Biological Nanomaterials NANO*4100 FALL 2014 Instructor:John
Dutcher Office:MacN 451 Phone + phone mail : Ext. 53950
E-mail:[email protected] Web:www.physics.uoguelph.ca/psi
Lectures:M W F13:30 14:20MacN 201 Course Website:
http://www.physics.uoguelph.ca/~dutcher/nano4100/
Slide 2
Objectives of the Course Understand the principles of the
quantitative biology approach Understand the basic building blocks
of biology and how they bind to form biological molecules
Understand different interactions between biological molecules and
the principles underlying the self- assembly of aggregates of
biological molecules and nanomaterials Appreciate the diversity and
complexity of self- assembled biological nanomaterials Expand
scientific writing skills to develop effective communication
Slide 3
Literature Required Text: CD directory with review &
research papers Available in the cd directory at:
http://www.physics.uoguelph.ca/~dutcher/download/nano_4100
Supplementary Reading : Various journals related to biological
molecules, biological materials, nanomaterials (see the website for
links) Please learn how to use internet to look for papers and to
find their full texts. You should be familiar with the following:
Entrez (PubMed); ISI Web of Knowledge (Science Citation Index and
Biological Abstracts); Chemical Abstracts; Scholars Portal (or
ScienceDirect); HighWire Press; Annual Reviews; ACS
Publications
Slide 4
Evaluation Problem Assignments30% Directed Reading Assignments
15% Marking of NANO*1000 Report 5% Midterm Test20% Final
Examination30% ____________________________________ Total100%
Slide 5
Course Topics introduction to quantitative biology - power of
physical approach to biological systems introduction to
biomolecules and biological membranes - building blocks and
interactions lipids and self-assembly of lipid structures
macromolecules: polymers - random walks & diffusion
macromolecules: proteins & DNA - building blocks and higher
order structure self-assembly of macromolecules - copolymers,
protein filaments, peptide-based self-assembly biological machines
- bacterial flagella, myosin & kinesin walking, Brownian
ratchet bionanocomposites - unique properties
Slide 6
Guest Instructors Rob Wickham (Physics):copolymers Leonid Brown
(Physics):proteins Doug Fudge (MCB):protein filaments
bonding between molecules is weak comparable to thermal energy
k B T ~ 1/40 eV (@RT) can have big changes to soft materials with
small changes in environment temperature, pH, ionic strength,
applied fields
Slide 9
Soft Materials hydrogels C. Chang et al. Euro Polym J 46, 92
(2010) Swollen in water As-prepared Dried Swollen in NaCl
solution
Soft Materials drug delivery heat-triggered dox release from
Temperature Sensitive Liposome due to MRI-guided high intensity
focused ultrasound Grull & Langereis, J Controlled Release 161,
317 (2012)
Slide 12
Large Range of Length Scales properties depend on length scale
of measurement complex, hierarchical structure processing is the
key [P. Ball, Made to Measure]
Slide 13
Physics Meets Biology bring together biology & physics to
get biological physics sophisticated experimental tools
sophisticated models of biological systems Quantitative Biology
quantitative data demand quantitative models www.qbio.ca
Slide 14
PSI Biological Physics Projects bacterial biophysics
viscoelastic properties of bacterial cells bacterial twitching
motility Min protein oscillations & patterns biopolymers at
surfaces & membranes single molecule pulling of proteins on
nano-curved surfaces single molecule imaging of peptides in lipid
matrix field driven changes in conformation & orientation
enzymatic degradation of cellulose imaging & kinetics of
