Why is the biological hydrophobicity scale more accurate than earlier experimental hydrophobicity scales?
2014 (English)In: Proteins: Structure, Function, and Genetics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 82, no 9, 2190-2198 p.Article in journal (Refereed) Published
The recognition of transmembrane helices by the translocon is primarily guided by the average hydrophobicity of the protential transmembrane helix, However, he exact hydrophobicity of each amino acid can he identified in several diferent ways. The free energy of transfer for amino acid analogues between a hydrophobic media, for example, octanol and water can be measured or obtained from simulations, the hydrophobicity can also be estimated by statistical properties from known transmembrane segments and finally the contribution of each amino acid type for the probability of traitslocon recognition has recently been measured directly. Although these scales correlate quite well, there are dear differences between them and it is not well understood which scale represents neither the biology best nor what the differences are. Here, we try to provide some answers to this by studying the ability of different scales to recognize transmembrane helices and predict the topology of transmembrane proteins. From this analysis it is clear that the biological hydrophobicity scale as well scales created from statistical analysis of membrane helices perform better than earlier experimental scales that are mainly based on measurements of amino acid analogs and not directly on transmeiribrane helix recognition. Using these results we identified the properties of the scales that perform better than other scales. We find, for instance, that the better performing scales consider proline more hydrophilic. This shows that tratismembrarie recognition is not only governed by pure hydrophobicity but also by the helix preferences for amino acids, as praline is a strong helix breaker.
Place, publisher, year, edition, pages
2014. Vol. 82, no 9, 2190-2198 p.
hydrophobicity scale, membrane proteins, traiislocon recognition, protein structure predictions, secondary structopology prediction
Biochemistry and Molecular Biology
Research subject Biochemistry
IdentifiersURN: urn:nbn:se:su:diva-107801DOI: 10.1002/prot.24582ISI: 000340940300040OAI: oai:DiVA.org:su-107801DiVA: diva2:752600