Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems
Open accessAbstract
Incorporating the dynamic nature of biomolecules in the modeling of their complexes is a challenge, especially when the extent and direction of the conformational changes taking place upon binding is unknown. Estimating whether the binding of a biomolecule to its partner(s) occurs in a conformational state accessible to its unbound form ("conformational selection") and/or the binding process induces conformational changes ("induced-fit") is another challenge. We propose here a method combining conformational sampling using ClustENM-an elastic network-based modeling procedure-with docking using HADDOCK, in a framework that incorporates conformational selection and induced-fit effects upon binding. The extent of the applied deformation is estimated from its energetical costs, inspired from mechanical tensile testing on materials. We applied our pre- and post-docking sampling of conformational changes to the flexible multidomain protein-protein docking benchmark and a subset of the protein-DNA docking benchmark. Our ClustENM-HADDOCK approach produced acceptable to medium quality models in 7/11 and 5/6 cases for the protein-protein and protein-DNA complexes, respectively. The conformational selection (sampling prior to docking) has the highest impact on the quality of the docked models for the protein-protein complexes. The induced-fit stage of the pipeline (post-sampling), however, improved the quality of the final models for the protein-DNA complexes. Compared to previously described strategies to handle conformational changes, ClustENM-HADDOCK performs better than two-body docking in protein-protein cases but worse than a flexible multidomain docking approach. However, it does show a better or similar performance compared to previous protein-DNA docking approaches, which makes it a suitable alternative.
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Evidence points to the conformational selection binding mechanism, which allows one to precompute the conformational ensemble of the interacting molecule(s) and dock the separate conformers with limited conformational search.
“In a long-standing debate between the proponents of the “induced-fit” and the “conformational selection” binding mechanisms [21–23], the evidence pointing to the latter allows one to precompute the conformational ensemble of the interacting molecule(s) and dock the separate conformers with limited conformational search [24,25].”
From Challenges in protein docking (2020) · cites this paper as [25]
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COMPLEX OF THE INTERLEUKIN-1 RECEPTOR WITH THE INTERLEUKIN-1 RECEPTOR ANTAGONIST (IL1RA)
Schreuder, H., Tardif, C., Tramp-Kalmeyer, S., et al. (1998) · Worldwide Protein Data Bank · doi:10.2210/pdb1ira/pdb
IL-1 RECEPTOR TYPE 1 COMPLEXED WITH ANTAGONIST PEPTIDE AF10847
Vigers, G. P. A., Dripps, D. J., Edwards, C. K., et al. (2000) · Worldwide Protein Data Bank · doi:10.2210/pdb1g0y/pdb
THE CRYSTAL STRUCTURE OF CALCIUM-FREE EQUINE PLASMA GELSOLIN.
Burtnick, L. D., Robinson, R., & Li, C. (1999) · Worldwide Protein Data Bank · doi:10.2210/pdb1d0n/pdb
Vorobiev, S. M., Bubb, M., & Almo, S. C. (2001) · Worldwide Protein Data Bank · doi:10.2210/pdb1ijj/pdb
HUMAN TISSUE FACTOR COMPLEXED WITH COAGULATION FACTOR VIIA INHIBITED WITH A BPTI-MUTANT
Zhang, E., Charles, R., & Tulinsky, A. (1998) · Worldwide Protein Data Bank · doi:10.2210/pdb1fak/pdb
Crystal structure of the tick carboxypeptidase inhibitor in complex with human carboxypeptidase B
Arolas, J. L., Popowicz, G. M., Lorenzo, J., et al. (2005) · Worldwide Protein Data Bank · doi:10.2210/pdb1zli/pdb
Solution Structure of Tick Carboxypeptidase Inhibitor
Pantoja‐Uceda, D., & Blanco, F. J. (2007) · Worldwide Protein Data Bank · doi:10.2210/pdb2jto/pdb
Crystal Structure of the Fucosylated Fc Fragment from Human Immunoglobulin G1
Matsumiya, S., Yamaguchi, Y., Saito, J., et al. (2011) · Worldwide Protein Data Bank · doi:10.2210/pdb3ave/pdb
COMPLEX OF RAN WITH IMPORTIN BETA
Vetter, I. R., Arndt, A., Kutay, U., et al. (1999) · Worldwide Protein Data Bank · doi:10.2210/pdb1ibr/pdb
Kent, H. M., Moore, M. S., Quimby, B., et al. (1999) · Worldwide Protein Data Bank · doi:10.2210/pdb1qg4/pdb
L.casei HprK/P in complex with B.subtilis HPr
Fieulaine, S., Moréra, S., Poncet, S., et al. (2001) · Worldwide Protein Data Bank · doi:10.2210/pdb1kkl/pdb
Lactobacillus casei HprK/P Bound to Phosphate
Fieulaine, S., Moréra, S., Poncet, S., et al. (2001) · Worldwide Protein Data Bank · doi:10.2210/pdb1jb1/pdb
Herzberg, O. (1992) · Worldwide Protein Data Bank · doi:10.2210/pdb2hpr/pdb
Crystal structure of Nidogen/Laminin Complex
Takagi, J., Yang, Y. T., Liu, J.-H., et al. (2003) · Worldwide Protein Data Bank · doi:10.2210/pdb1npe/pdb
PORCINE RIBONUCLEASE INHIBITOR
Kobe, B., & Deisenhofer, J. (1996) · Worldwide Protein Data Bank · doi:10.2210/pdb2bnh/pdb
STRUCTURE AND MECHANISM OF THE HOMODIMERIC ASSEMBLY OF THE RXR ON DNA
Zhao, Q., Chasse, S., Devarakonda, S., et al. (1998) · Worldwide Protein Data Bank · doi:10.2210/pdb1by4/pdb
HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D BOUND WITH KINKED DNA DUPLEX
Robinson, H. H., Gao, Y., McCrary, B. S., et al. (1997) · Worldwide Protein Data Bank · doi:10.2210/pdb1azp/pdb
Human papillomavirus type 18 E2 DNA-binding domain bound to its DNA target
Kim, S.-S., Tam, J. K., Wang, A. F., et al. (2001) · Worldwide Protein Data Bank · doi:10.2210/pdb1jj4/pdb
CRYSTAL STRUCTURE OF PUT3/DNA COMPLEX
Swaminathan, K., & Marmorstein, R. (1997) · Worldwide Protein Data Bank · doi:10.2210/pdb1zme/pdb
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- Authors
- Kurkcuoglu, Z., & Bonvin, A. M. J. J.
- Affiliations
- Utrecht University (NL)
- Corresponding author
- Kurkcuoglu, Zeynep
- Bonvin, Alexandre M. J. J.
- Venue
- Proteins Structure Function and Bioinformatics
- Publisher
- Wiley
- Published
- 2019-09-03
- Volume
- 88
- Issue
- 2
- Pages
- 292-306
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- PMC
- PMC6973081
- OpenAlex
- W2969910143
- Cited by
- 37
- References
- 82
- Citations by year
- 2026: 1 · 2025: 3 · 2024: 4 · 2023: 7 · 2022: 8 · 2021: 8 · 2020: 5 · 2019: 1
- FWCI
- 1.82
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Proteins Structure Function and Bioinformatics (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Funders
- Horizon 2020 Framework Programme
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- protein-protein docking, protein-DNA docking, conformational selection, induced fit, haddock, elastic network model, conformational sampling, flexible docking, multidomain proteins
- MeSH terms
- Algorithms, DNA, Nucleic Acid Conformation, Protein Binding, Protein Conformation, Proteins, Reproducibility of Results, Computational Biology, Protein Interaction Mapping, Molecular Docking Simulation
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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