摘要:

AbstractThe peptides Ac‐ΔPhe‐Ala‐ΔPhe‐NHMe (1), Ac‐ΔPhe‐Val‐ΔPhe‐NHMe (2), Ac‐ΔPhe‐Gly‐ΔPhe‐Ala‐OMe (3), and Boc‐Ala‐ΔtPhe‐Gly‐ΔPhe‐Ala‐OMe (4), containing two dehydro‐phenylalanine (ΔPhe) residues, were synthesized and the solution structure investigated in various solvents. The nmr and CD measurements indicate that all the dehydropeptides examined adopt 310‐helical conformations in solution. The tripeptides1and2exibited an intense negative CD exciton couplet, which was assigned to the right‐handed screw sense, while the tetrapeptide3displayed a CD couplet having opposite sign, which was assigned to the left‐handed helical sense. In the pentapeptide4the sense of the helix was found to vary with solvent and temperature, as demonstrated by the sign reversal of the CD spectrum. The right‐handed sense dominates in hexafluoro‐2‐propanol, whereas a left‐handed helix prevails in chloroform, acetonitrile and methanol. A crucial role for this behavior is likely to be played by the two alanine residues positioned respectively at the head and tail of the sequence, which favor confo

ISSN:0006-3525    

DOI:10.1002/bip.360330102

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

年代:1993

数据来源: WILEY

摘要:

AbstractPartial compressibilities of globular proteins in water are reviewed. Contribution of hydrational and of intrinsic compressibilities to experimental partial quantity have been evaluated from ultrasonic data using two independent methods: (a) additive calculation of the hydrational contributions of the surface atomic groups and (b) an analysis of correlation between partial compressibility and molecular surface area. The value (14 ± 3) × 10−6bar−1for the isothermal compressibility coefficient of the protein interior at 25°C was obtained as an average value for variety of globular proteins. This value is similar to that of solid organic polymers. Possible relaxation contribution to partial compressibility is roughly estimated from comparison of thermodynamic with x‐ray data on protein compressibility. The average compressibility of water in the hydration shell of proteins was found to be 35 × 10−6bar−1, which is 20% less than that of pure water. © 1993 John W

ISSN:0006-3525    

DOI:10.1002/bip.360330103

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

年代:1993

数据来源: WILEY

摘要:

AbstractOne‐dimensional and two‐dimensional (2D) nmr experiments were carried out on an oligonucleotide duplex that contains an unpaired cytosine, d(GCGAACAAGCG)·d(CGCTTTTCGC), which will be referred to as the C‐bulge decamer. Evidence from one‐dimensional nuclear Overhauser effect (NOE) experiments on the exchangeable protons indicates that the unpaired cytosine is extrahelical. This conclusion is also supported by numerous cross‐peaks in the 2D NOE spectroscopy (NOESY) spectrum of the nonexchangeable protons. The assignments for all of the resonances, with the exception of the H5′ and H5″ resonances, have been made through the use of 2D NOESY, correlated spectroscopy (COSY), and relayed COSY experiments. The temperature dependence of the C(H6) resonance chemical shifts indicates that the unpaired cytosine shows unusual behavior compared to other cytosines in the duplex. A comparison of chemical shifts for all, the assigned resonances of the duplexes with and without the unpaired cytosine suggests that the majority of the structural perturbation is localized in the A·T tract surrounding the unpaired base. The behavior of the imino resonances as a function of temperature also indicates that the perturbation to the duplex is localized and destabilizes the A·T base pairs adjacent to the unpaired base. © 1993 Joh

ISSN:0006-3525    

DOI:10.1002/bip.360330104

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

年代:1993

数据来源: WILEY

摘要:

AbstractThe influence of sugar ring flexibility in DNA on the mechanism of theB⇄Aconformational transition is studied. The dipole moment of the deoxyribose as a function of its puckered states is calculated by the quantum‐mechanical method using the MINDO/3 approximation. The interaction of the sugar dipole with the neighbor molecular groups in polynucleotide chains is estimated. The sugar dipole interaction with phosphate groups and counterions is shown to be strong and capable to deform the pseudorotation potential of deoxyribose. The effective pseudorotation potential of sugar ring in theBandAhelices is obtained. The results are used to explain the behavior of Raman bands in the region of sugar–phosphate vibrations. The mechanism of the effect of electrostatic forces on the sugar–phosphate backbone conformation, which is essential for theB⇄Aand other structure transitions, is offered. © 1993 John Wiley

