bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of chloroquine on the torsional dynamics and rigidities of linear and supercoiled DNAs at low ionic strength
Authors: Wu Pengguang , Schurr J. Michael 
Published: December 2004

AbstractThe magnitude and uniformity of the torsion elastic constant (α) of linear and supercoiled pBR322 DNAs are measured in 3 mM Tris as a function of added chloroquine/basepair ratio (chl/bp) by studying the fluorescence polarization anisotropy of intercalated ethidium dye. The time‐resolved FPA is measured using a picosecond dye‐laser for excitation and time‐correlated single‐photon counting detction. For both linear and supercoiled DNAs, α remains uniform except at the very highest chl/bp ratio examined. For the linear DNA, α decreases from 5.0 × 10−12 dyne‐cm at chl/bp = 0 to about 3.5 × 10−12 dyne‐cm at chl/bp = 0.5, and remains at that value up to chl/bp = 5, whereupon it increases back up to its original value. For the supercoiled DNA, α remains constant at about 5.2 × 10−12 dyne‐cm from chl/bp = 0 up to chl/bp = 5, whereupon it increases in parallel with the linear DNA. The effect of chloroquine on the secondary structure, torsion constant, and torsional dynamics evidently differs substantially between linear and supercoiled DNAs, even under conditions where the supercoiled DNA is completely relaxed and both DNAs bind the same amount of dye. This strongly contradicts any notion that the local structures of linear and relaxed supercoiled DNA/dye complexes with the same binding ratio are identical. The increase in apparent α at chl/bp = 5 for both DNAs may be due to stacking of the chloroquine in the major groove and consequent stiffening of the filament.
The biased reptation model of DNA gel electrophoresis: Mobility vs molecular size and gel concentration
Authors: Slater Gary W. , Noolandi Jaan 
Published: December 2004

AbstractThe biased reptation model provides a good framework for interpreting the results of continuous field DNA electrophoresis experiments performed in agarose gels. Here we discuss the main features of the mobility–molecular size and mobility–gel concentration diagrams as obtained from new extensive computer simulations of the model. Our aim is to suggest a global and coherent picture of this widely used yet poorly understood experimental technique, and to point out the areas where a systematic experimental study is still needed.
A Monte Carlo simulation study of the influence of internal motions on the molecular conformation deduced from two‐dimensional nmr experiments
Authors: Genest D. 
Published: December 2004

AbstractMonte Carlo methods have been used to simulate internal motions of aromatic protons of an oligonucleotide at the nanosecond time scale. Each proton is allowed to fluctuate about its equilibrium position. The longitudinal cross‐relaxation rates of such a system of spins have been determined by computing the appropriate correlation functions. Then the interproton distances have been deduced according to the procedure generally used in two‐dimensional nmr techniques (nuclear Overhauser effect spectroscopy—NOESY) and compared to the true values. The influence of the amplitude A and of the internal rotational diffusion constant Dint characterizing the dynamics of the system has been checked for in‐phase and for uncorrelated motions. It is shown that for the investigated models the distances deduced from NOESY experiments may be under or overestimated, depending strongly on the values of A and Dint. Furthermore, the cross‐relaxation rate of a couple of protons is very sensitive to the correlation level of the motions of both protons.
Effects of nucleotide bromination on the stabilities of Z‐RNA and Z‐DNA: A molecular mechanics/thermodynamic perturbation study
Authors: Ross Wilson S. , Hardin Charles C. , Tinoco, Ignacio , Rao Shashidhar N. , Pearlman David A. , Kollman Peter A. 
Published: December 2004

