Path-LZerD: Predicting Assembly Order of Multimeric Protein Complexes

Methods Mol Biol. 2020;2074:95-112. doi: 10.1007/978-1-4939-9873-9_8.

Abstract

Many important functions in a cell are carried out by protein complexes with more than two subunits. Similar to the folding of a single protein, multimeric protein complexes in general follow an energetically favored assembly path. Knowing the assembly path not only provides critical information about the molecular mechanism of the assembly but also serves as a foundation for artificial design of protein complexes, as well as development of drugs that interfere with complex formation. There are experimental approaches for determining the assembly path of a complex; however, such methods are resource intensive. We have recently developed a computational method, Path-LZerD, which predicts the assembly path of a complex by simulating the docking process of the complex. Here, we explain how to use the Path-LZerD software with examples.

Keywords: Assembly order; Multimeric protein complex; PPI; PPI network; Protein docking; Protein structure modeling; Protein–protein interaction; Structure prediction.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Computational Biology
  • Databases, Protein
  • Protein Binding
  • Protein Conformation
  • Protein Interaction Mapping
  • Protein Multimerization
  • Proteins / chemistry*
  • Software

Substances

  • Proteins