Download L1-2

Bionanotechnology
Dr Cait MacPhee ([email protected])
Dr Paul Barker ([email protected])
Mondays 12 pm, Tuesdays 11 am
Syllabus
The molecules of life
Proteins (6 lectures)
background
as components in nanodevices
biomolecular electronic devices
electron transport and photosynthesis
as fibrous materials
in motion – molecular motors
DNA (3 lectures)
background
as components in nanodevices: part I
as components in nanodevices: part II
Lipids (1 lecture)
background; as components in
nanostructures: artificial cells
(liposomes and membrane
nanotubes)
Bio-inorganic composites (1 lecture)
composites – including butterfly wings,
diatoms, mineralisation
The whole cell
Cell mechanotransduction (1 lecture)
bringing together physical, life, and applied
sciences; bone cell mechanobiology
Cell motility (1 lecture)
how cells travel and navigate through 2and 3 dimensional environments
Biomaterials (1 lecture)
surface science/ surface chemistry; tissue
engineering
Nanomedicine (1 lecture)
Nanotherapeutics, real and imagined
·
Qdots and developmental biology
Ethical considerations (1 lecture)
risk/benefit analysis focusing on bionanotechnology
Suggested texts:
Nanobiotechnology, edited by
CM Niemeyer and CA Mirkin
Bionanotechnology, DS Goodsell
http://bionano.rutgers.edu/mru.html
Proteins
The basics
• Proteins are linear heteropolymers: one or
more polypeptide chains
• Repeat units: one of 20 amino acid residues
• Range from a few 10s-1000s
• Three-dimensional shapes (“folds”) adopted
vary enormously
– Experimental methods: X-ray crystallography,
electron microscopy and NMR (nuclear magnetic
resonance)
L-amino
acids
The peptide bond
• has partial (40%) double bond
character
• ~ 1.33 Å long - shorter than a
single, but longer than a double
bond
• Ca usually trans
• the 6 atoms of the peptide bond
are always planar
• N partially positive; O partially
negative, gives rise to a
significant dipole moment
d-
Ca
d+
Ca
Free backbone rotation occurs only about the
bonds to the a-carbon
c

Y
F
Y: rotation about the Ca-C bond
F rotation about the Ca-N bond
Steric considerations restrict the possible values of Y and F
Ramachandran plots
Antiparallel b-sheet
Parallel b-sheet
Triple coiled-coil
a-helix (L)
a-helix (R)
Flat ribbon
Used to display
which
conformations are
allowed. All the
disallowed
conformations are
sterically
impossible
because atoms in
the backbone
and/or side chains
would overlap.
The amino acids
isoleucine
tryptophan
asparagine
glutamate
alanine
The amino acids
• Hydrophobic: Alanine(A), Valine(V), phenylalanine
(Y), Proline (P), Methionine (M), isoleucine (I), and
Leucine(L)
• Charged: Aspartic acid (D), Glutamic Acid (E), Lysine
(K), Arginine (R)
• Polar: Serine (S), Theronine (T), Tyrosine (Y);
Histidine (H), Cysteine (C), Asparagine (N),
Glutamine (Q), Tryptophan (W)
The disulphide bond
• Only in extracellular
proteins
• Formed by oxidation
of the SH (thiol)
group in cysteine
amino acids
• Forms a covalent
cross-link between
the Sg atoms of two
cysteines
Protein structure
Hierarchy of structures
1°
Sequence
2°
a/b
3°
Packaging
4°
Assembly
Hierarchy of structures
Primary structure: sequence of amino acids
Secondary structure:
• Alpha helix
• Beta sheet
• Beta turns
Local structures
stabilized by hydrogen bonds
within the backbone of the chain
The a-helix
C
• One of the two most common elements of
secondary structure
• Right-handed helix stabilized by hydrogen
bonds
• amide carbonyl group of residue i is Hbonded to amide nitrogen of residue i+4
• 3.6 amino acids per turn
• acts as a strong dipole
• H-bonds are parallel to the axis of the helix
