Principal component analysis of alpha-helix deformations in transmembrane proteins

alpha -helices are deformable secondary structural components regularly observed in protein folds. The overall flexibility of an alpha -helix can be resolved into constituent physical deformations such as bending in two orthogonal planes and twisting along the principal axis. We used Principal Component Analysis to identify and quantify the contribution of each of these dominant deformation modes in transmembrane alpha -helices, extramembrane alpha -helices, and alpha -helices in soluble proteins. Using three alpha -helical samples from Protein Data Bank entries spanning these three cellular contexts, we determined that the relative contributions of these modes towards total deformation are independent of the alpha -helix's surroundings. This conclusion is supported by the observation that the identities of the top three deformation modes, the scaling behaviours of mode eigenvalues as a function of alpha -helix length, and the percentage contribution of individual modes on total variance were comparable across all three alpha -helical samples. These findings highlight that alpha -helical deformations are independent of cellular location and will prove to be valuable in furthering the development of flexible templates in de novo protein design.