Modeling Symmetric Macromolecular Structures in Rosetta3

By Frank DiMaio, Andrew Leaver-Fay, Philip Bradley, David Baker, Ingemar André. 2011

210 citations recorded by the source corpus.

Symmetric protein assemblies play important roles in many biochemical processes. However, the large size of such systems is challenging for traditional structure modeling methods. This paper describes the implementation of a general framework for modeling arbitrary symmetric systems in Rosetta3. We describe the various types of symmetries relevant to the study of protein structure that may be modeled using Rosetta's symmetric framework. We then describe how this symmetric framework is efficiently implemented within Rosetta, which restricts the conformational search space by sampling only symmetric degrees of freedom, and explicitly simulates only a subset of the interacting monomers. Finally, we describe structure prediction and design applications that utilize the Rosetta3 symmetric modeling capabilities, and provide a guide to running simulations on symmetric systems.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

One contact for every twelve residues allows robust and accurate topology-level protein structure modeling (2013, positive): “Given this information, models with D2 dihedral symmetry were generated using the Rosetta symmetric modeling framework.35 The lowest energy models converged to a common quaternary fold with structural variation mainly within the short helices that are not involved in the interface between chains.”
High-accuracy refinement using Rosetta in CASP13 (2019, methodology): “The Rosetta symmetry modeling machinery used for homo-oligomer comparative modeling 17,18 was incorporated into the refinement pipeline in this CASP.”
Designing Peptides on a Quantum Computer (2019, background): “…quantum annealing hardware limits the size of design tasks that can be tackled, molecules with internal n -fold symmetry can have n -fold more amino acid positions without increasing the number of unique designable positions or the overall computational complexity of the design task ( 40 , 41 ) .”
HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry (2018, methodology): “With more and more symmetric structures available in the PDB, several web servers that use template-based methods like ROBETTA (23), SWISS-MODEL (24), and GalaxyGemini (25) have been proposed to predict the homo-oligomer structure.”
Computation and Functional Studies Provide a Model for the Structure of the Zinc Transporter hZIP4* (2015, methodology): “The selected model was then further energy-minimized with Rosetta to remove clashes, while respecting structural symmetry and GREMLIN restraints (27).”
Design of a hyperstable 60-subunit protein icosahedron (2016, unknown): “For T33-21, the sfGFP was fused to either the C-terminus of the first component (12 sfGFP molecules), or the C-terminus of both components (24 sfGFP molecules).”
An Integrated Framework Advancing Membrane Protein Modeling and Design (2015, methodology): “From the asymmetric unit, the full complex was reassembled by the symmetric docking routine and the interface score was computed as the cumulative score of all symmetric interfaces [65].”
High resolution microtubule structures reveal the structural transitions in αβ–tubulin upon GTP hydrolysis (2014, methodology): “The lattice was modeled in a 33 3 arrangement using symmetry operations as previously described (DiMaio et al., 2011).”