Notes 20100810 McConkey Meiering Meeting
From SnOwy - Ed's Wiki Notebook
20100810.112310
- Base case -- duplication event -- mechanism for the very first duplication
- Nothing to bunch up on -- no similar sequences to start
- Recommended the up-down barrels
- Fundamentally different: Beta propellers are kind of different, they are in the middle of the continuum for compact proteins and loose fibrillar proteins.
- We should work on the tightly packed proteins (that have more constraints)
- Hence TIM Barrels; however, suggest: Beta up-down barrels has a stronger signal -- 4 repeats in 8 strands
Bibliography
- Doug Barrick (John Hopkins) -- Ankryn
- Lynn Regan (EL)
- Matthew H Cordes (Arizona) -- Ark Repressor
- Brian K Davis -- Ferridoxin Review (2002, Biophysics molecular biology)
- Tight globular kind
- 23 residue primordial sequence
- Payandeh, Pie, E F -- JBC 2006
- Park, Mayo, Recipe for designing 33 residue beta sheet peptides
- Grichin N V
- Current opinion 2009 structural biology
- TPR repeat -- (tetra something repeat?) -- attempted to get 7 to n repeats -- the 'repeat' step is difficult
On Thesis Proposal
- LaTeX?
- Robert Sterner -- TIM Barrel
- Janet Thornton -- Superfold
- Orengo -- Superfold
- Return to the 4-helix bundle
- Ferridoxin
- Up-down barrels
- TIM Barrel?
- Albumin?
- Computational Methods Revamp
- Rosetta step after consensus sequence
- Describe possible direction
- Describe rationale
- Scope (the third problem is small for a PhD thesis)
