Unit 3 Question Bank
It arises when a series of consecutive aminoacyl residues adopt similar φ and ψ angles. The two commonest forms are the α-helix and the β-pleated sheet, together with bends, turns and loops. It is stabilised principally by hydrogen bonds between backbone carbonyl oxygens and amide hydrogens. Side chains are not involved in forming secondary structure, though they help determine its stability and type.Harper's ch.5, p.36 · TMU Lecture 3 Slide 9
A complete turn contains an average of 3.6 residues and rises 0.54 nm (the pitch). The R groups face outward. Because proteins contain only L-amino acids, only right-handed α-helices occur. Stability arises from hydrogen bonds parallel to the helix axis, between the carbonyl oxygen of one peptide bond and the amide hydrogen of the fourth residue down the chain.Harper's ch.5, p.38
Different domains work together to provide the complete function of the protein. A small polypeptide such as triose phosphate isomerase or myoglobin may consist of a single domain; protein kinases contain two — a β-sheet-rich amino-terminal domain that binds ATP and an α-helix-rich carboxyl-terminal domain that binds the substrate.Harper's ch.5, pp.40–41
Examples include the zinc finger (about 30 residues forming an elongated loop held at its base by a single Zn²⁺ ion coordinated to four residues — four Cys, or two Cys and two His) and nuclear localisation sequences.TMU Lecture 3 Slides 20, 22
The commonest are combinations of α-helix and β-sheet. The helix-loop-helix motif, which provides the oligonucleotide-binding portion of DNA-binding proteins such as repressors and transcription factors, is the standard example.Harper's ch.5, p.39 · TMU Lecture 3 Slide 20
Monomeric proteins consist of one chain and have no quaternary structure. Greek letters distinguish subunit types and subscripts their number: α₄ is a homotetramer, α₂β₂ (adult haemoglobin) a heterotetramer. It is stabilised by the same non-covalent forces as tertiary structure, and sometimes by interchain disulfide bonds.Harper's ch.5, p.41
Within it, the modules of secondary structure rearrange until the mature, native conformation is attained. The process is orderly but not rigid: considerable flexibility exists in the order in which elements may be rearranged.Harper's ch.5, pp.44–45
Prion diseases are protein conformation diseases: the pathological isoform PrPˢᶜ acts as a template that converts the host's normal PrPᶜ — monomeric and α-helix rich — into the β-sheet-rich PrPˢᶜ, which aggregates into insoluble, protease-resistant deposits. The amino acid sequence is unchanged; only the conformation differs.Harper's ch.5, pp.45–46
Configuration is the geometric relationship between a given set of atoms — for example that which distinguishes L- from D-amino acids — and its interconversion requires breaking covalent bonds.Harper's ch.5, p.36
Framing the answer
Protein structure is described in four orders. The primary structure is the basic structure, held together by covalent bonds; the secondary, tertiary and quaternary structures together constitute the spatial structure, or conformation, and are stabilised principally by non-covalent forces. Conformation is dictated by the primary sequence.
Primary structure
The sequence of amino acids in the polypeptide chain, read from the N-terminus to the C-terminus, joined by covalent peptide bonds. It is gene-encoded and determines all higher orders of structure.
Secondary structure
The folding of short (3–30 residue), contiguous segments of the polypeptide backbone into geometrically ordered units, arising when a series of consecutive residues adopt similar φ and ψ angles. Side chains are not involved, though they influence stability and type. Stabilised by hydrogen bonds between backbone carbonyl oxygens and amide hydrogens. The principal forms are:
| Form | Features |
|---|---|
| α-helix | 3.6 residues per turn, pitch 0.54 nm, φ ≈ −57° and ψ ≈ −47°; right-handed only; R groups face outward; hydrogen bonds parallel to the axis, to the fourth residue down the chain |
| β-pleated sheet | Highly extended backbone with a pleated zigzag appearance; R groups of adjacent residues point in opposite directions; hydrogen bonds formed with adjacent segments of chain; may be parallel or antiparallel |
| Turns, bends and loops | Connect adjacent regions of secondary structure; proline and glycine are common in β-turns; loops contain residues beyond the minimum needed, and often lie on the surface as epitopes |
Recurring combinations of these, 10–40 residues long, are termed supersecondary structures (e.g. helix-loop-helix), intermediate between secondary and tertiary structure.
Tertiary structure
The entire three-dimensional conformation of a polypeptide — how the secondary structural features (helices, sheets, bends, turns and loops) assemble into domains, and how those domains relate spatially to one another. A domain is a section of structure that folds independently into a stable conformation and is sufficient to perform a particular task; protein kinases, for example, have two, one binding ATP and one the substrate. Tertiary structure is stabilised mainly by hydrophobic interactions, with contributions from hydrogen bonds, salt bridges, van der Waals interactions and intrachain disulfide bonds.
