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1.  A Description of the Techniques and Application of Molecular Replacement Used to Determine the Structure of Polyoma Virus Capsid at 22.5 Å Resolution 
The electron density map of polyoma virus capsid crystals solved at 22.5 Å resolution by molecular replacement [Rayment, Baker, Caspar & Murakami (1982). Nature (London), 295, 110–115] shows that the 72 capsomeres that form the polyoma capsid are all pentamers. An extensive series of refinement calculations were undertaken to demonstrate the validity of this unexpected result. This report describes the details of the data collection, structure determination and the tests of the methods applied. The refinement calculations demonstrate that the refined phases are insensitive to the initial phasing model for a wide variety of models. They also show that it is vital to include in the refinement calculations interpolated values for the unrecorded data. A variety of tests demonstrate that the all-pentamer structure of the polyoma capsid is determined by the diffraction amplitudes and the self-consistent constraint that the 72 capsomeres are arranged with icosahedral symmetry within a well defined limiting envelope.
PMCID: PMC4167719  PMID: 25242833
2.  Towards crystal structure prediction of complex organic compounds – a report on the fifth blind test 
Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologies was used by the participating groups in order to evaluate the ability of the current computational methods to predict the crystal structures of the six organic molecules chosen as targets for this blind test. The first four targets, two rigid molecules, one semi-flexible molecule and a 1:1 salt, matched the criteria for the targets from CSP2007, while the last two targets belonged to two new challenging categories – a larger, much more flexible molecule and a hydrate with more than one polymorph. Each group submitted three predictions for each target it attempted. There was at least one successful prediction for each target, and two groups were able to successfully predict the structure of the large flexible molecule as their first place submission. The results show that while not as many groups successfully predicted the structures of the three smallest molecules as in CSP2007, there is now evidence that methodologies such as dispersion-corrected density functional theory (DFT-D) are able to reliably do so. The results also highlight the many challenges posed by more complex systems and show that there are still issues to be overcome.
PMCID: PMC3222142  PMID: 22101543
3.  Electrostatic and aspheric influence of the fluoro-substitution of 4-bromodiphenyl ether (PBDE 3) 
Accurate structure determinations by X-ray crystal analysis and computation using semi-empirical self-consistent field molecular orbital calculations are described and compared for 4-bromodiphenyl ether (PBDE 3), the 13C6-isotopic labeled PBDE 3 (13C6-PBDE 3) and its five corresponding monofluorinated analogues (F-PBDEs 3): 2-fluoro-4-bromodiphenyl ether (F-PBDE 3-2F), 2′-fluoro-4-bromodiphenyl ether (F-PBDE 3-2′F), 3-fluoro-4-bromodiphenyl ether (F-PBDE 3-3F), 3′-fluoro-4-bromodiphenyl ether (F-PBDE 3-3′F) and 4′-fluoro-4-bromodiphenyl ether (F-PBDE 3-4′F). The synthesis and full characterization by means of 1H, 13C, 19F nuclear magnetic resonance spectroscopy and mass spectrometry of the F-PBDEs 3 are presented for the first time. Intermolecular interactions for PBDE 3 and the F-PBDEs 3 isomers were dominated by weak C-H(F,Br) ····π and C-H····F interactions. The bond lengths of C-F varied between 1.347(2) Å and 1.362(2) Å, C4-Br between 1.880(3) Å and 1.904(19) Å. Both correlated with electron-density differences as determined by 13C shifts, but not with the strength of C-F couplings. The interior ring angles at ipso-fluoro-substitution increased to 121.95° due to hyperconjugation by p-π-orbital overlapping, a phenomenon that was also computed. An attraction between the vicinal fluoro-and bromo-substituents was not determined, as seen in fluoro-substituted chlorobiphenyls. The torsion angles measured and computed for the series of PBDE 3 and F-PBDEs 3 differed strongly from each other. Since the ether linkage (an average of 2.76 Å) provides more distance and the bonds are flexible up to a certain range, the influence of a fluoro-substituent is only detectable in PBDEs with high ortho-substitution. A concordance of computed and measured torsion angles can be observed with increasing size and/or grade of substitution comparing mono- to tetra- fluoro-, chloro-, bromo- and methyl-substitutions in the ortho-positions of diphenyl ether. Differences between computational versus measured data demonstrates a strong need to evaluate the results against independent techniques to conclude structure receptor activity relationships of PBDEs. Any discussion of the Ah or other biological receptor activity of certain PBDEs should take this in consideration. For the first time a complete overview of known and hypothetical biological activities of PBDEs is presented.
PMCID: PMC3120100  PMID: 18204217
4.  Genetic and Genomic Public Health Strategies: Imperatives for Neonatal Nursing Genetic Competency 
Genetics and genomics are emerging as the central science for 21st century health care. Proficient nursing care incorporates this central science. Nursing genetic competency includes anticipating future demands spurred by knowledge advancement. Three emerging public health areas that call for future neonatal nursing genetic competency development will be discussed here: increasing emphasis on neonatal family health histories, population genetic biobanking, and family genetic advocacy. Neonatal nurses can develop genetic competency by targeting: 1) Collaborative efforts between nurse and family regarding neonatal family health history preparation and understanding its genetic implications; 2) Referrals to and partnerships with genetic advocacy groups in programs that empower neonate's families; 3) Familiarity with biobank practices that interface nursing care domains.
PMCID: PMC2391006  PMID: 12324686

Results 1-4 (4)