Molecular simulation and docking studies of Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose: implication for transcriptional activation of GAL genes

Abstract

The Gal4p mediated transcriptional activation of GAL genes requires the interaction between Gal3p bound with ATP and galactose and Gal80p. Though numerous studies suggest that galactose and ATP activate Gal3p/Gal1p interaction with Gal80p, neither the mechanism of activation nor the interacting surface that binds to Gal80p is well understood. In this study we investigated the dynamics of Gal3p and Gal1p in the presence and absence of ligands ATP and galactose to understand the role played by dynamics in the function of these proteins through molecular dynamics simulation and protein-protein docking studies. We performed simulations totaling to 510 ns on both Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose. We find that, while binding of ligands ATP and galactose to Gal3p/Gal1p do not affect the global conformation of proteins, some local conformational changes around upper-lip helix including insertion domain are observed. We observed that only in the presence of ATP and galactose, Gal3p displays opening and closing motion between the two domains. And because of this motion, a binding interface, which is largely hydrophobic, opens up on the surface of Gal3p and this surface can bind to Gal80p. From our simulation studies we infer probable docking sites for Gal80p on Gal3p/Gal1p, which were further ascertained by the docking of Gal80p on to ligand bound Gal1p and Gal3p proteins, and the residues at the interface between Gal3p and Gal80p are identified. Our results correlate quite well with the existing body of literature on functional and dynamical aspects of Gal1p and Gal3p proteins.

Dynamics of Gal80p in the Gal80p–Gal3p complex differ significantly from the dynamics in the Gal80p–Gal1p complex: implications for the higher specificity of Gal3p

“…16 Our computationally predicted binding interface for the Gal3p-Gal80p complex showed excellent agreement with the recently published crystal complex of ATP and galactose bound Gal3p-Gal80p complex. 16 Our computationally predicted binding interface for the Gal3p-Gal80p complex showed excellent agreement with the recently published crystal complex of ATP and galactose bound Gal3p-Gal80p complex.…”

“…S4, ESI †). These observations further strengthened our proposed model of Gal80p binding with Gal3p, 16 and the nonappearance of SASA opening in the case of Gal3p in the presence of Gal80p suggests that the equilibrium was shifted towards a closed conformation (Fig. 16 While a fall in COM distances was observed for Gal3p in both the model and the crystal complex during complex formation with Gal80p (Fig.…”

“…17 The representative structure obtained from the later part of the trajectory (27-50 ns) was close (backbone RMSD = 3.1 Å) to the crystal complex compared to the initial structure (backbone RMSD = 6.05 Å) (Fig. 16 While a fall in COM distances was observed for Gal3p in both the model and the crystal complex during complex formation with Gal80p (Fig. The Center of Mass distance (COM) between the residue Lys 81 (Lys 87 in the case of Gal1p) from the N-terminal lip and Gln 378 (Gln 386 in Gal1p) from the C-terminal lip of Gal3p was calculated (Fig.…”

“…16 Also, the dynamics of Gal3p vary significantly from that of Gal1p in the presence of ligands, and a large continuous hydrophobic region opens only at the surface of Gal3p. 16 Also, the dynamics of Gal3p vary significantly from that of Gal1p in the presence of ligands, and a large continuous hydrophobic region opens only at the surface of Gal3p.…”

Identification of Angiotensin Converting Enzyme Inhibitor: An In Silico Perspective

“…The topology of ligand was generated using PRODRG server (Schuttelkopf and van Aalten 2004). The GROMOS force field has been used for MD simulation (Upadhyay and Sasidhar 2012;M'endez-Cuesta et al 2010). The complex of tACE-ZINC48251687 was fully surrounded by SPC water molecules (water density was 1.0).…”