Variation of amino acid properties in all-beta globular and outer membrane protein structures.
Discriminating outer membrane (OM) proteins from globular proteins is an important task. The structural analysis of beta-strands dominating globular (all-beta) proteins and OM proteins provides useful insight to distinguish between them. In this work, we analyze the characteristic features of the 20 amino acid residues in all-beta and OM proteins. We set up numerical indices for several properties of amino acid residues, such as, conformational parameters, surrounding hydrophobicity, accessible surface area and reduction in accessibility, and inter-residue contacts. We found that all the aromatic residues prefer to be in beta-strands of both globular and OM proteins. The surrounding hydrophobicity of aromatic and non-polar amino acid residues in globular proteins is significantly higher than that of OM proteins. The residues Trp, Arg, Phe and Gln show a remarkable difference of reduction in accessibility between all-beta globular (betaG) and OM proteins. The positively charged residues, Lys and Arg in the membrane part of OM proteins have more number of contacts than globular proteins. Further, the behavior of the 20 amino acid residues in beta-strand segments of globular and OM proteins have been discussed. The parameters developed in this work can be used for identifying transmembrane beta-strands in OM proteins and for discriminating betaG proteins from OM proteins.
Gromiha
M Michael
MM
Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan. michael-gromiha@aist.go.jp
Suwa
Makiko
M
D000596:Amino Acids / Q000737:chemistry*; D057927:Hydrophobic and Hydrophilic Interactions; D008565:Membrane Proteins / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012997:Solvents / Q000737:chemistry; D013499:Surface Properties
D000596:Amino Acids; D008565:Membrane Proteins; D012997:Solvents