Flexibility of aromatic residues in acetylcholinesterase: Difference between revisions
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=== | === Group I: residues with fixed side-chain conformation === | ||
[[Image:F120.png|thumb|Fig. 1. The χ<sub>1</sub>/χ<sub>2</sub> plot of F120.|300px|left]] | [[Image:F120.png|thumb|Fig. 1. The χ<sub>1</sub>/χ<sub>2</sub> plot of F120.|300px|left]] | ||
<scene name='Aromatic_residues/14_residues_group2/1'>F120 as well as W233, W432, Y70, Y121, F331, F288, and F290</scene> fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ<sub>1</sub> and χ<sub>2</sub> angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB. | <scene name='Aromatic_residues/14_residues_group2/1'>F120 as well as W233, W432, Y70, Y121, F331, F288, and F290</scene> fall into group I, the category of residues with fixed side-chain conformations in both crystal structures and MD simulation trajectory. Fig. 1 shows that both the experimental and MD data are concentrated in a specific region. In this figure, the grey dots are derived from a 20-ns MD trajectory of native ''Tc''AChE and each one represents a pair of χ<sub>1</sub> and χ<sub>2</sub> angles calculated based on snapshot structures of TcAChE extracted from the MD trajectory at 1 ps intervals. The plot contains 20,000 such dots in total. The red pentacle is the crystal structure (pdb code 1ea5) used for the MD simulation. The dark triangles present pairs of c1 and c2 angles calculated based on 89 crystal structures of AChE deposited in the PDB. | ||
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=== | === Group II: residues with flexible side chains === | ||
[[Image:W279_3_low.jpg|thumb|Fig. 2. The χ<sub>1</sub>/χ<sub>2</sub> plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]] | [[Image:W279_3_low.jpg|thumb|Fig. 2. The χ<sub>1</sub>/χ<sub>2</sub> plots of W279. Details in the plots are as in Fig. 1 except that the grey areas in the right plot are the favorable regions for the side-chain of Trp predicted by PROCHECK. |450px|right]] | ||
<applet load=Pp_W279_abcde_m3.pdb' size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." /> | <applet load=Pp_W279_abcde_m3.pdb' size='320' frame='true' scene='Flexibility_of_aromatic_residues_in_acetylcholinesterase/W279_animation3/1' align='left' caption="This is an animation to show the 7 conformations of W279 according to the 7 groups, a, b, c, d, e, f, and g, shown in Fig. 2. The side-chain of W279 is colored in red and the ligands in green." /> | ||
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[[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ<sub>1</sub>/χ<sub>2</sub> plot of F330. Details are as in Fig. 1. b)The χ<sub>1</sub>/χ<sub>2</sub> of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]] | [[Image:F330_3_low.jpg|thumb|Fig. 3. a) The χ<sub>1</sub>/χ<sub>2</sub> plot of F330. Details are as in Fig. 1. b)The χ<sub>1</sub>/χ<sub>2</sub> of all Phe residues in ''Tc''AChE (pdb code 1ea5) overlayed on the favored regions for these residues derived by the program PROCHECK. |500px|left]] | ||
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=== | === Group III: Residues with different degree of side-chain flexibility in MD simulations and crytal structures === | ||
[[Image:W84.jpg|thumb|Fig. 4. The χ<sub>1</sub>/χ<sub>2</sub> plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]] | [[Image:W84.jpg|thumb|Fig. 4. The χ<sub>1</sub>/χ<sub>2</sub> plots of W84. MD trajectory of the ''Tc''AChE monomer is shown without (a) or with (b) main-chain fixed during the simulation. |500px|right]] | ||