@article {388, title = {Identifying knots in proteins.}, journal = {Biochemical Society Transactions}, volume = {41}, year = {2013}, month = {2013 Apr}, pages = {533-7}, abstract = {Polypeptide chains form open knots in many proteins. How these knotted proteins fold and finding the evolutionary advantage provided by these knots are among some of the key questions currently being studied in the protein folding field. The detection and identification of protein knots are substantial challenges. Different methods and many variations of them have been employed, but they can give different results for the same protein. In the present article, we review the various knot identification algorithms and compare their relative strengths when applied to the study of knots in proteins. We show that the statistical approach based on the uniform closure method is advantageous in comparison with other methods used to characterize protein knots.}, keywords = {Animals, Humans, Models, Molecular, Protein Conformation, Proteins}, issn = {1470-8752}, doi = {10.1042/BST20120339}, author = {Millett, Kenneth C and Rawdon, Eric J and Stasiak, Andrzej and Joanna I. Sulkowska} } @article {389, title = {Knot localization in proteins.}, journal = {Biochemical Society Transactions}, volume = {41}, year = {2013}, month = {2013 Apr}, pages = {538-41}, abstract = {The backbones of proteins form linear chains. In the case of some proteins, these chains can be characterized as forming linear open knots. The knot type\ of the full chain reveals only limited information about the entanglement of the chain since, for example, subchains of an unknotted protein can form knots and subchains of a knotted protein can form different types\ of knots than the entire protein. To understand fully the entanglement within the backbone of a given protein, a complete analysis of the knotting within all of the subchains of that protein is necessary. In the present article, we review efforts to characterize the full knotting complexity within individual proteins and present a matrix that conveys information about various aspects of protein knotting. For a given protein, this matrix identifies the precise localization of knotted regions and shows the knot types\ formed by all subchains. The pattern in the matrix can be considered as a knotting fingerprint of that protein. We observe that knotting fingerprints of distantly related knotted proteins are strongly conserved during evolution and discuss how some characteristic motifs in the knotting fingerprints are related to the structure of the knotted regions and their possible biological role.}, keywords = {Animals, Humans, Models, Molecular, Protein Conformation, Proteins}, issn = {1470-8752}, doi = {10.1042/BST20120329}, author = {Rawdon, Eric J and Millett, Kenneth C and Joanna I. Sulkowska and Stasiak, Andrzej} }