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Canonical protein dynamics

Canonical protein dynamics. Flowchart. Differential equation. Solution. f. 0. Physical picture of protein translation and degradation. No degradation for this protein. No translations. 10. 0. 11. 1. 12. 2. 13. 3. 14. 4. 15. 5. 16. 6. 17. 7. 18. 8. 19. 9. +. +. +.

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Canonical protein dynamics

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  1. Canonical protein dynamics Flowchart Differential equation Solution f 0

  2. Physical picture of protein translation and degradation No degradation for this protein No translations 10 0 11 1 12 2 13 3 14 4 15 5 16 6 17 7 18 8 19 9 + + + No change 20 Note: Proteins can be distinguished by momentary distortions.

  3. Physical picture of protein translation and degradation Chance translation 10 0 11 1 12 2 13 3 14 4 15 5 16 6 17 7 18 8 19 9 + + + + 20 Note: Proteins can be distinguished by momentary distortions.

  4. Physical picture of protein translation and degradation Neglecting to roll dice on this freshly generated protein. 10 0 11 1 12 2 13 3 14 4 15 5 16 6 17 7 18 8 19 9 + + + + No change 20 Note: Proteins can be distinguished by momentary distortions.

  5. Physical picture of protein translation and degradation 10 0 11 1 12 2 13 3 14 4 15 5 16 6 17 7 18 8 19 9 + + + + No change 20 Note: Proteins can be distinguished by momentary distortions.

  6. Physical picture of protein translation and degradation 10 0 11 1 12 2 13 3 14 4 15 5 16 6 17 7 18 8 19 9 + + + + 20 Note: Proteins can be distinguished by momentary distortions.

  7. Physical picture of protein translation and degradation 10 0 11 1 12 2 13 3 14 4 15 5 16 6 17 7 18 8 19 9 Rolled dice for protein that was already degraded! + + + + No change 20 Note: Proteins can be distinguished by momentary distortions.

  8. Physical picture of protein translation and degradation 10 0 11 1 12 2 13 3 14 4 15 5 16 6 17 7 18 8 19 9 + + + + 20 Note: Proteins can be distinguished by momentary distortions.

  9. Physical picture of protein translation and degradation 10 0 11 1 12 2 13 3 14 4 15 5 16 6 17 7 18 8 19 9 + + + + 20 Note: Proteins can be distinguished by momentary distortions.

  10. Physical picture of protein translation and degradation Chance translation 10 0 11 1 12 2 13 3 14 4 15 5 16 6 17 7 18 8 19 9 + + + + + 20 Note: Proteins can be distinguished by momentary distortions.

  11. Physical picture of protein translation and degradation 10 0 11 1 12 2 13 3 14 4 15 5 16 6 17 7 18 8 19 9 + + + + + 20 Note: Proteins can be distinguished by momentary distortions.

  12. Physical picture of protein translation and degradation 10 0 11 1 12 2 13 3 14 4 15 5 16 6 17 7 18 8 19 9 + + + + + 20 Note: Proteins can be distinguished by momentary distortions.

  13. Physical picture of protein translation and degradation 10 0 11 1 12 2 13 3 14 4 15 5 16 6 17 7 18 8 19 9 + + + + + 20 Note: Proteins can be distinguished by momentary distortions.

  14. Physical picture of protein translation and degradation Chance translation 10 0 11 1 12 2 13 3 14 4 15 5 16 6 17 7 18 8 19 9 + + + + + + 20 Note: Proteins can be distinguished by momentary distortions.

  15. Physical picture of protein translation and degradation 10 0 11 1 12 2 13 3 14 4 15 5 16 6 17 7 18 8 19 9 + + + + + + 20 Note: Proteins can be distinguished by momentary distortions.

  16. Physical picture of protein translation and degradation 10 0 11 1 12 2 13 3 14 4 15 5 16 6 17 7 18 8 19 9 + + + + + + 20 Note: Proteins can be distinguished by momentary distortions.

  17. Physical picture of protein translation and degradation 10 0 11 1 12 2 13 3 14 4 15 5 16 6 17 7 18 8 19 9 + + + + + + 20 Note: Proteins can be distinguished by momentary distortions.

  18. Physical picture of protein translation and degradation Between times and 10 0 11 1 12 2 13 3 14 4 15 5 16 6 17 7 18 8 19 9 + + + + + + Proteins lost Proteins added 20 Note: Proteins can be distinguished by momentary distortions.

  19. Physical picture of protein translation and degradation 30 Limitation!!! (But we all do it this it this way) 29 10 0 1 11 12 2 13 3 14 4 15 5 16 6 17 7 18 8 19 9 28 Realistic trajectory f + + + + + + Unrealistically smooth trajectory STOP 20 Note: Proteins can be distinguished by momentary distortions. x(# proteins)

  20. Canonical protein dynamics Flowchart Differential equation Solution f 0

  21. Time-course and rise time Declare initial condition, for example, “start at time 0 with no protein” Look for possible steady states Estimate some slopes f 0

  22. Time-course and rise time f 0

  23. Time-course and rise time f 0

  24. Time-course and rise time Show f STOP 0

  25. Time-course and rise time f 0

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