‐stranded nucleic acid helices is studied by molecular mechanics and molecular dynamics calculations. Using standard TAT and CGG homopolymers, single, triple, and quintuple molecular replacements are made. Some of these replacements are expected to form Hoogsteen bonds and some are not. While the electrostatic and total energetic differences for base triplet mismatches were dependent on the electrostatic model chosen, clear trends in the local geometric distortions were apparent. Relationships between these model‐built strand geometries and chemical probe experiments are discussed.
Hydrodynamic study of flexibility in immunoglobulin igG1 using Brownian dynamics and the Monte Carlo simulations of a simple model
Authors: Díaz F. G. , Iniesta A. , De La Torre J. García 
Published: December 2004

AbstractA simple bead model is proposed for the antibody molecule immunoglobulin IgG1. The partial flexibility of the hinge is represented by a quadratic potential associated to the angles between arms. Conformational and hydrodynamic properties are calculated using Monte Carlo (rigid‐body) and Brownian dynamics simulations. Comparison of experimental and calculated values for some overall properties allows the assignment of dimensions and other model parameters. The Brownian dynamics technique is used next to simulate a rotational correlation function that is comparable with the decay of fluorescence emission anisotropy. This is done with varying flexibility at the hinge. The longest relaxation time shows a threefold decrease when going from the rigid Y‐shaped conformation to the completely flexible case. The calculations are in good agreement with the decay times observed for IgG1. A flexibility analysis of the latter indicates that a variability of ±55° (standard deviation) in the angle between the Fab arms.
The effect of conformation on the CD of interacting helices: A theoretical study of tropomyosin
Authors: Cooper Thomas M. , Woody Robert W. 
Published: December 2004

AbstractA recent report [M. E. Holtzer, et al. (1988) Biophysics Journal, 53, 96a] of the anomalous CD spectum of the tropomyosin (TM) fragment 11TM127 motivated us to model the system as two 21‐residue α‐helices distorted to a coiled‐coil conformation. We used strong‐coupling exciton theory to model the optical properties of the system. Two backbone amide excited states (nπ* and ππ*) were considered, as well as four excited states (Lb, La, Bb, Ba) for the phenolic side chain. We calculated the effect of superhelix formation on the backbone CD spectrum. The decrease in molar ellipticity of the α‐helix parallel‐polarized transition at 208 nm was found to be a simple function of superhelix tilt angle. We then modeled a coiled coil (radius = 5.5 Å, pitch = −140 Å) with one aromatic ring per superhelix. Steric interactions between aromatic side chains in a coiled coil were calculated as a function of side‐chain conformation and heptet position. Steric interactions between phenolic rings will be significant for heptet positions a and d, but not for positions b, c, e, f, or g. We calculated the phenolic Lb transition rotational strength as a function of position within the heptet repeats, and of all possible side‐chain dihedral angles, X1 and X2. When tyrosines were placed at heptet positions b, c, e, f, or g, the rotational‐strength surface was nearly identical to that of a single tyrosine in an undistorted helix. In contrast, the rotational‐strength surface for tyrosines in heptet positions a or d showed substantial intertyrosine coupling components. The rotational‐strength surfaces for the three types of heptet positions (position a, position d, and the others) allowed an interpretation of the aromatic CD spectra of TM and its fragments. It was predicted that the three types of heptet positions will be spectroscopically distinguishable.
A 23Na‐nmr study of sodium–DNA interactions in concentrated DNA solutions at low‐supporting electrolyte concentration
Authors: Strzelecka Teresa E. , Rill Randolph L. 
Published: December 2004

