Lecture 6: Protein Secondary and Tertiary Structure

this describes simple and highly regular and commonly found structural features of proteins that are generated primarily by hydrogen bonds between amide groups and carbonyl oxygens of the polypeptide backbone

protein secondary structure

which parts of a polypeptide chain mainly contribute to the establishment and stability of secondary structure? Explain which types of interactions stabilize secondary structure elements

carbonyl oxygen and amide group, H bonding stabilizes structure

what types of bonds (interactions) stabilize the alpha-helix? what are the functional groups that contain the atoms engaged in this interaction?

stabilized by H-bonds between backbone main chain carbonyl C=O and amine N-H groups

how far apart are the amino acids that are interacting (number of residues)?

The N-H group is 4 residues away from C=O

how many amino acid residues are in one turn of an alpha-helix?

3.6 amino acids in one 360 degree turn

what is the more frequent handedness (left of right handed) of helical portions of proteins?

right handed helices are more stable and thus more frequent die to less steric hindrance

what are characteristics of the alpha helix?

- spiral backbone with side chains pointing outward

- stabilized by H bonds in backbone

- intrachain bonds

what are characteristics of the beta sheet?

- forms an extended zig zag line

- H bonds between parallel strands, interstrand H-bonding

- typically depicted as broad arrows pointing in the same or opposite directions

what are the characteristics of loops and turns?

- turns are sharper changes in direction

- loops are more gentle turns in direction

- turns of the polypeptide chain, link successive runs of a alpha-helix or beta-conformation

what is a superhelix?

when 2 or more alpha-helices intertwine

name an example of a superhelix

keratin

how is the collagen helix different from an alpha helix?

collagen forms a unique helix distinct from the alpha-helix. The helix in collagen is left-handed and has 3 residues per turn not 3.6. Three of these helices (known as alpha-chains) are wound around each other to form a coil called the collagen triple helix

what is the term for the helices in collagen?

alpha-chains

how can individual strands of a beta-sheet be oriented relative to each other?

individual strands of beta sheets can be antiparallel, parallel, or mixed

which type of beta sheet is more stable?

antiparallel because the H-bonds between C=O and N-H are in a straight line

name four proteins with high content of Beta-sheets

1. silk

2. fatty acid binding protein

3. alpha-hemolysin

4. porin

what is the difference between a turn and a loop?

turns contain less than 5 residues with a sharp change in direction whereas loops contain more residues with a more gentle change in direction

what are two amino acids that occur frequently in turns?

proline and glycine

how many residues constitute an alpha- , beta-, and gamma- turn?

alpha turn- 5 residues

beta turn- 4 residues

gamma turn- 3 residues

for beta turns which amino acid is with each type?

Type 1 - proline

Type 2 - glycine

antiparallel, H-bond between residues 1 and 4

where are the h bonds in gamma turns?

between residues 1 and 3

what can be said about the ramachandran angles (dihedral angles) of an alpha helix and beta conformation (how scattered are they)?

Ramachandran angles of alpha right handed helices are more common. Beta sheets shown pattern of most favorable angles as well

the overall structure of a fully folded single polypeptide chain, determined by long range interactions of amino acids

protein tertiary structure

which parts of a polypeptide chain contribute to the establishment of tertiary structure (contrast with secondary structure)

not only backbone, but also amino acid side chains play an important role

not only H-bonds, but all types of non-covalent interactions determine tertiary structure

what types of amino acids (side chain classification) predominate inside and outside of a globular protein?

for a compact globular protein, hydrophilic side chains are on the surface interacting with water. most hydrophobic side chains are buried inside

what types of amino acids predominate inside and outside of membrane proteins?

for membrane globular proteins, hydrophobic side chains are on the outside interacting with lipids and hydrophilic side chains are either outside the membrane or form a water channel, cavity, or are salt bridged with each other (ex: porin)

which types of interactions hold a protein in its folded (=native) conformation?

van der waals interactions (short range) play a significant role in holding the polypeptide chain in its native conformation

when proteins acquire their unique 3D conformation

protein folding

what is the function of a chaperone?

to facilitate the folding of proteins during their synthesis

when the protein unfolds, leading to loss of function

denaturation

what leads to denaturation of proteins?

pH, temperature, detergents, urea, guanidium hydrochloride

distinct structural units that fold and move independently and often have different functions; sections of a single polypeptide chain

protein domain

a recognizable folding pattern involving 2 or more elements of secondary structure and the connections between them, reptitive

motif

a motif is also what?

supersecondary structure

similar to motifs, but larger and used to describe characteristic folding patterns of entire proteins or protein domains, may contain several motifs

folds