Group:SMART:2010 Pingry SMART Team: Difference between revisions
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<scene name='2010_Pingry_SMART_Team/1lwi_loops/1'>Purple and Blue highlight the two solvent exposed loops (Purple: Loop A, Blue: Loop B)</scene>. The loops are important for two different reasons. Loop A is responsible for the substrate binding. It holds many of the amino acids responsible for the hydrophobic substrate binding pocket. Loop B is also important to substrate binding as | <scene name='2010_Pingry_SMART_Team/1lwi_loops/1'>Purple and Blue highlight the two solvent exposed loops (Purple: Loop A, Blue: Loop B)</scene>. The loops are important for two different reasons. Loop A is responsible for the substrate binding. It holds many of the amino acids responsible for the hydrophobic substrate binding pocket. Loop B is also important to substrate binding, as it undergoes large conformational changes to accommodate the substrate. In this structure (1lwi), the substrate is absent and this loop is in its extended position. This opening and closing "garage door" mechanism is convenient for working through a large number of substrates, as the substrates can enter and exit easily. In the rat liver, each protein needs to convert as many steroids as possible to change the signal that is being sent out. In Dr. Banta's fuel cell, each protein would need to oxidize sugar molecules quickly to establish a current. | ||
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Dark Grey highlights the beta barrel and helix structure. The barrel consists of eight parallel beta strands and eight anti-parallel alpha helices. The bottom is sealed by two antiparallel beta strands (6-10 and 13-18). This structure is common to all members of the AKR family. It provides a convenient way to keep all reactants in the same vicinity and out of the external environment. This applies to reactions in both 3α-HSD and in alcohol dehydrogenase. <scene name='2010_Pingry_SMART_Team/1lwi_betabarrel/4'>Click Here to view the Beta barrel in blue and Helices in red.</scene> The top contains two solvent exposed loops (loop A: 116-142 and loop B: 217-235) | Dark Grey highlights the beta barrel and helix structure. The barrel consists of eight parallel beta strands and eight anti-parallel alpha helices. The bottom is sealed by two antiparallel beta strands (6-10 and 13-18). This structure is common to all members of the AKR family. It provides a convenient way to keep all reactants in the same vicinity and out of the external environment. This applies to reactions in both 3α-HSD and in alcohol dehydrogenase. <scene name='2010_Pingry_SMART_Team/1lwi_betabarrel/4'>Click Here to view the Beta barrel in blue and Helices in red.</scene> The top contains two solvent exposed loops (loop A: 116-142 and loop B: 217-235) | ||
<scene name='2010_Pingry_SMART_Team/1lwi_loops/1'>Purple and Blue highlight the two solvent exposed loops (Purple: Loop A, Blue: Loop B)</scene>. The loops are important for two different reasons. Loop A is responsible for the substrate binding. It holds many of the amino acids responsible for the hydrophobic substrate binding pocket. Loop B is also important to substrate binding, as it undergoes large conformational changes to accommodate the substrate. In contrast to the previous structure, the substrate is now present (in 1afs) and this loop takes a closed position. This opening and closing "garage door" mechanism is convenient for working through a large number of substrates, as the substrates can enter and exit easily. In the rat liver, each protein needs to convert as many steroids as possible to change the signal that is being sent out. In Dr. Banta's fuel cell, each protein would need to oxidize sugar molecules quickly to establish a current. | |||
