Lecture 3 - Protein Structure

What is a protein?

Linear polymer of L-amino acids connected by peptide bonds

How many levels of structure do proteins have?

4 (1^o, 2^o, 3^o, 4^o)

Primary Protein Structure

• Linear L-amino acid sequence held by covalent peptide bonds

• Determines properties of protein

Secondary Protein Structure

Spatial arrangement stabilized by hydrogen bonding; alpha helices and beta sheets

Tertiary Structure

Folding of secondary structure for packing (minimal volume); H-bonds, salt bridges, hydrophobic effect

Quaternary Structure

Interaction of multiple polypeptides (ex. hemoglobin - dimer of dimers)

Which structure is most favorable?

Primary; it is more disordered (extended)

Expect coupling not to be required

Which structure is least favorable?

Tertiary/Quaternary; less disordered (more compact)

Would expect coupling

Peptide Bond

Carbonyl carbon bonded to nitrogen of another amino acid

What reaction forms bond between two amino acids?

Dehydration reaction (water leaves)

What molecule leaves from peptide bond formation?

Water

Oxygen leaves from the hydroxyl group of one amino acid

2 hydrogens leave from nitrogen of the other

What 2 atoms is the peptide bond between?

Carbonyl carbon and amide nitrogen

Amino acid residue

Single amino acid on a polypeptide (different from free amino acid)

Partial double bond character results from…

Resonance between carbonyl oxygen and amide nitrogen (polypeptides are resonance-stabilized)

What orientation are peptide bonds in?

Planar; causes to be rigid, limits space for folding or rotation

Are polypeptides usually found cis or trans?

Trans, keeps R-groups further apart limiting steric hindrance

What is the problem in cis amino acids?

Steric repulsions will destabilize protein structure

Phi angle

Angle of rotation around the bond between alpha-carbon and nitrogen

Psi angle

Angle of rotation allowed between alpha-carbon and carbonyl carbon

Ramachandran Plot

Uses phi and psi angles on a graph to determine what structure is present in a protein (ex. alpha-helices have specific phi and psi values)

Secondary structure requires that R-groups are…

In trans arrangement

What bond stabilizes ALL secondary structures?

Hydrogen bonds between amide hydrogens and carbonyl oxygens

Alpha Helix Structure

Right-handed corkscrew; helical shape stabilized by H-bonds

Turn pattern/pitch of alpha helices

One turn every 4 residues, and each residue faces the same side of the helix

In alpha helices where are hydrogen bonds formed?

Within the structure, parallel to axis; carbonyl oxygen of residue n and amide hydrogen of n+4

In alpha-helices where do R-groups face?

All OUT

Proline’s Importance in secondary structure

Disrupts both alpha-helices and beta-sheets because of its rigidity and lack of hydrogen bonding ability

Why can’t proline hydrogen bond?

Its amide nitrogen has no hydrogen

A proline in amino acid sequence means…

There are two separate structure (either helix or sheet)

Amphipathic Helix

An alpha-helix has both non-polar and polar parts, allowing it to interact with water and hydrophobic environments.

Beta Sheet

Secondary structure with individual strands stabilized by hydrogen-bonding between

In beta sheets, where are the hydrogen bonds?

BETWEEN adjacent strands; not within

What way do B-sheet R-groups face?

Opposite each other (one left, one right)

Orientation of B-sheets can be…

Antiparallel or parallel

How are amino acid sequences written?

N to C terminus

Alpha helix vs. beta sheet

• Compact vs. Extended

• Hydrogen bonds within vs. between strands

  • Both H-bond

• R-groups all facing out vs. opposite directions (in and out)

• n+4 pitch vs. n+3 (X-P-G) pitch

• Can be single chain vs. must have multiple strands

• Keratin vs. Fibroin

• More stable vs. Less stable

  • (Entropy increases as you extend the molecule)

Beta-turns

Compact, abrupt turns (allow for 180 degree reversal) following n+3 pitch

Amino acid motif for beta turns

X-P-G

Proline at position 2, glycine at 3

Where are beta turns usually found?

Globular proteins

Types of beta turns

Depends on what orientation the R-groups are in (cis or trans = type 1 or 2)

What determines whether beta-sheet or alpha helix forms?

Primarily backbone hydrogen bonding, but also charge-pairing

Intermolecule = beta, intramolecule = alpha

How does Glycine affect secondary structure?

Not able to interact with other amino acids to stabilize; in too high amount, can even destabilize and break structure

Why does glycine destabilize secondary structures?

It has a a very small side chain, interfering with its ability to interact

(Only hydrogen is its side chain)

Intrinsically Disordered Proteins (IDP)

Proteins that retain little structure and are very flexible; NO tertiary structure (1/3 of eukaryotic cells)

Example of an IDP

Protein tau (found in Alzheimers)