AbstractAqueous solutions of DNA fragments with a contour length (500 Å) near the persistence length at DNA concentrations ranging from 10 to 290 mg/mL solvent and a constant supporting electrolyte concentration of 0.01 M (predominantly NaCl) were examined by 23Na‐nmr spectroscopy at temperatures of 20, 40, and 60°C. Over the higher portion of this concentration range (> 100 mg/ml) the DNA solutions undergo a complex series of transitions between different anisotropic, liquid crystalline phases (T. E. Strzelecka and R. L. Rill, Biopolymers, in press). Counterions in solutions of strong polyelectrolytes are usually described in terms of a two‐state model as free or “bound” (influenced by the electrostatic field of the polyanion). The longitudinal relaxation rate (R1 = 1/T1) at all DNA concentrations decreased with increasing temperature, demonstrating fast exchange between free and bound counterions. R1, increased nearly linearly with increasing DNA phosphate/sodium ratio in the isotropic domain until the onset of anisotropic phase formation, in agreement with similar nmr studies conducted at low DNA concentrations. The value of R1,b = 194 ± 7 Hz obtained for the isotropic phase from 10 to 100 mg DNA/mL at 20°C was in agreement with values reported previously. A nonlinear increase in R1 with DNA concentration was observed upon onset of anisotropic phase formation, indicating an increase in the product of the fraction of bond ions times their relaxation rate (r·R1,b).The spectral lineshape of all isotropic samples was Lorentzian. Spectra of anisotropic samples exhibited low magnitude quadrupole splitting of ≤400 Hz correlated with appearance of a cholesteric phase with pitch ≈ 2 μm. The magnitude of the quadrupole splitting decreased with increasing DNA concentration at low temperatures and increased with concentration at high temperature. At all concentrations the quadrupole splitting decreased then increased with temperature. These temperature‐ and concentration‐dependent changes in quadrupole splitting are consistent with an angle between the DNA helix axis and the principle component (VZZ) of the local electric field gradient tensor near the “magic angle” of 54.7°.
Internal dynamics of tRNAPhe studied by depolarized dynamic light scattering
Authors: Patkowski A. , Eimer W. , Dorfmüller Th. 
Published: December 2004

AbstractThe collective internal dynamics of transfer RNAphe from brewer's yeast in solution was studied by depolarized dynamic light scattering (DDLS). Within the melting region of tRNA the depolarized spectra consist of two Lorentzian, where the narrow (slow) component describes the overall rotation of the macromolecule. The broad component is attributed to the collective reorientation of the bases within the biopolymer. At high temperature only this relaxation process is observed in the spectrum. The viscosity dependence of the collective internal relaxation process is described by the Stokes–Einstein–Debye equation for rotational diffusion. Estimates of the internal orientational pair correlation factor from the integral depolarized intensities of tRNAPhe solutions indicates that the observed dynamics correspond to the collective reorientation of approximately 5 bases. A comparison of the results presented with DDLS studies on the aggregation of the mononucleotide guanosine‐5′‐monophosphate confirms this result. For a further characterization of the relaxation process we studied the effect of hydrostatic pressure (1–1000 bar) on the depolarized spectra of tRNA. While other spectroscopic methods like nmr, fluorescence polarization anisotropy decay, or ESR give information about the very local motion of a single base within the DNA or RNA, this study shows that by DDLS one can characterize collective internal motions of macromolecules.
Random coil scission rates determined by time‐dependent total intensity light scattering: Hyaluronate depolymerization by hyaluronidase
Authors: Reed Wayne F. , Reed Christopher E. , Byers Larry D. 
Published: December 2004

AbstractA recently developed theory of the light scattering by random coils undergoing random scission is applied to the digestion of hyaluronate by hyaluronidase. The time dependence of the scattered light from solutions undergoing digestion was monitored. Working at a high angle with high molecular weight hyaluronate allowed the use of a powerful approximation for determining initial velocities and the Henri–Michaelis–Menten coefficients, without explicit knowledge of the hyaluronate molecular weight, radius of gyration, second virial coefficient, or polydispersity. Effects due to a molecular weight dependent second virial coefficient and to non‐Gaussian behavior are briefly considered. Assays were performed over nearly two orders of magnitude in substrate concentration. The initial velocities are compared with those obtained by a standard reducing sugar assay, which was performed on identical samples. The main advantages of the light scattering assay procedure over the more traditional assays are that many relatively high‐precision data points can be quickly and automatically collected with simple apparatus, and that the technique is most sensitive for the initial period of digestion, where the other assays are least sensitive. The shapes of the scattering curves also provide evidence that hyaluronate in these solutions is not a stable double strand and that the hyaluronidase cleaves bonds randomly. The curves also indicate that enzyme deactivation occurs, which accounts for the lower velocities yielded by the slower reductimetric assay, which is measured over longer initial periods.
Restrained and unrestrained molecular dynamics simulations in the NVT ensemble of alamethicin
Authors: Fraternali F. 
Published: December 2004

