Exploring calcium ion-dependent effect on the intermolecular interaction between human secreted phospholipase A2 and its peptide inhibitors in coronary artery disease
| Autor: | Xiaoye Su, Dingkun Wu, Fang Cao, Guanggan Bo, Junwu Xing, Yunxian Zhu, Min Li |
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| Rok vydání: | 2019 |
| Předmět: |
Molecular model
chemistry.chemical_element Peptide binding Peptide Coronary Artery Disease Calcium Molecular Dynamics Simulation 01 natural sciences 03 medical and health sciences Phospholipase A2 Materials Chemistry Humans Platelet Physical and Theoretical Chemistry Enzyme Inhibitors Spectroscopy 030304 developmental biology chemistry.chemical_classification 0303 health sciences biology 010405 organic chemistry Computer Graphics and Computer-Aided Design 0104 chemical sciences Enzyme Activation Phospholipases A2 Enzyme chemistry Helix biology.protein Biophysics Peptides Protein Binding |
| Zdroj: | Journal of molecular graphicsmodelling. 93 |
| ISSN: | 1873-4243 |
| Popis: | Human secreted phospholipase A2 (hsPLA2) is a small calcium ion (Ca2+)-regulatory protein secreting from platelets, eosinophils and T-lymphocytes, which has been established as an important biomarker and potential target for the diagnosis and therapy of coronary artery disease. Short peptide inhibitors are used to competitively suppress the enzymatic activity of hsPLA2. Here, Ca2+ effect on the intermolecular recognition and interaction between hsPLA2 and its peptide inhibitors is investigated systematically by using molecular modeling and bioinformatics analysis. Dynamics simulations reveal that the hsPLA2 structure bound with Ca2+ is rather stable and has low thermal motion; removal of Ca2+ considerably increases structural flexibility and intrinsic disorder of the protein. Energetics calculations suggest that presence of Ca2+ can effectively promote the interaction of hsPLA2 with peptide inhibitors. In particular, the local substructures of hsPLA2 such as helix H1, loop L2 and double-stranded β-sheet DS that participate in peptide recognition are involved in or nearby Ca2+-coordinating site and can be directly stabilized by the Ca2+. In addition, a significant concentration-dependent effect of Ca2+ on peptide–hsPLA2 binding is observed in vitro, that is, a little of Ca2+ can largely improve peptide binding affinity, but high Ca2+ concentration does not increase the affinity substantially. The correlation between calculated free energy and experimental binding affinity over different peptide inhibitors is improved considerably by adding Ca2+ to hsPLA2. Specifically, the FLSYK peptide can generally bind to Ca2+-bound hsPLA2 with a moderate or high affinity (Kd ranges between 56 and 210 μM), but have only a modest affinity or even nonbinding to Ca2+-free hsPLA2 (Kd > 400 μM or = n.d.). |
| Databáze: | OpenAIRE |
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