摘要:

AbstractA formula for the apparent diffusion coefficient [Dapp(κ)] of a rigid ring is derived from the exact first cumulant of its dynamic structure factor.Dapp(κ) is expressed in terms of the ring radius, the diffusion coefficients (DzzandDxx) for translation parallel and perpendicular, respectively, to the symmetry axis, and the diffusion coefficients (D R∥and D R⟂) for rotation around the symmetry and transverse axes, respectively.Dapp(κ) exhibits oscillations as a function of the scattering vectork, which depend on D R⟂and the anisotropy of translational diffusion (Dzz−Dxx). The maxima inDapp(κ) are associated with minima in the static structure factorS(κ, 0), which are due to destructive intramolecular interference. The oscillations inDapp(κ) result from periodic variations in therelativeintensities of scattered light from different orientations of the ring, which manifest the various motions to different extents. The orientations contributing most to the scattered intensity are those that exhibit the least destructive interference and consequently contribute most to the decay of the dynamic structure factor. © 1993

ISSN:0006-3525    

DOI:10.1002/bip.360331202

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1993

数据来源: WILEY

摘要:

AbstractThe preparation and melting of a 16 base‐pair duplex DNA linked on both ends by C12H24(dodecyl) chains is described. Absorbance vs temperature curves (optical melting curves) were measured for the dodecyl‐linked molecule and the same duplex molecule linked on the ends instead by T4loops. Optical melting curves of both molecules were measured in 25, 55, and 85 mMNa+and revealed, regardless of [Na+], the duplex linked by dodecyl loops is more stable by at least 6°C than the same duplex linked by T4loops. Experimental curves in each salt environment were analyzed in terms of the two‐state and multistate theoretical models. In the two‐state, or van't Hoff analysis, the melting transition is assumed to occur in an all‐or‐none manner. Thus, the only possible states accessible to the molecule throughout the melting transition are the completely intact duplex and the completely melted duplex or minicircle. In the multistate analysis no assumptions regarding the melting transition are required and the statistical occurrence of every possible partially melted state of the duplex is explicitly considered. Results of the analysis revealed the melting transitions of both the dodecyl‐linked molecule and the dumbbell with T4end loops are essentially two state in 25 and 55 mMNa+. In contrast, significant deviations from two‐state behavior were observed in 85 mMNa+. From our previously published melting data of DNA dumbbells with Tnend loops wheren= 2, 3, 4, 6, 8, 10, 14 [T. M. Paner, M. Amaratunga, and A. S. Benight, (1992)Biopolymers, Vol. 32, pp. 881–892] and the dumbbell with T4end loops of this study, a plot ofd(Tm)/dln [Na+] was constructed. Extrapolation of this data ton= 1 intersects with the value ofd(Tm)/dln [Na+] obtained for the alkyl‐linked dumbbell, suggesting the salt‐dependent stability of the alkyl‐linked molecule behaves as though the duplex of this molecule were linked by end loops comprised of a single T residue. ©

ISSN:0006-3525    

DOI:10.1002/bip.360331203

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1993

数据来源: WILEY

摘要:

