The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology
Open accessAbstract
Cellular processes often depend on interactions between proteins and the formation of macromolecular complexes. The impairment of such interactions can lead to deregulation of pathways resulting in disease states, and it is hence crucial to gain insights into the nature of macromolecular assemblies. Detailed structural knowledge about complexes and protein-protein interactions is growing, but experimentally determined three-dimensional multimeric assemblies are outnumbered by complexes supported by non-structural experimental evidence. Here, we aim to fill this gap by modeling multimeric structures by homology, only using amino acid sequences to infer the stoichiometry and the overall structure of the assembly. We ask which properties of proteins within a family can assist in the prediction of correct quaternary structure. Specifically, we introduce a description of protein-protein interface conservation as a function of evolutionary distance to reduce the noise in deep multiple sequence alignments. We also define a distance measure to structurally compare homologous multimeric protein complexes. This allows us to hierarchically cluster protein structures and quantify the diversity of alternative biological assemblies known today. We find that a combination of conservation scores, structural clustering, and classical interface descriptors, can improve the selection of homologous protein templates leading to reliable models of protein complexes.
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Cites
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
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Leaver-Fay (2011) · doi:10.1016/b978-0-12-381270-4.00019-6 · Cited by 1,904
CAPRI: A Critical Assessment of PRedicted Interactions
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Emerging methods in protein co-evolution
de Juan, D., Pazos, F., & Valencia, A. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3414 · Cited by 607
Sequence co-evolution gives 3D contacts and structures of protein complexes
Hopf, T. A., Schärfe, C. P. I., Rodrigues, J. P. G. L. M., Green, A. G., Kohlbacher, O., Sander, C., Bonvin, A. M. J. J., & Marks, D. S. (2014) · eLife · doi:10.7554/elife.03430 · Cited by 515
Docking and scoring protein interactions: CAPRI 2009
Lensink, M. F., & Wodak, S. J. (2010) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.22818 · Cited by 226
Templates are available to model nearly all complexes of structurally characterized proteins
Kundrotas, P. J., Zhu, Z., Janin, J., & Vakser, I. A. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1200678109 · Cited by 179
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Haas, J., Barbato, A., Behringer, D., Studer, G., Roth, S., Bertoni, M., Mostaguir, K., Gumienny, R., & Schwede, T. (2018) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.25431 · Cited by 168
Self-citationGeneralized Biomolecular Modeling and Design with RoseTTAFold All-Atom
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New prediction categories in CASP15
Kryshtafovych, A., Antczak, M., Szachniuk, M., Zok, T., Kretsch, R. C., Rangan, R., Pham, P., Das, R., Robin, X., Studer, G., et al. (2023) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26515 · Cited by 54
“This is the oligomeric Template Modeling score (TM-score) 49 for overall topology (SCORE) and the contact based QS-score 50 which is interface centric (QSCORE).”
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Metadata
- Authors
- Bertoni, M., Kiefer, F., Biasini, M., Bordoli, L., & Schwede, T.
- Venue
- Scientific Reports
- Published
- 2017-09-05
- Volume
- 7
- Issue
- 1
- Pages
- 10480-10480
- ISSN
- 2045-2322 (ISSN-L)
- OpenAlex
- W2751260413
- Cited by
- 866
- References
- 7
- FWCI
- 24.85
- Type
- journal article
- Language
- en
- Open access
- gold
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- Bertoni, M., Kiefer, F., Biasini, M., Bordoli, L., & Schwede, T. (2017). Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. Scientific Reports. https://doi.org/10.1038/s41598-017-09654-8
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