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Taking advantage of local similarities of homologous structures

Taking advantage of local similarities of homologous structures. Rigid-body refinement of segments Fragment searches (FFFEAR, ESSENS) DEN or jelly-body refinement Rosetta modeling Morphing. Morphing. Local structures may superimpose very closely

darshan-gopal
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Taking advantage of local similarities of homologous structures

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  1. Taking advantage of local similarities of homologous structures • Rigid-body refinement of segments • Fragment searches (FFFEAR, ESSENS) • DEN or jelly-body refinement • Rosetta modeling • Morphing

  2. Morphing • Local structures may superimpose very closely • The position of a large group of atoms can be identified accurately with a poor map • Relationship between structures may be a simple distortion

  3. A challenging morphing problem: How can we use this map to identify the shifts needed? cab55342: final model green3PIC (32% identity) in blue

  4. Standard refinement does not move the structure very much.. cab55342: 3PIC (32% identity) in blueRefined template in orange

  5. Steps in morphing • A. Identify local translation to apply to one Ca atom and nearby atoms • B. Smooth the local translations in window of 10 residues • C. Apply the smoothed translation to all atoms in the residue

  6. Identify local translation to apply to one Ca atom and nearby atoms cab55342: final model (green)3PIC (32% identity, blue)prime-and-switch map (blue)

  7. Identify local translation to apply to one Ca atom and nearby atomsModel density in pink cab55342:3PIC (32% identity, blue) Ca 181

  8. Identify local translation to apply to one Ca atom and nearby atoms Model density offset to match map cab55342:3PIC (32% identity, blue)

  9. Smooth offset over nearby residues and apply to all atoms in the residue cab55342:3PIC (32% identity, blue)Morphed model (yellow) Ca 181 Geometry within each residue is maintained

  10. Refine morphed model 3PIC (32% identity) in blueMorphed model (yellow)Refined morphed model (orange) Ca 181

  11. Get new map Repeat morphing 6 times... 3PIC (32% identity) blue Refined morphed model (yellow)prime-and-switch map (purple)

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