AbstractThe structures of ZI‐ and ZII‐ form RNA and DNA oligonucleotides were energy minimized in vacuum using the AMBER molecular mechanics force field. Alternating C‐G sequences were studied containing either unmodified nucleotides, 8‐bromoguanosine in place of all guanosine residues, 5‐bromocytidine in place of all cytidine residues, or all modified residues. Some molecules were also energy minimized in the presence of H2O and cations. Free energy perturbation calculations were done in which G8 and C5 hydrogen atoms in one or two residues of Z‐form RNAs and DNAs were replaced in a stepwise manner by bromines. Bromination had little effect on the structures of the energy‐minimized molecules. Both the minimized molecular energies and the results of the perturbation calculations indicate that bromination of guanosine at C8 will stabilize the Z forms of RNA and DNA relative to the nonbrominated Z form, while bromination of cytidine at C5 stabilizes Z‐DNA and destabilizes Z‐RNA. These results are in agreement with experimental data. The destabilizing effect of br5C in Z‐RNAs is apparently due to an unfavorable interaction between the negatively charged C5 bromine atom and the guanosine hydroxyl group. The vacuum‐minimized energies of the ZII‐ form oligonucleotides are lower than those of the corresponding ZI‐ form molecules for both RNA and DNA. Previous x‐ray diffraction, nmr, and molecular mechanics studies indicate that hydration effects may favor the ZI‐ conformation over the ZII‐ form in DNA. Molecular mechanics calculations show that the ZII–ZI energy differences for the RNAs are greater than three times those obtained for the DNAs. This is due to structurally reinforcing hydrogen‐bonding interactions involving the hydroxyl groups in the ZII form, especially between the guanosine hydroxyl hydrogen atom and the 3′‐adjacent phosphate oxygen. In addition, the cytidine hydroxyl oxygen forms a hydrogen bond with the 5′‐adjacent guanosine amino group in the ZII‐ form molecule. Both of these interactions are less likely in the ZI‐ form molecule: the former due to the orientation of the GpC phosphate away from the guanosine ribose in the ZI form, and the latter apparently due to competitive hydrogen bonding of the cytidine 2′‐hydroxyl hydrogen with the cytosine carbonyl oxygen in the ZI form. The hydrogen‐bonding interaction between the cytidine hydroxyl oxygen and the 5′‐adjacent guanosine amino group in Z‐RNA twists the amino group out of the plane of the base. This may be responsible for differences in the CD and Raman spectra of Z‐RNA and Z‐DNA.
Ir vibrational CD in model deoxyoligonucleotides: Observation of the B → Z phase transition and extended coupled oscillator intensity calcuations
Authors: Gulotta Miriam , Goss Dixie J. , Diem Max 
Published: December 2004

AbstractThe first observation of ir vibrational CD (VCD) in small model DNA molecules is reported. The VCD signals in the 1550–1750‐cm−1 spectral region, which originate from coupling of carbonyl stretching modes of the nucleic acid bases, are found to be sensitive to the handedness of the polymer helix.The formalism to calculate VCD intensities of polymers is developed from the exciton model derived earlier by Tinoco [(1963) Radiation Res. 20, 133; (1960) J. Chem. Phys. 33, 1332; (1964) J. Am. Chem. Soc. 86, 297] and Schellman and co‐workers [(1975) Biopolymers 14, 173; (1969) J. Phys. Chem. 73, 28]. The resulting equations, which are a direct extension of the dimeric case known as the “coupled oscillator,” are used in model calculations of the helical polymers.
Cyclic pentapeptides as models for reverse turns: Determination of the equilibrium distribution between type I and type II conformations of Pro‐Asn and Pro‐Ala β‐turns
Authors: Stradley Sarah J. , Rizo Josep , Bruch Martha D. , Stroup Adam N. , Gierasch Lila M. 
Published: December 2004

AbstractCyclic pentapeptides are excellent models for reverse turns and have been used extensively in our laboratory to explore the influence of different amino acid sequences on turn preference. This paper is divided into two parts: In the first, we review our previous studies of cyclic pentapeptides. We summarize work that demonstrates the range of conformations possible within the cyclic pentapeptide backbone, the importance of sequence chirality in determining the backbone fold, and the utility of these cyclic pentapeptides as models for various turns. In the second, we present new results on two cyclic pentapeptides that contain β‐turns with Pro‐Ala or Pro‐Asn sequences in the i + 1 and i + 2 positions. By stereochemical criteria, a type I β‐turn is expected to be preferred by such L‐L sequences. On the other hand, in proteins Asn occurs frequently in the i + 2 position of type II turns. We asked whether the same propensity would be manifest in an isolated model peptide, and if so, what the interactions were that influenced the relative stability of the type I and type II turns. To address these questions we have compared the conformational behavior of two peptides: cyclo(Gly‐Pro‐Ala‐D‐Phe‐Pro) and cyclo(D‐Ala‐Pro‐Asn‐Gly‐Pro). From previous studies, we anticipated that both peptides would contain an inverse γ‐turn and a β‐turn which consisted of either Gly‐Pro‐Ala‐D‐Phe or D‐Ala‐Pro‐Asn‐Gly in positions i to i + 3, respectively. Nuclear magnetic resonance analysis confirms this overall backbone conformation. Furthermore, quantitative nuclear Overhauser effect measurements in combination with molecular dynamics simulations and torsionally‐forced energy minimizations have enabled us to determine that both type I and type II β‐turns are present in equilibrium in these peptides. The introduction of Asn in position i + 2 shifts this equilibrium significantly towards type II. We have done preliminary assessment of the possible side‐chain/backbone conformations that contribute to the shift in populations.
Biodegradation of copoly(L‐aspartic acid/L‐glutamic acid) in vitro
Authors: Hayashi Toshio , Iwatsuki Makoto 
Published: December 2004

