title: Dissection of the water cavity of yeast thioredoxin 1: the effect of a hydrophobic residue in the cavity.
abstract: The water cavity of yeast thioredoxin 1 (yTrx1) is an ancestral, conserved structural element that is poorly understood. We recently demonstrated that the water cavity is involved in the complex protein dynamics that are responsible for the catalytically relevant event of coupling hydration, proton exchange, and motion at the interacting loops. Its main feature is the presence of the conserved polar residue, Asp24, which is buried in a hydrophobic cavity. Here, we evaluated the role of the solvation of Asp24 as the main element that is responsible for the formation of the water cavity in thioredoxins. We showed that the substitution of Asp24 with a hydrophobic residue (D24A) was not sufficient to completely close the cavity. The dynamics of the D24A mutant of yTrx1 at multiple time scales revealed that the D24A mutant presents motions at different time scales near the active site, interaction loops, and water cavity, revealing the existence of a smaller dissected cavity. Molecular dynamics simulation, along with experimental molecular dynamics, allowed a detailed description of the water cavity in wild-type yTrx1 and D24A. The cavity connects the interacting loops, the central β-sheet, and α-helices 2 and 4. It is formed by three contiguous lobes, which we call lobes A-C. Lobe A is hydrophilic and the most superficial. It is formed primarily by the conserved Lys54. Lobe B is the central lobe formed by the catalytically important residues Cys33 and Asp24, which are strategically positioned. Lobe C is the most hydrophobic and is formed by the conserved cis-Pro73. The central lobe B is closed upon introduction of the D24A mutation, revealing that independent forces other than solvation of Asp24 maintain lobes A and C in the open configuration. These data allow us to better understand the properties of this enzyme.
authors.affiliation: †Institute of Medical Biochemistry, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
authors.forename: Anwar
authors.initials: A
authors.lastname: Iqbal
authors.affiliation: §Laboratory of Toxicology, Instituto Oswaldo Cruz, Fiocruz, 21045-900 Rio de Janeiro, Brazil.
authors.forename: Francisco
authors.initials: F
authors.lastname: Gomes-Neto
authors.affiliation: ∥Faculdades Integradas de Três Lagoas-AEMS, Três Lagoas, Brazil.
authors.forename: Catarina Akiko
authors.initials: CA
authors.lastname: Myiamoto
authors.affiliation: ‡Center of Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
authors.forename: Ana Paula
authors.initials: AP
authors.lastname: Valente
authors.affiliation: †Institute of Medical Biochemistry, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
authors.forename: Fabio C L
authors.initials: FC
authors.lastname: Almeida
mesh_terms: D019943:Amino Acid Substitution; D001224:Aspartic Acid / Q000737:chemistry / Q000235:genetics; D057927:Hydrophobic and Hydrophilic Interactions; D008565:Membrane Proteins / Q000737:chemistry* / Q000235:genetics; D056004:Molecular Dynamics Simulation; D020125:Mutation, Missense; D054464:Peroxiredoxins / Q000737:chemistry* / Q000235:genetics; D017433:Protein Structure, Secondary; D012441:Saccharomyces cerevisiae / Q000201:enzymology* / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000235:genetics; D013329:Structure-Activity Relationship
chemical_list: D008565:Membrane Proteins; D029701:Saccharomyces cerevisiae Proteins; C103243:TRX1 protein, S cerevisiae; D001224:Aspartic Acid; D054464:Peroxiredoxins