Investigation on two human defensin dimers: structure prediction and refinement using a combined simulation strategy

Abstract

Defensins are cationic cysteine-rich small molecules belonging to the innate immune system. Most defensins form dimers that can enhance their function. Thus, predicting their dimer structures, if unavailable, is important. In this project, a combined simulation strategy is applied to predict dimer structures of two defensins, human defensin type 2 (hBD-2) and human defensin type 5 (HD5), which includes predicting the initial dimer structure running implicit solvent replica-exchange (REX) simulations with a GBSW module, then running microsecond-long all-atom simulations with the CHARMM36 forcefield to refine the prediction. The combined simulations predicted the dimer structures in good agreement with crystal structures within simulation uncertainty. Microsecond-long refinement on the crystal structures of hBD-2 and HD5 dimers shows that CHARMM36 forcefield could contribute a structural deviation of 1.0–3.0 Å from their crystal structures. Comparing the RMSD, RMSF, radius of gyration, accessible surface area (ASA), number of hydrogen bonds (H-bonds) and residue distance map for simulations starting from the REX initiated structure and the crystal structure, consistent agreements were reached for both dimers. However, hBD-2 dimer has a larger hydrophobic ASA, while HD5 has a larger hydrophilic ASA; HD5 forms 45 H-bonds on the binding interface while 12 for hBD-2 dimer.