Open AccessBottom-up structural proteomics: cryoEM of protein complexes enriched from the cellular milieu
Author(s) -
Chin-Ming Ho,
Xiaorun Li,
Mason Lai,
Thomas C. Terwilliger,
Josh R. Beck,
James A. Wohlschlegel,
Daniel E. Goldberg,
Anthony Fitzpatrick,
Zhou Zh
Publication year - 2019
Publication title -
nature methods
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 19.469
H-Index - 318
eISSN - 1548-7105
pISSN - 1548-7091
DOI - 10.1038/s41592-019-0637-y
Subject(s) - proteomics , structural biology , computational biology , cryo electron microscopy , plasmodium falciparum , biology , ab initio , resolution (logic) , biophysics , protein structure , membrane protein , proteome , chemistry , microbiology and biotechnology , biochemistry , membrane , malaria , computer science , organic chemistry , artificial intelligence , gene , immunology
X-ray crystallography often requires non-native constructs involving mutations or truncations, and is challenged by membrane proteins and large multicomponent complexes. We present here a bottom-up endogenous structural proteomics approach whereby near-atomic-resolution cryo electron microscopy (cryoEM) maps are reconstructed ab initio from unidentified protein complexes enriched directly from the endogenous cellular milieu, followed by identification and atomic modeling of the proteins. The proteins in each complex are identified using cryoID, a program we developed to identify proteins in ab initio cryoEM maps. As a proof of principle, we applied this approach to the malaria-causing parasite Plasmodium falciparum, an organism that has resisted conventional structural-biology approaches, to obtain atomic models of multiple protein complexes implicated in intraerythrocytic survival of the parasite. Our approach is broadly applicable for determining structures of undiscovered protein complexes enriched directly from endogenous sources.