AbstractCD spectra and melting curves were collected for a 28 base‐pair DNA fragment in the form of a DNA dumbbell (linked on both ends by T4single‐strand loops) and the same DNA sequence in the linear form (without end loops). The central 16 base pairs (bp) of the 28‐bp duplex region is the poly(pu) sequence: 5′‐AGGAAGGAGGAAAGAG‐3′. Mixtures of the dumbbell and linear DNAs with the 16‐base single‐strand sequence 5′‐TCCTTCCTCCTTTCTC‐3′ were also prepared and studied. At 22°C, CD measurements of the mixtures in 950 mMNaCl, 10 mMsodium acetate, 1 mMEDTA, pH 5.5, at a duplex concentration of 1.8 μM, provided evidence for triplex formation. Spectroscopic features of the triplexes formed with either a dumbbell or linear substrate were quite similar. Melting curves of the duplex molecules alone and in mixtures with the third strand were collected as a function of duplex concentration from 0.16 to 2.15 μM. Melting curves of the dumbbell alone and mixtures with the third strand were entirely independent of DNA concentration. In contrast, melting curves of the linear duplex alone or mixed with the third strand were concentration dependent. At identical duplex concentrations, the dumbbell alone melts ∼20°C higher than the linear duplex. The curve of the linear duplex displayed a significant pretransition probably due to end fraying.On melting curves of mixtures of the dumbbell or linear duplex with the third strand, a low temperature transition with much lower relative hyperchromicity change (∼ 5%) was observed. This transition was attributed to the melting of a new molecular species, e.g., the triplex formed between the duplex and single‐strand DNA molecules. In the case of the dumbbell/single‐strand mixture, these melting transitions of the triplex and the dumbbell were entirely resolvable. In contrast, the melting transitions of the linear duplex and the triplex overlapped, thereby preventing their clear distinction. To analyze the data, a three‐state equilibrium model is presented. The analysis utilizes differences in relative absorbance vs temperature curves of dumbbells (or linear molecules) alone and in mixtures with the third strand. From the model analysis a straightforward derivation offT(T), the fraction of triplex as a function of temperature, was obtained. Analysis offTvs temperature curves, in effect melting curves of the triplexes, provided evaluation of thermodynamic parameters of the melting transition. For the triplex formed with the dumbbell substrate, the total transition enthalpy is ΔHT= 118.4 ± 12.8 kcal/mol (7.4 ± 0.8 kcal/mol per triplet unit) and the total transition entropy is ΔST= 344 ± 36.8 cal/K · mol (eu) (21.5 ± 2.3 eu per triple unit). The transition curves of the triplex formed with the linear duplex substrate displayed two distinct regions. A broad pretransition region fromfT= 0 to 0.55 and a higher, sharper transition abovefT= 0.55. The transition parameters derived from the lower temperature region of the curve are ΔH′T= 44.8 ± 9.6 kcal/mol and ΔS′T= 112 ± 33.6 eu (or ΔH′ = 2.8 ± 0.6 kcal/mol and ΔS′ = 7.0 ± 2.1 eu per triplet). These values are probably too small to correspond to actual melting of the triplex but instead likely reveal effects of end fraying of the duplex substrate on triplex stability. Transition parameters of the upper transition are ΔH′T= 128.0 ± 2.3 kcal/mol and ΔS′T= 379.2 ± 6.4 eu (ΔH′ = 8.0 ± 0.2 kcal/mol and ΔS′ = 23.7 ± 0.4 eu per triplet) in good agreement (within experimental error) with the transition parameters of the triplex formed with the dumbbell substrate. Supposing this upper transition reflects actual dissociation of the third strand from the linear duplex substrate this triplex is comparable in thermodynamic stability to the triplex formed with a dumbbell substrate. Even so, the biphasic melting character of the linear triplex obscures the whole analysis, casting doubt on its absolute reliability. Apparently triplexes formed with a dumbbell substrate offer technical advantages over triplexes formed from linear or hairpin duple

ISSN:0006-3525    

DOI:10.1002/bip.360331204

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1993

数据来源: WILEY

摘要:

AbstractDepolarization ratios of Raman bands, excited at 488.0 nm, of guanosine‐5′‐monophosphoric 4 acid, cytidine‐5′‐monophosphoric acid, adenosine‐5′‐monophosphoric acid, thymidine‐5′‐monophosphoric acid, and uridine‐5′‐monophosphoric acid have been measured in their H2O and D2O solutions in the spectral region from 300 to 1800 cm−1. For comparison, the disodium salt of 2′‐deoxyadenosine‐5′‐monophosphoric acid was also subjected to the depolarization measurement in its H2O solution. The results have been correlated with possible orientations of the principal axes of the Raman scattering tensors as well as with the relative magnitudes of the tensor components. Results should be useful for future polarized Raman studies of synthetic and

ISSN:0006-3525    

DOI:10.1002/bip.360331205

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1993

数据来源: WILEY

摘要:

