The mechanism of glycerol conduction in aquaglyceroporins

Background: The E. coli glycerol facilitator, GlpF, selectively conducts gl ycerol and water, excluding ions and charged solutes. The detailed mechanis m of the glycerol conduction and its relationship to the characteristic sec ondary structure of aquaporins and to the NPA motifs in the center of the c hannel are unknown. Results: Molecular dynamics simulations of GlpF reveal spontaneous glycerol and water conduction driven on a nanosecond timescale, by thermal fluctuat ions. he bidirectional conduction, guided and facilitated by the secondary structure, is characterized by breakage and formation of hydrogen bonds for which water and glycerol compete. The conduction involves only very minor changes in the protein structure, and cooperativity between the GlpF monome rs is not evident. The two conserved NPA motifs are strictly linked togethe r by several stable hydrogen bonds and their asparagine side chains form hy drogen bonds with the substrates passing the channel in single file. Conclusions: A complete conduction of glycerol through the GlpF was deduced from molecular dynamics simulations, and key residues facilitating the con duction were identified. The nonhelical parts of the two half-membrane-span ning segments expose carbonyl groups towards the channel interior, establis hing a curve-linear pathway. The conformational stability of the NPA motifs is important in the conduction and critical for selectivity. Water and gly cerol compete in a random manner for hydrogen bonding sites in the protein, and their translocations in single file are correlated. The suggested cond uction mechanism should apply to the whole family.