Flexible docking of peptides to proteins using CABS‐dock

Kurciński, Mateusz; Badaczewska-Dawid, Aleksandra E.; Koliński, Michał; Koliński, Andrzej; Kmiecik, Sebastian

doi:10.1002/pro.3771

Cited by 48 publications

(51 citation statements)

References 38 publications

(139 reference statements)

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“…Molecular docking simulation can predict the structures of the protein–peptide complex, and is widely used to study the inhibition of enzymatic reactions by inhibitors including peptides (He et al., 2019). In this study, it was an effective tool to screen peptides with certain activity (Kurcinski, Badaczewska‐Dawid, Kolinski, Kolinski, & Kmiecik, 2020). Total score can reflect the binding affinities and stability of ligand to receptor, comprehensively considering hydrophobic interaction, binding affinities and binding strength (Guo, He, & Hou, 2020).…”

Section: Resultsmentioning

confidence: 99%

Purification, identification, and computational analysis of xanthine oxidase inhibitory peptides from kidney bean

Hou

2021

Journal of Food Science

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Hyperuricemia is related to plenty of diseases, seriously damaging human health. Current clinical drugs used to treat hyperuricemia have many adverse effects. In this study, kidney bean hydrolysate (KBH) was found to exert high xanthine oxidase inhibitory (XOI) activity. Compared to KBH (50.31 ± 2.73%), XOI activities of three fractions (Mw <5 kDa, Mw<3 kDa, Mw < 1 kDa) by ultrafiltration were higher and increased to 58.58 ± 3.57%, 59.34 ± 1.78%, and 55.05 ± 5.00%, respectively (P < 0.05). A total of 69 peptides were identified by HPLC‐ESI‐MS/MS and analyzed binding affinities with XO with the help of molecular docking. AVDSLVPIGR, DWYDIK, LDNLLR, ISPIPVLK, ISSLEMTR showed well binding affinities with XO and DWYDIK presented the highest XOI activity (68.63 ± 5.07%) among five synthetic peptides (P < 0.05). Additionally, visual analysis results indicated that DWYDIK was pushed into the hydrophobic channel and formed hydrogen bonds with pivotal amino acids of xanthine oxidase. Overall, KBH could be a promising candidate as anti‐ hyperuricemia functional food. Practical Application This research initially revealed that kidney bean peptides could significantly inhibit the activity of xanthine oxidase, indicating kidney bean peptides could be a treatment for hyperuricemia. Kidney bean peptides may have commercial potentials as a safer alternative with few side effects to drugs.

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Section: Resultsmentioning

confidence: 99%

Purification, identification, and computational analysis of xanthine oxidase inhibitory peptides from kidney bean

Hou

2021

Journal of Food Science

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“…The flexible N terminus of ARIH2 was docked onto ASB9-CRL using GalaxyWEB PepDock ( 34 ), CABS-dock ( 35 ), and HPEPDOCK ( 36 ). These docking programs were selected for their ability to model long peptides (>20 aa) in large proteins (>300 aa) and to discriminately score various models.…”

Section: Methodsmentioning

confidence: 99%

“…Substitution of ARIH2 for ARIH1 gave the structure of ARIH2-UBE2L3-Ub based on the structure of the complex (PDB 5UDH).Docking the N-terminus of ARIH2 into ASB9-CRL. The flexible N-terminus of ARIH2 was docked onto ASB9-CRL using GalaxyWEB PepDock(35), CABS-dock(36), and HPEPDOCK (37). These docking programs were selected for their ability to model long peptides (>20 aa) in large proteins (>300 aa) and to discriminately score various models.…”

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confidence: 99%

The Mechanism of NEDD8 Activation of CUL5 Ubiquitin E3 Ligases

Lumpkin

Ahmad

Blake

et al. 2021

Molecular & Cellular Proteomics

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Cullin RING E3 Ligases (CRLs) ubiquitylate hundreds of important cellular substrates. Here we have assembled and purified the Ankyrin repeat and SOCS Box protein 9 CUL5 RBX2 Ligase (ASB9-CRL) in vitro and show how it ubiquitylates one of its substrates, CKB. CRLs occasionally collaborate with RING between RING E3 ligases (RBRLs) and indeed, mass spectrometry analysis showed that CKB is specifically ubiquitylated by the ASB9-CRL-ARIH2-UBE2L3 complex. Addition of other E2s such as UBE2R1 or UBE2D2 contribute to polyubiquitylation but do not alter the sites of CKB ubiquitylation. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) analysis revealed that CUL5 neddylation allosterically exposes its ARIH2 binding site, promoting high affinity binding, and it also sequesters the NEDD8 E2 (UBE2F) binding site on RBX2. Once bound, ARIH2 helices near the Ariadne domain active site are exposed, presumably relieving its autoinhibition. These results allow us to propose a model of how neddylation activates ASB-CRLs to ubiquitylate their substrates.

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“…CABS-dock is a well-established method for flexible protein-peptide docking and its current status has been summarized in the recent review [32]. CABS-dock uses a very efficient simulation approach, the CABS coarse-grained protein model (its broad applications in protein modeling, protein structure prediction, simulation of protein flexibility and disordered states have been recently summarized in the reviews [33][34][35].…”

Section: Stage 1: Molecular Docking Using Cabs-dockmentioning

confidence: 99%

Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement

Badaczewska-Dawid

Kmiecik

Koliński

2020

Preprint

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The structural description of peptide ligands bound to G protein-coupled receptors (GPCRs) is important for the discovery of new drugs and deeper understanding of the molecular mechanisms of life. Here we describe a three-stage protocol for the molecular docking of peptides to GPCRs using a set of different programs: (1) CABS-dock for docking fully flexible peptides; (2) PD2 method for the reconstruction of atomistic structures from C-alpha traces provided by CABS-dock and (3) Rosetta FlexPepDock for the refinement of protein-peptide complex structures and model scoring. We evaluated the proposed protocol on the set of 7 different GPCR-peptide complexes (including one containing a cyclic peptide) for which crystallographic structures are available. We show that CABS-dock produces high resolution models in the sets of top-scored models. These sets of models, after reconstruction to all-atom representation, can be further improved by Rosetta high-resolution refinement and/or minimization, leading in most of the cases to sub-Angstrom accuracy in terms of interface RMSD measure.

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Flexible docking of peptides to proteins using CABS‐dock

Cited by 48 publications

References 38 publications

Purification, identification, and computational analysis of xanthine oxidase inhibitory peptides from kidney bean

Purification, identification, and computational analysis of xanthine oxidase inhibitory peptides from kidney bean

The Mechanism of NEDD8 Activation of CUL5 Ubiquitin E3 Ligases

Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement

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