The link between amino acid sequence of a protein (the primary structure) and its precise three-dime — Analytical Chemistry Chemistry Question
Protein folding
The link between amino acid sequence of a protein (the primary structure) and its precise three-dimensional fold (the tertiary structure) remains one of the most important unsolved mysteries of modern science.
All protein backbones are identical: planar amide units are linked via tetrahedral methylene bridges, the so called α-carbons. Each α-carbon carries an R group of a specific α-amino acid (see the following diagram).
[VISUAL]
A unique sequence of amino acids characterizes a particular protein, determining how it folds and functions.
Every amide group in the polypeptide backbone, including its flanking α-carbons, is a planar unit. Explain.
Model Answer
The planar amide group, that is, Cα, O, H and the next Cα are in a single plane - is stabilized by resonance. The C-N bond of the amide assumes partial double bond character and the overlap between p orbitals of O, C and N is maximized. The C’s across this partial double bond can assume cis or trans arrangement.
[VISUAL]
The α-carbons across each amide unit occur in a trans geometrical arrangement. However, in case of the amino acid proline, both cis and trans amide arrangements are almost equally favored. Why?
Model Answer
With nineteen of the amino acids, the trans arrangement is sterically favoured (i. e. it is comparatively less crowded). In the case of proline, cis and trans arrangements are almost equally crowded.
[VISUAL]
The conformational choices of amino acid residues in a polypeptide chain are stereochemically controlled. For nineteen of the genetically coded amino acids, the conformational choice is largely restricted to the α (folded) and β (extended) regions of the Ramachandran diagram. For the amino acid glycine, however, the conformational choices are much wider. Explain.
Model Answer
Note about Ramchandran diagram: In a polypeptide, the amide units are planar (partial double bond character across the N-C bond) but the bonds connecting N and C, and the carbonyl carbon and C are free to rotate. These rotational angles are defined as φ and ψ, respectively. The conformation of the main chain is completely defined by these angles. Only some combinations of these angles are allowed while others are disallowed due to steric hindrance. The allowed range of φ and ψ angles are visualised as a steric contour diagram, shown below, known as the Ramachandran diagram.
For nineteen amino acids, the conformational choice is largely restricted to the so-called α and β regions on left half of the Ramachandran diagram (Panel A). This is due to the L - chiral nature of amino acids and the steric effects of their R groups.
Glycine is an achiral residue with H as the R group. Therefore, much larger conformational regions on both left and right halves of Ramachandran diagram are accessible to this residue (Panel B).
[VISUAL]
When a linear polypeptide folds forming a globular protein, an amino acid residue may assume α or β conformation. However it is observed that consecutive residues generally assume α or β conformation, rather than a random combination of α and β. Explain.
Model Answer
Consecutive residues in α conformation form the α-helix. Similarly, consecutive residues in β conformation form the β-sheet. Both α-helix and β-sheet structures feature extensive networks of hydrogen bonds which stabilise them. Thus random combinations of α and β conformations are rarely found.
[VISUAL]
In an aqueous environment polypeptides generally fold into compact globular protein structures. The reason is (select one)
i. The R groups in polypeptides are largely polar.
ii. The R groups in polypeptides are largely nonpolar.
iii. Both polar and nonpolar R groups occur in comparable proportion.
Justify your answer.
Model Answer
For a polypeptide to fold in an aqueous environment, nearly half the R groups should be non-polar (water hating) and the other half polar (water loving).
Upon folding to form a globular protein, the non-polar R groups are packed inside (away from water) while the polar groups are positioned on the surface (in contact with water). The phenomenon is similar to the hydrophobic aggregation of a micellar structure in water. If all the R groups are either polar or non-polar, no hydrophobic segregation is possible, and no folding will occur.
[VISUAL]
The pattern of R group polarities has an important role in determining whether α-helix or β-sheet will form when a polypeptide folds in water at an apolar surface. Explain the role of R group polarities.
Model Answer
Alternating polar/nonpolar periodicity of R groups favours β-sheets. All the non-polar groups will face the apolar surface while the polar groups will be exposed to water. So the net folding will be like a β-sheet. On the other hand, a complex periodic pattern of R group polarities is needed in forming the α-helix.
[VISUAL]