title: Targeted molecular dynamics (TMD) of the full-length KcsA potassium channel: on the role of the cytoplasmic domain in the opening process.
abstract: Some recent papers clearly indicate that the cytoplasmic domain of KcsA plays a role in pH sensing. We have performed, for the first time, a targeted molecular dynamics (TMD) simulation of the opening of full-length KcsA at pH 4 and pH 7, with a special interest for the cytoplasmic domain. Association energy calculations show a stabilization at pH 7 confirming that the protonation of some amino-acids at pH 4 in this domain plays a role in the opening process. A careful analysis of the pH dependent charges borne by residues in the cytoplasmic domain and their interactions confirms some literature experimental data and permits to give further insight into the role played by some of them in the opening process.
authors.affiliation: Department of Chemistry, Lanzhou University, Lanzhou, Gansu 730000, People's Republic of China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.forename: Florent
authors.initials: F
authors.lastname: Barbault
authors.forename: Michel
authors.initials: M
authors.lastname: Delamar
authors.forename: Ruisheng
authors.initials: R
authors.lastname: Zhang
authors.forename: Rongjing
authors.initials: R
authors.lastname: Hu
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D015640:Ion Channel Gating; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D015221:Potassium Channels / Q000737:chemistry*; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D048170:Streptomyces lividans / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; D015221:Potassium Channels; C107790:prokaryotic potassium channel