Likelihood-based structure solution in Phaser and Phenix By providing three-dimensional pictures of biological molecules, macromolecular crystallography underpins a deeper understanding of the processes that maintain life. As such, it plays a key role in the basic science of biochemistry and molecular biology, as well as the development of new therapies by the pharmaceutical industry. New algorithms, based on the statistical concept of maximum likelihood, will be developed in the program Phaser an6 incorporated in the Phenix package to determine the 3D structures of proteins and nucleic acids more quickly and more automatically. With these new tools, other crystallographers should gain a better return on the investment made in their research, and crystallographic methods should become accessible to researchers with less specialist expertise. The majority of crystal structures are now solved by the technique of molecular replacement, which exploits the known structure of a related molecule. By coupling the sensitivity of likelihood-based molecular replacement in Phaser with sophisticated modeling techniques in the program Rosetta developed by the group of David Baker, the reach of molecular replacement will be further extended to use starting models that are more distantly related than currently feasible. The next most popular method of structure solution is single-wavelength anomalous diffraction (SAD) phasing, which shares with molecular replacement the advantage of requiring data from only one good crystal. The strength of likelihood for phasing, once the positions of the anomalous scatterers are known, will be extended to improving methods for determining the initial substructure. Increased automation in the Phenix package will make advanced algorithms available to novice crystallographers, and will allow expert crystallographers to explore many more possibilities for structure solution. Methods will be developed to exploit a partial solution in one crystal form, either by molecular replacement or experimental phasing, to solve additional crystal forms. Advanced methods will be developed for refining pairs of structures, to give a clearer picture of the differences between them.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Program Projects (P01)
Project #
5P01GM063210-12
Application #
8382317
Study Section
Special Emphasis Panel (ZRG1-BCMB-H)
Project Start
Project End
Budget Start
2012-08-01
Budget End
2013-07-31
Support Year
12
Fiscal Year
2012
Total Cost
$158,319
Indirect Cost
$5,081
Name
Lawrence Berkeley National Laboratory
Department
Type
DUNS #
078576738
City
Berkeley
State
CA
Country
United States
Zip Code
94720
Hintze, Bradley J; Richardson, Jane S; Richardson, David C (2017) Mismodeled purines: implicit alternates and hidden Hoogsteens. Acta Crystallogr D Struct Biol 73:852-859
Demydchuk, Mykhaylo; Hill, Chris H; Zhou, Aiwu et al. (2017) Insights into Hunter syndrome from the structure of iduronate-2-sulfatase. Nat Commun 8:15786
Richardson, Jane S; Videau, Lizbeth L; Williams, Christopher J et al. (2017) Broad Analysis of Vicinal Disulfides: Occurrences, Conformations with Cis or with Trans Peptides, and Functional Roles Including Sugar Binding. J Mol Biol 429:1321-1335
Greber, Basil J; Nguyen, Thi Hoang Duong; Fang, Jie et al. (2017) The cryo-electron microscopy structure of human transcription factor IIH. Nature 549:414-417
McCoy, Airlie J; Oeffner, Robert D; Wrobel, Antoni G et al. (2017) Ab initio solution of macromolecular crystal structures without direct methods. Proc Natl Acad Sci U S A 114:3637-3641
Zheng, Min; Reimers, Jeffrey R; Waller, Mark P et al. (2017) Q|R: quantum-based refinement. Acta Crystallogr D Struct Biol 73:45-52
Hryc, Corey F; Chen, Dong-Hua; Afonine, Pavel V et al. (2017) Accurate model annotation of a near-atomic resolution cryo-EM map. Proc Natl Acad Sci U S A 114:3103-3108
Moriarty, Nigel W; Draizen, Eli J; Adams, Paul D (2017) An editor for the generation and customization of geometry restraints. Acta Crystallogr D Struct Biol 73:123-130
Liebschner, Dorothee; Afonine, Pavel V; Moriarty, Nigel W et al. (2017) Polder maps: improving OMIT maps by excluding bulk solvent. Acta Crystallogr D Struct Biol 73:148-157
Akey, David L; Terwilliger, Thomas C; Smith, Janet L (2016) Efficient merging of data from multiple samples for determination of anomalous substructure. Acta Crystallogr D Struct Biol 72:296-302

Showing the most recent 10 out of 126 publications