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Integrative structural modeling of macromolecular complexes using Assembline.

Vasileios Rantos1,2, Kai Karius1,2, Jan Kosinski3,4,5

  • 1Centre for Structural Systems Biology (CSSB), Hamburg, Germany.

Nature Protocols
|November 30, 2021
PubMed
Summary
This summary is machine-generated.

Assembline software enables integrative modeling of large macromolecular complexes using diverse experimental data. This computational tool efficiently determines complex structures, even for flexible or heterogeneous molecules not suitable for high-resolution cryo-electron tomography.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Integrative modeling combines multiple experimental data types (X-ray crystallography, cryo-electron microscopy, cross-linking mass spectrometry) for macromolecular complex structure determination.
  • This approach is crucial for large, flexible, or heterogeneous complexes often challenging for high-resolution cryo-electron microscopy or cryo-electron tomography.

Purpose of the Study:

  • To introduce Assembline, a streamlined software package for integrative modeling of multi-megadalton macromolecular complexes.
  • To provide a robust pipeline for building and analyzing ensembles of models that satisfy diverse experimental constraints.

Main Methods:

  • Assembline integrates existing software and novel algorithms into a unified modeling pipeline.
  • The protocol employs a multistep procedure for efficient conformational space sampling and incorporates unique modeling restraints and a configuration system.
  • It processes data from atomic structures, homology models, electron microscopy maps, and other experimental sources.

Main Results:

  • Assembline successfully models multi-megadalton complexes, including the nuclear pore complex.
  • The protocol achieves exhaustive conformational sampling within 100-1,000 CPU-hours for megadalton-scale complexes.
  • It offers tools for model analysis and provides comprehensive instructions for input preparation, execution, and performance assessment.

Conclusions:

  • Assembline provides an efficient and versatile computational tool for determining the structures of large and complex macromolecular assemblies.
  • The software facilitates the study of challenging biological systems by enabling integrative modeling with diverse experimental data.
  • It offers a user-friendly pipeline suitable for both individual researchers and high-performance computing cluster environments.