Paper Citing NAMD - Abstract
Jorgensen, Anne Marie; Tagmose, Lena; Jorgensen, Anne Marie M.; Bogeso, Klaus P.; Peters, Guenther H.
Molecular dynamics simulations of Na+/Cl--dependent neurotransmitter transporters in a membrane-aqueous system
CHEMMEDCHEM, 2:827-840, JUN 2007
We have performed molecular dynamics simulations of a homology model of the human serotonin transporter (hSERT) in a membrane environment and in complex with either the natural substrate S-HT or the selective serotonin reuptake inhibitor escitaloprom. We have also included a transporter homologue, the Aquifex aeolicus leucine transporter (LeuT), in our study to evaluate the applicability of a simple and computationally attractive membrane system. Fluctuations in LeuT extracted from simulations are in good agreement with crystal logrophic B factors. Furthermore, key interactions identified in the X-ray structure of, LeuT are maintained throughout the simulations indicating that our simple membrane system is suitable for studying the transmembrane protein hSERT in complex with 5-HT or escitoloprom. For these transporter complexes, only relatively small fluctuations are observed in the ligand-binding cleft. Specific interactions responsible for ligand recognition, are identified in the hSERT-5HT and hSERT-escitaloprom complexes. Our finding5 are in good agreement with predictions from mutagenesis studies.
