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In contrast to the previous topological model of the ATP binding domain of the F 1-ATPase β subunit based on analogies to those of rasp21 and adenylate kinase, a more consistent model can be constructed with the known structure of the recA protein as a reference. The secondary structure of the F 1-ATPase β subunit predicted from the primary structure agrees well with that of the recA protein. The topology includes a repetitive βα Cβαβαβαβ structure where all β strands are parallel and surround the central α Chelix above which bound ATP is located. Several residues thought to be located at catalytic site as reported in genetic and chemical labeling work can be consistently positioned in this model.

The amino acid composition or transmembrane proteins was analyzed for their three separate portions: the transmembrane apolar, cytoplasmic and extracellular regions. The composition was different between cytoplasmic and extracellular peptides; alanine and arginine residues were preferentially sited on the cytoplasmic side, while the threonine and cysteine/cystine were preferentially sited on the extracellular side. The composition of cytoplasmic and extracellular peptides of membrane proteins corresponded to those of intracellular and extracellular types of soluble proteins, respectively. This difference in composition was independent of the peptide orientation against the membrane. Peptide chains could be correctly assigned as either cytoplasmic or extracellular, solely from an analysis of sequence composition. For single-spanning membrane proteins the predictive accuracy was 90%, whereas for multi-spanning proteins this was 85%.

Structural analysis of chloroplast transit peptides (cTPs), including secondary structure prediction and analysis of ‘cTP-like’ peptides of known 3D structure, suggests that cTPs are essentially flexible peptides devoid of regular secondary or tertiary structure. It is proposed that cTPs may be designed to interact with a succession of different chaperones on the chloroplast protein-import pathway.