AbstractMolecular dynamics simulations on the transmembrane antibiotic peptide alamethicin have been performed in the NVT ensamble (i.e., the number of particles N, the volume V, and the temperature T of the system are kept constant). Results on the structure and conformational flexibility of this molecule are discussed and compared with previous experimental CD, x‐ray, nmr data and theoretical computations on fragments analogues.An extensive study of structural and dynamic properties from H‐bonding pattern analysis is presented. Evidences for a largely α‐helix structure with some extent of freedom in the C‐terminal region are found.Further, a partition of the molecule into three regions on the base of structural features and dynamic behavior has been proposed, and the correlation among the motions of the three regions is described.
Solvent‐ and salt‐induced coil–helix transition of alkali metal salts of poly(L‐glutamic acid) in aqueous organic solvents
Authors: Satoh Mitsuru , Fujii Yoshitake , Kato Fusaaki , Komiyama Jiro 
Published: December 2004

AbstractThe coil–helix transition has been studied for alkali metal salts of poly (L‐glutamic acid) (PLG), i.e., PLGLi, ‐Na, ‐K, and ‐Cs, in aqueous organic solvent systems. Dependence of the transition on the solvent composition has been qualitatively discussed in terms of the solvent dielectric constant D, Gutmann's acceptor number AN, and water activity aw. The helix formation induced by addition of alkali chlorides has also been studied. The sharpness of the transition has been interpreted as a measure of reduction of electrostatic energy of helical PLG through contact ion‐pair formation between a counterion and carboxyl anion.
Interaction of guanylic acid with the Mg(II), Ca(II), Sr(II), and Ba(II) ions in the crystalline solid and aqueous solution: Evidence for the ribose C2′‐endo/anti and C3′‐endo/anti conformational changes
Authors: Tajmir‐Riahi Heidar‐Ali 
Published: December 2004

AbstractThe interaction of guanosine‐5′‐monophosphoric acid (H2‐GMP) with the alkaline earth metal ions has been studied in aqueous solution at neutral pH. The crystalline salts of the type Mg‐GMP·5H2O, Ca‐GMP·6H2O, Sr‐GMP·7H2O, and Ba‐GMP·7H2O were isolated and characterized by Fourier transform ir, 1H‐nmr and x‐ray powder diffraction measurements. Two types of macrochelate complexes have been identified: (a) The direct metal–base and indirect metal–phosphate bindings (inner and outer sphere interaction) for the Mg(II), Ca(II), and Sr(II), ions; and (b) the indirect metal–base and direct metal–phosphate bindings (outer and inner sphere interaction) for the Ba(II) ion. In aqueous solution, an equilibrium exists between the base–metal–H2O…PO3 and base … H2O–M–PO3 interactions. The ribose moiety shows C3′‐endo/anti conformation in the free acid; C2′‐endo/anti in the Na2‐GMP salt; C3′‐endo/anti in the Mg(II)‐, Ca(II)‐, and Sr(II)‐GMP salts; and C2′‐endo/anti, in the Ba(II)‐GMP salt.
Transient electric birefringence study of highly dilute agarose solutions
Authors: Dormoy Y. , Candau S. 
Published: December 2004

AbstractIn order to characterize the first step of agarose gelation, highly dilute solutions (2·10−3 to 0.5 g/L) have been studied by means of the transient electric birefringence technique. The field‐free decay curves of the birefringence are well described by a stretched‐exponential B(t) ≈ exp(−t/τ)β; the value of the exponent β is close to 0.5 whatever the agarose concentration. The suspended particles observed by electron microscopy present a rod‐like shape with a constant diameter (∼50 Å), without any branching; they are polydisperse with a distribution of lengths approximately exponential. The mean length of these fibers, deduced from their mean rotational diffusion coefficient, is proportional to the 0.37 power of the agarose concentration in the solution. Furthermore, these particles possess a strong permanent electrical dipole confirming the side‐to‐side arrangement of helices into bundles; this dipole is roughly proportional to the particle length, indicating a self‐similarity in the unidirectional growth of the agarose fibers, even when approaching the gelling concentration.
Study of the “molten globule” intermediate state in protein folding by a hydrophobic fluorescent probe
Authors: Semisotnov G. V. , Rodionova N. A. , Razgulyaev O. I. , Uversky V. N. , Gripas' A. F. , Gilmanshin R. I. 
Published: December 2004

