Changes in Internal Structure and Dynamics upon Binding Stabilise the Nematode Anticoagulant NAPc2
Abstract
:1. Introduction
2. Materials and Methods
2.1. Molecular Dynamics Simulations
2.2. Plasmid Construction
2.3. Protein Expression and Purification
2.4. Prothrombin Time Coagulation Assays
3. Results
3.1. Simulations Capture Mobility of NAPc2
3.2. The fXa Bound Conformation Was Not Present in the Free NAPC2 Simulation
3.3. Binding to fXa Stabilizes NAPc2
3.4. Internal Salt Bridge Found in Bound Conformation
3.5. Internal Salt Bridge Required for Maximal Activity
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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NAPc2 | fXa | NAPc2-fXa | |
---|---|---|---|
PDB code | 1COU 1 | 2H9E | 2H9E |
PDB method | NMR | X-ray | X-ray |
residues | 85 | 281 | 366 |
protein atoms | 1267 | 4312 | 5579 |
counterions | 18 Na+, 6 Cl− | 28 Na+, 29 Cl− | 63 Na+, 50 Cl− |
water molecules | 4481 | 10,434 | 15,885 |
box size (Å) | 33 × 28 × 44 | 47 × 65 × 53 | 53 × 57 × 80 |
simulation length (ns) | 100 | 100 | 100 |
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Woodward, E.; Duggan, B.M. Changes in Internal Structure and Dynamics upon Binding Stabilise the Nematode Anticoagulant NAPc2. Biomolecules 2024, 14, 421. https://doi.org/10.3390/biom14040421
Woodward E, Duggan BM. Changes in Internal Structure and Dynamics upon Binding Stabilise the Nematode Anticoagulant NAPc2. Biomolecules. 2024; 14(4):421. https://doi.org/10.3390/biom14040421
Chicago/Turabian StyleWoodward, Elaine, and Brendan M. Duggan. 2024. "Changes in Internal Structure and Dynamics upon Binding Stabilise the Nematode Anticoagulant NAPc2" Biomolecules 14, no. 4: 421. https://doi.org/10.3390/biom14040421