| 학회 | 한국고분자학회 |
| 학술대회 | 2005년 가을 (10/13 ~ 10/14, 제주 ICC) |
| 권호 | 30권 2호 |
| 발표분야 | 의료용 고분자 부문위원회 |
| 제목 | Energetics of ion conduction through gramicidin channel |
| 초록 | Gramicidins are a family of antibiotics that exert their antibacterial activity by increasing the cation permeability of the target bacterial plasma membrane, due to the formation of bilayer-spanning channels. Gramicidin channels selectively permeate monovalent cations, such as H+, NH4+, Cs+, Rb+, K+, Na+, and Li+, across the inner membrane of gram-positive bacteria. We have investigated the translocation of a single ion through the gramicidin channel by using molecular dynamics (MD) simulations. To simulate complete, continuous conduction events of a single ion through the gramicidin channel within a feasible computing time, we employ the technique of steered MD (SMD) that accelerates the conduction by applying external forces on a single ion in a manner that still retains the intrinsic conduction mechanism. Employing Jarzynski's equality between free energy and irreversible work, we can obtain the free energy profile along the conduction pathway through a time series analysis of MD trajectories. The calculated profile pinppoints barriers inside the channel. We examine valence selectivity of the gramicidin channel by performing SMD of Na+, Ca2+ and Cl-. We also compare the conductivity of various monovalent cations by performing SMD of Cs+, K+, etc. Fig. 1. Microscopic simulation system: gramicidin channel embedded in a DMPC lipid bilayer and solvated with 9720 water molecules and a pair of NaCl ions. Na+ ion is indicated by yellow sphere and Cl- ion by green sphere. Lipid bilayer is not shown for the sake of clarity. The figure was generated using PyMOL. |
| 저자 | 박진우, 고연조, 허준, 조원호 |
| 소속 | 서울대 |
| 키워드 | steered molecular dynamics; gramicidin; ion channel |