AbstractBinding of the hydrophobia fluorescent probe, 1‐anilino‐naphthalene‐8‐sulfonate (ANS), to synthetic polypeptides and proteins with a different structural organization has been studied. It has been shown that ANS has a much stronger affinity to the protein “molten globule” state, with a pronounced secondary structure and compactness, but without a tightly packed tertiary structure as compared with its affinity to the native and coil‐like proteins, or to coil‐like, α‐helical, or β‐structural hydrophilic homopolypeptides.The possibility of using ANS for the study of equilibrium and kinetic molten globule intermediates is demonstrated, with carbonic anhydrase, β‐lactamase, and α‐lactalbumin as examples.
Preferred conformation of the terminally blocked (Aib)10 homo‐oligopeptide: A long, regular 310‐helix
Authors: Toniolo Claudio , Crisma Marco , Bonora Gian Maria , Benedetti Ettore , Dl Blasio Benedetto , Pavone Vincenzo , Pedone Carlo , Santini Antonello 
Published: December 2004

AbstractThe decapeptide pBrBz‐ (Aib)10‐OtBu, synthesized by the 5(4H)‐oxazolone method, crystallizes in the monoclinic space group C2/c with a = 43.901(2), b = 9.289(2), and c = 34.746(3) A; β = 114.69(3)°; and Z = 8. The crystals contain one molecule of water associated with each peptide. The structure has been solved by the Patterson method and refined to an R value of 0.073 for 6819 observed reflections. The peptide adopts a regular 310‐helical structure stabilized by eight NH …︁ OC intramolecular 1 ← 4 (or C10) H bonds. This study has allowed us to characterize this important peptide secondary structure in great detail. The crystal‐state conformation agrees well with proposals made on the basis of an ir absorption and 1H‐nmr study in solution.
A molecular dynamics study of the effect of G · T mispairs on the conformation of DNA in solution
Authors: Shibata Masayuki , Zielinski Theresa Julia , Rein Robert 
Published: December 2004

AbstractThe effect of G · T mispair incorporation into a double‐helical environment was examined by molecular dynamics simulation. The 60‐ps simulations performed on the two hexanucleotide duplexes d (G3C3)2 and d (G3TC2)2 included 10 Na+ counterions and first hydration shell waters. The resulting backbone torsional angle trajectories were analyzed to select time spans representative of conformational domains. The average backbone angles and helical parameters of the last time span for both duplexes are reported. During the simulation the hexamers retained B‐type DNA structures that differed from typical A‐ or B‐DNA forms. The overall helical structures for the two duplexes are vary similar. The presence of G · T mispairs did not alter the overall helical structure of the oligonucleotide duplex. Large propeller twist and buckle angles were obtained for both duplexes. The purine/pyrimidine crossover step showed a large decrease in propeller twist in the normal duplex but not in the mismatch duplex. Upon the formation of wobble mispairs in the mismatched duplex, the guanines moved into the minor groove and the thymines moved into the major groove. This helped prevent purine/purine clash and created a deformation in the relative orientation of the glycosidic bonds. It also exposed the free O4 of the thymines in the major groove and N2 of the guanines in the minor groove to interactions with solvent and counterions. These factors seemed to contribute to the apparently higher rigidity of the mismatched duplex during the simulation.
Molecular dynamics simulations of small peptides: Dependence on dielectric model and pH
Authors: Daggett Valerie , Kollman Peter A. , Kuntz Irwin D. 
Published: December 2004