AbstractThe preparation of copolypeptides consisting of L‐aspartic acid and L‐glutamic acid was performed to determine the effects of copolymer composition and sequential distributions on the rate of degradation by papain in a PECF (pseudoextracellular fluid) at pH 4.75 and 7.40, at 37.0°C, to simulate in vivo polymer degradation. Random copolymers consisting of β‐benzyl L‐aspartate and γ‐benzyl L‐glutamate were synthesized by the N‐carboxyanhydride method. Water‐soluble copolymers were obtained by successive reactions of side chains by anhydrous HBr treatment. All the samples were found to be degraded by random chain scission with papain. Further, the degradation data for the samples followed the Michaelis–Menten rate law, being the first order in papain concentration. The nature of side chains are important to the rate of degradation by papain and it was controlled by the comonomer composition as well as the sequential distribution of comonomers in the copolymer chains.
Solvent effects on protein association and protein folding
Authors: Ben‐Naim A. 
Published: December 2004

AbstractSolvent effects on the thermodynamics of two processes—folding of proteins and association between proteins—are examined in detail. A complete inventory of the multitude of solvent effects may be obtained by employing the concept of conditional solvation free energy. This theoretical tool allows for the isolation of specific side‐chain effects from the entire protein and for the study of its contribution to the overall free energy change in small model compounds. Some numerical examples are presented, and ways of estimating other cases, for which no relevant experimental data are available, are suggested. Our findings lead to the conclusion that the currently used hydrophobicity scales, based on partition coefficients between water and an organic solvent, are inadequate measures of the contribution of side chains being transferred from water to the interior of the protein. We have also tentatively concluded that correlation between hydrophilic functional groups might be more important than correlations between hydrophobic side chains.
The program FANTOM for energy refinement of polypeptides and proteins using a Newton – Raphson minimizer in torsion angle space
Authors: Schaumann Thomas , Braun Werner , Wüthrich Kurt 
Published: December 2004

AbstractThe program FANTOM (fast Newton–Raphson torsion angle energy minimizer) performs minimizations of the ECEPP/2 energy function for proteins with the Newton–Raphson method. It is implemented for use with conventional computer hardware. The torsion angles are chosen as independent variables. The first and second derivatives are calculated with a previously described rapid algorithm. For the matrix inversion a modified Cholesky factorization is used. A line search adjusts the step length and nonbonded interactions can be calculated with a cutoff. The following tests of the program are described: All local minima of the ECEPP/2 energy function for the amino acids glycine and alanine were determined. An exhaustive search by more than 16,000 independent energy minimizations was used to identify low‐energy structures of Met‐enkephalin, which were then compared with previously published structures of this pentapeptide. To investigate the use of FANTOM with disulfide bonds, it was applied with conotoxin. As an illustration of the intended primary use of the program, an energy refinement of the structure of the basic pancreatic trypsin inhibitor determined by nmr spectroscopy in solution is described.
Theoretical studies of cis‐Pt(II)‐diammine binding to duplex DNA
Authors: McCarthy Sharon L. , Hinde Robert J. , Miller Kenneth J. , Anderson Janet S. , Basch Harold , Krauss Morris 
Published: December 2004

