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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) Pulling compound R1 from its bound state to dissociated state. The 14-3-3σ protein is shown in a cartoon and a surface representation; Inhibitor R1 is shown in a ball representation. The pulling path is shown in red line. (B) PMFs as a function of the inhibitor displacement from its binding site along the pulling path. (C) The averaged number of hydrogen bonds formed between the 14-3-3σ protein and its inhibitor as a function of the inhibitor displacement.
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f7: (A) Pulling compound R1 from its bound state to dissociated state. The 14-3-3σ protein is shown in a cartoon and a surface representation; Inhibitor R1 is shown in a ball representation. The pulling path is shown in red line. (B) PMFs as a function of the inhibitor displacement from its binding site along the pulling path. (C) The averaged number of hydrogen bonds formed between the 14-3-3σ protein and its inhibitor as a function of the inhibitor displacement.

Mentions: SMD simulations were performed to investigate the dynamic processes of two inhibitors (say R1 and R8) unbinding from the 14-3-3σ protein. The starting structures of compounds R1 and R8 for SMD simulations were extracted from the last structure of the afore-presented MD simulations. Then the starting structures were rotated for the orifice of the inhibitor binding pocket toward the +z direction, put them in a box of water, and neutralized the systems. Then 10 ns equilibrated MD simulation was carried out for each system. In our SMD simulations, each inhibitor is represented by two centers. Both centers were steered at the same time along z direction. The pulling speed was set at 0.01 Å/ps in z direction. In order to reduce the impact of pulling on the 14-3-3σ protein, the inhibitor can move freely in x and y directions, and the whole pulling path was divided into 16 segments along the z-direction with 1 Å for each segment. One pulling path way of compound R1 was show in Fig. 7A, the displacement is 16 Å from the bound state to the dissociated state, as well as 25 Å in the xy plane. For each segment, two types of SMD simulations were performed: one for pulling back to (denoted as reverse) the binding site and one for pulling away (denoted as forward) from the binding site. We sampled four forward and reverse pulling paths during which the work done to the system was recorded for each segment. The curves of works done to the systems along the pulling paths are shown in Fig. S2. From these works, we calculated the PMFs as a function of the displacement of inhibitors along z-axis by using the BD-FDT and the results are shown in Fig. 7B. We can see that the PMF difference between the bound state to the dissociated state are −13.88 and −9.24 kcal/mol for compounds R1 and R8, respectively. For compound R1, the PMF rises all the way until the displacement reaches to 7 Å where the inhibitor is steered out of the binding pocket. After that, the PMF reaches a plateau. For compound R8, the PMF rises with the displacement <3 Å and reaches an interesting intermediate state around the displacement within 3.5 Å to 4.5 Å. After that, the PMF rises again and then levels off after 6 Å, indicating the inhibitor is in the dissociate state.


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) Pulling compound R1 from its bound state to dissociated state. The 14-3-3σ protein is shown in a cartoon and a surface representation; Inhibitor R1 is shown in a ball representation. The pulling path is shown in red line. (B) PMFs as a function of the inhibitor displacement from its binding site along the pulling path. (C) The averaged number of hydrogen bonds formed between the 14-3-3σ protein and its inhibitor as a function of the inhibitor displacement.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f7: (A) Pulling compound R1 from its bound state to dissociated state. The 14-3-3σ protein is shown in a cartoon and a surface representation; Inhibitor R1 is shown in a ball representation. The pulling path is shown in red line. (B) PMFs as a function of the inhibitor displacement from its binding site along the pulling path. (C) The averaged number of hydrogen bonds formed between the 14-3-3σ protein and its inhibitor as a function of the inhibitor displacement.
Mentions: SMD simulations were performed to investigate the dynamic processes of two inhibitors (say R1 and R8) unbinding from the 14-3-3σ protein. The starting structures of compounds R1 and R8 for SMD simulations were extracted from the last structure of the afore-presented MD simulations. Then the starting structures were rotated for the orifice of the inhibitor binding pocket toward the +z direction, put them in a box of water, and neutralized the systems. Then 10 ns equilibrated MD simulation was carried out for each system. In our SMD simulations, each inhibitor is represented by two centers. Both centers were steered at the same time along z direction. The pulling speed was set at 0.01 Å/ps in z direction. In order to reduce the impact of pulling on the 14-3-3σ protein, the inhibitor can move freely in x and y directions, and the whole pulling path was divided into 16 segments along the z-direction with 1 Å for each segment. One pulling path way of compound R1 was show in Fig. 7A, the displacement is 16 Å from the bound state to the dissociated state, as well as 25 Å in the xy plane. For each segment, two types of SMD simulations were performed: one for pulling back to (denoted as reverse) the binding site and one for pulling away (denoted as forward) from the binding site. We sampled four forward and reverse pulling paths during which the work done to the system was recorded for each segment. The curves of works done to the systems along the pulling paths are shown in Fig. S2. From these works, we calculated the PMFs as a function of the displacement of inhibitors along z-axis by using the BD-FDT and the results are shown in Fig. 7B. We can see that the PMF difference between the bound state to the dissociated state are −13.88 and −9.24 kcal/mol for compounds R1 and R8, respectively. For compound R1, the PMF rises all the way until the displacement reaches to 7 Å where the inhibitor is steered out of the binding pocket. After that, the PMF reaches a plateau. For compound R8, the PMF rises with the displacement <3 Å and reaches an interesting intermediate state around the displacement within 3.5 Å to 4.5 Å. After that, the PMF rises again and then levels off after 6 Å, indicating the inhibitor is in the dissociate state.

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.