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Modeling Protein Complexes and Molecular Assemblies Using Computational Methods

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Computational Biology and Machine Learning for Metabolic Engineering and Synthetic Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2553))

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Abstract

Many biological molecules are assembled into supramolecular complexes that are necessary to perform functions in the cell. Better understanding and characterization of these molecular assemblies are thus essential to further elucidate molecular mechanisms and key protein-protein interactions that could be targeted to modulate the protein binding affinity or develop new binders. Experimental access to structural information on these supramolecular assemblies is often hampered by the size of these systems that make their recombinant production and characterization rather difficult. Computational methods combining both structural data, molecular modeling techniques, and sequence coevolution information can thus offer a good alternative to gain access to the structural organization of protein complexes and assemblies. Herein, we present some computational methods to predict structural models of the protein partners, to search for interacting regions using coevolution information, and to build molecular assemblies. The approach is exemplified using a case study to model the succinate-quinone oxidoreductase heterocomplex.

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Author notes

  1. Romain Launay and Elin Teppa contributed equally with all other contributors.

Authors and Affiliations

  1. Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse Cedex 04, France

    Romain Launay, Elin Teppa, Jérémy Esque & Isabelle André

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  1. Romain Launay
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  2. Elin Teppa
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  3. Jérémy Esque
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  4. Isabelle André
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Corresponding authors

Correspondence to Jérémy Esque or Isabelle André .

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Editors and Affiliations

  1. Bioinformatics Institute, Agency for Science, Technology & Research, Singapore, Singapore

    Kumar Selvarajoo

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Launay, R., Teppa, E., Esque, J., André, I. (2023). Modeling Protein Complexes and Molecular Assemblies Using Computational Methods. In: Selvarajoo, K. (eds) Computational Biology and Machine Learning for Metabolic Engineering and Synthetic Biology. Methods in Molecular Biology, vol 2553. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2617-7_4

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  • DOI: https://doi.org/10.1007/978-1-0716-2617-7_4

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2616-0

  • Online ISBN: 978-1-0716-2617-7

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