Quaternary structure
The number and types of polypeptide subunits of an oligomeric protein and their spatial arrangement. Present only in proteins of more than one chain: monomeric proteins have none. Homodimers contain two identical chains, heterodimers two different ones; Greek letters and subscripts denote composition, so α₄ is a homotetramer and α₂β₂ — adult haemoglobin — a heterotetramer. Stabilised by the same non-covalent forces, and in some proteins by interchain disulfide bonds.
The general principle
Primary structure is stabilised by covalent peptide bonds. The higher orders of structure are stabilised primarily — and often exclusively — by non-covalent interactions. Each individual interaction is weak; their number is what makes the folded conformation stable.
The non-covalent forces
| Force | Nature and importance |
|---|---|
| Hydrogen bonds | Between the carbonyl oxygen and the amide hydrogen of peptide bonds. The dominant force in secondary structure — parallel to the axis in the α-helix, between adjacent segments in the β-sheet. Also stabilise loops and tertiary contacts |
| Hydrophobic interactions | Non-polar side chains segregate into the interior of the protein, away from solvent. The dominant force in tertiary and quaternary structure, and the driving force of the molten globule stage of folding |
| Salt bridges (electrostatic or ionic bonds) | Between oppositely charged side chains, for example a lysine ammonium group with an aspartate carboxylate |
| van der Waals interactions | Weak and short-range, but numerous in the tightly packed core of a folded protein |
The covalent exception
Some proteins contain disulfide (–S–S–) bonds linking the sulfhydryl groups of two cysteinyl residues. These are covalent, and therefore the exception to the rule above.
- Intrachain disulfide bonds form within a single polypeptide and further enhance the stability of its folded tertiary conformation.
- Interchain disulfide bonds link different polypeptides and stabilise the quaternary structure of certain multimeric proteins.
Summary statement
Primary structure — covalent peptide bonds. Secondary structure — mainly hydrogen bonds. Tertiary and quaternary structure — mainly hydrophobic interactions, supported by hydrogen bonds, salt bridges and van der Waals forces, and in some proteins reinforced by covalent disulfide bonds.
The problem
A typical polypeptide can adopt ≥10⁵⁰ distinct conformations. If a chain searched them at random, folding would take billions of years; in reality proteins fold in milliseconds. Folding cannot therefore be a random search.
Thermodynamics provides the direction
The biologically relevant, or native, conformation is generally the one that is most energetically favoured. Knowledge of the native conformation is therefore already specified in the primary sequence — conformation is dictated by primary structure.
Folding is modular — two stages
- Local order. As the newly synthesised polypeptide emerges from the ribosome, short segments fold into secondary structural units that provide local regions of organised structure. The problem is thereby reduced from an astronomical search to the selection of an appropriate arrangement of a relatively small number of pre-formed elements.
- The molten globule. Forces driving hydrophobic regions into the interior, away from solvent, collapse the partially folded chain into a molten globule, within which the modules of secondary structure rearrange until the mature conformation is reached. The process is orderly but not rigid. For oligomeric proteins, individual protomers tend to fold before associating with other subunits.
Auxiliary proteins assist folding
| Protein | Function |
|---|---|
| Chaperones | Bind polypeptides before synthesis is complete, preventing premature folding into an incorrect conformation; and rescue proteins thermodynamically trapped in a misfolded dead end by unfolding hydrophobic regions and providing a second chance. They participate in the folding of over half of mammalian proteins |
| Protein disulfide isomerase | Disulfide bond formation is non-specific; by catalysing disulfide exchange — rupture of an S–S bond and its reformation with a different partner cysteine — the enzyme drives the protein toward its native pairings |
| Proline-cis,trans-isomerase | All X-Pro bonds are synthesised trans, but about 6% of those in mature proteins are cis, particularly in β-turns; this enzyme catalyses the isomerisation |
Note the contrast with the laboratory: many denatured proteins refold spontaneously in vitro, but far more slowly, and some fail entirely, forming insoluble aggregates of unfolded or partly folded chains held together by hydrophobic interactions.
Consequences of failure — protein conformation diseases
Prion diseases. Prions are protein particles that lack nucleic acid, causing fatal transmissible spongiform encephalopathies — Creutzfeldt-Jakob disease, scrapie, bovine spongiform encephalopathy. Normal human PrPᶜ is monomeric and rich in α-helix; the pathological PrPˢᶜ is rich in β-sheet, with hydrophobic side chains exposed to solvent, so the molecules associate into insoluble, protease-resistant aggregates. Transmission occurs because PrPˢᶜ serves as a template for the conformational conversion of PrPᶜ: the amino acid sequence is unchanged, and only the conformation is propagated.
Alzheimer's disease. Misfolding of β-amyloid, a 4.3-kDa polypeptide produced by proteolytic cleavage of amyloid precursor protein, is a prominent feature.
Nutritional failure of maturation. Scurvy illustrates the same principle from a different direction: vitamin C deficiency impairs prolyl and lysyl hydroxylase, so collagen fibres never acquire conformational stability.