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Cited by 15Supramolecular Self-Assembly in MaterialsProtein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

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A computational toolbox for the assembly yield of complex and heterogeneous structures

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Curatolo, Agnese I., Kimchi, Ofer, Goodrich, Carl P., Krueger, Ryan K., Brenner, Michael P.·2023·Nature Communications
DOI 10.1038/s41467-023-43168-4PMC PMC10721878

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Abstract

The self-assembly of complex structures from a set of non-identical building blocks is a hallmark of soft matter and biological systems, including protein complexes, colloidal clusters, and DNA-based assemblies. Predicting the dependence of the equilibrium assembly yield on the concentrations and interaction energies of building blocks is highly challenging, owing to the difficulty of computing the entropic contributions to the free energy of the many structures that compete with the ground state configuration. While these calculations yield well known results for spherically symmetric building blocks, they do not hold when the building blocks have internal rotational degrees of freedom. Here we present an approach for solving this problem that works with arbitrary building blocks, including proteins with known structure and complex colloidal building blocks. Our algorithm combines classical statistical mechanics with recently developed computational tools for automatic differentiation. Automatic differentiation allows efficient evaluation of equilibrium averages over configurations that would otherwise be intractable. We demonstrate the validity of our framework by comparison to molecular dynamics simulations of simple examples, and apply it to calculate the yield curves for known protein complexes and for the assembly of colloidal shells.

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Metadata

Authors
Curatolo, A. I., Kimchi, O., Goodrich, C. P., Krueger, R. K., & Brenner, M. P.
Affiliations
  • Harvard University (US)
  • Princeton University (US)
  • Institute of Science and Technology Austria (AT)
Corresponding author
Brenner, Michael P.
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2023-12-14
Volume
14
Issue
1
Pages
8328-8328
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-023-43168-4
PMC
PMC10721878
OpenAlex
W4389726621
Cited by
15
References
3
Citations by year
2026: 7 · 2025: 5 · 2024: 2 · 2023: 1
FWCI
0.96
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • Research Square (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • United States Department of Defense | United States Navy | Office of Naval Research (N00014-17- 1-3029, N00014-17- 1-3029,)
  • Simons Foundation (Investigator Award)
  • National Science Foundation (PHY-1734030)
Topics
  • Physical Sciences › Materials Science › Biomaterials › Supramolecular Self-Assembly in Materials
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
Keywords
self-assembly, assembly yield, entropic contribution, free energy, automatic differentiation, protein complexes, colloidal clusters, statistical mechanics

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