Protein Dynamics Flowchart and Physical Changes in Translation and Degradation
Explore the canonical protein dynamics flowchart and witness the physical alterations in protein translation and degradation processes, including chances of change and neglect in a series of visuals. Dive into the various scenarios where protein dynamics unfold with or without specific actions, depicting a comprehensive view of protein behavior.
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Presentation Transcript
Canonical protein dynamics Flowchart Differential equation ? ?? ??= ? ?? ? ? Solution ? ? ?? ? 0 1
Physical picture of protein translation and degradation No degradation for this copy of protein No translation No change ? ????? 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 2
Physical picture of protein translation and degradation Chance translation + + ? ????? 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 3
Physical picture of protein translation and degradation Neglected to roll dice on this freshly generated copy of protein + No change + ? ????? 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 4
Physical picture of protein translation and degradation + No change + ? ????? 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 5
Physical picture of protein translation and degradation + + ? ????? 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 6
Physical picture of protein translation and degradation + Rolled dice for copy of protein that was already degraded! No change + ? ????? 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 7
Physical picture of protein translation and degradation + + ? ????? 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 8
Physical picture of protein translation and degradation + + ? ????? 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 9
Physical picture of protein translation and degradation Chance translation + + + + ? ????? 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 10
Physical picture of protein translation and degradation + + + + ? ????? 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 11
Physical picture of protein translation and degradation + + + + ? ????? 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 12
Physical picture of protein translation and degradation + + + + ? ????? 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 17
Physical picture of protein translation and degradation Chance translation + + + + + + ? ????? 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 18
Physical picture of protein translation and degradation + + + + + + ? ????? 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 19
Physical picture of protein translation and degradation + + + + + + ? ????? 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 20
Physical picture of protein translation and degradation + + + + + + ? ????? 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
Mathematical description of protein translation and degradation Between times ?0 and ?0+ ? 3 translations 20 time steps ? ? # time steps Proteins added + 28 56 2 degradations 20 time steps 28 proteins ? ? ? ?0 # time steps # proteins Proteins lost + ? ?0+ ? ? ?0 + ? ? ? ? ? ?0 ? ?0+ ? ? ?0 ? ? ? ? ? ?0 + ?? ???=?0 ? ?0+ ? ? ?0 ? ?? ?0 ? ? + + + ?0 ? ????? 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 22
Mathematical description of protein translation and degradation ? ? ?? ??= ? ?? ? + Differential equation has limitations x (# proteins) STOP + 30 29 + Realistic trajectory 28 + + + ? ????? 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 23
Canonical protein dynamics Flowchart Differential equation ? ?? ??= ? ?? ? ? Solution ? ? ?? ? 0 24
Time-course and rise time ? ? ?? ??= ? ?? ? Declare initial condition, for example, start at time 0 with no protein Look for possible steady states 0 =?? ??= ? ???? ???=? ? 0 = 0 ? ? ? Estimate some slopes ?? ? 0 25
Time-course and rise time ? ? ?? ??= ? ?? ? ? ? = ? +? ?? ??= ? ? ? ? ? ? ?? ?? ? 1 ??? = ? ?? =? ? ? ? ? 0 ?=0 ?=? ? 0 ? ?? ??= ?? ? ??? = ? ?+? ?= 0 ??1 ?? ?? ???? = ? ?? ?? ??=?? ?? ?? ? ?=0 ?=0 ?? ?? ??= ? ?? ? +? ?? ?? ? ? ? ?? ?? ??= ?? ?? ? 0 26
Time-course and rise time ? ? ?? ??= ? ?? ? ? ? = ? +? ? ? ?? ?? ? 1 ??? = ? ?? =? ? ? 0 ?=0 ?=? ? 0 ? ? ? ?? ? ? ? ??? = ? ?+? ln = ? ?? 0 = ??? ln ? ? ?? ln ?? ?= 0 ?? ??=?? ?? ?? ? ? ?? ?? = ? ??? ?? ? =? ?? ??= ? ?? ? +? ?? ?? ?? ??? ? ? ? ?? ?? ??= ?? ?? ? 0 27
Time-course and rise time ? ? ?? ??= ? ?? ? ? =? ?? ??? Show 12=ln 2 STOP ? ? ? ? ?? ?? ?? ? ? ?? ?? 2? 2? ? 2? ? 2? ? 2? ? 0 ? 12 28
Time-course and rise time ? ? ?? ??= ? ?? ? ? =? ?? ??? 12=ln 2 ? ? ? ? ?? ? 2? ? 0 ? 12 ? 12 ? 12 ? 12 ? 12 29
