Bionanotechnology

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Bionanotechnology

• Dr Cait MacPhee (cem48_at_cam.ac.uk)
• Dr Paul Barker (pdb30_at_cam.ac.uk)
• Mondays 12 pm, Tuesdays 11 am

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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
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• Cell motility (1 lecture)
• how cells travel and navigate through 2- and 3
  dimensional environments
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• Biomaterials (1 lecture)
• surface science/ surface chemistry tissue
  engineering
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• Nanomedicine (1 lecture)
• Nanotherapeutics, real and imagined
•         Qdots and developmental biology
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• Ethical considerations (1 lecture)
• risk/benefit analysis focusing on
  bio-nanotechnology

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Suggested texts
Nanobiotechnology, edited by CM Niemeyer and CA
Mirkin
Bionanotechnology, DS Goodsell
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http//bionano.rutgers.edu/mru.html
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(No Transcript)
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Proteins
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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)

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L-amino acids
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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

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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
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Ramachandran plots
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.
Antiparallel b-sheet
Parallel b-sheet
Triple coiled-coil
a-helix (L)
a-helix (R)
Flat ribbon
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The amino acids
tryptophan
isoleucine
asparagine
glutamate
alanine
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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)

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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

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Protein structure
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Hierarchy of structures
1
2
3
4
Sequence
a/b
Assembly
Packaging
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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
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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 H-bonded to
  amide nitrogen of residue i4
• 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
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The a-helix
C

• 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
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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)

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The coiled-coil

• Heptad repeat in sequence
• a b c d e f gn
• Hydrophobic residues at a and d
• Charged residues at e and g

/-
Hydrophobic residues at a and d
Charged residues at e and g
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The coiled-coil
C
C
N
N
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The b-Pleated Sheet

• Composed of b-strands, where adjacent strands may
  be parallel, antiparallel, or mixed
• Brings together distal sections of the 1-D
  sequence
• Can be amphipathic

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The b-Sheet
AntiParallel
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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)

2
3
1

• Highly variable in sequence
• Often flexible
• Frequently a component of active sites

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Amino acid propensities
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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 gt 75 residues)
• Formation of disulfide bridges
• Interactions with metal ions

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Hierarchical organisation
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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
Ig
F3
EG
EG
EG
Ser/Thr Kinase
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Quaternary structure

• Assembly of homo- or heteromeric chains
• Symmetry constraints

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Hierarchy of structures
1
2
3
4
Sequence
a/b
Assembly
Packaging
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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

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Prosthetic groups
Small blue proteins (azurin)