| Autor: |
Priest C; Sandia National Laboratories, Albuquerque, NM, USA., VanGordon MR; Department of Chemistry, University of New Orleans, New Orleans, LA, USA., Rempe C; Sandia National Laboratories, Albuquerque, NM, USA., Chaudhari MI; Sandia National Laboratories, Albuquerque, NM, USA., Stevens MJ; Sandia National Laboratories, Albuquerque, NM, USA., Rick S; Department of Chemistry, University of New Orleans, New Orleans, LA, USA., Rempe SB; Sandia National Laboratories, Albuquerque, NM, USA. slrempe@sandia.gov. |
| Abstrakt: |
Umbrella sampling, coupled with a weighted histogram analysis method (US-WHAM), can be used to construct potentials of mean force (PMFs) for studying the complex ion permeation pathways of membrane transport proteins. Despite the widespread use of US-WHAM, obtaining a physically meaningful PMF can be challenging. Here, we provide a protocol to resolve that issue. Then, we apply that protocol to compute a meaningful PMF for sodium ion permeation through channelrhodopsin chimera, C1C2, for illustration. |
