[Chimera-users] FAD binding site on Cryptochrome

Margiotta, Joseph Joseph.Margiotta at utoledo.edu
Thu Oct 10 09:34:37 PDT 2019

I am very new to molecular modeling and have a very basic novice user issue.  We are studying cryptochrome proteins some of which are known to bind the chromophore Flavin adenine dinucleotide (FAD) and for this and other reasons are considered photopigments.  We have looked at a cryptochrome in chicken that binds FAD and is light sensitive (GallusCRY4) and have sent the AA sequence to Zhang’s COACH site for Protein-ligand binding site prediction (https://zhanglab.ccmb.med.umich.edu/COACH/) at the University of Michigan.  The results come up with a C-score confidence prediction of 0.59 with a cluster size of 63 for FAD binding to GallusCRY4.  The results allow you to download the 3D model and the residue-specific binding probability, which is estimated by SVM, the predicted bound ligands and detailed prediction summary, and the templates clustering results. We’d now like to extend this modeling to GallusCRY1 and GallusCRY2 to see get a FAD binding prediction and the complex structure with the most representative ligand in the cluster.

The COACH site lets you export the model and complex structure in PDB format and I downloaded Chimera to visualize and analyze the PDB results.   I would like to be able to label the structures using the binding probabilities, and template clustering results to include the predicted FAD binding pocket on the three CRY proteins and also label a tetrad of Trp residues that are thought to be responsible for electron transfer.  Can you give me some general guidance on how to start this analysis?

-- Joseph F. Margiotta, PhD
Professor of Neurosciences
UT College of Medicine & Life Sciences
Block HS 120A   Mail Stop 1007
Toledo, OH  43614

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