Identification of critical heterodimer protein interface parameters by multi-dimensional scaling in euclidian space

Protein subunit dimers are either homodimers (consisting of identical polypeptides) or heterodimers (consisting of different polypeptides). Protein dimers are involved in several cellular processes and an understanding of their molecular principle in complexations (subunit-subunit interaction) is essential. This is generally studied using 3D structures of homodimers and heterodimers determined by X-ray crystallography. However, the current knowledge on subunit interaction is limited due to lack of sufficient 3D dimer structures. It is our interest to study heterodimers using 3D structures to identify interaction parameters that would help in the development of a model to predict heterodimer interaction sites just from protein sequences. The efficiency of such models depends on the weighted contribution of numerous parameters characterizing heterodimer interfaces. Therefore, we studied the salient features of 111 interface parameters in 65 heterodimer structures. In this study, we applied multi-dimensional scaling for dimensionality reduction on these parameters to select the most critical ones that best characterize heterodimer interfaces. The significance of these parameters in subunit interaction is discussed.