AbstractThe binding of cis‐Pt(II) diammine (cis‐DP) to double‐stranded DNA was studied with several kinked conformations that can accommodate the formation of a square planar complex. Molecular mechanics (MM) calculations were performed to optimize the molecular fit. These results were combined with quantum mechanical (QM) calculations to ascertain the relative energetics of ligand binding through water vs direct binding of the phosphate to the ammine and platinum, and to guide the selection of DNA conformations to model complex formation. Based on QM and MM calculations, models are proposed that may be characterized by several general features. A structure involving hydrogen bonding between each ammine and distinct adjacent phosphate groups, referred to as closed conformation (CC), has already been reported. This is also found in the crystal structure of small dimers. We report alternative conformations that may be important in platination of duplex DNA. They are characterized by an intermediate conformation (IC), involving hydrogen bonding between one ammine and phosphate group, and an open conformation (OC), without ammine phosphate hydrogen bonding. The IC and OC can be stabilized by water bridges in the space between the ammine and the phosphate groups. Sugar puckers alternate from the type C(2′)‐endo or C(1′)‐exo (S), to the type C(3′)‐endo or C(2′)‐exo (N), with intermediate types near O(1′)‐endo (O). In general, the sugar puckers alternate from S to N to S through the platinated region (3′‐TpG*pG*p‐5′), with the complexed strand exhibiting, (3′)‐S*‐N*‐S‐(5′) alternation, while the complementary strand shows either (3′)‐S*‐N*‐S(5′) or (3′)‐S*‐N*‐O‐(5′) alternation. In both the OC and IC, a hydrogen bond is found between the ammine and O4(T) on thymine (T) at the (3′) end, adjacent to the complex site. There is a continuous range of backbone conformations through the platinated region which relate the OC to the IC. The models presented suggest that the dynamics of the binding of the cis‐Pt(II)‐diammines to adjacent N7(G) in double‐stranded DNA may encompass several conformational possibilities, and that water bridges may play a roll in supporting open and intermediate conformations. Proton–proton distances are reported to assist in the experimental determination of conformations.
B to Z transition in poly(dG‐dC) modified with benzo(a)pyrene diol epoxides studied with polarized light spectroscopy
Authors: Eriksson Magdalena , Nordén Bengt , Jernström Bengt , Gräslund Astrid 
Published: December 2004

AbstractThe NaCl‐induced transition from B to Z conformation in poly (dG‐dC), covalently modified with benzo(a)pyrene diol epoxides (BPDE), has been studied by use of flow linear dichroism (LD), CD, and fluorescence spectroscopy. In contrast to unmodified poly (dG‐dC), the BPDE‐modified polynucleotide displays a B to Z conversion that is incomplete in 2.7 M NaCl. This and a number of other observations are found consistent with a locally retained BPDE perturbed B‐like conformation in the vicinity of the BPDE adduct. In 2.7 M NaCl the polynucleotide orientation in flow is strongly reduced, which could indicate flexibility at the junctions between domains of BPDE perturbed B‐like conformation and Z conformation. A virtually stable high‐salt B form is found in 2.25 M NaCl at 0°C; its CD spectrum resembles that of the transient so‐called B* form, which is observed at an early stage of the B to Z transition. Characteristic B to Z transition times were evaluated by taking this B*‐form CD spectrum as the initial state spectrum. The kinetics of the B to Z transition, monitored by the CD signal at 287 nm, shows an increased transition rate with (+)‐anti‐BPDE modification whereas the (−)‐anti‐ and (±)‐syn‐BPDE adducts have retarding effects. The difference is discussed against the background of the different binding geometries of the BPDE isomer adducts.
Secondary‐structure dependent chemical shifts in proteins
Authors: Williamson Michael P. 
Published: December 2004

AbstractChemical shift data have been collected on eight proteins that have the same conformation in solution as in their crystal structures. Ring‐current shifts have been calculated and subtracted from the experimentally measured shifts, to leave shifts that depend only on local conformation. Overall, the shifts show an approximately normal distribution with no appreciable skewness, thus confirming that ring‐current shifts have the overall effect of skewing the distribution to high field. In helices, NH and CαH have a highly significant tendency to resonate to high field, whereas they resonate to low field in β‐sheets. Side‐chain protons resonate slightly to high field in γ‐sheets. Chemical shift distributions are narrowest for side‐chain protons, and widest for amide protons. When only slowly exchanging amide protons are considered, the high field shift for amide protons in helices is more pronounced, but there is only a small difference in sheets. CαH signals at the N‐terminal end of helices tend to resonate to higher field than those at the C‐terminal end, whereas for NH signals it is the C‐terminal end that resonates to higher field. There is no significant effect of position within the helix on side‐chain signals, implying that the helix dipole has little effect on shifts within the helix.
Physicochemical studies on tomato bushy stunt virus variants
Authors: Molina‐Garcia Antonio D. , Harding Stephen E. , Fraser Ronald R. S. 
Published: December 2004

