Author response: A synthetic peptide that prevents cAMP regulation in mammalian hyperpolarization-activated cyclic nucleotide-gated (HCN) channels

Saponaro, Andrea; Cantini, Francesca; Porro, Alessandro; Bucchi, Annalisa; DiFrancesco, Dario; Maione, Vincenzo; Donadoni, Chiara; Introini, Bianca; Mesirca, Pietro; Mangoni, Matteo E.; Thiel, Gerhard; Banci, Lucia; Santoro, Bina; Moroni, Anna

doi:10.7554/elife.35753.022

Cited by 1 publication

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“…(for details see Saponaro et al, 2018). These results suggest that Cluster 1 can be chosen as the bona fide model for the CNBD-TRIP8bnano complex.…”

Section: Submission Datamentioning

confidence: 84%

“…In this context, computational approaches offer valuable alternatives, opening the possibility to describe, at atomic level, physiologically relevant macromolecular complexes (Saponaro et al, 2018) integrative modelling platform, possesses the powerful advantage of being able to implement experimental data directly into the docking process to guide the computations (Dominguez et al, 2003).…”

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confidence: 99%

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Understanding Docking Complexes of Macromolecules Using HADDOCK: The Synergy between Experimental Data and Computations

Saponaro¹,

Maione²,

Bonvin³

et al. 2020

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This protocol illustrates the modelling of a protein-peptide complex using the synergic combination of in silico analysis and experimental results. To this end, we use the integrative modelling software HADDOCK, which possesses the powerful ability to incorporate experimental data, such as NMR Chemical Shift Perturbations and biochemical protein-peptide interaction data, as restraints to guide the docking process. Based on the modelling results, a rational mutagenesis approach is used to validate the generated models. The experimental results allow to select a final structural model best representing the bona fide protein-peptide complex. The described protocol can also be applied to model protein-protein complexes. There is no size limit for the macromolecular complexes that can be characterized by HADDOCK as long as the 3D structures of the individual components are available.

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“…(for details see Saponaro et al, 2018). These results suggest that Cluster 1 can be chosen as the bona fide model for the CNBD-TRIP8bnano complex.…”

Section: Submission Datamentioning

confidence: 84%

mentioning

confidence: 99%