Molecular Dynamic Studies Of The MethionineABC Transporter

Cell survival requires the regulated and selective passage of specific moleculesacross these membranes, not only to acquire nutrients and excrete waste products, butalso for a multitude of regulatory and other functions. Transmembrane transport ismediated by specific proteins associated with the membrane. The characterizations ofthese proteins and their roles in cellular physiology have been a focus of intensiveresearch for many years. It is now apparent that these myriad membrane transportsystems can be grouped into a limited number of families. Within any one family,members are related to each other in sequence and molecular mechanisms andprobably have a common evolutionary origin. This study considers the largest andmost diverse of these families, the ABC superfamily. Each ABC transporter isrelatively specific for a given substrate. Nevertheless, the variety of substrateshandled by different transporters is enormous: ABC transporters specific for aminoacids, sugars, inorganic ions, polysaccharides, peptides, and even proteins have beencharacterized. ABC transporters have received considerable attention recently becausethey are associated with many important biological processes in both prokaryotes andeukaryotes, as well as with clinical problems such as cystic fibrosis, antigenpresentation, and multidrug resistance of cancers. The designation ABC transporterrecognizes a highly conserved ATP-binding cassette, which is the most characteristicfeature of this superfamily. Since the first high-resolution structure of an ABCtransporter, the Escherichia coli vitamin B12importer, was reported in2002, crystalstructures of many importers and exporters have been solved. ABC transporterscontain two transmembrane domains or subunits (TMDs) that form the translocationpathway and two cytoplasmic nucleotide-binding domains or subunits (NBDs) that hydrolyze ATP. ABC transporters diverged very early into two classes that correlatewith the direction of substrate transport. Importers, found in prokaryotes, containadditional periplasmic or cell-surface-associated binding proteins that bind substrateswith high affinity and deliver them to the TMDs. Exporters recruit their substratesdirectly from the cytoplasm or lipid bilayer. Whereas the TMDs have low sequencesimilarity, the NBDs are highly conserved, each consisting of a RecA-like subdomaincontaining Walker A and B motifs and a helical subdomain containing the LSGGQsignature motif. In addition to the common NBDs and TMDs, the methionine ABCtransporter has C-terminal regulatory domains (C2domains) that belong to ACTprotein family. When the amount of methionine in the cell is high, the transport stops.This phenomenon is called trans-inhibition. To understand how a trans-inhibitedprotein returns to an uninhibited, resting state, we performed steered moleculardynamic (SMD) simulations with and without the substrates. From the simulations,we observed some important conformational changes in the whole ABC transporter,including the constriction in the translocation pathway in the TMDs and approach ofthe NBDs. However, the C2domains behaved different in two types of thesimulations. These findings might help to explain the relationship of theconformational changes of the C2domains with the rearrangements of the NBDs orTMDs, and providing a way to understand the trans-inhibition from an oppositedirection.