摘要:

AbstractEnergy minimization has been carried out on three poly(purine) · poly(pyrimidine) sequences—d(G)10· d(C)10, d(A)10, d(T)10and d(AG)5· d(CT)5—using the molecular mechanics program AMBER (Assisted Model Building and Energy Refinement). In order to extensively scan the conformational space available, five different helical models were studied, three of them being right‐handed helices while the other two were left helical. For all three sequences the right‐handed A‐ and B‐type helices are energetically slightly preferred over the left helices, but the energy difference between the various right‐handed helices is only marginal. A detailed analysis has been carried out to characterize the local structural variability in the refined structures, both in terms of torsion angles as well as other parameters such as base‐pair tilt, wedge roll, and wedge tilt, etc. All three sequences exhibit similar structural features for a particular form, but both the forms A and B show significant deviations from fiber models. In particular, the A‐form structures have higher unit rise (2.7 Å), and lower unit twist (31°) and base‐pair tilt (12°), compared to the fiber model, which has corresponding values of 2.56 Å, 32.7°, 20°, respectively. All these changes indicate that the refined models are closer to the A‐form structure observed in crystals of oligonucleotides. In the refined B‐for models, the helical parameters are close to the fiber B‐form, although the torsion angles show considerable variations. None of the three sequences examined, including the d(A)n· d(T)nsequence, show any pronounced

ISSN:0006-3525    

DOI:10.1002/bip.360280202

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

年代:1989

数据来源: WILEY

摘要:

AbstractWe have investigated the site and conformational preference of the reaction of a formaldehyde/amine reagent with DNA. Previous investigations of this laboratory have established that this reagent will react with native DNA, placing a positively charged amine moiety on the duplex that will survive exhaustive dialysis. The resulting adduct is duplex and base stacked in character, possessing B backbone geometry with a higher average winding angle and exhibiting remarkable stability with respect to the A‐form, Z‐form, or the single‐strand denaturated species. In this current investigation, we have found that the stability of the adduct is dramatically reduced if the DNA is converted to mononucleotides, thus obviating the usual approach of nuclease digestion and chromatography for the identification of the modified nucleotides. Using indirect approaches, we have established that the reactive site that survives removal of the equilibrium concentrations of CH2O and amine is the exocyclic amino group of the guanine bases. This conclusion is based on (1) the positive correlation between GC content and the extent of of adduct formation under standard reaction conditions (27°C, 0.63MCH2O, 0.007Mn‐butylamine, pH 7); (2) decreases in the level of substitution of amine in DNA, which has this site blocked by trinitrobenzene modification; and (3) failure of poly(dI‐dC) to retain amine upon dialysis. Raman spectra of the derivatized poly(dG‐dC) show enhanced 2′‐endoB character, with no marked shifts in the position of any of the lines, indicating the absence of any ring structures involving the N7 and the 06 of G. In standard reaction mixtures, other sites may react but this phenomenon appears to be minimal under conditions that do not favor fluctuational opening of base pairs. In the latter case, excess loading of amine on high GC content polymers produces a CD spectrum that is similar to one produced by poly(dA‐dT) in the “X”‐form [M. Vorlickova, E. Minyat, and J. Kypr (1984)Biopolymers23, 1–4]. This conformation is lost, however, upon removal of excess reagents by dialysis and cannot be reestablished, in the absence of unbound amine and formaldehyde. The reaction is specific for the B‐form of polynucleotides as demonstrated by the failure of poly(dG‐m5dC) in the stable Z‐form to exhibit substantial reaction. The B‐form of this polymer will react readily with the retention of 0.23 moles amine/mole nucleotide under our standard reaction conditions. Although retaining B‐form geometry, this adduct will lose significant amounts of amine when exposed to conditions that stabilize the Z‐form. This behavior is in contrast to that previously reported for poly(dG‐dC), which retains both the B‐form and all of its amine content under equivalent conditions. The present results reflects the greater Z‐forming potential of the methylated polymer. These observations lead us to the conclusion that the B‐form provides a GC locus that favors site binding of cations in the minor groove and stabilizes B geometry. This specific site is lost in the B → Z conversion. Thus, the cationic interactions that s

