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Using ProMol to Study Zinc Finger Motifs
Author(s) -
Albalwi Majied,
Bernstein Herbert,
Craig Paul
Publication year - 2015
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.29.1_supplement.567.20
Subject(s) - zinc finger , structural motif , template , computational biology , motif (music) , gene isoform , protein superfamily , computer science , chemistry , biology , biochemistry , gene , programming language , physics , transcription factor , acoustics
Currently, template‐based alignments focus on detection of motifs in novel structures that correspond to specific functions. ProMOL is a plugin for the PyMOL molecular graphics environment that has been used to detect motifs for enzyme active sites. The purpose of this study is to create non‐active site structural motifs in proteins, with a focus on the Zinc finger (ZnF) families from Pfam ‐ Cys2His2, Gag knuckle, Treble clef, Zinc ribbon, and Zn2/Cys6. While these motifs are not catalytic, zinc domains contribute to structure and function of proteins involved in many essential cellular processes. The methodology begins with creation and testing of the ZnF motifs against themselves followed by testing on homologs. A series of user‐created motif templates (the U set) will be prepared and characterized. Those with high specificity and selectivity will then be further refined and form the basis for the ProMOL S set (structural motifs). These motif templates will then be used to propose functions for unannotated structures in the Protein Data Bank. This work has been funded in part by National Institute of General Medical Sciences 2R15GM078077‐02, 3R15GM078077‐02S1 and 3R15GM078077‐02S2.