• Y = -47, F = -57°
N
The a-helix
C
• One of the most closelypacked arrangements of
amino acids
• Sidechains project outwards
• Can be amphipathic
• Average length: 10 amino
acids, or 3 turns
• Varies from 5 to 40 amino
acids
N
The coiled-coil
• “Supersecondary” structural motif
• Two or more a-helices wrapped around
each other
• Stable, energetically favorable protein
structure
• “Heptad Repeat”: pattern of side chain
interactions between helices is
repeated every 7 Amino Acids (or every
two “turns”)
The coiled-coil
• Heptad repeat in sequence
– [a b c d e f g]n
• Hydrophobic residues at “a” and “d”
• Charged residues at “e” and “g”
+/b
e
a
Hydrophobic residues
at “a” and “d”
f
d
c
g
Charged residues at “e” and “g”
The coiled-coil
C
C
Residues at “d” and “a”
form hydrophobic core
Residues at “e” and “g”
form ion pairs
-/+
b
g
e
a
+/-
c
d
f
f
a
d
c
g
e
+/-
b
-/+
N
N
The b-Pleated Sheet
• Composed of bstrands, where
adjacent strands may
be parallel,
antiparallel, or mixed
• Brings together distal
sections of the 1-D
sequence
• Can be amphipathic
The b-Sheet
Mixed
Parallel
AntiParallel
Loops
• Regions between a helices and b sheets
• Various lengths and three-dimensional configurations
• Located on surface of the structure (charged and polar
groups)
• Hairpin loops: complete turn in the polypeptide chain, (antiparallel b sheets)
2
3
1
• Highly variable in
sequence
4
• Often flexible
• Frequently a component
of active sites
Amino acid propensities
Helix
Sheet
Ala
High
inhibitory
Cys
inhibitory
Intermediate
Asp
inhibitory
Breaker
Glu
High
Breaker
Phe
Intermediate
Intermediate
Gly
Breaker
No preference
His
No preference
Intermediate
Ile
Intermediate
High
Lys
Intermediate
No preference
Leu
High
Intermediate
Met
High
Intermediate
Asn
No preference
No preference
Pro
Breaker
Breaker
Gln
Intermediate
Intermediate
Arg
inhibitory
inhibitory
Ser
inhibitory
No preference
Thr
inhibitory
Intermediate
Val
Intermediate
High
Trp
Intermediate
Intermediate
Tyr
No preference
High
Driving forces in protein folding
• Stabilisation by formation of hydrogen bonds
• Burying hydrophobic amino acids (with
aliphatic and aromatic side-chains)
• Exposing hydrophilic amino acids (with
charged and polar side-chains)
• For small proteins (usually > 75 residues)
– Formation of disulfide bridges
– Interactions with metal ions
Hierarchical organisation
Tertiary structure
• Packing of secondary structure elements into a compact
independently-folding spatial unit (a domain)
• Each domain is usually associated with a function
(“Lego”)
• Comprises normally only one protein chain: rare
examples involving 2 chains are known.
• Domains can be shared between different proteins.
Ig
EG EG EG
Ig
F3
Ser/Thr Kinase
Quaternary structure
• Assembly of homo- or
heteromeric chains
• Symmetry constraints
Hierarchy of structures
1°
Sequence
2°
a/b
3°
Packaging
4°
Assembly
Protein folds
• ~70,000 proteins in humans
• ~21,000 structures known
• Only 6 classes of protein folds
– Class a: bundles of a helices connected by loops on surface
of proteins
– Class b: antiparallel b sheets, usually two sheets in close
contact forming sandwich
– Class a/b: mainly parallel b sheets with intervening a
helices; may also have mixed b sheets (metabolic enzymes)
– Class a+ b: mainly segregated a helices and antiparallel b
sheets
– Multidomain proteins(a and b) - more than one of the above
four domains
– Membrane and cell-surface proteins and peptides excluding
proteins of the immune system
Prosthetic groups
Small blue proteins (azurin)
His
R
Glu
N
Cu
Cys
His
Cys
His
S
Cu
O
Cu
S
Met
Cys
His
Cytochrome c oxidase
Retinal
C
+
N
R
Haemoglobin