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Exploring NMR ensembles of calcium binding proteins: perspectives to design inhibitors of protein-protein interactions.

Isvoran A, Badel A, Craescu CT, Miron S, Miteva MA - BMC Struct. Biol. (2011)

Bottom Line: We employed several scoring methods in order to find the best protein conformations.Our results show that docking on NMR structures of calmodulin and centrin can be very helpful to take into account conformational changes occurring at protein-protein interfaces.NMR structures of protein-protein complexes nowadays available could efficiently be exploited for further structure-based drug design/virtual screening processes employed to design small molecule inhibitors of protein-protein interactions.

View Article: PubMed Central - HTML - PubMed

Affiliation: MTi, Inserm U973 - University Paris Diderot, 35 rue Helene Brion, Bat, Lamarck, 75013 Paris, France.

ABSTRACT

Background: Disrupting protein-protein interactions by small organic molecules is nowadays a promising strategy employed to block protein targets involved in different pathologies. However, structural changes occurring at the binding interfaces make difficult drug discovery processes using structure-based drug design/virtual screening approaches. Here we focused on two homologous calcium binding proteins, calmodulin and human centrin 2, involved in different cellular functions via protein-protein interactions, and known to undergo important conformational changes upon ligand binding.

Results: In order to find suitable protein conformations of calmodulin and centrin for further structure-based drug design/virtual screening, we performed in silico structural/energetic analysis and molecular docking of terphenyl (a mimicking alpha-helical molecule known to inhibit protein-protein interactions of calmodulin) into X-ray and NMR ensembles of calmodulin and centrin. We employed several scoring methods in order to find the best protein conformations. Our results show that docking on NMR structures of calmodulin and centrin can be very helpful to take into account conformational changes occurring at protein-protein interfaces.

Conclusions: NMR structures of protein-protein complexes nowadays available could efficiently be exploited for further structure-based drug design/virtual screening processes employed to design small molecule inhibitors of protein-protein interactions.

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Related in: MedlinePlus

Flowchart of the employed docking-scoring protocol.
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Figure 4: Flowchart of the employed docking-scoring protocol.

Mentions: The docking-scoring protocol employed to dock 1-naphthyl terphenyl into the selected structures is shown in Figure 4 (see for details in the Methods section). In order to identify the "best" protein conformations for further analysis, we calculated the RMSD between each pose obtained after docking with DOCK6.0 [45] and the reference points of smMLCK and P17-XPC for CaM and HsCen2, respectively (see Figure 1). The obtained RMSD values are shown in Figure 5A and 5B. Overall, docking results are best for the structures of C-HsCen2. We compared the binding zones of the two proteins to analyze these results. For C-CaM, the binding pocket consists of one cavity (volume 314.22 Å3, code 1CLL) containing residues F88, I96, L101, M105, M120, E123, M140 and M141. The residue F88 placed in the center of the binding zone is in contact with W4 and T7 of the smMLCK peptide. The binding site of HsCen2 is larger (volume 417.27 Å3, code 2GGM) and consists of two hydrophobic cavities separated by F113 interacting with L5 of the P17-XPC peptide, and L126 and M145 interacting with W2 of the peptide. The close contact of F113 and L5 of the bound peptide has also been observed in the structure of HsCen2 complexed with another protein partner targeting the same HsCen2 zone [46]. The deeper and bigger cavity contains the residues F113, I146, E148, V157, I165 and M166, and the smaller one contains the residues L126, V129, A130, L137, L142 and M145. The replacement of one Met residue (M105) of C-CaM with a smaller one, an Ala residue (A130), enlarges the hydrophobic cavity of the C-HsCen2. This facilitates a potential anchoring of 1-naphthyl terphenyl into the C-HsCen2.


Exploring NMR ensembles of calcium binding proteins: perspectives to design inhibitors of protein-protein interactions.

Isvoran A, Badel A, Craescu CT, Miron S, Miteva MA - BMC Struct. Biol. (2011)

Flowchart of the employed docking-scoring protocol.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3116463&req=5

Figure 4: Flowchart of the employed docking-scoring protocol.
Mentions: The docking-scoring protocol employed to dock 1-naphthyl terphenyl into the selected structures is shown in Figure 4 (see for details in the Methods section). In order to identify the "best" protein conformations for further analysis, we calculated the RMSD between each pose obtained after docking with DOCK6.0 [45] and the reference points of smMLCK and P17-XPC for CaM and HsCen2, respectively (see Figure 1). The obtained RMSD values are shown in Figure 5A and 5B. Overall, docking results are best for the structures of C-HsCen2. We compared the binding zones of the two proteins to analyze these results. For C-CaM, the binding pocket consists of one cavity (volume 314.22 Å3, code 1CLL) containing residues F88, I96, L101, M105, M120, E123, M140 and M141. The residue F88 placed in the center of the binding zone is in contact with W4 and T7 of the smMLCK peptide. The binding site of HsCen2 is larger (volume 417.27 Å3, code 2GGM) and consists of two hydrophobic cavities separated by F113 interacting with L5 of the P17-XPC peptide, and L126 and M145 interacting with W2 of the peptide. The close contact of F113 and L5 of the bound peptide has also been observed in the structure of HsCen2 complexed with another protein partner targeting the same HsCen2 zone [46]. The deeper and bigger cavity contains the residues F113, I146, E148, V157, I165 and M166, and the smaller one contains the residues L126, V129, A130, L137, L142 and M145. The replacement of one Met residue (M105) of C-CaM with a smaller one, an Ala residue (A130), enlarges the hydrophobic cavity of the C-HsCen2. This facilitates a potential anchoring of 1-naphthyl terphenyl into the C-HsCen2.

Bottom Line: We employed several scoring methods in order to find the best protein conformations.Our results show that docking on NMR structures of calmodulin and centrin can be very helpful to take into account conformational changes occurring at protein-protein interfaces.NMR structures of protein-protein complexes nowadays available could efficiently be exploited for further structure-based drug design/virtual screening processes employed to design small molecule inhibitors of protein-protein interactions.

View Article: PubMed Central - HTML - PubMed

Affiliation: MTi, Inserm U973 - University Paris Diderot, 35 rue Helene Brion, Bat, Lamarck, 75013 Paris, France.

ABSTRACT

Background: Disrupting protein-protein interactions by small organic molecules is nowadays a promising strategy employed to block protein targets involved in different pathologies. However, structural changes occurring at the binding interfaces make difficult drug discovery processes using structure-based drug design/virtual screening approaches. Here we focused on two homologous calcium binding proteins, calmodulin and human centrin 2, involved in different cellular functions via protein-protein interactions, and known to undergo important conformational changes upon ligand binding.

Results: In order to find suitable protein conformations of calmodulin and centrin for further structure-based drug design/virtual screening, we performed in silico structural/energetic analysis and molecular docking of terphenyl (a mimicking alpha-helical molecule known to inhibit protein-protein interactions of calmodulin) into X-ray and NMR ensembles of calmodulin and centrin. We employed several scoring methods in order to find the best protein conformations. Our results show that docking on NMR structures of calmodulin and centrin can be very helpful to take into account conformational changes occurring at protein-protein interfaces.

Conclusions: NMR structures of protein-protein complexes nowadays available could efficiently be exploited for further structure-based drug design/virtual screening processes employed to design small molecule inhibitors of protein-protein interactions.

Show MeSH
Related in: MedlinePlus