AbstractTomato bushy stunt virus particles have previously been physically and chemically well characterized. Different strains, however, are known to have different host plants and symptoms, and they can be distinguished serologically. In an attempt to correlate this behaviour with physicochemical properties, we have performed a comparative study on isolates of four of the main variants of this virus (Type strain, petunia asteroid mosaic virus, pelargonium leaf curl virus, and carnation Italian ringspot virus) with regard to sedimentation velocity characteristics, translation diffusivity (from quasi‐elastic light scattering measurements), and molecular weight (from both low‐speed sedimentation equilibrium and the Svedberg equation).It is demonstrated that there are no clear differences between the four strains, particularly insofar as their sedimentation characteristics (both velocity and low‐speed equilibrium). There is some suggestion from diffusion measurements that the Type strain virus particles may have a higher mass, although the presence of some aggregation phenomena may provide an alternative explanation for the diffusion data.
Adenine and guanine 8CH exchange in nucleic acids: Resolution and measurement by Raman optical multichannel analysis
Authors: Lamba Om P. , Becka Renee , Thomas George J. 
Published: December 2004

AbstractDeuterium exchange of 8C protons of adenine and guanine in nucleic acids is conveniently monitored by laser Raman spectrophotometry, and the average exchange rate so determined (〈kA + kG〉) can be exploited as a dynamic probe of the secondary structure of DNA or RNA [J. M. Benevides and G. J. Thomas, Jr. (1985) Biopolymers 24, 667–682]. The present work describes a rapid Raman procedure, based upon optical multichannel analysis, which permits discrimination of the different 8CH exchange rates, kA of adenine and kG of guanine, in a single experimental protocol. For this procedure, simultaneous measurements are made of the intensity decay or frequency shift in separately resolved Raman bands of adenine and guanine, each of which is sensitive only to 8C deuteration of its respective purine. Resolution of the rates kA and kG is demonstrated for the mononucleotide mixtures, 5′‐rAMP + 5′‐rGMP and 5′‐dAMP + 5′‐dGMP, for the polynucleotides poly (dA‐dT) . poly (dA‐dT) and poly (dG‐dC)·poly (dG‐dC), for calf thymus DNA, and for the 17 base‐pair operator OR3. We show that the different exchange rates of adenine and guanine, in nucleotide mixtures and in DNA, may also be calculated independently from intensity decay of the composite 1481‐cm−1 band, comprising overlapped adenine and guanine components, over a time domain that encompasses two distinct regimes: (1) a relatively more rapid exchange of guanine, and (2) a concurrent slower exchange of adenine. Both methods developed here yield consistent results. We find, first, that exchange of guanine is approximately twofold more rapid than that of adenine when both purines are present in the same structure and solvent environment, presumably a consequence of the greater basicity of the 7N site of guanine. Second, we find that adenine suffers greater retardation of exchange than guanine when both purines are incorporated into a “classical” B‐DNA secondary structure, such as that of calf thymus DNA. This finding suggests different microenvironments at the 7N‐8C loci of adenine and guanine in aqueous B‐DNA. We also confirm that adenine residues of B‐form poly (dA‐dT)·poly (dA‐dT) exchange much more slowly than those of other B‐DNA sequences, implying a secondary structure for the alternating‐AT sequence with unusual stereochemistry in the major groove. The greater resistance of adenine than guanine to 8CH exchange in the B‐DNA secondary structure is more evident in high molecular weight calf thymus DNA and in the alternating AT and GC copolymer duplexes than in the smaller 17 base‐pair operator OR3. The present results provide direct experimental evidence for structural heterogeneity of B‐DNA in aqueous solution, involving the purine 7N‐8C imidazole network. The methods developed here establish an experimental basis for future study of purine‐specific interactions that may be important in gene regulatory complexes and in nucleic acid condensation and packaging processes.