Nanobiology
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Enzymes as nanomachines
Molecular motors
Fluctuations in gene expression
Fluctuations in gene splicing
Copyright Stuart Lindsay 2009
The Cell Machine
• The genetic material
(DNA) is contained inside
the nucleus.
• Genetic information is
transported
to
the
cytoplasm as an RNA copy.
• ribosomes translate the
RNA code to proteins
• the entire cell is packaged
in
a
lipid
bilayer
membrane.
Copyright Stuart Lindsay 2009
Proteins: the nanomachines
(A) AP1: Transcription factor binding DNA to regulate the
expression of genes (DNA double helix in green)
(B)Protein kinase: a dimer that phosphorylates a target
(C) Actin, a filamentous protein acting as a structural scaffold.
Copyright
Lindsay 2009
The
20Stuart
amino
acid building-blocks
Genes code for amino acids
The sequence of residues
is specified by the
sequence of basis in RNA.
Each residue is codified
by a sequence of 3 bases
(codon).
The genetic code:
Note the stop codons
and degeneracy.
Note that 42=16 (<20), 43=64 (>20), so a three bases code is
necessary to specify the 20 different amino acids.
The cell machinery
out to the cytoplasm
trRNA
Into the nucleus
Copyright Stuart Lindsay 2009
Mechanical properties of proteins
Stiffness
Young’s modulus: ratio of stress to strain for a given material.
Young’s modulus
Stress =
Force per
unit area
F

E
A

Strain =
Fractional change in
dimension
In terms of a Hookean spring (A=l2):
F  El
Spring constant: k = El
Ex. Tubulin (transport in the cell)
MW=50KDa, E=2GPa, r=2.4nm, k = 10 N·m-1
Ex. Elastin (muscle and ligaments)
MW=75KDa, E=0.002GPa, r=2.75nm, k = 0.01 N·m-1
Density
Typical density of a well-packed protein is ρ ≈1.4·103 kg·m-3.
3MW
r
 0.073 MW nm
4 822
3
A (typical) 100kDa protein has a radius of ~3nm.
Viscosity
Typical viscosity for a globular protein (MW=100kD; r=3nm) is
η ≈1·10-3 Pa·s.
Drag coefficient in water:
  6 r  56 1012 Nsm 1
Diffusion
k BT
D
6a
Typical diffusion coefficient is D ≈7.3·10-11 m2·s-1.
Protein motions
Long range, collective fluctuations:
 
6a

Damped elastic fluctuations: from ps (tubulin) to ns (elastin)
Diffusive fluctuations: tens of ns
 2t

D
Actual catalyzed ET rate is kHz, so only ca. 1 in 106 longrange fluctuations drive the system to the transition state.
Copyright Stuart Lindsay 2009
Voltage gated channel
Living cells exchange materials by means of channels proteins,
chemically selective and under the control of signaling mechanisms.
The switch from open to closed is driven by the potential gradient
across the cell membrane.
AFM images of a monolayer of voltage-gated Porin OmpF on a
graphite surface in an electrolyte solution.
Energy for Molecular Motors and
ATP-dependent enzymes
ATP Hydrolysis
K eq
[ ADP ][ Pi ]

 4.9 x10 5
[ ATP]
Copyright Stuart Lindsay 2009
Thermal ratchet driven by ATP hydrolysis
Reactants = protein motor + H2O
Reactants +
ATP
Products + ADP
Products = protein
motor one step forward

 Ea 
k
exp 

6a
 kT 
Copyright Stuart Lindsay 2009
Molecular motors in muscle cells
Motor function in muscle cells is carried out by an actin-myosin
complex.
The active components of muscle tissues are the sarcomers, thick
filaments to which are attached many myosin molecules.
• Sarcomeres
appear as ca.
100,000 bands in
cardiac muscle
(TEM image)
Sarcomers, thick filaments, are interdigitated with thin filaments,
composed of bundles of the actin protein.
Crossbridge model
Myosin molecules consist of a long stalk that is permanently
attached to the tick filament and a pair of head units that
transiently contact the actin filaments.
The myosin moves along the interleaved actin filaments to draw
the crossbridge together, resulting in muscle contraction.
Muscle tissues can contract by more than 20% in length on a
period of tens of milliseconds.
Myosin-actin motor motion
Myosin
molecule
Crystal
structure of
head unit.
Note two
“feet”.
Arrows
point to
heads
(AAAS)
Myosin motor
ATP binding,
hydrolysis
and head
motion
Actin Filament
Copyright Stuart Lindsay 2009
“Walking”
action: step is
5 nm
(amplified by
lever arm to 36
nm). Force is
1.5 pN.
A Rotary Motor – ATP Synthase
A reversible motor:
• Proton gradient drives F1
rotation accompanied by
ATP synthesis from ADP.
• High ATP concentration
drives rotation in opposite
direction
with
ATP
hydrolysis which pumps
protons.
Copyright Stuart Lindsay 2009
clockwise rotation
counter-clockwise rotation
Copyright Stuart Lindsay 2009
Watching ATP synthase at work
F1 unit tethered with dyeloaded actin attached to F0
Movement of the gold bead was
detected by laser optical imaging.
The motor takes three 120° steps to
complete one rotation, hydrolizing
one ATP molecule per step.
(F1Prop4C.gif)
http://www.k2.phys.waseda.ac.jp/Researc.html
Copyright Stuart Lindsay 2009
(Courtesy of Professor Kazuhiko
Kinosita, Waseda University.)
Helix repeat: 3.4 nm
Copyright Stuart Lindsay 2008
DNA Nanotechnology
About 8 bases must be paired for a double helix to be stable at room
Temperature.
Copyright Stuart Lindsay 2008
A DNA-based four-way crossover structures producing a rigid
planar tile. The distance between adjacent tile is 20nm.
The structure, imaged by AFM, is produced by spontaneous selfassembly of the individual crosses.
Copyright Stuart Lindsay 2008
DNA Origami
A long template strand is annealed with a numebr of short strands
that either form cross-links at fixed points (loops) or fill regions to
form double helices.
Biomimetic nanostructures
Mineralization
These structures consist of
mineral layers held
together with proteins that
acts as surface-specific
‘glues’ (SEM images).
Abalone shell
Copyright Stuart Lindsay 2009
Diatom
Peptide glues for specific surfaces
• Make a random peptide library on the surface of a phage by
inserting random DNA into phage genome (Phage display)
• Select those phage that stick and grow them up.
• Repeat cycle for highly specific interaction
• Sequence “successful” phage genome to decode peptide
sequence
Filamentous bacteriophage
sticking to an InP (100)
surface. They express a
surface protein that sticks to
just this particular surface.
Whaley, S.R. et al. Nature,2000, 405: 665-668.
Mimicking Bio-nano-optics
Lenses
modeled
mimicking
brittlestar
Brittlestar
nanolenses
Lee and Szema, Science 2005
but flexible
so the
refractive
index can
be adjusted
by pumping
different
fluid.