ISSN:0006-3525    

DOI:10.1002/bip.360330105

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

年代:1993

数据来源: WILEY

摘要:

AbstractA theory describing the shapes of polarized fluorescence photobleaching recovery (PFPR) curves for a population of fluorophores undergoing restricted rotational diffusion in two‐dimensional systems such as planar membranes has been developed. In this model, restricted rotational diffusion of the fluorophores is described by using reflective boundary conditions, in which the fluorophores are assumed to diffuse freely but only within an angular space of width 2ω. The magnitude and apparent rate of the PFPR postbleach fluorescence curves are a function of both ω and the angle between the bleaching and observation beam polarizations ψ. It is shown that estimates of the degree of rotational restriction ω may be obtained from changes in the ψ‐dependent postbleach fluorescence intensities.Using angle‐dependent PFPR, slow rotational reorientations of the fluorescent lipid analogue 1,1′‐dioctadecyl‐3,3,3′,3′‐tetramethylindocarbocyanine in distearoylphosphatidylcholine Langmuir–Blodgett monolayers deposited on octadecyltrichlorosilane‐treated fused quartz were measured. As theoretically predicted for a rotationally restricted fluorophore population, both the initialFψ(0) and finalFψ(∞) postbleach fluorescence intensities varied as a function of ψ, and no measurable change in the postbleach fluorescence intensities was observed for ψ = 45°. Using the theory for restricted rotational motion, the ψ‐dependent variations of the final fluorescence intensitiesFψ(∞) obtained at two bleaching intensities gave an average apparent ω ≈︁ 52°. However, to adequately fit theFψ(0) data, inclusion of the theoretical effects of rapid (faster than the duration of the photobleaching pulse) fluorophore dynamics was also required. Best fits of theFψ(0) andFψ(∞) data were obtained when the fluorophores were assumed to rapidly wobble within a cone of semiangle δ ≈︁ 30°–50° while slowly rotating within an angular space defined by semiangle ω ≈︁ 35°–60°. Subsequent analysis of the time‐ and ψ‐dependent changes in the postbleach fluorescence curvesFψ(t) gave apparent diffusion coeff

ISSN:0006-3525    

DOI:10.1002/bip.360330106

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

年代:1993

数据来源: WILEY

摘要:

AbstractThe dipole moments of small protein molecules were determined experimentally in order to validate the calculated dipole moments by previous investigators. We found that the agreements are satisfactory for some proteins. There are, however, many proteins for which the agreement is less than satisfactory. In order to find the cause of the disagreement, the dipole moments of these proteins were recalculated using the Brookhaven Protein Data Bank. We calculated the dipole moment due to fixed surface charges and the bond moments of all the carbonyl groups in main chain and side chains. The calculation consists of the mean moments and their mean square fluctuations. In addition, we investigated the effect of electrostatic interactions between charged sites for several proteins. These results show that incorporation of the interactions does not affect substantially the calculated dipole moments. The rms fluctuation of the dipole moment is found to be small but not negligible. In conclusion, recalculated dipole moments are in good agreement with the observed values. © 1993 John Wiley&Sons, Inc

ISSN:0006-3525    

DOI:10.1002/bip.360330107

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

年代:1993

数据来源: WILEY

摘要:

AbstractSouthern bean mosaic virus (SBMV) is a spherical plant virus. It possesses an intrinsic (structural) anisotropy due to the orientation of valence bonds of the amino acid and/or nucleic acid residues. According to the light scattering theory of Rayleigh and Gans for optically anisotropic spheres, the degree of linear polarization of the scattered light depends on the intrinsic anisotropy, the relative refractive index of the sphere to the solvent, the scattering angle, and the inclination angle of linearly polarized incident light to the scattering plane. By using the theoretical expression of the degree of linear polarization, the intrinsic anisotropy parameter of southern bean mosaic virus in the compact spherical state was calculated with the appropriate experimental values. This novel method should be useful in elucidating the internal structure of spherical viruses and other spherical complexes of macromolecules. © 1993 John Wiley&Sons, Inc

