Amino acid hydrophobicity and accessible surface area

Area of Science:

• Protein structure and biophysics
• Computational biology
• Biochemistry

Background:

• The hydrophobic effect is a primary driver of protein folding and collapse.
• Understanding amino acid properties is crucial for predicting protein structure and function.

Purpose of the Study:

• To analyze the variation of solvent-accessible surface area (SASA) in protein fragments.
• To infer amino acid hydrophobicity based on SASA changes.
• To propose an alternative hydrophobicity scale derived from SASA behavior.

Main Methods:

• Analysis of solvent-accessible surface area in small protein fragments (3N45).
• Examination of 5526 protein chains from the Brookhaven Protein Data Bank.
• Power law analysis of accessible surface area for varying fragment sizes (N).

Main Results:

• Solvent-accessible surface area exhibits power law behavior for protein fragments.
• SASA variation and self-similar behavior provide a measure of amino acid side chain polarity.
• The findings allow inference of amino acid hydrophobicity (hydrophobic vs. hydrophilic).

Conclusions:

• The variation in solvent-accessible surface area offers a novel method for assessing amino acid hydrophobicity.
• This approach provides an alternative hydrophobicity scale independent of traditional methods.
• The study contributes to a deeper understanding of the forces governing protein folding.