ArticleJournal of Zhejiang University. Science. B2015
Molecular dynamics simulation of the interactions between EHD1 EH domain and multiple peptides.
Article in Journal of Zhejiang University. Science. B, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- Investigating the effects of missense mutations on the dual Ras/Rap activation mechanism of SYNGAP1 using molecular modelling.Journal of structural biology: X · 2026Article
- Unraveling the Interaction Mechanism of the Compounds From Cladophora sp to Recognize Prospective Larvicidal and Bactericidal Activities: In vitro and In Silico Approaches.Molecular biotechnology · 2025Article
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- Computational design and evaluation of a polyvalent vaccine for viral nervous necrosis (VNN) in fish to combat Betanodavirus infection.Scientific reports · 2024Article
- Unraveling modulation effects on albumin synthesis and inflammation by Striatin, a bioactive protein fraction isolated fromHeliyon · 2024Article
- Atomistic simulations reveal impacts of missense mutations on the structure and function of SynGAP1.Briefings in bioinformatics · 2024Article
- An immunoinformatics and extensive molecular dynamics study to develop a polyvalent multi-epitope vaccine against cryptococcosis.PloS one · 2024Article
- Designing a polyvalent vaccine targeting multiple strains of varicella zoster virus using integrated bioinformatics approaches.Frontiers in microbiology · 2023Article
- A novel variant fibrinogen, AαE11del, demonstrating the importance of AαE11 residue in thrombin binding.International journal of hematology · 2021Article
- Simulating Peptide Monolayer Formation: GnRH-I on Silica.International journal of molecular sciences · 2021Article
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5 authors.
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Abstract
objectiveTo provide essential information for peptide inhibitor design, the interactions of Eps15 homology domain of Eps15 homology domain-containing protein 1 (EHD1 EH domain) with three peptides containing NPF (asparagine-proline-phenylalanine), DPF (aspartic acid-proline-phenylalanine), and GPF (glycine-proline-phenylalanine) motifs were deciphered at the atomic level. The binding affinities and the underlying structure basis were investigated.
methodsMolecular dynamics (MD) simulations were performed on EHD1 EH domain/peptide complexes for 60 ns using the GROMACS package. The binding free energies were calculated and decomposed by molecular mechanics/generalized Born surface area (MM/GBSA) method using the AMBER package. The alanine scanning was performed to evaluate the binding hot spot residues using FoldX software.
resultsThe different binding affinities for the three peptides were affected dominantly by van der Waals interactions. Intermolecular hydrogen bonds provide the structural basis of contributions of van der Waals interactions of the flanking residues to the binding.
conclusionsvan der Waals interactions should be the main consideration when we design peptide inhibitors of EHD1 EH domain with high affinities. The ability to form intermolecular hydrogen bonds with protein residues can be used as the factor for choosing the flanking residues.
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