Publication Date:
2011-05-03
Description:
Molecular replacement procedures, which search for placements of a starting model within the crystallographic unit cell that best account for the measured diffraction amplitudes, followed by automatic chain tracing methods, have allowed the rapid solution of large numbers of protein crystal structures. Despite extensive work, molecular replacement or the subsequent rebuilding usually fail with more divergent starting models based on remote homologues with less than 30% sequence identity. Here we show that this limitation can be substantially reduced by combining algorithms for protein structure modelling with those developed for crystallographic structure determination. An approach integrating Rosetta structure modelling with Autobuild chain tracing yielded high-resolution structures for 8 of 13 X-ray diffraction data sets that could not be solved in the laboratories of expert crystallographers and that remained unsolved after application of an extensive array of alternative approaches. We estimate that the new method should allow rapid structure determination without experimental phase information for over half the cases where current methods fail, given diffraction data sets of better than 3.2 A resolution, four or fewer copies in the asymmetric unit, and the availability of structures of homologous proteins with 〉20% sequence identity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365536/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365536/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉DiMaio, Frank -- Terwilliger, Thomas C -- Read, Randy J -- Wlodawer, Alexander -- Oberdorfer, Gustav -- Wagner, Ulrike -- Valkov, Eugene -- Alon, Assaf -- Fass, Deborah -- Axelrod, Herbert L -- Das, Debanu -- Vorobiev, Sergey M -- Iwai, Hideo -- Pokkuluri, P Raj -- Baker, David -- 082961/Wellcome Trust/United Kingdom -- 5R01GM092802/GM/NIGMS NIH HHS/ -- GM074898/GM/NIGMS NIH HHS/ -- P01 GM063210/GM/NIGMS NIH HHS/ -- P41RR002250/RR/NCRR NIH HHS/ -- R01 GM092802/GM/NIGMS NIH HHS/ -- U54 GM074898/GM/NIGMS NIH HHS/ -- U54 GM074958/GM/NIGMS NIH HHS/ -- U54 GM094586/GM/NIGMS NIH HHS/ -- U54GM074958/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- Intramural NIH HHS/ -- Wellcome Trust/United Kingdom -- England -- Nature. 2011 May 26;473(7348):540-3. doi: 10.1038/nature09964. Epub 2011 May 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Washington, Department of Biochemistry and HHMI, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21532589" target="_blank"〉PubMed〈/a〉
Keywords:
Computational Biology/*methods
;
Crystallography, X-Ray
;
Databases, Protein
;
Electrons
;
*Models, Molecular
;
Proteins/*chemistry
;
Sequence Alignment
;
Sequence Homology, Amino Acid
;
*Structural Homology, Protein
Print ISSN:
0028-0836
Electronic ISSN:
1476-4687
Topics:
Biology
,
Chemistry and Pharmacology
,
Medicine
,
Natural Sciences in General
,
Physics
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