Discovering critical residues in glutathione reductase - Gentoo

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with one exception (Figure 2). There was about 90-100% support for the entire tree except for placement of the plants within the tree, which only had about 65- 70% support. Other than that, as expected, animals split out from plants, and both of them split apart from prokaryotes. No further analysis of the tree itself will be made, because it was intended as an intermediate for input into further programs. ConSurf is a program to calculate evolutionarily conserved residues and map them onto a protein structure. The true power of it is in its flexibility – it will take a list of sequences and a PDB ID as input, or you can input a precalculated sequence alignment, or even a precalculated phylogenetic tree, along with your own PDB. This allows for potential creation of better structural conservation maps, because ConSurf just uses ClustalW for alignment and a simple neighborjoining tree. ConSurf outputs a large table of conservation values, and optionally replaces the B factors in the PDB file with conservation values, so any molecular graphics program can be used for the analysis. However, ConSurf does not yet allow delving into tree-determinant residues. In other words, no simple way exists to analyze changes on smaller level than the entire tree to examine changes in function between different Grs.
Figure 4: Ile26 in FAD binding. See text for discussion. Initial analysis focused on the active site, where there is already a long list of residues suspected important in binding and catalysis. Near the NADPH (Figure 3), one can see that many of the expected residues were conserved: Arg291, Glu201, and others. But there are more conserved residues: Ser177, Asp178, Gln445, and interestingly, Ile198. Ser177 appears to hydrogen bond with the nicotinamide ring, which may serve to orient it correctly for hydride transfer. It's already known that generally the positive residue of ion pairs is nearer to the flavin, but what grows more clear here is that there are conserved positive residues above the flavin (Gln445 and Arg291 on the NADPH side), and the conserved negative Asp178 below the flavin. This negative charge just below the carbon that accepts a hydride from NADPH may serve some purpose in
Page 1 and 2: Discovering critical residues in gl
Page 3 and 4: To understand possible changes in G
Page 5 and 6: Materials and Methods Multiple sequ
Page 7 and 8: Figure 1: Alignment of Arg218. From
Page 9: sequences, a convenient feature of
Page 13 and 14: Figure 6: The Cys58-Cys63 disulfide
Page 15 and 16: Figure 8: Phe254, a surface hydroph
Page 17 and 18: Figure 10: Structural stabilization

Discovering critical residues in glutathione reductase - Gentoo

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