Protein Structure and Folding Lecture

Tertiary and Quaternary Structure of Proteins
Lecture 8. 10/15/2014
Reading: Lehninger Ch. 4.3, 4.4

Voet, Voet and Pratt Pg. 148-151; 155-172
Key terms and topics:

Tertiary Structure
Motifs
Domains
Globular proteins
Quaternary Structure
Subunit - monomer v. dimer v. trimer etc.
Protein Folding
Denaturation/Renaturation
Molten globule
Folding Chaperones
PyMOL molecules/PDB files which
contain examples of domains, motifs,
and interesting 3 and 4 structures
Hemoglobin (1THB)
-Hemolysin (7AHL)
Green Fluorescent Protein (1EMA)
Trilobed protease (2GOP)
Triose-phosphate isomerase (2YPI)
Voltage-Dependent Anion Channel 2JK4
Factors affecting the stability of an -helix

Amino Acid sequence:
Relative side chain position:
Helices that are hydrophilic on one face and hydrophobic

on the other are
a helical-wheel projection
Stabilizing effects of the helical dipole:
-conformation and the -sheet

An extended zig-zag conformation
-turns allow the strand to reverse direction

Type I contains
Type II contains
Random Coil
Finally - a random coil is a region of a protein that doesnt adopt a 2 structure, though
technically, it is not random - it adopts a conformation defined by the sequence and the
protein which contains it - to reduce the overall free energy.
Circular Dichroism (CD) allows spectroscopic

determination of 2 structure conformation
A scan of wavelength in the far UV region
(where the peptide bond absorbs) is plotted
against (the difference in molar extinction
coefficients of left handed and right handed
plane polarized light).
The tertiary structure of proteins
The components of a tertiary structure: Motifs

Protein structure heirarchy:
1 structure } 2 structure }
motifs } domains}
3 structures
(be careful when talking about these as a hierarchy of structures; an entire protein can be 1 motif,
or 1 motif or more can make up a domain)
4-helix bundle
-- loop
-meander
Greek Key
-coiled coil
-barrel
Tertiary structure are often represented as ribbon-like cartoons that emphasize -helices
and -sheets, (arrows indicate N-term to C-term direction)
Motifs
Large motifs can be constructed from smaller ones:
Proteins can be broadly classified based on their motifs

An all protein
An all protein
an / protein
Clicker Question
Beta-sheets
A) have extensive H-bond among main chain atoms.
B) can have parallel and anti-parallel strands.
C) often have alternating hyrdophobic and hydrophilic amino acids.
D) have H-bonds that are roughly perpendicular to the direction of the strand.
E) All of the above are true of beta-sheets.
Domains in the 3 Structure - An Independently

Stable Portion of the Protein
Domains:
Nuclease domain
Linker
dsRNA binding motif (it is also a domain)
Summary of Factors that Stabilize 3 Structures

1) Hydrophobic residues in the protein core.
Exposed hydrophobic side chains forces water to become ordered around them and
decreases the entropy. As these residues are buried in the interior, the water is
released and the entropy increases (energetically favorable).
2) Maximum van der Waals contacts in the core.

Nature abhors a vacuum - i.e. gaps in the core will be filled due to the attractive
forces between atoms.
3) Hydrogen bonded 2 structures
Maximized hydrogen bonding and van der Waals contacts in main chain atoms.
4) Amphipathic 2 structures
Increase hydrophobic interactions in the interior; increse H-bonding with water or other
residues on the exterior.
5) Reverse turns
Allow for the peptide chain to reverse direction - requires unusual conformational
flexibility provided by proline and/or glycine and H-bonding.
6) Disulfide bonds
Covalently crosslinks 2 Cys residues that maybe be very far apart in 1 structure but
close in the folded 3 structure.
7) Long range H-bonds - Similar effect as a disulfide, but non-covalent.
Quaternary Structure
If two polypeptides are the same it is a homodimer; if they are different it is a heterodimer.
Dimer (2), trimer (3), tetramer (4), hexamer (6), dodecamer (12). Each monomeric unit is a subunit.
Subunits can have very different functions such as catalysis, regulation, and ligand binding.
Examples: hemoglobin is a tetramer, NDKB is a hexamer
Hb
NDKB
How Does a Protein go from String of Amino Acids

to a Beautiful 3-D Structure?
The sequence determines structure:
The Protein Folding Problem

A 100 amino acid protein is synthesized in 5 seconds
Assume one amino acid can have 10 conformations. Thats 10100 conformations/peptide.
Assume a protein folds randomly, trying every possible conformation and each trial
takes 10-13 seconds (the time of a molecular vibration).
it would take 1077 years to fold a protein.....
Since this is obviously not random a random process, a folding pathway must be built
into the protein (via the sequence).
xkcd.com
Protein Folding Models:

The Stepwise Model:
The Hydrophobic Collapse Model:
Some proteins use Chaperones to help them fold
Protein Folding and Disease

Mis-folding can occur, but the proteins are usually degraded
Can lead to certain diseases - Alzheimers, Parkinsons and the prion protein diseases:
Creutzfeldt-Jakob (humans), Bovine spongiform encephalopathy (mad cow), chronic wasting (deer)
Amyloidoses - generation of amyloid fibers - consisting mostly

-sheets - deposited extracellularly. seen as a plaque
Thought to cause Alzheimers.
PrP PrPSc
In prions, the mis-folded form

catalyzes the mis-folding of
other prion proteins.
Folding Energetics and Gibbs Free Energy

N
When going from unfolded (U) to folded (N) it should be a decrease in free energy, or G,
and we can measure the change in standard free energy when 1 mole of reactants are converted
to 1 mole of products
The G is dependent on the changes in entropy (S) and enthalpy (H) of the system,
related through the Gibbs equation:
G = H - TS
G = H - TS
An energetics review sheet - think about why the following are true:
G is +
reaction is unfavorable, requires energy
G is -
reaction is favorable, releases energy
H is large
G is large
H is small
G is small
S is large
G is small
S is small
G is large
H is -
heat is released, bonds are formed
H is +
heat is absorbed, bonds are broken
S is large
increase in entropy (disorder)
S is small
decrease in entropy (disorder)

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How does a protein achieve its tertiary structure?

How does a protein achieve its tertiary structure?

What factors influence protein folding?

What factors influence protein folding?

Tertiary and Quaternary Structure of Proteins

Reading: Lehninger Ch. 4.3, 4.4

Key terms and topics:

Voltage-Dependent Anion Channel 2JK4

Factors affecting the stability of an -helix

Relative side chain position:

Helices that are hydrophilic on one face and hydrophobic

-conformation and the -sheet

-turns allow the strand to reverse direction

Circular Dichroism (CD) allows spectroscopic

The tertiary structure of proteins

The components of a tertiary structure: Motifs

Proteins can be broadly classified based on their motifs

Domains in the 3 Structure - An Independently

dsRNA binding motif (it is also a domain)

Summary of Factors that Stabilize 3 Structures

2) Maximum van der Waals contacts in the core.

How Does a Protein go from String of Amino Acids

The Protein Folding Problem

Protein Folding Models:

The Hydrophobic Collapse Model:

Some proteins use Chaperones to help them fold

Protein Folding and Disease

Amyloidoses - generation of amyloid fibers - consisting mostly

In prions, the mis-folded form

Folding Energetics and Gibbs Free Energy

reaction is unfavorable, requires energy

reaction is favorable, releases energy

heat is released, bonds are formed

heat is absorbed, bonds are broken

increase in entropy (disorder)

decrease in entropy (disorder)

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