TY - JOUR T1 - Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks A1 - Vijayabaskar, M. S. A1 - Vishveshwara, Saraswathi Y1 - 2012/05/17 N2 - Author Summary Proteins are polymers of amino-acids that fold into unique three-dimensional structures to perform cellular functions. This structure formation has been shown to depend on the amino-acid sequences. But examples of proteins with diverse sequences retaining a similar structural fold are quite substantial that we can no longer consider such phenomenon as exceptions. Therefore, this non-canonical relationship has been studied extensively mostly by studying the remote sequence similarities between proteins. Here we have attempted to address the above-mentioned problem by analyzing the similarities in the spatial interactions among amino-acids. Since the protein structure is a resultant of different interactions, we have considered the proteins as networks of interacting amino-acids to derive the common interactions within a popular structural fold called the TIM barrel fold. We were able to find common interactions among different families of the TIM fold and generalize the patterns of interactions by which the fold is being maintained despite sequence diversity. The results substantiate our hypothesis that interaction conservation might by a driving factor in fold formation and this new outlook can be used extensively in engineering proteins with better biophysical characteristics. JF - PLOS Computational Biology JA - PLOS Computational Biology VL - 8 IS - 5 UR - https://doi.org/10.1371/journal.pcbi.1002505 SP - e1002505 EP - PB - Public Library of Science M3 - doi:10.1371/journal.pcbi.1002505 ER -