AbstractThere has been much interest recently in the structure of small peptides in solution. A recent study by Bradley and co‐workers [(1989) in Techniques of Protein Chemistry, Hugli, T. E., Ed., Academic Press, Orlando, FL, pp. 531–546; (1990) Journal of Molecular Biology, 215, pp. 607–622] describes a 17‐residue peptide that is stable as a monomeric helix in aqueous solution at low pH, as determined by two‐dimensional nmr and CD spectroscopy. They also have determined the helix content of the peptide as a function of pH using CD. We performed molecular dynamics simulations, with an empirical force field, of this peptide at low pH, with three different dielectric models: a linear distance‐dependent dielectric function (ε = R); a modified form [J. Ramstein and R. Lavery (1988) Proceedings of the National Academy of Science, USA, Vol. 85, pp. 7231–7235] of the sigmoidal distance‐dependent dielectric function of Hingerty and co‐workers [(1985) Biopolymers, Vol. 24, pp. 427–439]; and ε = 1 with the peptide immersed in a bath of water molecules. We found that simulations with the sigmoidal dielectric function and the model with explicit water molecules resulted in average distances for particular interactions that were consistent with the experimental nmr results, with the sigmoidal function best representing the data. However, these models exhibited very different helix‐stabilizing interactions. We also performed simulations using the sigmoidal function at moderate and high pH to compare to experimental determinations of the pH dependence of helix content. Helix content did not decrease with increases in pH, as shown experimentally. We did, however, observe changes in a specific side chain–helix dipole interaction that was implicated in determining the pH‐dependent behavior of this peptide. Overall, the sigmoidal dielectric function was a reasonable alternative to adding explicit water molecules. In comparing 100 ps molecular dynamics simulations, the sigmoidal function was much less computer intensive and sampled more of conformational space than the treatment using explicit water molecules. Sampling is especially important for this system since the peptide has been shown experimentally to populate both helical and nonhelical conformations.
Proton and tritium nmr relaxation studies of peptide inhibitor binding to bacterial collagenase: Conformation and dynamics
Authors: Dive Vincent , Lai Adolfo , Valensin Gianni , Saba Giuseppe , Yiotakis Athanasios , Toma Flavio 
Published: December 2004

AbstractThe interaction of succinyl‐Pro‐Ala, a competitive inhibitor of Achromobacter iophagus collagenase, with the enzyme was studied by longitudinal proton and tritium relaxation. Specific deuterium and tritium labeling of the succinyl part at vicinal positions allowed the measurement of the cross‐relaxation rates of individual proton or tritium spin pairs in the inhibitor–enzyme complex as well as in the free inhibitor. Overall correlation times, internuclear distances, and qualitative information on the internal mobility in Suc1 (as provided by the generalized order parameter S2) could be deduced by the comparison of proton and tritium cross‐relaxations of spin pairs at complementary positions in the CH2CH2 moiety as analyzed in terms of the model‐free approach by Lipari and Szabo.The conformational and motional parameters of the inhibitor in the free and enzyme‐bound state were directly compared by this method. The measurement of proton cross‐relaxation in the Ala residue provided additional information on the inhibitor binding. The determination of the order parameter in different parts of the inhibitor molecule in the bound state indicates that the succinyl and alanyl residues are primarily involved in the interaction with the enzyme active site. The succinyl moiety, characterized in solution by the conformational equilibrium among the three staggered rotamers–i.e., trans: 50%; g+: 20%; g−; 30%–adopted in the bound state the unique trans conformation.
The Electrostatically Driven Monte Carlo method: Application to conformational analysis of decaglycine
Authors: Ripoll Daniel R. , Vásquez Max J. , Scheraga Harold A. 
Published: December 2004

AbstractThe Electrostatically Driven Monte Carlo (EDMC)method was applied in a study of a decamer of glycine whose conformational behavior is described by the Empirical Conformational Energy Program for Peptides (ECEPP/2) potential energy model. When free neutral end groups were used, it was found that conformations that were not α‐helical had significantly lower potential energies than fully α‐helical ones. However, when the N‐ and C‐termini were blocked by acetyl and methyl amide groups, respectively, the number of unsatisfied hydrogen‐bond donors and acceptors at the helix termini was diminished from 8 to 6; in this case, the possibility of forming two additional α‐helical hydrogen bonds was an important enough factor in making the α‐helical conformation the one with the lowest energy. The EDMC method was used as a global energy optimizer since it does not often become trapped in high‐energy local minima.
A method for estimating the nearest neighbor base‐pair content of RNAs using CD and absorption spectroscopy
Authors: Johnson Kenneth H. , Gray Donald M. 
Published: December 2004

AbstractCD and absorption spectra are sensitive to the secondary structure of RNAs. By fitting the spectra contained in our basis set to the CD and absorption spectra of an RNA of known sequence, we could determine the fractions of base pairs, the fractions of each of the nearest neighbor base pairs, and the fractions of the single‐stranded nucleotides in that RNA. The basis set included 58 CD and 58 absorption spectra. The fitting was done with a guided selection routine. The estimated error was about 0.05 for predicting the fractions of the nearest neighbor base pairs, 0.06 for predicting the fractions of A · U, G · C, and G · U base pairs, and 0.04 for predicting the fractions of the single‐stranded nucleotides.