Exercises for Chapter 8 – Channel Characteristics

1. Gramicidin D pore Identify a pore spanning through the structure of gramicidin D (PDB ID 1grm). What is its hydropathy? Which compounds are likely to pass through the chan nel? 2. Cytochrome P450 3A4 Using the default settings of MOLEonline, identify channels for Cytochrome P450 (PDB ID 1tqn). How many channels can you identify? Which of them is most likely the water channel based on the Hydropathy index? 3. Substrate tunnel How do you have to preprocess the structure of sterol 14-α demethylase (PDB ID 3k1o), in order to identify the access channel for the posaconazole inhibitor. What is the nature of this channel? 4. Bottleneck Identify a bottleneck in aquaporine (PDB ID 3gd8). What is the composition and Hydropathy of the bottleneck region?