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Physical aspects in the self-assembly of biological complexes
Bogdan Dragnea Chemistry Department Indiana UniversityBloomington IN [email protected]
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Self-assembling supra-molecular systemsExample of supramolecularhierarchy: the skeleton of a sea sponge (Eupectella, J. Aizenberg, 2003).
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What questions can physicists answer?
What is the mechanism of self-assembly?What intermediates, kinetic bottlenecks?How do the assembly pathways depend on environment?
What are the dynamics of the final complex?What physical properties emerge from a given hybrid structure?
How to design a biological metamaterial.
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Viruses: best size/complexity ratio?
Most viruses are symmetric: icosahedral or helical capsid structures.Most capsids are composed of a small number of types of proteins.
CAPSID
NUCLEICACID
Session L34: Virus-Inspired Supramolecular StructuresTuesday afternoon, March 6, 2007, APS Meeting.
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Mechanism of self-assembly: theory
Thermodynamics Physical Kinetics
R. Bruinsma et al., Phys. Rev. Lett., 2003
A. Zlotnick, J. Mol. Rec., 2005
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Mechanism of self-assembly: experiment
Thermodynamics Kinetics (DLS)Cryo-TEM
Zlotnick et coll.: Capsid formation is a nucleated process and the nucleus is a pentamer of dimers.
Gelbart et coll., PNAS, 2003λ-phage packages DNA at a pressure of 20 atm.
NOTE: ensemble averaging methods do not provide direct insights into the pathways of assembly.
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Assembly and dynamics – single virus
Optical tweezers Atomic force microscopy
Φ29: the strongest motor knownCharacterization of the mechanical work cycleBustamante et coll., Cell, 2005
G. Wuite et coll., PRL, 2006Continuum theory holds –important for interpretation of dynamics
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Detection and manipulation of single viruses – a need for new methods
DetectionIgnatovich and Novotny, PRL 2006
Manipulation
Klenerman et coll., JACS, 2006
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F = -α ∇E2
Two ways to reach subwavelength particle manipulation
Increase polarizability Use near-field: sharper gradients and field enhancementsProtein coat
(capsid)
Metal core
VLP’sC. Chen et al., Nano Lett., 2006 Okamoto and Kawata, PRL, 1999
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The first questions
Will VLP models be relevant for studying viral processes?What forces and what optical signals can be expected from near-field?
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Aperture-trap: experimental setup
Scan direction
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First results
V44.00008 Lensless focusing and optical trappingThursday, March 8, 2007, 12:39PM -12:51PM, Chris DuFort
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3D field intensity mapping
Amarie D, Rawlinson ND, Schaich WL, et al.Three-dimensional mapping of the light intensity transmitted through nanoaperturesNANO LETTERS 5: 1227-1230 JUL 2005
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Tailoring field distributions and enhancements
Max. Enhancement: 3000
SP Modes
Tonuta et al., NanoLetters, 2007
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On-going projects
Optothermal ratchet
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Virus-like particles-from probes to metamaterials-
Chen, C. et al. Nanoparticle-Templated Assembly of Viral Protein Cages. Nano Letters 6, 611-616 (2006).
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Particle acts as a template promoting self-assembly
~ 90% encapsulation efficiency.(As good as viral RNA)
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Core-induced polymorphism
Sun et al., PNAS, 2007
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Photothermal in-vivo tracking of metal nanoparticles
Single Nanoparticle Photothermal Tracking of 5-nm Gold Beads in Live Cells
B. Lounis et coll., Biophys. J., 2006.
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Towards bio-metamaterials
Metamaterials: optical properties determined by their organized structure rather than inherited directly from the material properties of individual subunits.Metallodielectric metamaterials are composed of resonant metal inclusions in a dielectric matrix and have subwavelength lattice periods.
Smith et al., Metamaterials and negative refractive index. Science 305, 788-792 (2004). Brown et al., Large Electromagnetic Stop Bands in Metallodielectric Photonic Crystals. Applied Physics Letters67, 2138-2140 (1995).Fan et al., Large omnidirectional band gaps in metallodielectric photonic crystals. Physical Review B 54, 11245-11251 (1996).
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Symmetric protein shells: 3D structures with sub-100 nm lattice parameter
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Plasmon hybridization (Nordlander, 2003)
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3D metallodielectric plasmonic band structure
De Abajo et coll., 2005
d
2R
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σposition = N1/2·σAu
σposition = σAu
Why VLPs?Why VLPs?To preserveTo preserve long range orderlong range order
Colloidal crystal:
VLP crystal:
Characteristic lengths:λ0 ≈ 0.6 μmλSP ≈ ? λdecay ≈ 20 μm
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VLPs crystallize in 3D metallodielectric arrays
10 μm
VLP
BMV
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Band splitting observed
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Conclusions
There is a vast unexplored territory in the area of mechanisms of self-assembly.New Tools (both theoretical and experimental) are needed to access:
Dynamics,Intermediates,Relationship between structure and properties.
Optics provides convenient ways to manipulate, probe and build.Examples: near-field forces for trap integration, virus-mimic probes, biological metamaterials.
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AcknowledgementsGroupDr. Marie-Christine DanielC. Chen (P-Chem)T. Onuta (Phys.)S. Anyagyei (Anal. Chem.) N. Goicochea (P-Chem)S. Dixit (P-Chem)X. Huang (P-Chem)M. Vieweger (P-Chem)D. Amarie(Phys/Jacobson/Glazier)Chris DuFort (Anal. Chem.)Chelsea KennedyZachary QuinkertSteve IrishDavid Pavkovich
Collaborators
Dr. W. L. SchaichDr. C. Cheng KaoDr. S. JacobsonDr. J. Glazier
Funding:
NSF-BioPhotonics, PRF, CLSIR