ISSN:0006-3525    

DOI:10.1002/bip.360280203

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

年代:1989

数据来源: WILEY

摘要:

AbstractThe conformation of cyclolinopeptide A [cyclo(Pro–Pro–Phe–Phe–Leu–Ile–Ile–Leu–Val)], a naturally occurring cyclic nonapeptide has been investigated in dimethylsulfoxide solution by 270 MHz1H‐nmr. A complete assignment of all CαH and NH resonances has been accomplished using two‐dimensional correlated spectroscopy and nuclear Overhauser effects (NOEs). Analysis of interresidue NOEs andJ HNC αHvalues permit construction of a molecular model for the cyclic peptide backbone. The crude model derived from nmr has been used as a starting point for energy minimization, which yields a refined structure largely compatible with nmr observations. The major features of the conformation of cyclolinopeptide A are a Type VI β‐turn centered at Pro(1)‐Pro(2), with acispeptide bond between these residues and a γ‐turn (C7) structure centered at Ile(6). Two intramolecular hydrogen bonds Val(9) CO—Phe(3)NH (4 → 1) and Leu(5) CO—Ile(7)NH (3 → 1) are observed in the low‐energy conformation. The limited solvent accessibility observed for the Val(9) and Leu(5) NH groups in the nmr studies ar

ISSN:0006-3525    

DOI:10.1002/bip.360280204

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

年代:1989

数据来源: WILEY

摘要:

AbstractFormation and thermodynamic characteristics of CH ⃛ O hydrogen bonding of methylated uracils and caffeine have been studied by nmr along two lines.1The concentration and temperature dependencies of the PMR spectra of 1,3‐dimethyluracil (m21,3Ura), 1,3‐dimethylthymine (m21,3Thy), and 1,3,6‐trimethyluracil (m31,3,6Ura) in chloroform at high concentrations of base analogs indicated the self‐association of m21,3Ura and m21,3Thy via C(6)H ⃛ O hydrogen bonding and the competitive formation of CH ⃛ O bonds between carbonyl oxygens and chloroform. The intermolecular interaction energy and the arrangement of molecules in the local minima of various m21,3Ura dimers were calculated by the method of atom‐atom potentials. The deepest minimum for the m21,3Ura coplanar dimer corresponds to a C(6)H ⃛ O hydrogen‐bond formation.2At low concentration of m21,3Ura and caffeine in CCl4, C(6)H ⃛ O bonding for m21,3Ura and C(8)‐H ⃛ O bonding for caffeine with oxygens of dimethyl sulfoxide (DMSO) and acetone were observed. The association constants of these complexes were obtained at different temperatures. The enthalpies ΔH, of the m21,3Ura–DMSO, m21,3Ura–accetone, caffeine–DMSO, and caffeine–acetone complexes were −2 ⃛ 0.1 kcal/mol. The calculations showed that the deepest minimum of the caffeine‐acetone coplanar complex corresponds to C(8)H ⃛ O bonding with energy of −3.5 kcal/mol and that of the m21,3Ura‐acetone complexes corresponds to C(6)H ⃛ O bonding with energy of −3.4 kcal/mol. The approximate correction for the solvent effect provides

ISSN:0006-3525    

DOI:10.1002/bip.360280205

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

年代:1989

数据来源: WILEY

摘要:

AbstractThe ion‐exchange transition of Na‐DNA → H‐DNA in concentrated salt‐free solutions is accompanied by strong variations in CD spectra. The rotational force of the negative band |Δε249| decreases when going to H‐DNA by about 4 times, and the value of Δε279, by 1.2 times. These changes are irreversible to a considerable extent, which is evident because the spectra of Na‐DNA obtained by neutralizing isoionic H‐DNA solutions with NaOH or by the ion‐exchange method significantly differ from those of Na‐DNA taken by dissolving solid Na‐DNA in deionized water. It has been shown that additions of NaCl to an isoionic solution of DNA leads to variations of spectra, typical for deprotonation processes as well as for an

