Optimizing model representation for integrative structure determination of macromolecular assemblies

Proc Natl Acad Sci U S A. 2019 Jan 8;116(2):540-545. doi: 10.1073/pnas.1814649116. Epub 2018 Dec 26.


Integrative structure determination of macromolecular assemblies requires specifying the representation of the modeled structure, a scoring function for ranking alternative models based on diverse types of data, and a sampling method for generating these models. Structures are often represented at atomic resolution, although ad hoc simplified representations based on generic guidelines and/or trial and error are also used. In contrast, we introduce here the concept of optimizing representation. To illustrate this concept, the optimal representation is selected from a set of candidate representations based on an objective criterion that depends on varying amounts of information available for different parts of the structure. Specifically, an optimal representation is defined as the highest-resolution representation for which sampling is exhaustive at a precision commensurate with the precision of the representation. Thus, the method does not require an input structure and is applicable to any input information. We consider a space of representations in which a representation is a set of nonoverlapping, variable-length segments (i.e., coarse-grained beads) for each component protein sequence. We also implement a method for efficiently finding an optimal representation in our open-source Integrative Modeling Platform (IMP) software (https://integrativemodeling.org/). The approach is illustrated by application to three complexes of two subunits and a large assembly of 10 subunits. The optimized representation facilitates exhaustive sampling and thus can produce a more accurate model and a more accurate estimate of its uncertainty for larger structures than were possible previously.

Keywords: coarse graining; integrative structure modeling; model selection; multiscale modeling; structural biology.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Databases, Protein*
  • Models, Molecular*
  • Protein Domains