Protein structure and function:

folding, misfolding,
degradation, and denaturation
DLA video
Andrew K. Sobering, PhD
asobering@sgu.edu
Department of Biochemistry
Science Building – Ground Floor

1
Protein structure: Learning Objectives
• Describe the geometry and the properties of the peptide bond.
• Be able to define the following terms: multimeric, prosthetic group, native conformation, loops, bends, motif and
domain.
• Describe the levels of protein structure: primary, secondary, tertiary, quaternary
• Explain how the primary sequence of a polypeptide might be obtained both from biochemical and genetic approaches
• Describe the structure of the α-helix and the β-sheet.
• Identify the bonds that stabilize the structure of α-helix and the β-sheet
• Identify amino acids that can disrupt the α-helix
• Describe what constitutes “supersecondary” structure
• Differentiate between the structure and function of fibrous and globular proteins.
• Explain the structure of silk as a protein that is predominantly composed of β-sheet
• Describe the bonds that stabilize tertiary and quaternary structures.
• List the advantages of quaternary structure, and explain the terminology that describes multimeric proteins
• Describe protein denaturation and list some common denaturing agents.
• Briefly describe the role of chaperones
• Describe the sequencing of a polypeptide by Edman degradation
• Compare and contrast the structure and function of myoglobin and hemoglobin
Protein folding
• Folding allows formation of the native (functional) protein form
• Folding is complex, may think of it as a trial and error process that
depends on:
1. Composition of side chains
2. hydrogen-bonding
3. Disulfide bonds
4. Ionic interactions
5. Hydrophobic effect
6. All in the context of repulsion of some shapes (steric, charge, bond angle
constraints, etc)

• To result in the most stable or favorable structure (usually lowest energy)

Protein folding
Denaturation of Proteins
• The primary structure stays intact
• All other shape/conformational structure → lost
• Denaturing agents include heat, organic solvents,
mechanical shearing, heavy metals, detergents, chaotropic
agents

• Denaturation is usually irreversible

• In rare cases, denaturation is reversible (RNAse A)

• Loss of biological activity

Most proteins do not revert to their original
tertiary structures after denaturation.

Ribonuclease A enzyme is a rare exception

RNAse
Chaperones
• Chaperones: play a role in protein folding during synthesis
• Keep unfolded proteins separate
• Enhance folding rate
• Protect side chains from inappropriate interactions

• Many chaperones are called Heat Shock Proteins

• Their synthesis increases in response to high temperature and other
conditions which increase protein denaturation in the cell
• Example HSP70
 mRNA
transcript
ribosome

Side chains of newly

formed protein are kept
Nascent away from each other by
polypeptide chaperones
being
translated
After proper folding,
chaperones come off,
and may be used again
Enzymatic degradation of proteins
• Enzymes are biological catalysts
• An enzyme that degrades protein is called a protease
Protein degradation
• Breaking the peptide bond

• Non-enzymatic OR enzymatic
 Non enzymatic protein degradation
• Very low pH, or very high pH
• Heat
• Time
• Of course this doesn’t happen naturally

• Degradation of proteins does not occur in the stomach

❑pH is not low enough, heat is not high enough, and not enough time.
• In the stomach, dietary protein is not degraded, but it is denatured
❑Denatured means the protein unfolds
❑Loss of the native conformation (shape)
• Job of stomach is to denature proteins, so they are easier to degrade
by digestive enzymes
Chemicals and conditions that might promote
protein denaturation
• Heat (thermal energy)
❑Pulls stuff apart
❑Think about frying an egg
• Stuff that alters / changes ionic bonds, and hydrogen bonding
❑Salt
❑Acid
❑Base
• Detergent
❑Allows hydrophobic areas of the protein to interact with water
• Reducing agents
❑Breaks disulfide bonds
 SDS – sodium dodecyl sulfate (a detergent) can denature proteins

Attribution: [[File:Protein-SDS interaction.png|Protein-SDS interaction]]

Beta-mercaptoethanol
Sometimes misfolded proteins are resistant to
degradation - disease
• Two examples

• Alzheimer disease
• Prion disease
Protein misfolding
• Spontaneous events in a cell
• Some genetic variants (mutation) might increase likelihood

• Alzheimer disease:
• The amyloid-β protein (neuronal) must sometimes be degraded
• Amyloid-β protein undergoes proteolytic cleavage as part of a normal degradation
❑ A non-toxic fragment may be created, this is cleared, and disposed of
❑ A neurotoxic form may be created, this accumulates, and will eventually lead to Alzheimer disease
• Other proteins aggregate to form tangles
❑Abnormal form of tau accumulation in neurofibrillary tangles
b-Sheet in fibrous (Amyloid) protein
• Amyloid protein deposited in brain of
a person with Alzheimer disease
❑ The twisted b-pleated sheet fibrils have
a 3-d structure that resembles silk fibrils
Prion diseases:
• Scrapie in sheep
• Creutzfeldt-Jakob disease in humans
• Mad cow disease
However, the shape of
All mammals have
PrPc can change to
the prion protein The normal shape of the
become the disease-
(PrP) as a normal protein is referred to as PrPc
causing form which is
brain protein (prion protein cellular)
called PrPSc
(unknown function)
(prion protein - scrapie)
 Prion (PrPc)
PrPc

Structure of
the protein
changes

predominant alpha helix
Protein of unknown
brain function
PrPSc
predominant beta sheet
Super-duper resistant to degradation
Damages neurons
Formation of one
PrPSc causes
conversion of all
PrPc to take the
PrPSc form
It just takes one PrPSc to
form from the normal PrPc,
and then all PrP will be
converted to the disease
state

“Catalytic
conversion”

PrPSc
accumulates
causing damage to
Like a zombie army brain tissue
 The transmissible spongiform encephalopathy (TSE)

Attribution: Photo Credit: Sherif Zaki; MD; PhD; Wun-Ju Shieh; MD; PhD; MPH; public domain; Datum Creation Date: 2004 Källa Public Health Image Library (PHIL) ID#: 10131