Protein Functions:

catalyze reactions (enzymes)

receptors (eg. pain receptors)

transport (ions across membranes, oxygen in blood)

molecular motors

recognition (eg. antibodies)

signals (eg. insulin)

structural support

Protein structure

chains of amino acids4 levels of structurerange of functional groups

carb. acidsamidesamineshydroxylthiolaromatic rings

interact with other proteins: assembliesflexibility, movement (doors, hinges, levers, etc.)

Amino acids:

20 building blocks

characterized by R group

in nature, S (L) configuration

Notice: glycine is not chiral! Conformationally free

Hydrophobicside-chains

Proline: side chain is bonded to main chain amine

conformationally restricted - effect on structure

Aromatic

planar

Hydroxyl

Thiol

Cysteine thiols can form disulfide linkages

important for 3, 4 structure

Positively charged

Lys: pKa ~ 10.8Arg: pKa ~ 12.5His: pKa ~ 6.0

Depends on environment!

Question: Why is Lys more acidic than Arg?

Lys: pKa ~ 10.8Arg: pKa ~ 12.5

Lys: pKa ~ 10.8Arg: pKa ~ 12.5

+ is stabilized in Arg“happier” with +

Arg less like to give up proton

Arg less acidic

Acids

Amides

pKa of acid ~ 4.1

amides not acidic or basic!

AA chain formed via peptide bonds - polypeptide

Carbox acid + amine forms amidelose water

50-2000 amino acids: protein<50 amino acids: peptide (eg. insulin, spider venom)

primary structure: a.a. sequence

AA sequence is specific to each protein/peptide

Sequence coded by DNA (gene): 3 base ‘codon’ encodes one amino acid, plus start/stop codons.

eg: GAC = aspartate

Peptide bonds are planar: 6 atoms in a planeC, C, O, N, H, C

Source of planarity: N is sp2

barrier to rotation about C-N bondfree rotation between C-C, N-Cflexibility/rigidity

Notice: R group on opposite sides

Peptide bonds are trans:

If cis, R groups clash

Free rotation, but only some angles possible due to steric clashes - limits possible folding patterns

phi psi

Secondary structure: helices

R groups point outright handed/clockwise (alpha) found in proteins (energetically favorable)3.6 residues per turnH-bonds between main chain O and N 4 aa’s down (next slide)

Ribbon form for depicting helices

Secondary structure: Beta sheetfully extended: parallel, anti-parallelH-bond between main-chain N and O

R groups perpendicular

Ribbon depiction of Beta-sheets

hairpin turn

Tertiary structure

(myoglobin) (oxygen carrier in muscle

heme prosthetic group (contains iron)

Tertiary structure

Beta-sheet rich

many proteins have both helices and sheets

Notice loops (no regular structure, but often still ordered (not random).

Often act as doors or flaps

A: space-fill picture of myoglobin;blue = chargedyellow - hydrophobic

B: cross-section:hydrophilic outsidehydrophobic inside

When unfolded, most proteins are insoluble in water

Some proteins form distinct domains

CD4 cell-surface protein: HIV virus attaches to this

Quaternary structure:22 hemoglobin

F6P aldolase (use Jmol – 1L6W)

Notice:

Quaternary structure (homodecamer)‘tails’ tie subunits together

Beta barrel (conserved tert. structure motif)

Primary structure determines higher structure, function

Classic study with ribonuclease

(cuts RNA)

Enzyme loses function when denatured, reduced

regains activity when dialized

all the info necessary is contained in sequence (originally in DNA sequence!

Primary structure (sequence) is easy to determine: sequence DNA

So shouldn’t we be able to predict structure from sequence?

Yes, in theory - but haven’t figured out yet!

Secondary structure prediction is somewhat accurate

We can predict structure, function by sequence alignment

myoglobin: carries oxygen in musclehemoglobin: carries oxygen in bloodstructure and function are related: sequences are similar

Protein structure is visualized by x-ray crystallography (Chapter 4)

Static picture - but proteins are dynamic!

Small peptides can be visualized by NMR - but complex!

Proteins are often post-translationally modified

(in eukaryotes)

expands repertoire of 20 aa’s

eg. phosphorylation often turns proteins ‘on and off’