title: Understanding the -C-X1-X2-C- motif in the active site of the thioredoxin superfamily: E. coli DsbA and its mutants as a model system.
abstract: E. coli DsbA is an intensively studied enzyme of the thioredoxin superfamily of thiol-disulfide oxidoreductases. DsbA catalyzes the disulfide bond formation and folding of proteins in the bacterial periplasm. DsbA and its mutants have highlighted the strong and puzzling influence of the -C-X1-X2-C- active site variants, found across the thioredoxin superfamily, on the ionization and redox properties of this site. However, the interpretation of these observations remains wanting, largely due to a dearth of structural information. Here, molecular dynamics simulations are used to provide extensive information on the structure and dynamics of reduced -C30-X31-X32-C33- motifs in wild type DsbA and 13 of its mutants. These simulations are combined with calculations of the pK of H32 and of the very low pK of the catalytic cysteine C30. In wild type DsbA, the titrations of C30 and H32 are shown to be coupled; the protonation states and dynamics of H32 are examined. The thiolate of C30 is stabilized by hydrogen bonds with the protein. Modulation of these hydrogen bonds by alteration of residue X32 has the greatest impact on the pK of C30, which rationalizes its higher pK in thioredoxin and tryparedoxin. Because of structural constrains, residue X31 has only an indirect and weak influence on the pK of C30. The dynamics of C30 is clearly related to its stabilizing interactions and pK value. Although relatively small differences between pKs were not reproduced in the calculations, the major trends are explained, adding new insights to our understanding of enzymes in this family.
authors.affiliation: Institute of Molecular Biology, Bulgarian Academy of Sciences , Acad. G. Bonchev Str., bl. 21, Sofia 1113, Bulgaria.
authors.forename: Andrey
authors.initials: A
authors.lastname: Karshikoff
authors.forename: Lennart
authors.initials: L
authors.lastname: Nilsson
authors.forename: Nicolas
authors.initials: N
authors.lastname: Foloppe
mesh_terms: D020816:Amino Acid Motifs; D020134:Catalytic Domain; D003545:Cysteine / Q000737:chemistry; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics*; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D019704:Protein Disulfide-Isomerases / Q000737:chemistry* / Q000235:genetics*; D013879:Thioredoxins / Q000737:chemistry
chemical_list: D029968:Escherichia coli Proteins; D013879:Thioredoxins; D019704:Protein Disulfide-Isomerases; C526648:dsbA protein, E coli; D003545:Cysteine