Class 6 Lecture

Protein folding is influenced by:

• Conformational degeneracy of the peptide chain.

• Hydrophobic effect

• Non-covalent interactions of atoms within the peptide backbone

• Non-covalent interactions of amino acid side chains

• Covalent disulfide bonds between cysteine side chains

favors U or F

Protein folding is influenced by:

• Conformational degeneracy of the peptide chain U

• Hydrophobic effect F

• Non-covalent interactions of atoms within the peptide backbone F

• Non-covalent interactions of amino acid side chains F

• Covalent disulfide bonds between cysteine side chains F

protein folding logistics

proteins are not stabilized by a lot (ex. 1-2 H-bonds)

proteins kind of go bad after a while (get oxidized)

ubiquitin destabilizes proteins and can’t do that if the protein is extremely stable

Non-covalent bonds/interactions

Chemical groups that are not close in a protein’s linear sequence can be close and interact in the folded state

Non-covalent bonds/interactions image helix

Intrahelical (within a single helix) and interhelical (between separate helices)

Cysteine

forms disulfide bonds

cell environment

outside cell: oxidizing, favors disulfide bonds

opposite inside

bacteria make proteins that digest the macromolecules of other bacteria (self-resistance)

insulin disulfide bonds

top first cystein bond with other cystein further away, one next to it bond below

Characteristics of misfolded proteins associated with disease

switch to beta-sheets → many copies form aggregates

Why do misfolded proteins have b- strands and not a-helices?

difference in alpha helix and beta strand interaction

Why do misfolded proteins have b- strands and not a-helices? deepseek

β-strands dominate in disease-causing aggregates because:

1. β-strands H-bond between chains → form stable, self-templating intermolecular β-sheets (amyloid cross-β structure).

2. α-helices H-bond within the same chain → internally satisfied, so they don't aggregate or propagate.

3. Cross-β stacks are extremely stable — protease-resistant, heat-resistant, and act as a template for more misfolding.

4. Kinetics: when normal folding fails, exposed backbone readily forms intermolecular β-sheets; α-helical aggregates have no equivalent stable, repeating architecture.

One-liner: β-strands win in misfolding because their hydrogen bonds are intermolecular and self-propagating, whereas α-helix H-bonds are intramolecular and self-contained.

Transmissible Spongiform Encephalopathies (TSEs) – Misfolding of PrP

formation of fibrils that are long enough to break cells via mechanical stress

1-121: disordered

122-180 (end or protein): structured (alpha-helix)

Experimental techniques for proteins

By charge/isoelectric point

• ion exchange chromatography

• isoelectric focusing

By molecular weight

• Size exclusion chromatpgraphy (gel filtration)

• SDS-PAGE

Both

• 2-dimensional gel electrophoresis

SDS-PAGE Assumptions for this class:

• SDS is added and proteins are unfolded

• Unaffected by charge of chemical groups of the protein

• Disulfide bonds are reduced

• Samples always start at the top of the gel represented in an image

• The experiment works as described

Chromatography