Molecular dynamics simulations of human glutathione transferase P1-1: Analysis of the induced-fit mechanism by GSH binding

• Published in: Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 1999-10, Vol.37 (1), p.1-9
• Main Authors: Stella, Lorenzo, Nicotra, Maria, Ricci, Giorgio, Rosato, Nicola, Di Iorio, Ernesto E.
• Format: Article
• Language: English
• Subjects: Binding Sites; Computer Simulation; Cysteine - chemistry; detoxification; fluctuations; Glutathione - metabolism; Glutathione S-Transferase pi; Glutathione Transferase - chemistry; Glutathione Transferase - metabolism; Humans; Isoenzymes - chemistry; Isoenzymes - metabolism; Models, Chemical; Models, Molecular; Motion; Protein Binding; Protein Conformation; protein dynamics; Spectrometry, Fluorescence; structure; sulfhydryl reactivity; Tryptophan - chemistry
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/(SICI)1097-0134(19991001)37:1<1::AID-PROT1>3.0.CO;2-B

We report here a 1‐ns molecular dynamics simulation on the ligand‐free monomer of human glutathione transferase P1‐1 in bulk water. The average conformation obtained from the last 500 ps of simulation is taken as a model for the apo‐structure of this protein and compared to the available crystallographic data. Remarkable changes in the tertiary structure take place during the simulation and are ascribed to the removal of the ligand. They support an induced fit mechanism occurring upon glutathione binding, whose major features can be described in detail. A portion of helix 2 (residues 42–50), which participates in the formation of the active site, undergoes the most prominent conformational changes. Other protein segments, such as the C‐terminal loop and helix 4, also show relevant structural rearrangements. All these transitions cause a significant shielding from the solvent of the hydrophobic binding site of the co‐substrate, whose exposed surface goes from 4.6 nm2in the holo‐structure to about 3.1 nm2in the apo‐conformation. The results of this simulation are consistent with numerous experimental observations previously obtained on GST P1‐1 and provide new insights for their explanation at the molecular level. Proteins 1999;37:1–9. © 1999 Wiley‐Liss, Inc.