Biol/Chem 5310

Lecture:10

September 25, 2001

Protein Folding

Protein denaturation is the reverse of protein folding. It can be observed by changing from normal conditions to conditions that favor the unfolding direction.

Examples:

Others:

Protein folding is highly cooperative

Quaternary Structure

Many proteins are complexes of multiple polypeptide chains. the spatial arrangement of these polypeptides is called the "quaternary structure". See animation of Fig. 6-33

These subunits may be identical or different. They are often indicated by letters or numbers

Hemoglobin

a2b2

2 types of subunits: a and b

2 copies of each

Proteins with identical subunits are called oligomers.

Such identical subunits are called protomers.

Hemoglobin could be called a dimer with an ab protomer

In practice it is called a tetramer because it has 4 subunits

 

Oligomers generally have internal symmetry

This is always rotational symmetry, C2, C3, ...

Some proteins have dihedral symmetry, with 2 additional axes of 2-fold rotational symmetry perpendicular to an axis of 2 (D2), 3(D3), or higher order.

Because amino acids are L-form, symmetry cannot be inversion or mirror plane symmetry.

 

Subunit interactions include the same noncovalent interactions that occur within proteins. (Electrostatic, h-bonds, van der waals)

But they tend to be more hydrophobic.

They also include disulfide bonds

 

 

 

Dynamics of protein folding

 

Early experiments indicated that proteins fold spontaneously, in an isolated form (i.e. without other proteins or other factors)

This suggested that the information for the 3-dimensional structure of a protein must be contained in its amino acid sequence.

These experiments were carried out by Christian Anfinsen.

(See link) & also

 

Ribonuclease A: 124 amino acids, 4 disulfide bonds

1) Denature isolated protein in 8M urea

2) Reduce disulfide bonds using 2-mercaptoethanol: S-S -> -SH

3a) Renature slowly by slowly diluting the urea, in the presence of oxygen, pH 8.0

OR

3b) Renature slowly in the presence of 2-mercaptoethanol, allowing exchange between S-S and SH bonds

• Disulfides form correctly, enzyme activity is about 100%

Conclusion, under the right conditions, proteins can fold correctly to the native structure.

Probability of 4 disulfides forming correctly in a random process is:

1/7 x 1/5 x 1/3 = 1/105 = about 1 %

Other proteins such as insulin cannot be refolded correctly, because of covalent modification. Such modification after folding and disulfide formation can mean that the protein after further modification is no longer in the state of lowest free energy.

Folding Accessory Proteins

Protein Dynamics

• Proteins are not static structures. Motions include:
  Atomic fluctuations
  Collective motions, of groups of atoms
  Conformational changes, with two or more stable conformations. See Calmodulin link
  Mouse Control

Last updated Tuesday, September 25, 2001

Comments/questions: svik@mail.smu.edu

Copyright 2001, Steven B. Vik, Southern Methodist University