adsorption & degradation polysaccharide nanoparticles startup
company
Slide 15
Quantitative Biology eight fundamental concepts provide toolbox
for interpreting biological data simple harmonic oscillator ideal
gas & ideal solutions Ising model random walks, entropy &
diffusion Poisson-Boltzmann model of charges in solution elastic
theory of 1D rods & 2D sheets Newtonian fluid model &
Navier-Stokes equations rate equation models of chemical kinetics
Adapted from Phillips et al., Physical Biology of the Cell
Slide 16
Quantitative Biology simple harmonic oscillator Phillips et
al., Physical Biology of the Cell
Slide 17
Quantitative Biology different levels of modeling beyond the
spherical cow Phillips et al., Physical Biology of the Cell DNA
membrane
Slide 18
Rules of Thumb Phillips et al., Physical Biology of the
Cell
Slide 19
Rules of Thumb Phillips et al., Physical Biology of the
Cell
Slide 20
Drunkards walk Courtesy of George Gamow Random Walks
Slide 21
Random Walk Common Theme random walk is a recurring concept in
course helps with seemingly unrelated problems diffusion of
molecules, cells & nanomachines polymer conformation protein
conformation compact random walk other non-obvious implementations
packing of chromosomes in nuclei looping of DNA fragments DNA
melting molecular motors
Slide 22
N = 1000 (a)Gaussian random walk random walk (b) self-avoiding
random walk random walk Polymer Conformation a b
Slide 23
Self-Similarity of a Polymer Molecule
Slide 24
Swimming of Bacteria
Slide 25
Contribution of Physical Science to Biology Is Hard to
OverestimateX-ray NMR ESR EM PDE RGS9-1 G t/i1 -1.5+1.5 -5.5+5.5
ppm ( 1 H) ppm ( 13 C) from Ridge et al.
Slide 26
Case Study of Bacteriorhodopsin - Contribution of Physical
Methods from Luecke et al. 7 transmembrane helices light-driven ion
pump Youtube video on bacteriorhodopsin from Alberts et al.
Slide 27
Case Study of Bacteriorhodopsin - Contribution of Physical
Methods UV/Vis spectroscopy - kinetics and thermodynamics of the
photocycle, orientation of the chromophore (LD) Raman spectroscopy
- configuration of the retinal chromophore and its changes in the
photocycle FTIR spectroscopy - conformational changes of the
protein and its chromophore in the photocycle, protonation changes
of carboxylic acids NMR spectroscopy - structure of protein
fragments, orientation of the chromophore, dynamics of certain
residues ESR spectroscopy - protein topology, conformational
changes Electron, Neutron, X-ray diffraction - structure of the
protein and its intermediates, location of water molecules Atomic
force microscopy - single molecule imaging & spectroscopy
Quantum chemistry/Molecular Dynamics - properties of the
chromophore and its binding site
Slide 28
Cells Many different kinds of cells Prokaryotic cells
Relatively simple membrane structure Few internal membranes
Eukaryotic cells Plant cells Plasma membrane inside the cell wall
Internal chloroplasts Animal cells Plasma membrane Nuclear
membrane
Slide 29
Dynamics of Cells Youtube video on the Inner Life of the Cell
from Biovisions project @ Harvard Swimming bacteria (Howard Berg)
Pilus retraction (Howard Berg)
Slide 30
Biological Membranes Major functions of cell membranes: 1.To
separate interior and exterior of the cell 2.To maintain
concentration gradients of various ions, which serve both as
sources of energy and as a basis for excitability 3.To house
functionally important protein complexes such as energy-producing
machines, transporters, enzymes, and receptors From Lodish et
al
Slide 31
Biological Membranes Cryo-electron microscopy reveals detailed
structure Phillips V. Matias, U of Guelph PhD thesis (A) (A) C.
