Abstract
We have investigated the structure and energetics of alamethicin oligomers in cylindrical pores using molecular dynamics simulations with a modified version of implicit membrane model 1 (IMM1-pore). We have added a new energy term to IMM1-pore to include the free energy cost of hydrophobic area exposure. With this new energy function, we have studied monomer to nonamer in cylindrical pores with radii ranging from 5 to 12 A. Stable, low energy pores are obtained for the right combination of radius and oligomeric number. The smaller oligomers (trimer to tetramer) formed closed pores for pore radius 6 A while the larger oligomers formed open pores at their optimal pore size. The octamer in a pore of radius 11 A gives the lowest effective energy per monomer. The tilt angles of the helices in the pore are 10-25° with respect to the membrane normal. The kink produced by Pro14 makes the pore funnel-like. Voltage seems to have little effect on the structure and stability of the pore.
Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