AbstractSolutions of modified adult human hemoglobin (Hb) have potential applications as physiological oxygen carriers. The chemical modification that has been the most studied during the last few years is the cross‐linking of the protein between its two αβ dimers, in order, first, to hamper their diffusion through the kidney and therefore increase the plasma persistence of Hb, and second, to decrease its oxygen affinity. However, despite the cross‐linking, the vascular retention time is only increased by a factor of three, and a supplementary modification of cross‐linked Hb is needed in order to further improve its in vivo half‐life. The Hb derivatives described in this paper were obtained by the covalent fixation of benzene tetracarboxylate‐substituted dextran onto oxyHb. The resulting conjugates all exhibited a higher P50than native Hb. The experiments carried out in the presence of inositolhexaphosphate showed that the allosteric sites of Hb molecules were occupied by the polymeric reagent. The important decrease in the Bohr effect and the lack of the Cl−effect on the oxygen‐binding properties proved that the Val 1α residue was also substituted. Finally, the ability of some conjugates to unload as much O2as blood, together with their other properties, make them quite promising candidates as red cell substitutes. © 1993 Joh

ISSN:0006-3525    

DOI:10.1002/bip.360331206

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1993

数据来源: WILEY

摘要:

AbstractA molecular mechanics study of polydehydroalanine [poly‐(Δ Ala)] is presented. For this purpose the AMBER 3a program has been used to perform the calculations. With exception of the point charges, the parameters for the terminal groups were taken from AMBER 3a libraries, whereas those for the Δ Ala residue from Alagona et al. [J. Comp. Chem.(1991) Vol.12, pp. 934–942]. Charges for the residue and terminal groups have been fitted from the MNDO electrostatic potential and scaled to achieve an ab initio 6‐31G* quality. Calculations have been carried out using the continuous solvent approximation with three different dielectrics ε = 1, 1r, and 4r. The results show that, despite the preferred structure for the isolated residue is an extended conformation, a 310‐helix is the preferred conformation in the solid state (ε = 1 and 1r), whereas a peculiar structure with ψ = 0° is preferred with ε = 4r. © 1993 John

ISSN:0006-3525    

DOI:10.1002/bip.360331207

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1993

数据来源: WILEY

摘要:

AbstractThe interaction of calf thymus DNA with Cu2+and Pb2+was studied in aqueous solution at pH 6.5 with metal/DNA (P) (P = phosphate) molar ratios (r) 1/80, 1/40, 1/20, 1/10, 1/4, 1/2, and 1, using Fourier Transform ir (FTIR) spectroscopy. Correlations between the ir spectral changes, metal ion binding mode, DNA condensation, and denaturation, as well as conformational features, were established.Spectroscopic evidence has shown that at low metal/DNA (P) molar rations 1/80 and 1/40, copper and lead ions bind mainly to the PO 2−of the backbone, resulting in increased base‐stacking interaction and duplex stability. The major copper ion base binding via G‐C base pairs begins atr>1/40, while the lead ion base binding occurs atr>1/20 with the A‐T base pairs. The denaturation of DNA begins atr= 1/10 and continues up tor= 1/2 in the presence of copper ions, whereas a partial destabilization of the helical structure was observed for the lead ion at high metal ion concentration (r= 1/2). Metal‐DNA binding also results in DNA condensation. No major departure from the B‐family structure was observed, upon DNA interaction with these metal ions. © 1993 John W

ISSN:0006-3525    

DOI:10.1002/bip.360331208

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1993

数据来源: WILEY

摘要:

