Library

X
feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
  • 1
    Electronic Resource
    Electronic Resource
    Solvent structure in vitamin B12 coenzyme crystals (1985)
    Springer
    European biophysics journal 11 (1985), S. 225-237 
    Details
    ISSN: 1432-1017
    Keywords: Solvent structure ; hydrogen bond networks ; computer simulation ; B12 coenzyme crystals ; probability density
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract Both the ordered and disordered solvent networks of vitamin B12 coenzyme crystal hydrate have been generated by Monte Carlo simulation techniques. Several different potential functions have been use to model both water-water and water-solute (i.e., water-coenzyme) interactions. The results have been analysed in terms of the structural properties of the water networks, such as mean water oxygen and hydrogen positions, coordination of each water molecule, and maxima of probability density maps in all four asymmetric units of this crystal. The following results were found: (I) Within each asymmetric unit only one hydrogen bonding network was predicted although there were several hydrogen atom positions for any one solvent molecule (defined as maxima in probability density). (II) Reasonable agreement was obtained between predicted and experimental positions in the ordered solvent region, independent of the potential function used. (III) The positions of the calculated probability density maxima for the disordered channel region were different in different asymmetric units; this led to different simulated hydrogen bond networks which were not always consistent with the experimentally determined alternative (lower occupancy) sites. The results suggest that it is advisable to simulate more than one asymmetric unit if one wishes to look at disorder in the solvent regions. Probability density maps were qualitatively very useful for picturing these disordered regions. However, there were no significant differences between quantitative results predicted using either average atomic positions or maxima of the probability density distributions. Problems in quantifying agreement between experimental and predicted disordered solvent networks are discussed. The potential which included hydrogen atoms explicitly (EMPWI) seemed to give the best overall agreement, mainly because it was successful in predicting the unusually short hydrogen bonds which are found in this crystal.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00261999
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 2
    Electronic Resource
    Electronic Resource
    Biomolecular energy calculations using transputer technology (1989)
    Springer
    European biophysics journal 17 (1989), S. 167-172 
    Details
    ISSN: 1432-1017
    Keywords: Transputer ; Occam 2 ; tyrosine ; peptide ; energy ; minimisation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract We report an application of current parallel processing transputer technology which has readily achieved a 25-fold reduction in computational time of peptide-solvent interactions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00254771
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 3
    Electronic Resource
    Electronic Resource
    Applications of synchrotron radiation to protein crystallography. II. Anomalous scattering, absolute intensity and polarization (1977)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 33 (1977), S. 445-455 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The synchrotron X-ray beam produced by the SPEAR storage ring at the Stanford Linear Accelerator Center has been used as a tuneable and intense source for single-crystal-protein diffraction experiments. A measurement of the absolute intensity of a focused, monochromatized X-ray beam gave a value of 3 × 109 photons s-1 at a wavelength of 1.74 Å for typical machine operating conditions. A series of hk0 precession photographs were obtained from a crystal of the Fe-containing protein rubredoxin to investigate anomalous scattering effects and study their use in phase determination. Seven discrete wavelengths of radiation were used, some above and some below the Fe K absorption edge (1.743 Å = 7.111 keV). The rubredoxin diffraction data showed intensity changes due to f' varying with wavelength as well as from Bijvoet differences. The Fe site could be correctly located from difference Patterson and Fourier maps based either on f' or f”. The signal to noise ratio at the iron site was enhanced by calculating combined f' and f” maps. The phases of the Bragg reflections were also obtained from three films collected at different wavelengths. When compared with the known phases for rubredoxin, the differences average to 60°, which indicates that some phasing information was available even from the relatively poor data and that this method will be potentially useful in future applications. A method for calculating the Lp factor which has to be applied to precession photographs taken with the polarized synchrotron X-ray beam is described in the Appendix.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0567739477001168
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 4
    Electronic Resource
    Electronic Resource
    Effect of molecular shape and electrostatic interactions on the water layer around polar and apolar groups in solution (1999)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 110 (1999), S. 7943-7950 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We have carried out neutron diffraction using hydrogen/deuterium isotope substitution and molecular dynamics simulations in order to investigate intermolecular water structure in aqueous solutions of phenol, ethanol, propanoic acid, and glucose. Partial radial distribution functions (rdfs) calculated from both experiment and simulation are compared. These show good overall agreement although the simulation gives more structure than the experimental data in the intramolecular region. From the simulation, the relative number of water molecules coordinated to different chemical groups are calculated and the three-dimensional water density around the different chemical groups on the solute molecule is obtained. For both the experimental and simulated rdfs the intermolecular region is relatively featureless but the simulated water structure shows significant differences between the water coordination around polar and apolar groups. The water is strongly coordinated to the polar groups (OH and COO−), although the hydroxyl groups have fewer close waters than would be possible if all hydrogen bonds were satisfied. There is little evidence for stable water networks around apolar groups. There is also some evidence that the polarized regions of the solutes influence the water coordination around neighboring apolar groups. Apart from the relatively strong polar interactions, the overall shape of the solute molecule is the most important determinant of the shape of the hydration shell. In the case of glucose, the OH groups take part in a well-defined hydrogen-bonded network around the glucose molecule which incorporates the solute molecule in a similar way to water molecules. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.478699
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 5
    Electronic Resource
    Electronic Resource
    Small-angle X-ray and neutron diffraction from corneal stroma (1978)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 11 (1978), S. 496-496 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The corneal stroma is a connective tissue which combines the usual properties of strength and resilience with one property, transparency, unusual in such tissues. Several models have been put forward to account for this transparency, these differ in detail but in almost all cases the regularity of arrangement of the collagen fibrils is taken to be an important parameter of the model (Maurice, 1957; Farrell & Hart, 1969; Benedek, 1971). So far the only experimental evidence about this arrangement comes from electron microscopy, and we have therefore applied small-angle diffraction techniques because they involve less preparative procedures which might cause artifacts.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889878013709
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 6
    Electronic Resource
    Electronic Resource
    DNA conformation and dynamics (1999)
    Springer
    Radiation and environmental biophysics 38 (1999), S. 23-29 
    Details
    ISSN: 1432-2099
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract Nucleotide conformation and dynamics are important for the study of radiation damage to DNA at the atomic level. It is necessary to study not only normal oligonucleotide structure but also those containing modified bases which result from interaction with OH-radicals. There are now over 8000 atomic coordinate entries in the Brookhaven Protein Data Bank, of which over 900 relate to experimentally determined structures of nucleic acids and nucleic acid/protein complexes. We review some of these data which have led to the elucidation of novel DNA conformations, insight into DNA sequence specificity and knowledge of protein/DNA interactions. Further understanding of the conformation, stability and dynamics of nucleic acids has come from molecular modelling. We have used such techniques to study chemical modifications to bases such as alkylation of thymine and guanine and the effects of curvature in longer sequences. Recent improvements in this area include the inclusions of explicit counter-ions and solvent molecules, the use of Particle Mesh Ewald methods to incorporate the long-range electrostatic interactions and the use of longer time scale simulations. We have employed these methods to analyse the effects of incorporation of 8-oxodeoxyguanosine into duplex DNA. This lesion is a common result of radiation damage and is known to have important effects in mutagenesis, cancer and ageing.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004110050134
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...