Sandbox Reserved 895: Difference between revisions
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From an evolutionary standpoint it might be expected that the RPE65 catalytic mechanism would resemble that of the carotenoid oxygenase as sequence homology places RPE65 in the same family as the CCOs, this is not the case. Although the current enzymatic mechanism for RPE65 is only hypothesized with current research, there is not enough experimental evidence to definitively rule out that RPE65 catalyzes its function with molecular oxygen in the isomerization reaction. However, if such were the case the reaction would require even more complex chemistry which is not justifiable by the current scientific evidence. A study by Oberhauser and colleagues in 2008 on NinaB, a member of the CCO family from moths with isomerooxygenase activity was described, indicating that the members of this family originally developed isomerase activity while keeping the carotenoid oxygenase activity. The results of this study suggested a functional link between vertebrate RPE65 and insect NinaB which are both essential for the synthesis of key visual cycle chromophores. The function of NinaB showed that RPE65, a retinoid isomerase in the CCO family, retained the emergent activity that was found in a common ancestor. Comparing the topologies between the enzyme and substrate between NinaB and RPE65 showed that the iron cofactor was not directly involved in the double bond isomerization activity. Although further research would be needed to determine the ancestry of RPE65, it is fascinating to study the evolution and the diversification of protein family in animals by following the trace from a single multifunctional ancestral protein to several highly specialized enzymes seen in vertebrates. <ref> DOI 19020100 </ref> Using Cluster Omega, the amino acid sequence of NinaB and bovine RPE65 was compared. Although the structure alignment is quite different, there are still some sequence homology between the two enzymes that may suggest an ancestor linkage. | From an evolutionary standpoint it might be expected that the RPE65 catalytic mechanism would resemble that of the carotenoid oxygenase as sequence homology places RPE65 in the same family as the CCOs, this is not the case. Although the current enzymatic mechanism for RPE65 is only hypothesized with current research, there is not enough experimental evidence to definitively rule out that RPE65 catalyzes its function with molecular oxygen in the isomerization reaction. However, if such were the case the reaction would require even more complex chemistry which is not justifiable by the current scientific evidence. A study by Oberhauser and colleagues in 2008 on NinaB, a member of the CCO family from moths with isomerooxygenase activity was described, indicating that the members of this family originally developed isomerase activity while keeping the carotenoid oxygenase activity. The results of this study suggested a functional link between vertebrate RPE65 and insect NinaB which are both essential for the synthesis of key visual cycle chromophores. The function of NinaB showed that RPE65, a retinoid isomerase in the CCO family, retained the emergent activity that was found in a common ancestor. Comparing the topologies between the enzyme and substrate between NinaB and RPE65 showed that the iron cofactor was not directly involved in the double bond isomerization activity. Although further research would be needed to determine the ancestry of RPE65, it is fascinating to study the evolution and the diversification of protein family in animals by following the trace from a single multifunctional ancestral protein to several highly specialized enzymes seen in vertebrates. <ref> DOI 19020100 </ref> Using Cluster Omega, the amino acid sequence of NinaB and bovine RPE65 was compared. Although the structure alignment is quite different, there are still some sequence homology between the two enzymes that may suggest an ancestor linkage. | ||
Comparing bovine RPE65 across different species using a BLAST search showed that RPE65 is highly conserved between animals. From mammals, to rodents there was at least a 97% similarity in sequences. As an example shown below in '''Figure | Comparing bovine RPE65 across different species using a BLAST search showed that RPE65 is highly conserved between animals. From mammals, to rodents there was at least a 97% similarity in sequences. As an example shown below in '''Figure 7A''' is a sequence alignment between bovine RPE65 and hamster RPE65. Throughout the sequence alignment there are only 12 amino acid residues that are different between the two species. By showing RPE65 is conserved, researchers are able to use bovine RPE65 to predict the structure and activity of human RPE65 in drug testing and drug development. '''Figure 7B''' shows the lineage of all know RPE65 enzymes. | ||
[[Image:sequence_alignment.jpg|thumb|center|512 px|alt=Figure | [[Image:sequence_alignment.jpg|thumb|center|512 px|alt=Figure 7A: bovine and hamster RPE65 sequence alignment| '''Figure 7A:''' Sequence Alignment between Bovine RPE65 and hamster RPE65 showing highly conserved amino acid residue between organisms.]] | ||
[[Image:Lineage_RPE65_Full.jpg|thumb|center|512 px|alt=Figure 7B: Full RPE65 lineage| '''Figure 7B:''' RPE65 lineage tree using BLAST. Note that the red arrow is a continuation of the lineage tree after "multiple organisms" and is not to scale. Note that the scale changes from 0.01 to 0.006 between the two portions of the lineage]] | |||
=== '''[1.3.2] Mutations leading to disease''' === | === '''[1.3.2] Mutations leading to disease''' === | ||
