NDLI: Preference of Amino Acids in Different Protein Structural Classes: A Database Analysis

Content Provider	IEEE Xplore Digital Library
Author	Ismail, W.M. Chowdhury, S.
Copyright Year	2010
Abstract	Understanding sequence-structure relationship is the key step in protein modeling and de novo protein design. Although almost 55,000 protein structures are solved and stored in protein data bank, elucidating sequence-structure relationship is still a challenging task. To understand sequence-structure relationship better, a statistical analysis of amino acid residues in four major structural classes of protein viz. α proteins, β proteins, α/β proteins and α+β proteins is performed. We use non-homologous proteins from (< 30% identity) October 2008 release Brookhaven Protein Data Bank (PDB) with resolution better than 2.5 angstrom. Interestingly, in comparison to the helical protein, the helical propensities of hydrophobic residues in mix proteins (containing both α helix and β sheet) are increased significantly. On the other hand, the helical propensities of hydrophilic residues are reduced in mixed proteins. A reverse trend is observed in strand propensity. The difference in helical propensity of hydrophobic and hydrophilic residues in different fold may be due to differential folding mechanism. The size of protein may also play a crucial role. A position specific analysis of helices is also done in all α and α/β proteins. The detailed analysis of helix dissection revealed that, the presence of β sheet influences the individual preference of amino acids in different positions within helix. This result indicates that the preference of amino acid in different positions (N terminus, C terminus and middle) within α helix are influenced by long range interactions with other structural elements.
Starting Page	1
Ending Page	5
File Size	628715
Page Count	5
File Format	PDF
ISBN	9781424447121
ISSN	21517622
DOI	10.1109/ICBBE.2010.5514826
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2010-06-18
Publisher Place	China
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Proteins Coils Algorithm design and analysis Data analysis Databases Statistical analysis Biological system modeling Amino acids Prediction algorithms Biology
Content Type	Text
Resource Type	Article

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