AlphaFold2 Protein Structure Prediction of JCVI-syn3A Protein-coding Genes

David M. Bianchi1, James F. Pelletier2, Clyde A. Hutchison III3, John I. Glass3, Zaida Luthey-Schulten1*

1Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA, 2Centro Nacional de Biotecnologia, Madrid, ESP, 3J. Craig Venter Institute (JCVI), La Jolla, CA, USA,

*Correspondence to zan@illinois.edu.

Please Cite: David M. Bianchi, James F. Pelletier, Clyde A. Hutchison III, John I. Glass, Zaida Luthey-Schulten, Towards the Complete Functional Characterization of a Minimal Bacterial Proteome Journal of Physical Chemistry B, "Jose Onuchic Festschrift" (2022).

DOI: 10.1021/acs.jpcb.2c04188

ylbN AlphaFold Bioinformatic Analysis
The AlphaFold2 predicted structure of JCVI-syn3A protein-coding gene JCVISYN3A_0527, with lddT (AlphaFold confidence measure) coloring with a cold-to-hot color palette (i.e. Blue-green-yellow-red, more confidence/"lower error" to less confidence/"higher error").

Please address any correspondence regarding code to:

CONTACT: davidmb2@illinois.edu

Archive of predicted structures for JCVI-syn3A protein coding genes and Associated Analysis Notebook. (700 MB, 2.5 GB Unzipped)

README file for the JCVI-syn3A protein structural prediction database and analysis notebook (also present in ZIP).

Supplemental Spreadsheet containing functional predictions for JCVI-syn3A protein-coding genes with associated gene essentiality data from Breuer et al 2019.

Link to the JCVI-syn3A prediction database including associated sequence analysis (CAUTION>125GB). Not necessary for structural analysis.

Acknowledgements

D.M.B. thanks Troy Brier, Benjamin Gilbert, and Zane Thornburg for helpful review of analysis code. This work would not have been possible without support from NSF MCB-1818344 and NSF MCB-1840320. We also acknowledge support from NSF Physics Frontiers Center PHY 1430124 "The Center for the Physics of Living Cells'' (CPLC) and the NSF Physics of Living Systems (PoLS) Initiative NSF PHY-2014027.