ISSN:0006-3525    

DOI:10.1002/bip.360330108

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

年代:1993

数据来源: WILEY

摘要:

AbstractA Monte Carlo method has been developed for generating the conformations of short single‐stranded DNAs from arbitrary starting states. The chain conformers are constructed from energetically favorable arrangements of the constituent mononucleotides. Minimum energy states of individual dinucleotide monophosphate molecules are identified using a torsion angle minimizer. The glycosyl and acyclic backbone torsions of the dimers are allowed to vary, while the sugar rings are held fixed in one of the two preferred puckered forms. A total of 108 conformationally distinct states per dimer are considered in this first stage of minimization. The torsion angles within 5 kcal/mole of the global minimum in the resulting optimized states are then allowed to vary by ±10° in an effort to estimate the breadth of the different local minima. The energies of a total of 2187 (37) angle combinations are examined per local conformational minimum. Finally, the energies of all dinucleotide conformers are scaled so that the populations of differently puckered sugar rings in the theoretical sample match those found in nmr solution studies. This last step is necessitated by limitations in the theoretical methods to predict DNA sugar puckering accurately. The conformer populations of the individual acyclic torsion angles in the composite dimer ensembles are found to be in good agreement with the distributions of backbone conformations deduced from nmr coupling constants and the frequencies of glycosyl conformations in x‐ray crystal structures, suggesting that the low energy states are reasonable. The low energy dimer forms (consisting of 150–325 conformational states per dimer step) are next used as variables in a Monte Carlo algorithm, which generates the conformations of single‐stranded d(CXnG) chains, where X = A, T andn= 3, 4, 5. The oligonucleotides are built sequentially from the 5′ end of the chain using random numbers to select the conformations of overlapping dimer units. The simulations are very fast, involving a total of 106conformations per chain sequence. The potential errors in the buildup procedure are minimized by taking advantage of known rotational interdependences in the sugar–phosphate backbone. The distributions of oligonucleotide conformations are examined in terms of the magnitudes, positions, and orientations of the end‐to‐end vectors of the chains. The differences in overall flexibility and extension of the oligomers are discussed in terms of the conformations of the constituent dinucleotide steps, while the general methodology is discussed and compared with other nucleic acid model building techniques. © 1993 Jo

ISSN:0006-3525    

DOI:10.1002/bip.360330109

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

年代:1993

数据来源: WILEY

摘要:

AbstractAssignment of the hydrogen spectrum is the first step in the conventional procedure for the determination of molecular structure by1H‐nmr. In this paper, we explore the possibility of directly exploiting the distances derived from nuclear Overhauser effect experiments to generate a three‐dimensional structure that is then assigned based on knowledge of the connectivity or primary sequence. This effort is analogous to that of the protein crystallographers in tracing electron density of the peptide chain. In particular, we compare structures produced by distance geometry to known peptide secondary structures to see what level of information is required to “trace” the backbone α‐carbon and amide hydrogens and the β‐carbon hydrogens. We conclude that this approach is only useful with excellent quality stereo‐resolved data. © 1993 John

ISSN:0006-3525    

DOI:10.1002/bip.360330110

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

年代:1993

数据来源: WILEY

摘要:

AbstractWe have used a combination of densimetric, calorimetric, and uv absorption techniques to obtain a complete thermodynamic characterization for the formation of nucleic acid homoduplexes of known sequence and conformation. The volume change ΔVaccompanying the formation of four duplexes was interpreted to reflect changes in hydration based on the electrostriction phenomenon. In 10 mMsodium phosphate buffer at pH 7, the magnitude of the measured ΔV's ranged from −2.0 to +7.2 ml/mol base pair and followed the order of poly(rA) · poly(dT) ∼ poly(dA) · poly(dT)

ISSN:0006-3525    

DOI:10.1002/bip.360330111

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

年代:1993

数据来源: WILEY