Self-Assembly Dynamics of Linear Virus-like Particles: Theory and - - PowerPoint PPT Presentation
Self-Assembly Dynamics of Linear Virus-like Particles: Theory and Experiment TMV Model 200 nm VLP Paul van der Schoot www.virology.wisc.edu/virusworld Collaborators Experiments Theory Armando Renko Daniela Melle Willem
200 nm
www.virology.wisc.edu/virusworld
Armando Hernandez-Garcia Renko de Vries Daniela Kraft Melle Punter Willem Kegel
deskeng.com/articles/aaahnd.htm www.vcbio.science.ru.nl/en/fesem/tem/
www.apsnet.org/edcenter/intropp/lessons/viruses/pages/tobaccomosaic.aspx
www.sweetpics.site/t/tobacco-mosaic-virus-model.html
coat protein (180 copies) ss RNA (3000 nts) 100 nm ss RNA (6400 nts) coat protein (2100 copies)
[G]/[dTq]= 40
Janssen et al. JACS 131 (2009), 1222.
stacking - 5 kBT
theory
binding - 10 kBT
Jabbari et al. Macromol. 43 (2010), 5833.
self-assembly templated assembly theory
T = 263 K [dTq] = 0.25 mM competition! enthalpy - 20 kBT
Koch et al. Beilstein J. Nanotechnol. 7 (2016), 613. Lebeurier et al. PNAS 74 (1977), 149. Chandrika et al. Virol 273 (2000) 198
OAS = packaging signal
6400 nt 5’ 3’
cap
W
18 kDa coat protein 34 cp bilayer disk lockwasher “threading”
OAS
growing helical virus
http://www.rsc.org/ej/CS/2001
allosteric binding
Caspar Biophys J 32 (1980) 103
binding → templated assembly interaction → co-operativity → self-assembly switching → suppresses self-assembly allostery → co-operativity
1 , n
*
P P P
P T
mass action → stoichiometry → co-operativity →
non-equilibrium distribution
Punter et al. J Phys Chem B 120 (2016), 6286.
P T
stoichiometry
∗ mass action
co-operativity
Kraft et al. Biophys J 102 (2012), 2845. Punter et al. J Phys Chem B 120 (2016), 6286.
sharp transition intermediates are suppressed longer template q increases co-operativity binding affinity
Punter et al. J Phys Chem B 120 (2016), 6286.
undershoot!
q = 51 𝜏 = 0.007 𝑇 = 𝑓2 excess template excess protein
silk-like block Sn: (GAGAGAGQ)n basic block B: K12 collagen-like block C: hydrophilic random coil (400 amino acids)
Garcia-Hernandez et al. Nature Nano 9 (2014), 698.
200 nm
2.5 kbp dsDNA
300 nm
C-S10-B 500 nm 200 nm λ = 0.101 λ = 0.134 C-S14-B C-S10-B C-S14-B ϵ + g (kBT) −17 −17 h − ϵ (kBT) 6 3 k+ (min−1) 4 × 109 4 × 109
Punter et al. J Phys Chem B 120 (2016), 6286.
q = 417
2.5 kDa DNA cDNA = 0.65 nM
theory:
TMV −17 7 3 × 108
Kraft et al. Biophys J 102 (2012), 2845.
Joris Sprakel
Cigil et al. J. Am. Chem. Soc. 139 (2017), 4962
polyfluorene: optomechanical proxy genome
𝑔
+ ≡
1 1 + 𝜇 Langmuir nucleation
zipping C-S10-B:
50
Garcia-Hernandez et al. Nature Nano 9 (2014), 698.
fraction taut excess protein!
Cigil et al. J. Am. Chem. Soc. 139 (2017), 4962
polyfluorene: optomechanical proxy genome C-S10-B: Joris Sprakel 𝑔
+ = 0.1
𝑔
+ = 0.3
𝑔
+ = 0.5
𝑔
+ = 0.7
micelle coat protein
Langmuir template OAS Zipper
Sander Kuipers
12 * ,
Z P
11 * ,
L P
9 * ,
M P
2 * ,
Z P P
T
M
Kuipers, bachelor thesis (Utrecht U, 2017)
Sander Kuipers Langmuir zipper dimensionless time fraction packaged templates sites
9
Z M
Z L k
7
5
3