Why is the hydrophobic effect essential in protein folding?

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Question restatement: Why is the hydrophobic effect essential in protein folding?

Option a: It forces charged residues to the protein surface. This is misleading. The hydrophobic effect primarily drives nonpolar, water-fearing residues to the interior to reduce water structuring, while charged or polar residues are more commonly exposed on the surface where they can interact with the aqueous environment or form salt bridges. Therefore, this option inaccurately characterizes the general outcome of hydrophobic collapse.

Option b: It stabilizes the peptide bond. The stability of the peptide bond itself is not governed by the hydrophobic effect. Peptide bonds are stabilized by resonance and hydrogen bonding within the backbone and side chains; hydrophobic effects influence tertiary structure, not the intrinsic chemical stability of the bond. Hence, this statement confuses backbone chemistry with folding drivers.

Option c: It promotes burial of hydrophobic residues. This is the core idea of the hydrophobic effect: nonpolar amino acid side chains seek to minimize unfavorable interactions with water, leading to their sequestration in the protein interior (the hydrophobic core) during folding. This burial increases overall system entropy of water and stabilizes the folded state. The logic aligns with classical protein folding theory.

Option d: It neutralizes all dipoles in the structure. The hydrophobic effect does not neutralize dipoles or cancel dipole moments across the protein. Dipole interactions, including hydrogen bonds and ionic interactions, contribute to folding and stability, but neutralizing all dipoles is neither a defined consequence nor a mechanism of hydrophobic collapse. This overstates the effect and misattributes it to dipole neutralization.

Option e: It enhances the resolution of X-ray crystallography. The hydrophobic effect pertains to thermodynamics of folding in solution, not to the technical outcomes of X-ray crystallography. Crystallography resolution depends on crystal quality, data collection, and diffraction properties, not on the hydrophobic driving force of folding. This option confuses structural biology concepts with methodological aspects.

Summary perspective: Among the choices, option c accurately captures the essential role of the hydrophobic effect in protein folding by describing the burial of hydrophobic residues into the protein core, which is a fundamental driving force for achieving a stable folded structure in aqueous environments.

BINF3010/BINF9010-Applied Bioinformatics - 2025 T2

Why is the hydrophobic effect essential in protein folding?

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