Analysis of mutations of defensin protein using accelerated molecular dynamics simulations

• Published in: PloS one Vol. 15; no. 11; p. e0241679
• Main Authors: Pandey, Bharati, Tyagi, Chetna, Prajapati, Gopal Kumar, Mishra, Awdhesh Kumar, Hashem, Abeer, Alqarawi, Abdulaziz A, Abd Allah, Elsayed Fathi, Mohanta, Tapan Kumar
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 30.11.2020; Public Library of Science (PLoS)
• Subjects: Amino Acid Sequence; Amino acids; Antifungal activity; Antifungal agents; Biology and Life Sciences; Chemical bonds; Defensins; Defensins - chemistry; Defensins - genetics; Deuterium - chemistry; Disulfide bonds; Free energy; Fungicides; Gene mutation; Genetic research; Homology; Identification and classification; Lipids; Medicine and Health Sciences; Membranes; Molecular dynamics; Molecular Dynamics Simulation; Molecular Sequence Data; Mutants; Mutation; Mutation - genetics; Peptides; Physical Sciences; Plant proteins; Properties; Proteins; Sequence Alignment; Sequence Homology, Amino Acid; Simulation; Trypsin; α-Amylase; India; Saudi Arabia; Hungary; Riyadh Saudi Arabia
• DOI: 10.1371/journal.pone.0241679
• ISSN: 1932-6203

Plant defensins possess diverse biological functions that include antifungal and antibacterial activities and α-amylase and trypsin inhibitory properties. Two mutations, G9R and V39R, were confirmed to increase the antifungal activity of Raphanus sativus antifungal protein 2 (RsAFP2). Accelerated Molecular Dynamics (aMD) were carried out to examine the conformational changes present in these RsAFP2 mutants, and its two closest homologs compared to the wild-type protein. Specifically, the root mean square fluctuation values for the eight cysteine amino acids involved in the four disulfide bonds were low in the V39R mutant compared to the wild-type. Additionally, analysis of the free energy change revealed that G9R and V39R mutations exert a neutral and stabilizing effect on RsAFP2 conformation, and this is supported by the observed lower total energy of mutants compared to the wild-type, suggesting that enhanced stability of the mutants. However, MD simulations to a longer time scale would aid in capturing more conformational state of the wild-type and mutants defensin protein. Furthermore, the aMD simulations on fungal mimic membranes with RsAFP2 and its mutants and homologs showed that the mutant proteins caused higher deformation and water diffusion than the native RsAFP2, especially the V39R mutant. The mutant variants seem to interact by specifically targeting the POPC and POPI lipids amongst others. This work highlights the stabilizing effect of mutations at the 9th and 39th positions of RsAFP2 and their increased membrane deformation activity.