Group:SMART:2010 Pingry SMART Team: Difference between revisions
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<scene name='2010_Pingry_SMART_Team/1lwi_default/5'>The non-polar cavity for substrate binding is colored CPK and contains Leu54, Trp86, Phe118, Leu122, Phe128, Phe129, Leu137, and Phe139.</scene> The substrate binding pocket is non-polar because the substrate, testosterone, is a lipid, and therefore non-polar. This is an important factor when considering how to modify substrate specificity. In Dr. Banta's fuel cell protein, the most common substrate will be a sugar,a hydrophilic molecule. Therefore, the substrate binding pocket must match the substrate. The catalytic triad, which includes the most important amino acids in regards to reacting with the substrate, is located at the distal, or far, end of the pocket. | <scene name='2010_Pingry_SMART_Team/1lwi_default/5'>The non-polar cavity for substrate binding is colored CPK and contains Leu54, Trp86, Phe118, Leu122, Phe128, Phe129, Leu137, and Phe139.</scene> The substrate binding pocket is non-polar because the substrate, testosterone, is a lipid, and therefore non-polar. This is an important factor when considering how to modify substrate specificity. In Dr. Banta's fuel cell protein, the most common substrate will be a sugar,a hydrophilic molecule. Therefore, the substrate binding pocket must match the substrate. The catalytic triad, which includes the most important amino acids in regards to reacting with the substrate, is located at the distal, or far, end of the pocket. | ||
<scene name='2010_Pingry_SMART_Team/1lwi_cofactorbonding/1'>Orange highlights the co-factor specificity side-chains.</scene> Gln190, Asn167, Ser166 form hydrogen bonds with the nicotinamide ring. For more details about co-factor specificity, see the other two protein structures. | <scene name='2010_Pingry_SMART_Team/1lwi_cofactorbonding/1'>Orange highlights the co-factor specificity side-chains.</scene> Gln190, Asn167, Ser166 form hydrogen bonds with the nicotinamide ring in the cofactor. Tyr216 performs pi-stacking against the nicotinamide ring of the cofactor. For more details about co-factor specificity, see the other two protein structures, which explain the subject in more depth. | ||
<scene name='2010_Pingry_SMART_Team/1afs_safetybelt/1'>Green highlights the safety belt mechanism that is present only in 1AFS.</scene> Formed by Asp224 and Lys28, the safety belt locks the cofactor in the binding site through residues that form hydrogen bonds to the oxygens on the phosphate. This safety belt is formed when Loop B binds the substrate, and is broken upon release. As a result, this safety mechanism is present in 1AFS, but missing in 1LWI where the substrate is absent. In addition, this safety belt seems to be missing residues from Lys28 to Asp224. This is due to the fuzzy positions in the x-ray crystallography image, which leaves the exact locations of the residues unresolved. | <scene name='2010_Pingry_SMART_Team/1afs_safetybelt/1'>Green highlights the safety belt mechanism that is present only in 1AFS.</scene> Formed by Asp224 and Lys28, the safety belt locks the cofactor in the binding site through residues that form hydrogen bonds to the oxygens on the phosphate. This safety belt is formed when Loop B binds the substrate, and is broken upon release. As a result, this safety mechanism is present in 1AFS, but missing in 1LWI where the substrate is absent. In addition, this safety belt seems to be missing residues from Lys28 to Asp224. This is due to the fuzzy positions in the x-ray crystallography image, which leaves the exact locations of the residues unresolved. | ||
