Signal sequences conformation, predictions

The importance of signal-sequence conformation for proper function has been tested by determining the effect on activity of sequence changes that are predicted to change conformational tendencies these are discussed below. Only in the case of the LamB mutants (see below and Section III,F) have correlations been made between the actual and predicted conformational preferences of the altered and native sequences. 

The c region is more sensitive to conformational alterations. The . coli wild-type lipoprotein signal sequence is predicted to form a )3 turn at positions —7 to -4. Alanine was substituted for serine (position —6), which occurs frequently in ji turns, or threonine (position -5), which is also found in turns, but less often than serine, or both (Vlasuk et al.,... 

Brown et al. (1984) introduced insertions of three or four amino acids into the yeast invertase signal sequence near its amino terminus. The insertions were predicted to stabilize an a helix, favor a )3 turn, or to destabilize both a-helix and 3-sheet formation. None of these alterations prevented proper secretion of the protein. Thus, the amino-terminal domain of the signal sequence is relatively unconstrained as to conformation. 

Substitution of Ala for Thr -5 alone did not cause a predicted loss of -turn conformation, while replacement of Ser —6 or both Ser —6 and Thr —5 yielded a structure predicted to lack a )3 turn. The phenotypes of the mutants correlate with the predicted presence or absence of the turn. Those predicted to lack a turn accumulate membrane-bound precursor lipoprotein, which is slowly processed to mature lipoprotein. Thus, the absence of a region favoring /3 turn in the c domain can inhibit removal of the signal sequence. 

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