Question

Describe the typical principles used to identify topogenic sequences within proteins and how these principles can be used to develop computer algorithms. How does the identification of topogenic sequences lead to prediction of the membrane arrangement of a multipass protein

Answer 1

Topogenic sequences share a series of structural features, and thereby computational algorithms can be used to predict these protein-membrane segments

Step-by-step explanation:

Topogenic sequences are protein segments formed by alpha-helical transmembrane domains, which are required for the insertion of membrane proteins. These domains share a series of well-defined features: they are composed of segments of about 20 hydrophobic amino-acid residues. In consequence, computational algorithms can be designed to identify protein patterns that fulfill these structural requirements (i.e. segments with a length of 20 residues, hydrophobic level, etc). The models assign a similarity threshold (threshold value) that predict if the similarity level of the protein pattern is good enough to detect a topogenic segment.