crescentus (B) (B)Intestinal epithelial cells (C) (C)Photoreceptors
in rod cell (D) (D)Mitochondrian surrounded by endoplasmic
reticulum S. aureus septum
Slide 32
Major Components of a MembraneMembraneProteins LipidBilayer
Characteristic molecular weights Lipids: 0.5-2 kDa Proteins: 5-6000
kDa from Luecke et al. Other components: carbohydrates, water,
ions
Slide 33
Fluid Mosaic Model From Cooper Singer & Nicolson, Science
(1972)
Slide 34
Evolution of Membrane Models Phillips, Physical Biology of the
Cell Sackmann (1995) Singer & Nicolson (1972) Israelachvili
(1978)
Slide 35
Restrictions to Free Diffusion of Membrane Proteins from Vereb
et al. A lipid microdomains B, C cytoskeleton D protein
association
Slide 36
Hydration of a Lipid Bilayer (MD Simulation) from Popot and
Engelman
Slide 37
Membrane Proteins and Lipids Are Often Linked with
Carbohydrates (glycoproteins and glycolipids) From Lodish et
al
Slide 38
Building a Lipid Molecule Start with fat Long chain hydrocarbon
Different numbers of carbons with either Single bonds (saturated)
Double bonds (unsaturated) Convert hydrocarbon chain to fatty acid
by attaching carboxyl (-COOH) group at end Fatty acids are
fundamental building block of lipids 2 to 36 carbons long, with
most common between 14 & 22 Usually even number of carbons most
fatty acid chains are unsaturated single double bond most common,
up to 6 double bonds e.g. oleic acid e.g. DHA (docosahexaenoic
acid)
Slide 39
Building a Lipid Molecule fatty acids rarely found free in cell
chemical linking to hydrophobic group, e.g. glycerol, produces
non-polar lipid di-acylglycerol has 2 fatty acids Key lipid in
signaling pathways tri-acylglycerol is typical storage fat can
replace one of the fatty acids with a polar group polar lipid or
glycero-phospholipid hydrophobic tail & hydrophilic head e.g.
PC, PE, PG, PI PC: phosphatidylcholine or lecithin PE:
phosphatidylethanolamine PG: phosphatidylglycerol PI:
phosphatidylinositol neutralcharged
Slide 40
Building a Lipid Molecule polarhydrophobic Fatty acid myristic
acid (14:0) Oleic acid (18:1) DHA (22:6) Di-acylglycerol of
myristic acid Tri-acylglycerol of stearic acid (triglyceride)
glycerol From Mouritsen
Slide 41
Building a Lipid Molecule polarhydrophobic DMPC lipid:
di-acylglycerol & phosphatidylcholine lysolipid Phosphatic acid
phosphate glycerol choline From Mouritsen
Major Phospholipids From Alberts et al glycerol phosphate
choline
Slide 44
Major Phospholipids From Mouritsen
Slide 45
Major Phospholipids From Mouritsen
Slide 46
Glyco(sphingo)lipids From Alberts et al
Slide 47
Cholesterol Stiffens Fluid Membranes From Alberts et al
Slide 48
Lipid Rafts From Dykstra et al
Slide 49
Phase Transitions in Lipid Layers Can use differential scanning
calorimetry (DSC) Heat sample and reference (material similar to
sample but not does have phase transition in the region of
interest) at identical rate e.g. sample is lipid + solvent,
reference is solvent At phase transition, more heat must be applied
to the sample to maintain the linear increase in temperature with
time The excess or differential heat supplied to the sample is
recorded as a function of temperature The sensitivity depends on
the sample size, but also on scan rate At a phase transition, get a
peak T m : peak position (phase transition temperature) T 1/2 :
FWHM of peak H: area under the peak (enthalpy of transition) S =
H/T m : entropy of transition
Slide 50
Differential Scanning Calorimetry variation of excess specific
heat with temperature for two-state, endothermic process
Slide 51
Differential Scanning Calorimetry
Slide 52
Slide 53
DSC curves of distearoyl PC (DSPC) layers as a function of
water content C Chapman et al., Chem. Phys. Lipids (1967)
Slide 54
Lipid Layer Ordering Short range order described by : chains
are disordered (melted) Trans-gauche isomerization Rapid diffusion
