(626f) Alternating Mechanism in Transporters: Insights From MD and NMA

During nerve impulse transmission, neurotransmitters are released into the synaptic cleft and once the signal cease are taken back up into the presynaptic cell. This re-uptake is catalyzed by a family of membrane transport proteins known as the neurotransmitter/sodium symporters (NSS). The NSSs couple the uptake of specific neurotransmitters to the transmembrane gradients of ions (e.g. Na,Cl, K). Within this family, the biogenic amine subfamily is responsible for the reuptake of serotonin, dopamine, and norepinephrine. These transporters are the targets of antidepressants, cocaine, and amphetamines. The high sequence homology among the NSS transporters suggests a common architecture constituted of 12 membrane spanning alpha-helices. The three-dimensional structure of these protein is still largely unknown and lately, models have been constructed from the recently crystallized bacterial leucine transporter (LeuTAa). In spite of these efforts the molecular mechanism by which these transporters bind and translocate their substrates remains unknown. One of the proposed mechanisms involves conformational changes that alternately expose the central biding site to each side of the membrane.

We combined normal mode analysis and full atomistic molecular dynamics (MD) simulations to test the feasibility of the alternating mechanism hypothesis. We found that an small set of the low frequency normal modes, which are known to be a good description for protein conformational changes, are able to describe a fair amount of the displacement produced in a perturbed MD trajectory designed to force the opening of the periplasmic half the protein. Based on the elastic network approximation, we tested the robustness of the method comparing different force constant functionality and using several LeuTAa crystallized structures. The relevance of this method relies in the predicting power of the normal modes analysis, which based only in topological properties of the protein can predict how it will face a perturbation.