Flexibility of a polypeptide chain

the peptide bond is essentially planar (6 atoms are in plane: C, C=O, N-H,and Crespectively)

40% double bond character around C-N

constrains the conformation of the protein backbone

the double bond character is also expressed in the respective

C-N bond length:

C-N: 1.49 Å, C=N: 1.27 Å

phi psi

HN-C and C-CO are pure single bonds, high degreeof freedom for rotation around these bonds

Protein conformation

lots of ways for a protein to fold if each amino acid has two main chain bonds to rotate about

torsion (or dihedral) angles

BUT! Any combination of phi and psi is possible?

Ramachandran plot

many combinations are disfavored due to steric collisions

(green regions are allowed, white regions are not)

What does thermodynamics have to say about protein folding?

each copy of an unfolded polymer exists in a different conformation (ran-dom coil) yielding a mixture of many possible conformations, which would theoretically oppose folding due to favorable enthropy

but in proteins, rigidity of peptide units and the restricted set of allowedphi and psi values actually limit the number of possible structures

and it is overcome by interactions that favor the folded form e.g. hydro-phobic interactions among apolar side-chains (rather than being exposed to polar water), H-bonding network, S-S bridges, ion pairs, etc.

a highly flexible polymer, of any kind, with large number of possible conformations to adopt would NEVER fold into a unique 3D

structure!!

Secondary structural elements

alpha helixbeta pleated sheetbeta turnomega loop

all forms stabilize via H-bridges between amino acids nearby in

linear sequence

alpha helix

3.6 residues/turn100o rotation/residuerise/residue: 1.5 Åpitch of helix: 5.4 Å

Screw sense of an alpha helix

right-handed (clockwise)

or

left-handed (counterclockwise)

more stable, less steric clashes

between side chains andbackbone

helical content of a protein may vary from 0-100%

Ferritin (iron storage protein) contains 75% alpha helix

~25% of all soluble proteins are largely helical

an alpha helix is usually smaller than 45 Å

proteins embedded in or crossing biological membranes buildalso up mainly from alpha helices

Beta (pleated) sheets(beta because this structure was the 2nd one, after the alpha helix, that Linus Pauling

and Robert Corey envisioned/proposed in 1951, 6 years before the first everprotein structure determined by X-ray crystallography by Kendrew in 1957, myoglobin )

composed of 2 or more beta strands (fully extended chains)

stabilized by H-bonding between polypeptide chains

purely parallel, purely antiparallel or mixed beta sheets exist

4-5 but even 10 or more strands make up a beta sheet

beta sheets generally adopt a twisted shape:

fatty acid binding proteins (important in lipid metabolism) almost entirely are built from beta sheets:

MUSCLE FATTY ACIDBINDING PROTEIN

(1FTP.pdb)

Loops and turns

globular proteins can be made up if turns and loops are incor-porated in structure

beta turn = reverse turn = hairpin turn

loop = omega loop (generally rigid, well-defined structures)

loops and turns generally lie on the protein surfaces and par-ticipate in protein-protein and other types of interactions

turn loops

Superhelices

-keratin (main component of wool and hair) consists of two right-handed -helices intertwined to form a left-handed superhelix called coiled coil (superfamily of coiled-coil proteins, ~60 proteins in humans)

2 or more helices can entwine and form a stable, even 1000 Å (0.1 m) or longer, structure found in cytoskeleton, filaments, muscle proteins

3.5 residues/turn, heptad repeats, every 7th residue is Leu on each strandand these two Leu interact (hydrophobic interaction), 2 Cys can also interact (S-S) stabilizing fiber

wool can be stretched (some interactions among helices brake, S-S does not and pulls back after release)

hair and wool have fewer cross-links, horn, claw, hoof are hard

Collagen

most abundant protein in mammals, main fibrous component of skin, bone, teeth, cartilage and tendon

extracellular protein, rod shape, ~3000 Å long/15 Å in diameter, 3 helical protein chains (~1000 residues each, every 3rd residue is Gly, Gly-Pro-(Pro-OH) triad is frequent, Pro-OH (4-hydroxyproline) is a naturalamino acid derivative)

no H-bonds inside the helical strands, stabilization occurs via steric repulsion between Pro and Pro-OH

~3 residues/turn, 3 helices wind in a superhelical cable that is stabilizedby H-bond in between strands (Pro-OH participates in H-bonding networkand lack of –OH on Pro in collagen lead to the disease scurvy (Vitamin C deficiency, ascorbate reduces Fe3+ to Fe2+ in prolyl hydroxylase for its continuous activity)

Pro rings are on the outside, Gly in every 3rd position is needed because the superhelix is very crowded inside and there is no place for any otherbigger amino acid

Tertiary structure

the very first protein to be seen in atomic detail was myoglobin, the O2-carrier protein in muscle, determined by Kendrew in 1957 (6 Å resolution)

Kendrew's original model of the myoglobin molecule, 1957, made of plasticine.

single polypeptide chain, 153 residues, heme prosthetic (helper) group [heme: protoporphyrin IX and central iron ion], very compact molecule (45 X 35 X 25 Å), 70% of amino acids are in 8 helices, the rest are in loops and turns

hydrophobic amino acids are yellow, charged onesare blue, others are white

cross-section

Heme

interior of globular proteins are rich in hydrophobic amino acids like Leu, Val, Met, Phe

charged and rather polar residues, like Glu, Asp, Lys, Arg (Gln, Asn) localizeon the exterior of proteins

in myoglobin there are two critical His in the interior that conduct binding of O2

helices and sheets may often have an amphipathic character: one part points towards the hydrophobic interior core of the protein, the other side points into solution

burying polar main chain atoms in the hydrophobic interior is possible if allN-H and C=O moieties are in a H-bonding network ( helix, sheet)

proteins spanning biological membranes are the “exceptions that prove therule” as they have a reverse distribution of hydrophobic and hydrophilic amino acids, like in porins, found in the outer membranes of bacteria (they are “inside out” relative to proteins function in aqueous environment)

Motifs and supersecondary structures

certain combinations of secondary structure are present in many proteins and frequently exhibit similar functions, these combinations are called motifs or supersecondary structures

For instance, a helix-turn-helix motif, often found in DNA-binding proteins

some polypeptide chains fold into 2 or more compact globular units or regionsthat are connected by flexible regions, these are called domains (30-400 aminoacids long)

cell-surface protein CD4 consists of 4 similar domains

Quaternary structure

proteins containing more than one polypeptide chains adopt a quaternary structure which describes the spatial arrangement of the subunits and theinteraction between them

each polypeptide chain is called a subunit

the number of subunits may vary and we designate this by calling the protein a dimer, trimer, tetramer, etc.

there can be homo- and hetero-multimers which may be tightened togethercovalently or non-covalently

the Cro protein of bacteriophage is a dimer of identical subunits

human hemoglobin , the O2-carrying protein of blood, consists of two -type and two -type subunits, a 22 hetero-tetramer

viruses make the most out of limited genetic information: they have a protein coat thatuses many, often identical, subunits repetitively in a symmetric array for their build-up:e.g. the rhinovirus, the cause of the common cold, includes 60 copies of each of four subunits forming a nearly spherical shell that encloses the viral genome

schematic viewelectron micrographof virus particles