Amino acid hydrophobicity and accessible surface area

It is well known that the hydrophobic effect is the major factor that drives a protein toward collapse and folding. We analyze the variation of the solvent-accessible surface area of amino acids in small fragments of protein (3N45) . In this way, we look into 5526 protein chains deposited in the Bro...

Full description

Saved in:
Bibliographic Details
Published in:Physical review. E, Statistical, nonlinear, and soft matter physics Statistical, nonlinear, and soft matter physics, 2007-01, Vol.75 (1 Pt 1), p.011920-011920, Article 011920
Main Authors: Moret, M A, Zebende, G F
Format: Article
Language:English
Subjects:
Amino Acids - chemistry
Biophysics - methods
Hydrophobic and Hydrophilic Interactions
Models, Biological
Molecular Conformation
Polymers - chemistry
Protein Conformation
Protein Folding
Proteins - chemistry
Solvents - chemistry
Surface Properties
Water
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:It is well known that the hydrophobic effect is the major factor that drives a protein toward collapse and folding. We analyze the variation of the solvent-accessible surface area of amino acids in small fragments of protein (3N45) . In this way, we look into 5526 protein chains deposited in the Brookhaven Protein Data Bank. The accessible surface area behaves as a power law for N9 . The comparison between the loss of accessible area and the self-similar behavior gives us a measure of the possibility of an amino acid to have apolar or polar side chain. It is therefore possible to infer about amino acid hydrophobicity, i.e., if one amino acid has a hydrophobic side chain or if it has a hydrophilic one. Furthermore, the present findings indicate that the variation of the accessible surface area describes an alternative hydrophobicity scale.
ISSN:1539-3755
1550-2376
DOI:10.1103/PhysRevE.75.011920