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Cha M, Emre EST, Xiao X, Kim JY, Bogdan P, VanEpps JS, Violi A, Kotov NA. Unifying structural descriptors for biological and bioinspired nanoscale complexes. NATURE COMPUTATIONAL SCIENCE 2022; 2:243-252. [PMID: 38177552 DOI: 10.1038/s43588-022-00229-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 03/17/2022] [Indexed: 01/06/2024]
Abstract
Biomimetic nanoparticles are known to serve as nanoscale adjuvants, enzyme mimics and amyloid fibrillation inhibitors. Their further development requires better understanding of their interactions with proteins. The abundant knowledge about protein-protein interactions can serve as a guide for designing protein-nanoparticle assemblies, but the chemical and biological inputs used in computational packages for protein-protein interactions are not applicable to inorganic nanoparticles. Analysing chemical, geometrical and graph-theoretical descriptors for protein complexes, we found that geometrical and graph-theoretical descriptors are uniformly applicable to biological and inorganic nanostructures and can predict interaction sites in protein pairs with accuracy >80% and classification probability ~90%. We extended the machine-learning algorithms trained on protein-protein interactions to inorganic nanoparticles and found a nearly exact match between experimental and predicted interaction sites with proteins. These findings can be extended to other organic and inorganic nanoparticles to predict their assemblies with biomolecules and other chemical structures forming lock-and-key complexes.
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Affiliation(s)
- Minjeong Cha
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Emine Sumeyra Turali Emre
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Xiongye Xiao
- Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, USA
| | - Ji-Young Kim
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Paul Bogdan
- Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, USA
| | - J Scott VanEpps
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
- Program in Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, USA
- Department of Emergency Medicine, University of Michigan, Ann Arbor, MI, USA
- Michigan Center for Integrative Research in Critical Care, University of Michigan, Ann Arbor, MI, USA
| | - Angela Violi
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
- Biophysics Program, University of Michigan, Ann Arbor, MI, USA
| | - Nicholas A Kotov
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI, USA.
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
- Program in Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, USA.
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