Limits...
Revealing the binding modes and the unbinding of 14-3-3σ proteins and inhibitors by computational methods.

Hu G, Cao Z, Xu S, Wang W, Wang J - Sci Rep (2015)

Bottom Line: We found that the binding free energies are mainly from interactions between the phosphate group of the inhibitors and the hydrophilic residues.However, we also found that the binding free energy of inhibitor R9 is smaller than that of inhibitor R1.The information obtained from this study may be valuable for future rational design of novel inhibitors, and provide better structural understanding of inhibitor binding to 14-3-3σ proteins.

View Article: PubMed Central - PubMed

Affiliation: Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics and College of Physics and Electronic Information, Dezhou University, Dezhou, 253023, China.

ABSTRACT
The 14-3-3σ proteins are a family of ubiquitous conserved eukaryotic regulatory molecules involved in the regulation of mitogenic signal transduction, apoptotic cell death, and cell cycle control. A lot of small-molecule inhibitors have been identified for 14-3-3 protein-protein interactions (PPIs). In this work, we carried out molecular dynamics (MD) simulations combined with molecular mechanics generalized Born surface area (MM-GBSA) method to study the binding mechanism between a 14-3-3σ protein and its eight inhibitors. The ranking order of our calculated binding free energies is in agreement with the experimental results. We found that the binding free energies are mainly from interactions between the phosphate group of the inhibitors and the hydrophilic residues. To improve the binding free energy of Rx group, we designed the inhibitor R9 with group R9 = 4-hydroxypheny. However, we also found that the binding free energy of inhibitor R9 is smaller than that of inhibitor R1. By further using the steer molecular dynamics (SMD) simulations, we identified a new hydrogen bond between the inhibitor R8 and residue Arg64 in the pulling paths. The information obtained from this study may be valuable for future rational design of novel inhibitors, and provide better structural understanding of inhibitor binding to 14-3-3σ proteins.

No MeSH data available.


(A) Structure-based electrostatic potentials at neutral pH for the 14-3-3σ protein shown in surface representation. The inhibitor R1 is shown in ball and stick representation. (B) The distances between the oxygen atoms of the phosphate group of inhibitor R1 and the atoms of side chain of residues in the binding pocket of the phosphate group in crystallographic structure (shown in red color). Their average distances in the last 5 ns MD structures are shown in blue color.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4644958&req=5

f2: (A) Structure-based electrostatic potentials at neutral pH for the 14-3-3σ protein shown in surface representation. The inhibitor R1 is shown in ball and stick representation. (B) The distances between the oxygen atoms of the phosphate group of inhibitor R1 and the atoms of side chain of residues in the binding pocket of the phosphate group in crystallographic structure (shown in red color). Their average distances in the last 5 ns MD structures are shown in blue color.

Mentions: The crystallographic complex of the phosphate peptide and the 14-3-3σ protein (PDB ID: 1YWT)4950 revealed that the phosphate group of the binding peptide forms several hydrogen bonds with 14-3-3σ protein. The structure-based net charges at neutral pH for the 14-3-3σ protein were calculated by using the Adaptive Poisson-Boltzmann Solver (APBS) and PDB2PQ program51 and visualized resulting electrostatic potentials in VMD software52 (Fig. 2A). It is clear that the groove in 14-3-3σ protein is hydrophilic53. The hydrophilic pocket of the phosphate group is formed by several hydrophilic residues (Arg60, Arg133, Tyr134 and so on). In our previous work, the phosphate group in phosphoserine residue was in unprotonated state50. So we set the phosphate group of inhibitors in unprotonated state in this work. To evaluate the validity of unprotonated phosphate group of inhibitors, we calculated five averaged distances between the atoms of protein and the atoms of the phosphate group based on the MD trajectory from 15 ns to 20 ns in compound R1. As shown in Fig. 2B, the calculated values are in good agreement with the crystallographic values.


Revealing the binding modes and the unbinding of 14-3-3σ proteins and inhibitors by computational methods.

Hu G, Cao Z, Xu S, Wang W, Wang J - Sci Rep (2015)

(A) Structure-based electrostatic potentials at neutral pH for the 14-3-3σ protein shown in surface representation. The inhibitor R1 is shown in ball and stick representation. (B) The distances between the oxygen atoms of the phosphate group of inhibitor R1 and the atoms of side chain of residues in the binding pocket of the phosphate group in crystallographic structure (shown in red color). Their average distances in the last 5 ns MD structures are shown in blue color.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4644958&req=5

f2: (A) Structure-based electrostatic potentials at neutral pH for the 14-3-3σ protein shown in surface representation. The inhibitor R1 is shown in ball and stick representation. (B) The distances between the oxygen atoms of the phosphate group of inhibitor R1 and the atoms of side chain of residues in the binding pocket of the phosphate group in crystallographic structure (shown in red color). Their average distances in the last 5 ns MD structures are shown in blue color.
Mentions: The crystallographic complex of the phosphate peptide and the 14-3-3σ protein (PDB ID: 1YWT)4950 revealed that the phosphate group of the binding peptide forms several hydrogen bonds with 14-3-3σ protein. The structure-based net charges at neutral pH for the 14-3-3σ protein were calculated by using the Adaptive Poisson-Boltzmann Solver (APBS) and PDB2PQ program51 and visualized resulting electrostatic potentials in VMD software52 (Fig. 2A). It is clear that the groove in 14-3-3σ protein is hydrophilic53. The hydrophilic pocket of the phosphate group is formed by several hydrophilic residues (Arg60, Arg133, Tyr134 and so on). In our previous work, the phosphate group in phosphoserine residue was in unprotonated state50. So we set the phosphate group of inhibitors in unprotonated state in this work. To evaluate the validity of unprotonated phosphate group of inhibitors, we calculated five averaged distances between the atoms of protein and the atoms of the phosphate group based on the MD trajectory from 15 ns to 20 ns in compound R1. As shown in Fig. 2B, the calculated values are in good agreement with the crystallographic values.

Bottom Line: We found that the binding free energies are mainly from interactions between the phosphate group of the inhibitors and the hydrophilic residues.However, we also found that the binding free energy of inhibitor R9 is smaller than that of inhibitor R1.The information obtained from this study may be valuable for future rational design of novel inhibitors, and provide better structural understanding of inhibitor binding to 14-3-3σ proteins.

View Article: PubMed Central - PubMed

Affiliation: Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics and College of Physics and Electronic Information, Dezhou University, Dezhou, 253023, China.

ABSTRACT
The 14-3-3σ proteins are a family of ubiquitous conserved eukaryotic regulatory molecules involved in the regulation of mitogenic signal transduction, apoptotic cell death, and cell cycle control. A lot of small-molecule inhibitors have been identified for 14-3-3 protein-protein interactions (PPIs). In this work, we carried out molecular dynamics (MD) simulations combined with molecular mechanics generalized Born surface area (MM-GBSA) method to study the binding mechanism between a 14-3-3σ protein and its eight inhibitors. The ranking order of our calculated binding free energies is in agreement with the experimental results. We found that the binding free energies are mainly from interactions between the phosphate group of the inhibitors and the hydrophilic residues. To improve the binding free energy of Rx group, we designed the inhibitor R9 with group R9 = 4-hydroxypheny. However, we also found that the binding free energy of inhibitor R9 is smaller than that of inhibitor R1. By further using the steer molecular dynamics (SMD) simulations, we identified a new hydrogen bond between the inhibitor R8 and residue Arg64 in the pulling paths. The information obtained from this study may be valuable for future rational design of novel inhibitors, and provide better structural understanding of inhibitor binding to 14-3-3σ proteins.

No MeSH data available.