Paper Citing NAMD - Abstract
Klauda, Jeffery B.; Brooks, Bernard R.
Sugar binding in lactose permease: Anomeric state of a disaccharide influences binding structure
JOURNAL OF MOLECULAR BIOLOGY, 367:1523-1534, APR 13 2007
Lactose permease in Escherichia coli (LacY) transports both anomeric states of disaccharides but has greater affinity for a-sugars. Molecular dynamics (MD) simulations are used to probe the protein-sugar interactions, binding structures, and global protein motions in response to sugar binding by investigating LacY (the experimental mutant and wild-type) embedded in a fully hydrated lipid bilayer. A total of 12 MD simulations of 20-25 ns each with beta(alpha)-D-galactopyranosyl-(1,1)-beta-D-galactopyranoside (beta beta-(Galp)(2)) and alpha beta-(Galp)(2) result in binding conformational families that depend on the anomeric state of the sugar. Both sugars strongly interact with Glu126 and alpha beta-(Galp)(2) has a greater affinity to this residue. Binding conformations are also seen that involve protein residues not observed in the crystal structure, as well as those involved in the proton translocation (Phe118, Asn119, Asn240, His322, Glu325, and Tyr350). Common to nearly all protein-sugar structures, water acts as a hydrogen bond bridge between the disaccharide and protein. The average binding energy is more attractive for alpha beta-(Galp)(2) than beta beta-(Galp)(2), i.e. -10.7(+/- 0.7) and -3.1(+/- 1.0) kcal/mol, respectively. Of the 12 helices in LacY, helix-IV is the least stable with beta beta-(Galp)(2) binding resulting in larger distortion than alpha beta-(Galp)(2). Published by Elsevier Ltd.
