bionanotechnology dr cait macphee (cem48@cam.ac.uk) dr paul barker (pdb30@cam.ac.uk) mondays 12 pm,...
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Bionanotechnology
Dr Cait MacPhee (cem48@cam.ac.uk)Dr Paul Barker (pdb30@cam.ac.uk)Mondays 12 pm, Tuesdays 11 am
SyllabusThe molecules of lifeProteins (6 lectures)
backgroundas 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 Ias 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 2- and 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 bio-nanotechnology
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
• has partial (40%) double bond character
• ~ 1.33 Å long - shorter than a single, but longer than a double bond
• C 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
+
-C
C
The peptide bond
Free backbone rotation occurs only about the bonds to the -carbon
rotation about the C-N bond
: rotation about the C-C bond
Steric considerations restrict the possible values of and
Ramachandran plots
Parallel -sheetAntiparallel -sheet Triple coiled-coil
-helix (R)
-helix (L)
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 S atoms of two cysteines
Protein structure
Hierarchy of structures
1° 2° 3° 4°
Sequence / AssemblyPackaging
Hierarchy of structures
• Alpha helix • Beta sheet• Beta turns
Local structures stabilized by hydrogen bondswithin the backbone of the chain
Primary structure: sequence of amino acids
Secondary structure:
• One of the two most common elements of secondary structure
• Right-handed helix stabilized by hydrogen bonds• amide carbonyl group of residue i is H-bonded 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• = -47, = -57°
N
C
The -helix
• One of the most closely-packed 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
CThe -helix
The coiled-coil
• “Supersecondary” structural motif• Two or more -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
Hydrophobic residues at “a” and “d”
Charged residues at “e” and “g”
ab
cd
e
f
g
+/-
• Heptad repeat in sequence
– [a b c d e f g]n
• Hydrophobic residues at “a” and “d”• Charged residues at “e” and “g”
The coiled-coil
N N
CC
ab
cd
e
f
g
ab
cd
e
f
g
Residues at “d” and “a”form hydrophobic core
Residues at “e” and “g”form ion pairs
+/-
+/-
-/+
-/+
The -Pleated Sheet
• Composed of -strands, where adjacent strands may be parallel, antiparallel, or mixed
• Brings together distal sections of the 1-D sequence
• Can be amphipathic
AntiParallel
The -Sheet
ParallelMixed
Loops
• Regions between helices and 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, (anti-
parallel sheets)1
23
4
• Highly variable in sequence
• 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° 2° 3° 4°
Sequence / AssemblyPackaging
Protein folds
• ~70,000 proteins in humans• ~21,000 structures known• Only 6 classes of protein folds
– Class : bundles of helices connected by loops on surface of proteins
– Class : antiparallel sheets, usually two sheets in close contact forming sandwich
– Class : mainly parallel sheets with intervening helices; may also have mixed sheets (metabolic enzymes)
– Class : mainly segregated helices and antiparallel sheets
– Multidomain proteins( and ) - 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)
HaemoglobinC N R
+C N R
+C N R
+
Retinal
Cytochrome c oxidase
CuCu
HisS
S
Cys
Cys
O
GluN
Met
His
His
His
Cys
R
Cu
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