Bionanotechnology Dr Cait MacPhee Dr Paul Barker 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 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

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 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  -sheet Antiparallel  -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°1°2°2°3°3°4°4° Sequence // AssemblyPackaging

Hierarchy of structures Alpha helix Beta sheet Beta turns Local structures stabilized by hydrogen bonds within 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 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 C The  -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” +/- 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 C C 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 Parallel Mixed

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

Amino acid propensities HelixSheet AlaHighinhibitory CysinhibitoryIntermediate AspinhibitoryBreaker GluHighBreaker PheIntermediate GlyBreakerNo preference HisNo preferenceIntermediate IleIntermediateHigh LysIntermediateNo preference LeuHighIntermediate MetHighIntermediate AsnNo preference ProBreaker GlnIntermediate Arginhibitory SerinhibitoryNo preference ThrinhibitoryIntermediate ValIntermediateHigh TrpIntermediate TyrNo preferenceHigh

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 IgF3 Ser/Thr Kinase

Quaternary structure Assembly of homo- or heteromeric chains Symmetry constraints

Hierarchy of structures 1°1°2°2°3°3°4°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) Haemoglobin Retinal Cytochrome c oxidase Cu His S S Cys O Glu N Met His Cys R Cu