ISSN:0006-3525    

DOI:10.1002/bip.360280206

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

年代:1989

数据来源: WILEY

摘要:

AbstractOptical rotation data indicate that xanthan can exist both in an ordered and a disordered conformation. Using molecular weights obtained from light scattering measurements and contour length distributions obtained from electron micrographs, we find that a native, filtered xanthan exposed to low salinity (<10−4MNaCl) and subsequently returned to 0.1MNaCl has a highly elongated structure with a mass per unit length of 1950 ± 200 Dalton/nm. Our data thus suggest that the ordered conformation of this xanthan is double stranded. We find that native, filtered xanthan in 0.1MNH4Ac has a nearly similar structure, but exists in part as aggregates of varying shape and size. Electron micrographs of these xanthans in 10−4MNH4Ac (the disordered conformation) display a mixture of species ranging from unaggregated single‐ or perfectly matched double‐stranded species, to double‐stranded chains branching into its two subunits as well as double‐stranded chains with different degrees of mismatching. This study suggests that the perfectly matched antiparallel or parallel double‐stranded chain constitutes the lowest free energy state of the ordered conformation of xanthan in dilute aq

ISSN:0006-3525    

DOI:10.1002/bip.360280207

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

年代:1989

数据来源: WILEY

摘要:

AbstractThe thermal conformational transitions of two sonicated samples of schizophyllan were studied in water‐dimethylsulfoxide (DMSO) mixtures by high‐sensitivity differential scanning calorimetry (DSC). Two transitions were observed over most of the range of solvent compositions. These were assigned to an internal change of the triple helix [T. Itou et al. (1986)Macromolecules19, 1234–1240] and a triple‐helix–single‐coil transition [T. Sato et al. (1981)Carbohydr. Res.95, 195–204], respectively. In water, the former transition observed at lower temperature for a low molecular weight sample, U‐1, is centered at 3°C and characterized by the specific enthalpy, Δhcal= 3.29 J g−1. A higher molecular weight sample, M‐2, showed this transition at 7°C with Δhcal= 4.39 J g−1. The transition temperature for both samples increased with increasing DMSO concentration up to about 50°C at 70 weight % DMSO, and then rapidly decreased with increasing DMSO concentration, with about 3°C higher for M‐2 than for U‐1 over the DMSO concentration. The transition was not observed when the concentration of DMSO exceeded 87%. It was found that Δhcalfor both samples was a linear function oft1/2, the temperature of half‐completion in °C, Δhcal= 0.177t+ 2.96. The triple helix‐coil transition was observed at around 127°C for U‐1 and above 130°C for M‐2 in the range of DMSO composition below about 70%. The transition temperature decreased with increasing DMSO concentration at above 70%, and the transition finally disappeared when the DMSO concentration exceeded 90%. The plot of Δhcalvs.t1/2for the transition of both samples gave a linear relation, Δhcal= 0.253t– 10.58. The reversibility of the transition at lower temperature was demonstrated by the reversibility of the curves when the first heating was stopped before the second transition. Once the heating was performed over the second transition, the reheating DSC curves showed several endothermic peaks, indicating the irreversibility of the transition and heterogeneity

ISSN:0006-3525    

DOI:10.1002/bip.360280208

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

年代:1989

数据来源: WILEY

摘要:

AbstractThe diffusion coefficients of monodisperse polystyrene latex spheres in solutions of polymerized actin were measured using dynamic light scattering. Four different probes with radiiR, ranging from 50 to 500 nm, were separately used in actin solutions with concentrationsc, ranging from 1.5 to 21 μM, which had been polymerized with either 1 mMMgCl2, 1mMCaCl2, or 100 mMKCl. Under all conditions, and at four different scattering angles in the range of 30°–90°, the measured average diffusion coefficientsDof the probes were systematically smaller for samples of increased actin concentration or of increased probe radius. Control experiments indicated that the probes did not bind to the actin. These data for Mg2+‐ and Ca2+‐polymerized actin agree and were found to be quite well summarized by the scaling relationD/D0= exp[–αRδCν], whereD0is the measured diffusion coefficient of the probes in water (and, as also measured, in the starting actin solutions prior to polymerization with added salt), with values of δ = 0.73 ± 0.05, ν = 1.08 ± 0.09, and α = (1.1 ± 0.6) × 10−3(withcin μMandRin nm). Data for KCl‐polymerized actin show much more restricted diffusivities of the probes at comparable actin concentrations. Inhomogeneities in the solution are reflected in the “effective polydispersity” of the probe diffusion coefficients, which depend on loc

