Amino acid distributions in integral membrane protein structures
Autor: | Martin B. Ulmschneider, Mark S.P. Sansom |
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Jazyk: | angličtina |
Předmět: |
Proline
Lipid Bilayers Statistics as Topic Biophysics Glycine 010402 general chemistry 01 natural sciences Biochemistry Protein Structure Secondary 03 medical and health sciences Orientations of Proteins in Membranes database Protein structure Methods Animals Humans Amino Acids Hydrophobicity scales Integral membrane protein 030304 developmental biology 0303 health sciences Bacteria Chemistry Peripheral membrane protein β-Barrel Membrane Proteins Cell Biology Transmembrane protein 0104 chemical sciences Transmembrane domain Membrane protein α-Helix Amino acid distribution |
Zdroj: | Biochimica et Biophysica Acta (BBA) - Biomembranes. (1):1-14 |
ISSN: | 0005-2736 |
DOI: | 10.1016/S0005-2736(01)00299-1 |
Popis: | Advances in structure determination of membrane proteins enable analysis of the propensities of amino acids in extramembrane versus transmembrane locations to be performed on the basis of structure rather than of sequence and predicted topology. Using 29 available structures of integral membrane proteins with resolutions better than 4 A the distributions of amino acids in the transmembrane domains were calculated. The results were compared to analysis based on just the sequences of the same transmembrane alpha-helices and significant differences were found. The distribution of residues between transmembrane alpha-helices and beta-strands was also compared. Large hydrophobic (Phe, Leu, Ile, Val) residues showed a clear preference for the protein surfaces facing the lipids for beta-barrels, but in alpha-helical proteins no such preference was seen, with these residues equally distributed between the interior and the surface of the protein. A notable exception to this was alanine, which showed a slight preference for the interior of alpha-helical membrane proteins. Aromatic residues were found to follow saddle-like distributions preferring to be located in the lipid/water interfaces. The resultant 'aromatic belts' were spaced more closely for beta-barrel than for alpha-helical membrane proteins. Charged residues could be shown to generally avoid surfaces facing the bilayer although they were found to occur frequently in the transmembrane region of beta-barrels. Indeed detailed comparison between alpha-helical and beta-barrel proteins showed many qualitative differences in residue distributions. This suggests that there may be subtle differences in the factors stabilising beta-barrels in bacterial outer membranes and alpha-helix bundles in all other membranes. |
Databáze: | OpenAIRE |
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