Improving integrative 3D modeling into low‐ to medium‐resolution electron microscopy structures with evolutionary couplings
Abstract
Electron microscopy (EM) continues to provide near‐atomic resolution structures for well‐behaved proteins and protein complexes. Unfortunately, structures of some complexes are limited to low‐ to medium‐resolution due to biochemical or conformational heterogeneity. Thus, the application of unbiased systematic methods for fitting individual structures into EM maps is important. A method that employs co‐evolutionary information obtained solely from sequence data could prove invaluable for quick, confident localization of subunits within these structures. Here, we incorporate the co‐evolution of intermolecular amino acids as a new type of distance restraint in the integrative modeling platform in order to build three‐dimensional models of atomic structures into EM maps ranging from 10–14 Å in resolution. We validate this method using four complexes of known structure, where we highlight the conservation of intermolecular couplings despite dynamic conformational changes using the BAM complex. Finally, we use this method to assemble the subunits of the bacterial holo‐translocon into a model that agrees with previous biochemical data. The use of evolutionary couplings in integrative modeling improves systematic, unbiased fitting of atomic models into medium‐ to low‐resolution EM maps, providing additional information to integrative models lacking in spatial data.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Apr 09, 2021
- Source ID
- 10.1002/pro.4067
Entities
People
- Caitlyn L McCafferty
- David W Taylor
- Edward Marcotte
Organizations
- Army Research Office
- Cancer Prevention and Research Institute of Texas
- Dell Medical School at The University of Texas at Austin
- National Institute of General Medical Sciences
- National Institutes of Health
- National Science Foundation
- Robert A. Welch Foundation
- University of Texas at Austin