Table 1.
Docking results from M-α1AT, Z-α1AT, and M* model with S-(4-nitrobenzyl)-6-thioguanosine and the 79 other small molecules.
Fig 1.
Kinetic diagram of bPEG-peptide binding to α1AT.
(A) Four micrograms per well of attached (■) Z-α1AT or (●) M-α1AT were incubated for various times in presence of 38.4 μM bPEG-peptide. (B) Z-α1AT was incubated in presence of 5% DMSO and bPEG-peptide for 16 h. Errors bars reflect the standard deviation of three replicates.
Fig 2.
Pattern of inhibition resulting from the screening of 80 unknown LOPAC compounds.
A 96-well plate was coated with 4 μg/well of Z-α1AT and incubated for 16 h with 100 μM of various compounds and 38.4 μM of bPEG-peptide. The black arrow indicates the compound that corresponds to S-(4-nitrobenzyl)-6-thioguanosine and gives an inhibition effect of 67 ± 2% and. The error bars are the standard deviation of three individual experiments.
Fig 3.
S-(4-nitrobenzyl)-6-thioguanosine inhibits bPEG-peptide binding to Z-α1AT.
(A) Dose-response curves were assayed for various concentrations of (●) S-(4-nitrobenzyl)-6-thioguanosine and (■) its homologue S-(4-nitrobenzyl)-6-thioinosine. (B) Chemical structures of (left) S-(4-nitrobenzyl)-6-thioguanosine and (right) S-(4-nitrobenzyl)-6-thioinosine. The errors bars are the standard deviation of an experiment conducted in triplicate.
Fig 4.
Effect of S-(4-nitrobenzyl)-6-thioguanosine on Z-α1AT polymerization.
The protein was incubated with (●) or without (■) 100 μM of S-(4-nitrobenzyl)-6-thioguanosine for various time at 37°C. The error bars are the standard deviation of three separate experiments.
Fig 5.
The three models of α1AT protein.
(Top left) Structure of wild type (PDB: 1QLP) (Top right) Structure of Z-mutant (PDB: 3T1P) (Bottom middle) Intermediate M* model with an expanded β-sheet A (retained from structure 3T1P), RCL not inserted into the RCL cavity (retained from structure 1QLP), and Cterm loop inserted into β-sheet B (retained from structure 1QLP). β-sheet A is colored red and β-sheet B is colored green. Shades of green and red distinguish discontinuous fragments from the same initial crystal structure (light/dark green for 1QLP fragments and light/dark red for 3T1P fragments) used to generate the M* model. Grey colored regions represent residues that were not used to generate the M* model.
Fig 6.
The fragments of structures 1QLP (green) and 3T1P (red) used to homology model the M* intermediate state of α1AT.
β-sheet A is the red beta sheet across the top half of the model and β-sheet B is the green beta sheet across the bottom of the model. Residue numbers at the start and end of each fragment transition are labeled with an arrow in the Nterm to Cterm direction. Shades of green and red distinguish discontinuous fragments from the same initial crystal structure (light/dark green for 1QLP fragments and light/dark red for 3T1P fragments).
Fig 7.
Binding Sites for S-(4-nitrobenzyl)-6-thioguanosine.
Two protein ribbon models are shown for each structure: (A) 3CWM, (B) 3T1P and (C) M* Model. The left model and right representations in each panel are rotated 90° with respect to one another. The best binding poses for S-(4-nitrobenzyl)-6-thioguanosine at each available binding site are shown with space filling atoms with the carbon atoms colored green. (Purple) Strands 3 and 5 from β-sheet A. (Dark blue) Cterm loop within β-sheet B. (Light blue) RCL. (Orange) Residues of the RCL corresponding to the analogous 6-mer peptide.
Table 2.
Residues interacting with S-(4-nitrobenzyl)-6-thioguanosine in top scoring binding sites.