title: Probing water environment of Trp59 in ribonuclease T1: insight of the structure-water network relationship.
abstract: In this study, we used the tryptophan analogue, (2,7-aza)Trp, which exhibits water catalyzed proton transfer isomerization among N(1)-H, N(7)-H, and N(2)-H isomers, to probe the water environment of tryptophan-59 (Trp59) near the connecting loop region of ribonuclease Tl (RNase T1) by replacing the tryptophan with (2,7-aza)Trp. The resulting (2,7-aza)Trp59 triple emission bands and their associated relaxation dynamics, together with relevant data of 7-azatryptophan and molecular dynamics (MD) simulation, lead us to propose two Trp59 containing conformers in RNase T1, namely, the loop-close and loop-open forms. Water is rich in the loop-open form around the proximity of (2,7-aza)Trp59, which catalyzes (2,7-aza)Trp59 proton transfer in the excited state, giving both N(1)-H and N(7)-H isomer emissions. The existence of N(2)-H isomer in the loop-open form, supported by the MD simulation, is mainly due to the specific hydrogen bonding between N(2)-H proton and water molecule that bridges N(2)-H and the amide oxygen of Pro60, forming a strong network. The loop-close form is relatively tight in space, which squeezes water molecules out of the interface of α-helix and β2 strand, joined by the connecting loop region; accordingly, the water-scant environment leads to the sole existence of the N(1)-H isomer emission. MD simulation also points out that the Trp-water pairs appear to preferentially participate in a hydrogen bond network incorporating polar amino acid moieties on the protein surface and bulk waters, providing the structural dynamic features of the connecting loop region in RNase T1.
authors.affiliation: Department of Chemistry and Center for Emerging Material and Advanced Devices, National Taiwan University , Taipei 10617, Taiwan.
authors.forename: Wei-Chih
authors.initials: WC
authors.lastname: Chao
authors.forename: Jiun-Yi
authors.initials: JY
authors.lastname: Shen
authors.forename: Jyh-Feng
authors.initials: JF
authors.lastname: Lu
authors.forename: Jinn-Shyan
authors.initials: JS
authors.lastname: Wang
authors.forename: Hsiao-Ching
authors.initials: HC
authors.lastname: Yang
authors.forename: Kevin
authors.initials: K
authors.lastname: Wee
authors.forename: Li-Ju
authors.initials: LJ
authors.lastname: Lin
authors.forename: Yi-Ching
authors.initials: YC
authors.lastname: Kuo
authors.forename: Cheng-Han
authors.initials: CH
authors.lastname: Yang
authors.forename: Shih-Hui
authors.initials: SH
authors.lastname: Weng
authors.forename: Huai-Ching
authors.initials: HC
authors.lastname: Huang
authors.forename: You-Hua
authors.initials: YH
authors.lastname: Chen
authors.forename: Pi-Tai
authors.initials: PT
authors.lastname: Chou
mesh_terms: D019943:Amino Acid Substitution; D001236:Aspergillus oryzae / Q000201:enzymology; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D017433:Protein Structure, Secondary; D006163:Ribonuclease T1 / Q000737:chemistry* / Q000235:genetics; D014364:Tryptophan; D014867:Water / Q000737:chemistry*
chemical_list: D014867:Water; D014364:Tryptophan; D006163:Ribonuclease T1