Exercises for Chapter 6 – Detection of Channels

1. Gramicidin D channel Identify a pore penetrating the structure of the small gramicidin ion channel (PDB ID 1grm). How long is the pore and how narrow is the bottleneck? 2. ProbeRadius and InteriorThreshold settings for channel identification What is the suitable value for the ProbeRadius and InteriorThreshold parameter for channel identification? Use the following systems: a. Acetylcholine receptor channel (PDB ID 4boi) b. Carbonic anhydrase tunnel from the active site Cys 57, His 112, Cys 115 (PDB ID 3eyx) c. Haloalkane dehalogenase from the buried iodine ion coordinates (PDB ID 1cqw) 3. Channel starting point What is the best way to identify a starting point prior to channel identification? a. For channels leading to a buried volume in the protein structure b. For pores spanning the whole structure 4. Polyamine oxidase binding channel Identify the U-shaped polyamine oxidase (PDB ID 1b37) binding channel, as described in the literature. 5. Polypeptide channel in ribosome Identify a polypeptide channel in a large ribosomal subunit (PDB ID 1jj2). Use U 2620 and A 2486 located on chain 0 as the starting point for channel identification.