AbstractA procedure is developed and applied to characterize the globalshapeandfolding featuresof the backbone of a chain molecule. The methodology is based on the following concept:the probability of observing a rigid placement of a backbone in 3‐space as a projected curve withNovercrossings.The numerical computation of these probabilities allows one to construct theovercrossing spectrumof a macromolecule at a given configuration. Although the spectrum is built from the knowledge of the nuclear geometry of the main‐chain atoms, the shape descriptor overlooks local geometrical features (such as distances and contacts) and provides a characterization of essential (topological) features of the overall fold, such as its compactness and degree of entanglement. In contrast with other shape descriptors, the present approach gives an absolute characterization of the configuration considered, and not one that is relative to an arbitrarily chosen reference structure. Moreover, it is possible to discriminate between folding features that otherwise may not be distinguished when using other geometrical or topological global descriptors. The overcrossing spectrum is proposed as a tool that complements current structural analyses of macromolecules, especially when monitoring structural homologies within a group of related or unrelated polymers. In this work, we apply the methodology to the analysis of proteins having the globin fold. The results are compared with those of other proteins exhibiting similar size and number of residues. Some basic properties of the spectra as a function of the chain length are also discussed. © 1993 John Wiley&Sons,

ISSN:0006-3525    

DOI:10.1002/bip.360331209

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1993

数据来源: WILEY

摘要:

AbstractIn this paper, we explore the possibility of using experimental observations in the Monte Carlo chain growth method that we have previously developed. In this method, the macromolecule (peptide, protein, nucleic acid, etc.) is grown atom‐by‐atom (or residue‐by‐residue, etc.) and partial chains are replicated according to their Boltzmann weights. Once the molecule completed, we are left with a Boltzmann‐distributed ensemble of configurations. For long molecules, an efficient sampling of the (extremely large) phase space is difficult for obvious reasons (existence of many local minima, limited computer memory, etc.). In the case in which one is mainly interested in the low energy conformations, we have incorporated in the growth scheme experimental observations taken from the Protein Data Banks. More precisely, we have considered the case of twenty‐L‐alanine and we have used the (experimental) Ramachandran's plot for this residue. The biased growth procedure goes as follows: (a) each time one adds along the main backbone chain, either a carbon atom belonging to a carbonyl group, or a nitrogen atom, its dihedral angle (ϕ) or (ψ) is drawn with a probability law that reflects the experimental Ramachandran (ϕ,ψ) plot; (b) the bias introduced in this way is canceled through an extra term in the energy (replication energy = true energy + bias energy); (c) the configurations, generated atT= 1000 K, are then energy minimized. We have worked with an all‐atom CHARMM force field, and Ramachandran's plot for the alanine was modeled through three angular zones (α‐helix, β‐sheet, coil). In our calculations, the probabilities of the α (pα) and β (pβ) regions have been varied in large proportions (pαbetween 0.64 and 0.19, the “experimental” value being 0.59). The results, based on 35 “unbiased” and 25 “biased” (or “guided”) distinct minimized configurations clearly demonstrate the efficiency of the method. The low energy configurations, for all tested values ofpα, have a total (or almost total) a helix content. The unbiased configurations have much higher energies (in general, even higher than the left‐handed helix). Note that the method is not “α helix in‐α helix out,” since working atT= 300 K with the experimental (pα= 0.59) value yields configurations partially frozen in aC ed7alanine

ISSN:0006-3525    

DOI:10.1002/bip.360331210

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1993

数据来源: WILEY

摘要:

AbstractThe effect of the solvent in the molecular properties of DNA bases has been explored by using a self‐consistent reaction field (SCRF) method based on the AM1 (Austin Model 1) Hamiltonian and a modified version of the high level Miertus–Scrocco–Tomasi (MST) algorithm. MST/AM1 estimates of free energies of hydration compare qualitatively well with the available experimental data, as well as with the results obtained from molecular dynamic simulations. Furthermore, the changes in the dipole predicted by the MST/AM1 method are in good agreement with Monte Carlo/quantum mechanical data, as well as with AM1‐SM2 (Soluation Model 2) estimates. AM1/MST calculations of Mulliken, and electrostatic charges, dipoles, molecular electrostatic potentials and molecular interaction potentials in both vacuum and solution allowed us to quantify the effect of the water on the reactive characteristics of the DNA bases. This effect is large and complex, and cannot be neglected in theoretical calculations where an accurate representation of the DNA bases is needed. The possibility of including the polarization effect of the water into force‐field simulations of DNA structures is discussed. © 1993 John Wiley

ISSN:0006-3525    

DOI:10.1002/bip.360331211

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1993

数据来源: WILEY