(translation & rotation) : chains stiff, oriented parallel to
each other, perpendicular to bilayer plane : chains tilted with
respect to bilayer normal c: crystalline phase (L c is lamellar but
crystalline within the plane) Long range order described by L: 1D
lamellarT: 3D tetragonal P: 2D rectangularR: rhombohedral H: 2D
hexagonalQ: cubic
Slide 55
Lipid Layer Ordering
Slide 56
Lipid Phase Diagram Blume, Acta ThermChimActa (1991) Phase
diagram for PC/water systems
Slide 57
Lipid Phase Transition Gel to liquid crystal phase transition
involves Cooperative melting of hydrocarbon chains Introduces large
number of trans-gauche isomerizations Introduces kinks and jogs
into chains Large increase in lateral diffusion rate of lipids in
plane of bilayer Small increase in volume Large increase in area
per polar head Decrease in bilayer thickness Observed not only in
model systems but also in whole cells
Slide 58
Lipid Phase Transitions Can investigate changes in transition
temps with chain length, etc. Blume, Acta ThermChimActa (1991)
Slide 59
Lipid Phase Transitions Blume, Acta ThermChimActa (1991)
Dependence of H and T m on position of double bond in PCs with
chain length of 18 carbons Nature can control T m by placement of
double bond
Slide 60
Influence of Polar Head Group PEs have a higher T m than PCs
smaller headgroup for PE hydrogen bonding of PE protonated amino
group with adjacent negatively charged phosphate group note effect
of pH increase pH to 12 to deprotonate PE headgroup T m decreases
from 63 o C to 41 o C for DPPE PG negatively charged in high ionic
strength solvent, charges are shielded at neutral pH, T m, H and S
for PGs are similar to those for PCs PS at neutral pH, 2 negative
charges and 1 positive charge T m influenced by pH and ionic
strength
Slide 61
Lipid Monolayers Not a bilayer, but Well defined geometry with
which to study the intermolecular interactions between lipids and
between lipids & proteins Create a so-called Langmuir monolayer
by spreading amphiphilic molecules at the air-water interface using
a Langmuir trough Movable barriers allow the control of the surface
area A which causes a change in the surface pressure This allows
measurement of the -A isotherm, which has characteristic shape for
each type of molecule and provides information about the
orientation and packing of the molecules
Slide 62
Langmuir Trough Norde, Colloids and Interfaces in Life Sciences
(2003) Schematic of Langmuir trough
Slide 63
Surface Pressure-Area Isotherm Norde, Colloids and Interfaces
in Life Sciences (2003) G: gas; LE: liquid expanded; LC: liquid
condensed; S: solid
Slide 64
Phase Coexistence Norde, Colloids and Interfaces in Life
Sciences (2003) Brewster angle microscopy of monolayers showing the
Coexistence of LC (light) and LE (dark) phases
Slide 65
Compressibility slope of -A isotherm is measure of isothermal
compressibility monolayer in gas state is highly compressible but
it is less in more condensed states
Slide 66
Phase Coexistence Norde, Colloids and Interfaces in Life
Sciences (2003) Orientations of amphiphilic molecules for the
various phases on the pressure-area isotherms
Slide 67
Temperature Dependence of -A Isotherms Norde, Colloids and
Interfaces in Life Sciences (2003) as temperature increases
pressure at onset of LE LC transition increases corresponding value
of a m decreases coexistence region decreases
Slide 68
Albrecht et al., J. Phys. (Paris) (1978) -A isotherms for DPPC
at different temperatures Temperature Dependence of -A
Isotherms
Slide 69
Langmuir-Blodgett Film Formation Norde, Colloids and Interfaces
in Life Sciences (2003) formation of Y-type Langmuir-Blodgett film
transfer rates of ~1 mm/s
Slide 70
Langmuir-Blodgett Film Formation Norde, Colloids and Interfaces
in Life Sciences (2003) X-type transfer Z-type transfer can also
use Langmuir-Schaefer deposition horizontal touch of substrate on
monolayer