1-20 - Hong Guo F223 WLS BCMB University of Tennessee...

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Unformatted text preview: Hong Guo F223 WLS BCMB University of Tennessee [email protected], 865-974-3610 Jan. 20, 2011 BCMB422: Computational Biology/Protein Modeling (3) Examine 3D Structure of Chymotrypsin Open the structure of 5SGA in Z:/BCMB422/1-13. Open Sequence Editor (SE) window as well and Display -> Residue UID, Actual Secondary Structure and Single Letter Residues. Display ribbon by using MOE->Render-> Backbone->Cartoon. Catalytic Triad Select water chain (3) in SE and then use SE->Editor- >Delete Selected Chains to delete water molecules . Hide all the residues first in the MOE window. Then in SE window, highlight His57 (H57), Asp102 (D102) and Ser195 (S195) using Ctrl key and mouse and show them in the MOE window (ball and stick). Measure the interaction distances between D102 and H57 and between H57 and S195, Inhibitor Binding and Oxyanion Hole Select the inhibitor in SE (the second chain) and show it in stick representation in the MOE window. Display G193 as well in ball and stick and show oxyanion hole interactions. Specificity pocket Oxyanion hole Examine 3D Structure of Chymotrypsin with MOE 2009.10 (2) Open the 1CSE structure in MOE window Z:/BCMB422/1-13/1CSE.pdb . Display-> Residue UID , Actual Secondary Structure and Single Letter Residues . Display ribbon . Select water chain (4) in SE and then use SE-...
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This note was uploaded on 05/05/2011 for the course BIOL 400 taught by Professor Dr.biology during the Spring '11 term at University of Tennessee.

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1-20 - Hong Guo F223 WLS BCMB University of Tennessee...

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