ArticleMolecules (Basel, Switzerland)2018
Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes.
Article in Molecules (Basel, Switzerland), 2018. 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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Who cites it
10 citing papers in PubMed.
- Nanomechanical response of peptide-bound DNA as a model molecular bio-nanocomposite: a steered molecular dynamics study.Journal of molecular modeling · 2026Article
- Novel asymmetrical azines appending 1,3,4-thiadiazole sulfonamide: synthesis, molecular structure analyses,RSC advances · 2023Article
- Using steered molecular dynamic tension for assessing quality of computational protein structure models.Journal of computational chemistry · 2022Article
- Molecular mechanisms of amyloid disaggregation.Journal of advanced research · 2022Review
- In Silico Investigation of Phytoconstituents of Medicinal Herb 'Results in chemistry · 2021Article
- A New Family of Benzo[International journal of molecular sciences · 2021Article
- Article
- Investigation of Some AntiviralInternational journal of molecular sciences · 2020Article
- Pharmacophoric Site Identification and Inhibitor Design for Autotaxin.Molecules (Basel, Switzerland) · 2019Article
- Molecular Modeling in Drug Design.Molecules (Basel, Switzerland) · 2019Article
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Authors and funding
5 authors.
Funding
Abstract
Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered molecular dynamics (SMD) to assess the strength of protein-peptide interactions. The idea behind using SMD simulations is that the mechanical stability can be used as a promising and an efficient alternative to computationally highly demanding estimation of binding affinity. However, mechanical stability defined as a peak in force-extension profile depends on the choice of the pulling direction. Here we propose an uncommon choice of the pulling direction along resultant dipole moment (RDM) vector, which has not been explored in SMD simulations so far. Using explicit solvent all-atom MD simulations, we apply SMD technique to probe mechanical resistance of ligand-receptor system pulled along two different vectors. A novel pulling direction-when ligand unbinds along the RDM vector-results in stronger forces compared to commonly used ligand unbinding along center of masses vector. Our observation that RDM is one of the factors influencing the mechanical stability of protein-peptide complex can be used to improve the ranking of binding affinities by using mechanical stability as an effective scoring function.
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Registered trials
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