ISSN:0006-3525    

DOI:10.1002/bip.360280209

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

年代:1989

数据来源: WILEY

摘要:

AbstractNormal modes of vibration of DNA in the low‐frequency region (10–300 cm−1interval) have been identified from Raman spectra of crystals of B‐DNA [d(CGCAAATTTGCG)], A‐DNA [r(GCG)d(CGC) and d(CCCCGGGG)], and Z‐DNA [d(CGCGCG) and d(CGCGTG)]. The lowest vibrational frequencies detected in the canonical DNA structures—at 18 ± 2 cm−1in the B‐DNA crystal, near 24 ± 2 cm−1in A‐DNA crystals, and near 30 ± 2 cm−1in Z‐DNA crystals—are shown to correlate well with the degree of DNA hydration in the crystals structures, as well as with the level of hydration in calf thymus DNA fibers. These findings support the assignment [H. Urabe et al. (1985)J. Chem. Phys.82, 531–535; C. Demarco et al. (1985)Biopolymers24, 2035–2040] of the lowest frequency Raman band of each DNA to a helix mode, which is dependent primarily upon the degree of helix hydration, rather than upon the intrahelical conformation. The present results show also that B‐, A‐, C‐, and Z‐DNA structures can be distinguished from one another on the basis of their characteristics Ramanintensityprofiles in the region of 40–140 cm−1, even through all structures display two rather similar and complex bands centered within the intervals of 66–72 and 90–120 cm−1. The similarity of Raman frequencies for B‐, A‐, C‐, and Z‐DNA suggests that these modes originate from concerted motions of the bases (librations), which are not strongly dependent upon helix backbone geometry or handedness. Correlation of the Raman frequencies and intensities with the DNA base compositions suggests that the complex band near 90–120 cm−1in all double‐helix structures is due to in‐plane librational motions of the bases, which involve stretching of the purine‐pyrimidine hydrogen bonds. This would explain the centering of the band at higher frequencies in structures containing G ⃛ C pairs (>100 cm−1) than in structures containing A ⃛ T pairs (<10

ISSN:0006-3525    

DOI:10.1002/bip.360280210

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

年代:1989

数据来源: WILEY

摘要:

AbstractExperimentally observed solution conformations of carbohydrate molecules might correspond to a dynamical average of several interconverting conformers in solution. In order to understand and describe more precisely molecular flexibility and motions, new computational routes have to be envisaged. Compared to conventional approaches where sugar residues are treated as rigid, the optimization of all the internal parameters—i.e., bond angles, valence angles, and all torsional angles—is an important step toward more realistic information. Here we report the calculations of potential energy surfaces where all the internal coordinates of the molecules were “relaxed” and minimized through an extensive molecular mechanics scheme. For this work, a prototypical carbohydrate system, the disaccharide α‐maltose, was selected. The inclusion of the relaxed principle into conformational description of maltose does not generally alter the overall shape of the allowed low‐energy regions, or the position of the local minima. However, flexibility within the ring plays a crucial role. Its principle effect is the lowering of energy barriers to conformational transitions about the glycosidic bonds, permitting pathways among the low‐energy minima. This occurs with retaining the overall4C1conformation of the glucose residues. The torsional angles corresponding to the orientations of the hydroxyl groups, especially the primary hydroxyl ones, display stable arrangements separated by energy barriers. They create subpopulations of stable conformers and it has not been possible to take into consideration interconversion of one subpopulation to another one. A “synthetic” relaxed potential energy surface is proposed, which can provide a realistic starting base for further investigation of solution behavior of d

ISSN:0006-3525    

DOI:10.1002/bip.360280211

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

年代:1989

数据来源: WILEY