Bioc 192 Tutorial 2 Notes: Elements of Protein Structure and Folding

Define the four levels of protein structure: primary, secondary, tertiary, and quaternary.
Define the properties of the α-helix, β-sheet, and turns and recognise them in protein structures.
Outline the steps involved in folding a newly synthesized protein, including the role of chaperones.
Provide examples of misfolded proteins and the diseases associated with them.

There are 4 levels of protein structure.
- Primary structure
- Secondary structure
- Tertiary structure
- Quaternary structure (only some proteins have this)
All proteins have: primary, secondary, and tertiary structures.
Some proteins have quaternary structure.
Understanding these four levels helps explain how proteins achieve their final shape.

A protein forms following the order of structure levels: primary → secondary → tertiary → quaternary.
Between the formation of secondary structures and tertiary structures there are two additional protein structure concepts:
- Supersecondary structures: combinations of secondary structures that form recognisable patterns.
- Domains: a relatively stable folded region of a protein with a particular function.
Supersecondary structures and domains (or motifs) describe levels bridging from simple, repetitive secondary structures to more complex and unique tertiary structures.

The α-helix is a right-handed helix.
It has $3.6$ residues per turn.
Each residue is about $1.5\ \text{Å}$ apart along the helical axis.
Hydrogen bonds form between the carbonyl oxygen of residue $n$ and the amide hydrogen of residue $n+4$ .
Side chains point outward from the helix core.
Glycine and proline are helix breakers.

A β-sheet consists of two or more β-strands that are hydrogen bonded together.
Typically, there are $2\text{ to }10$ strands per sheet.
Each strand contains about $6\ to\ 15$ residues.
Side chains point alternately up and down along the sheet.
A stretch of residues that alternates polarity (P-NP-P-NP-P) is likely a β-strand.

Turns link helices and strands.
They are usually $3\text{ to }4$ residues long.
They have high glycine and proline content.
There are more than $16$ types of turns; most are Type I and Type II.
Turns often form a hydrogen bond across the width of the turn.
Coils and loops are longer forms of turns, involving more residues.
Turns do not necessarily require the dramatic angle change that a strict turn has.

Folding is an ordered, stepwise process:
1) Formation of short secondary structural elements.
2) Supersecondary structures come together to form domains.
3) Domains come together to form a slightly disordered tertiary structure.
4) Small conformational adjustments finalize the tertiary structure.
The process is guided by the intrinsic propensities of amino acids and the physical chemistry of interactions (non-covalent and some covalent factors).
The role of chaperones is acknowledged as part of folding, helping proteins achieve their correct folds, though detailed mechanisms are not described in these notes.

Proteins unfold when their environment changes, including:
- Heat
- pH changes
- Salt content changes
- Detergents
Non-covalent interactions break during denaturation, including:
- Hydrogen bonds
- Ionic (electrostatic) interactions
- Hydrophobic interactions
Covalent bonds (the strongest bonds) generally stay intact during denaturation.
Native protein shape is essential for function; denaturation destroys the 3D structure and therefore the function.
Everyday examples of denaturation include:
- Cooking (e.g., egg albumen turning from clear to white)
- Hand sanitizer relies on protein denaturation for antimicrobial activity
- Fever can denature proteins in the body, contributing to illness

Protein denaturation can lead to diseases when misfolding or aggregation occurs.
Alzheimer’s disease: Aggregation of proteins leads to amyloid plaques thought to play a role in disease pathology.
Prion diseases: A single misfolded protein can induce other proteins to misfold, propagating disease.
Misfolding and aggregation have significant biomedical relevance and motivate research into folding mechanisms, chaperone function, and therapeutic interventions.

The four structure levels connect to function: structure dictates function, and folding determines activity.
Misfolding is directly linked to diseases, highlighting the importance of proper protein folding in biology and medicine.
Understanding secondary structures and their patterns (α-helix, β-sheet, turns) helps in predicting protein architecture from sequence and in interpreting structural data.
Chaperones represent cellular strategies to ensure correct folding under physiological conditions.

α-helix: $3.6$ residues per turn; $1.5\ \text{Å}$ between consecutive residues; HB: carbonyl O of residue $n$ to amide H of residue $n+4$ .
β-sheet: $2\text{ to }10$ strands per sheet; $6\ to\ 15$ residues per strand.
Turns: $3\ to\ 4$ residues; more than $16$ turn types; most are Type I and II; turns often have intra-turn H-bonds across width.
Turn-based and loop regions can extend into coils/loops, which are longer forms of turns.
Structural hierarchy order (typical): primary → secondary → tertiary → quaternary; supersecondary structures and domains bridge secondary to tertiary.
Denaturation involves disruption of non-covalent bonds; covalent bonds remain intact; functional loss accompanies structural loss.

Proper protein folding is essential for biological activity; misfolding is a central theme in major diseases.
Denaturation is not only a laboratory concept but reflects everyday processes (cooking, disinfection) and clinical phenomena (fever).
Structural motifs (α-helix, β-sheet, turns) recur across proteins, enabling modular understanding of protein architecture and function.