Developments in X-ray Crystallographic Structure Determination of Biological Macromolecules

@article{Garman2014DevelopmentsIX,
  title={Developments in X-ray Crystallographic Structure Determination of Biological Macromolecules},
  author={E. Garman},
  journal={Science},
  year={2014},
  volume={343},
  pages={1102 - 1108}
}
  • E. Garman
  • Published 2014
  • Chemistry, Medicine
  • Science
The three-dimensional structures of large biomolecules important in the function and mechanistic pathways of all living systems and viruses can be determined by x-ray diffraction from crystals of these molecules and their complexes. This area of crystallography is continually expanding and evolving, and the introduction of new methods that use the latest technology is allowing the elucidation of ever larger and more complex biological systems, which are now becoming tractable to structure… Expand

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References

SHOWING 1-10 OF 51 REFERENCES
Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems.
TLDR
Some of the advances in the algorithms used for crystallographic structure determination in the Phenix and Crystallography & NMR System software packages are reviewed and how methods from ab initio structure prediction and refinement in Rosetta have been applied to challenging crystallographic problems are described. Expand
Femtosecond X-ray protein nanocrystallography
TLDR
This work offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage, by using pulses briefer than the timescale of most damage processes. Expand
Structures from Anomalous Diffraction of Native Biological Macromolecules
TLDR
Robust procedures for enhancing the signal-to-noise ratio in the slight anomalous scattering from generic native structures by combining data measured from multiple crystals at lower-than-usual x-ray energy are devised. Expand
Predicting the X-ray lifetime of protein crystals
TLDR
A predictive metric diffraction-weighted dose is presented for modeling the rate of decay of total diffracted intensity from protein crystals in macromolecular crystallography, and hence it is possible to directly compare potential data-collection strategies to optimize the diffraction for a given level of damage under specific experimental conditions. Expand
Towards an understanding of radiation damage in cryocooled macromolecular crystals.
TLDR
Although progress is being made, the understanding of radiation damage is far from complete and methods for recognizing the damage and treating the data are being made available but they are still at an early stage of development. Expand
De novo protein crystal structure determination from X-ray free-electron laser data
TLDR
X-ray FEL data can be used for de novo protein structure determination, that is, without previous knowledge about the structure, and high-quality diffraction intensities are obtained, resulting in an experimental electron density map good enough for automated building of the protein structure. Expand
Natively Inhibited Trypanosoma brucei Cathepsin B Structure Determined by Using an X-ray Laser
TLDR
The structure reveals the mechanism of native TbCatB inhibition and demonstrates that new biomolecular information can be obtained by the “diffraction-before-destruction” approach of x-ray free-electron lasers from hundreds of thousands of individual microcrystals. Expand
Specific chemical and structural damage to proteins produced by synchrotron radiation.
  • M. Weik, R. Ravelli, +7 authors J. Sussman
  • Chemistry, Medicine
  • Proceedings of the National Academy of Sciences of the United States of America
  • 2000
TLDR
This work shows for the enzymes Torpedo californica acetylcholinesterase and hen egg white lysozyme that synchrotron radiation also can cause highly specific damage, and provides a direct approach for studying the radiation chemistry of proteins and nucleic acids at a detailed, structural level. Expand
Efficient anisotropic refinement of macromolecular structures using FFT.
TLDR
All the tests show that anisotropic refinement not only reduces the R value and Rfree but also improves the fit to geometric targets, indicating that this parameterization is valuable for improving models derived from experimental data. Expand
Experimental determination of the radiation dose limit for cryocooled protein crystals.
TLDR
The calculated dose limit of 2 x 10(7) Gy for the diffracting power of cryocooled protein crystals to drop by half has been experimentally evaluated at a third-generation synchrotron source. Expand
...
1
2
3
4
5
...