Investigation of Putative Metal Binding by Npp-domain of Collagen XI
Dr. Henry Charlier and Dr. Julia Oxford
The crystal structure for the NC4 domain of collagen IX (NC4) has recently been reported (2uur). NC4 has significant sequence homology to the Npp domain of collagen XI (Npp) and therefore was used to construct a model for the structure of Npp. Using the reported zinc binding site of NC4 and other homologs, a putative metal binding site was identified in the Npp structural model. Molecular Dynamics (MD) were performed with calcium bound versus not bound to the putative site. After MD calculations were performed, the structure had lost some β-sheet, while the putative zinc binding site remained intact. Stepwise addition of prolines followed by MD achieved a properly folded Npp protein as assessed by RMSD being measured under 3.5 A. Preliminary metal binding studies are underway. (NIH Grant # P20 RR016454)
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