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