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Cited by 115Advanced Electron Microscopy Techniques and ApplicationsEnzyme Structure and FunctionProtein Structure and Dynamics

Bottom-up structural proteomics: cryoEM of protein complexes enriched from the cellular milieu

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Ho, Chi-Min, Li, Xiaorun, Lai, Mason, Terwilliger, Thomas C., Beck, Josh R., Wohlschlegel, James, Goldberg, Daniel E., Fitzpatrick, Anthony W. P. +1 more·2020·Nature Methods
DOI 10.1038/s41592-019-0637-yPMC PMC7494424
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Abstract

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.

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Cited by

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Authors
Ho, C.-M., Li, X., Lai, M., Terwilliger, T. C., Beck, J. R., Wohlschlegel, J., Goldberg, D. E., Fitzpatrick, A. W. P., & Zhou, Z. H.
Affiliations
  • California NanoSystems Institute (US)
  • University of Science and Technology of China (CN)
  • Los Alamos National Laboratory (US)
  • Iowa State University (US)
  • University of California, Los Angeles (US)
  • Washington University in St. Louis (US)
  • Mortimer B. Zuckerman Mind Brain Behavior Institute (US)
Corresponding author
Zhou, Z. Hong
ORCID
Venue
Nature Methods
Publisher
Springer Science and Business Media LLC
Published
2019-11-25
Volume
17
Issue
1
Pages
79-85
ISSN
  • 1548-7091 (ISSN-L)
  • 1548-7105
DOI
10.1038/s41592-019-0637-y
PMC
PMC7494424
OpenAlex
W2990714798
Cited by
115
References
3
Citations by year
2026: 13 · 2025: 21 · 2024: 14 · 2023: 20 · 2022: 19 · 2021: 16 · 2020: 12
FWCI
5.87
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Methods (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • eScholarship (California Digital Library) (submittedVersion)
  • OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
Funders
  • U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (R01GM071940, U24GM116792)
  • U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (AI094386, T32 AI007323)
  • U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (DE025567, S10RR23057)
  • U.S. Department of Health & Human Services | NIH | NIH Office of the Director (S10OD018111)
  • National Science Foundation (DBI-1338135, DMR-1548924)
  • U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (K99/R00 HL133453)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords
protein complex structure, ab initio structure determination, Plasmodium falciparum, Plasmodium, protein complex identification, atomic models, membrane proteins
MeSH terms
Erythrocytes, Humans, Image Processing, Computer-Assisted, Models, Molecular, Plasmodium falciparum, Protein Conformation, Mass Spectrometry, Protozoan Proteins, Malaria, Falciparum, Cryoelectron Microscopy, Proteomics, Multiprotein Complexes, Amyloid Precursor Protein Secretases

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