Defining the membrane disruption mechanism of kalata B1 via coarse-grained molecular dynamics simulations.
Kalata B1 has been demonstrated to have bioactivity relating to membrane disruption. In this study, we conducted coarse-grained molecular dynamics simulations to gain further insight into kB1 bioactivity. The simulations were performed at various concentrations of kB1 to capture the overall progression of its activity. Two configurations of kB1 oligomers, termed tower-like and wall-like clusters, were detected. The conjugation between the wall-like oligomers resulted in the formation of a ring-like hollow in the kB1 cluster on the membrane surface. Our results indicated that the molecules of kB1 were trapped at the membrane-water interface. The interfacial membrane binding of kB1 induced a positive membrane curvature, and the lipids were eventually extracted from the membrane through the kB1 ring-like hollow into the space inside the kB1 cluster. These findings provide an alternative view of the mechanism of kB1 bioactivity that corresponds with the concept of an interfacial bioactivity model.
Biological Engineering Program, King Mongkut's University of Technology Thonburi, 126 Pracha Uthit Rd., Bang Mod, Thung Khru, Bangkok, Thailand, 10140.
Wanapinun
W
Nawae
Department of Chemistry, Kasetsart University, 50 Phaholyothin Rd., Ladyao Chatuchak, Bangkok, Thailand, 10900.
Supa
S
Hannongbua
1] School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian Campus), 49 Soi Thian Thale 25, Bang Khun Thian Chai Thale Rd., Tha Kham, Bang Khun Thian, Bangkok, Thailand, 10150 [2] Bioinformatics and Systems Biology program, King Mongkut's University of Technology Thonburi (Bang Khun Thian Campus), 49 Soi Thian Thale 25, Bang Khun Thian Chai Thale Rd., Tha Kham, Bang Khun Thian, Bangkok, Thailand, 10150.
Marasri
M
Ruengjitchatchawalya
D023181:Antimicrobial Cationic Peptides / Q000494:pharmacology*; D002462:Cell Membrane / Q000187:drug effects / Q000502:physiology*; D047169:Cyclotides / Q000494:pharmacology*; D008051:Lipid Bilayers / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D010940:Plant Proteins / Q000494:pharmacology; D011485:Protein Binding; D014867:Water / Q000737:chemistry
D023181:Antimicrobial Cationic Peptides; D047169:Cyclotides; D008051:Lipid Bilayers; D010940:Plant Proteins; C091930:kalata B1; D014867:Water