Automated evaluation of quaternary structures from protein crystals

被引:61
作者
Bliven, Spencer [1 ]
Lafita, Aleix [1 ,2 ]
Parker, Althea [1 ,3 ]
Capitani, Guido [1 ,4 ]
Duarte, Jose M. [1 ,5 ,6 ]
机构
[1] Paul Scherrer Inst, Lab Biomol Res, Villigen, Switzerland
[2] NIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bldg 10, Bethesda, MD 20892 USA
[3] Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland
[4] Swiss Fed Inst Technol, Sci IT Serv, Zurich, Switzerland
[5] Swiss Fed Inst Technol, Dept Biol, Zurich, Switzerland
[6] Univ Calif San Diego, SDSC, RCSB Prot Data Bank, La Jolla, CA 92093 USA
基金
瑞士国家科学基金会; 美国国家卫生研究院; 美国国家科学基金会;
关键词
DATA-BANK; INFERENCE; ASSEMBLIES; FRAMEWORK; SYMMETRY;
D O I
10.1371/journal.pcbi.1006104
中图分类号
Q5 [生物化学];
学科分类号
070307 [化学生物学];
摘要
A correct assessment of the quaternary structure of proteins is a fundamental prerequisite to understanding their function, physico-chemical properties and mode of interaction with other proteins. Currently about 90% of structures in the Protein Data Bank are crystal structures, in which the correct quaternary structure is embedded in the crystal lattice among a number of crystal contacts. Computational methods are required to 1) classify all protein-protein contacts in crystal lattices as biologically relevant or crystal contacts and 2) provide an assessment of how the biologically relevant interfaces combine into a biological assembly. In our previous work we addressed the first problem with our EPPIC (Evolutionary Protein Protein Interface Classifier) method. Here, we present our solution to the second problem with a new method that combines the interface classification results with symmetry and topology considerations. The new algorithm enumerates all possible valid assemblies within the crystal using a graph representation of the lattice and predicts the most probable biological unit based on the pairwise interface scoring. Our method achieves 85% precision (ranging from 76% to 90% for different oligomeric types) on a new dataset of 1,481 biological assemblies with consensus of PDB annotations. Although almost the same precision is achieved by PISA, currently the most popular quaternary structure assignment method, we show that, due to the fundamentally different approach to the problem, the two methods are complementary and could be combined to improve biological assembly assignments. The software for the automatic assessment of protein assemblies (EPPIC version 3) has been made available through a web server at http://www.eppic-web.org.
引用
收藏
页数:19
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