Peptide Suboptimal Conformation Sampling for the Prediction of Protein-Peptide Interactions

Lamiable, Alexis; Thévenet, Pierre; Eustache, Stephanie; Saladin, Adrien; Moroy, Gautier; Tufféry, Pierre

doi:10.1007/978-1-4939-6798-8_3

Cited by 3 publications

(3 citation statements)

References 24 publications

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“…Initial peptide inputs were predicted using PEP-FOLD 3, an in silico conformational prediction tool. 62,63 The output of these calculations was used as an input for 200 ns simulations of each peptide, using the CHARMM36 force field and explicit water under constant NPT conditions. The temperature was maintained at 310 K. Simulations were performed in dodecahedral unit cells with periodic boundary conditions, and charges were neutralized using sodium/chloride ions, as necessary.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Conformational Dynamics in Extended RGD-Containing Peptides

et al. 2020

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Cell binding experiments were designed and performed by J.L.A. with support of M.A.A. J.H.O. provided project administration, funding acquisition, and supervision. A version of this work is reproduced with permission in W.R.L.'s thesis document.50 Supporting Information The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.biomac.0c00506. Additional data and information describing peptide synthesis and characterization, MD simulations, EPR, and DEER (PDF)

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Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Conformational Dynamics in Extended RGD-Containing Peptides

et al. 2020

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“…21 Sequence alignment showed that the SBP sequence for IP 3 R2 contained an additional stretch of amino acids absent in IP 3 R1 and partly lacking in IP 3 R3 (Figure 1B). Within the putative SBP sequence of IP 3 R2, we identified a cluster of closely apposed glutamate (Glu, E) residues and delineated several candidate peptides that were tested with PEP-SiteFinder 40,41 for their interaction with a homology model of the human IP 3 R2 protein constructed with Modeller software. 42 Hereby, two peptides emerged with high interaction scores with the IP 3 -binding site of IP 3 R2: IP3RPEP5 (human) and IP3RPEP6 (mouse/rat version) (Figure 1C).…”

Section: Ip3rpep6 As a Potential Ip 3 R2 Antagonistmentioning

confidence: 99%

IP3RPEP6, a novel peptide inhibitor of IP₃ receptor channels that does not affect connexin‐43 hemichannels

Tao,

Hulpiau,

Wagner

et al. 2024

Acta Physiologica

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AimInositol 1,4,5‐trisphosphate receptors (IP3Rs) are intracellular Ca2+‐release channels with crucial roles in cell function. Current IP3R inhibitors suffer from off‐target effects and poor selectivity towards the three distinct IP3R subtypes. We developed a novel peptide inhibitor of IP3Rs and determined its effect on connexin‐43 (Cx43) hemichannels, which are co‐activated by IP3R stimulation.MethodsIP3RPEP6 was developed by in silico molecular docking studies and characterized by on‐nucleus patch‐clamp experiments of IP3R2 channels and carbachol‐induced IP3‐mediated Ca2+ responses in IP3R1, 2 or 3 expressing cells, triple IP3R KO cells and astrocytes. Cx43 hemichannels were studied by patch‐clamp and ATP‐release approaches, and by inhibition with Gap19 peptide. IP3RPEP6 interactions with IP3Rs were verified by co‐immunoprecipitation and affinity pull‐down assays.ResultsIP3RPEP6 concentration‐dependently reduced the open probability of IP3R2 channels and competitively inhibited IP3Rs in an IC50 order of IP3R2 (~3.9 μM) < IP3R3 (~4.3 μM) < IP3R1 (~9.0 μM), without affecting Cx43 hemichannels or ryanodine receptors. IP3RPEP6 co‐immunoprecipitated with IP3R2 but not with IP3R1; interaction with IP3R3 varied between cell types. The IC50 of IP3RPEP6 inhibition of carbachol‐induced Ca2+ responses decreased with increasing cellular Cx43 expression. Moreover, Gap19‐inhibition of Cx43 hemichannels significantly reduced the amplitude of the IP3‐Ca2+ responses and strongly increased the EC50 of these responses. Finally, we identified palmitoyl‐8G‐IP3RPEP6 as a membrane‐permeable IP3RPEP6 version allowing extracellular application of the IP3R‐inhibiting peptide.ConclusionIP3RPEP6 inhibits IP3R2/R3 at concentrations that have limited effects on IP3R1. IP3R activation triggers hemichannel opening, which strongly affects the amplitude and concentration‐dependence of IP3‐triggered Ca2+ responses.

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“…Structure prediction for CoilE peptide model with PEPFOLD3. 24,25 Live tracking of cellular dynamics using HGN-CoilR (a) HeLa cells transfected with Mito-CoilE-mEmerald were treated with 3.2 pM HGN-CoilR and irradiated using a two-photon microscope at 800 nm. Twenty-four hour post-laser-irradiated images were collected using a Leica SP8 resonant scanning confocal microscope over a period of 2.5 h to demonstrate the ability to track mitochondria movement over time.…”

Section: Confocal Imaging For Colocalization Analysismentioning

confidence: 99%

VIPER^nano: Improved Live Cell Intracellular Protein Tracking

Morgan

Doh

Beatty

et al. 2019

ACS Appl. Mater. Interfaces

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Tracking intracellular proteins in live cells has many challenges. The most widely used method, fluorescent protein fusions, can track proteins in their native cellular environment and has led to significant discoveries in cell biology. Fusion proteins add steric bulk to the target protein and can negatively affect native protein function. The use of exogenous probes such as antibodies or protein labels is problematic because these cannot cross the plasma membrane on their own and thus cannot label intracellular targets in cells. We developed a labeling platform, VIPER nano , for live cell imaging of intracellular proteins using a peptide fusion tag (CoilE) to the protein of interest and delivery of a fluorescently labeled probe peptide (CoilR). CoilR and CoilE form an αhelical heterodimer with the protein of interest, rendering a labeled protein. Delivery of CoilR into the cell uses hollow gold nanoshells (HGNs) as the primary delivery vehicle. The technology relies on the conjugation and light-activated release of the CoilR peptide on the surface of the HGNs. We demonstrate light-activated VIPER nano delivery and labeling with two intracellular proteins, localized either in the mitochondria or the nucleus. This technology has the ability to study intracellular protein dynamics and spatial tracking while lessening the steric bulk of tags associated with the protein of interest.

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Peptide Suboptimal Conformation Sampling for the Prediction of Protein-Peptide Interactions

Cited by 3 publications

References 24 publications

Conformational Dynamics in Extended RGD-Containing Peptides

Conformational Dynamics in Extended RGD-Containing Peptides

IP3RPEP6, a novel peptide inhibitor of IP₃ receptor channels that does not affect connexin‐43 hemichannels

VIPER^nano: Improved Live Cell Intracellular Protein Tracking

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Peptide Suboptimal Conformation Sampling for the Prediction of Protein-Peptide Interactions

Cited by 3 publications

References 24 publications

Conformational Dynamics in Extended RGD-Containing Peptides

Conformational Dynamics in Extended RGD-Containing Peptides

IP3RPEP6, a novel peptide inhibitor of IP3 receptor channels that does not affect connexin‐43 hemichannels

VIPERnano: Improved Live Cell Intracellular Protein Tracking

Contact Info

Product

Resources

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IP3RPEP6, a novel peptide inhibitor of IP₃ receptor channels that does not affect connexin‐43 hemichannels

VIPER^nano: Improved Live Cell Intracellular Protein Tracking