%0 Journal Article %J Biochemical Society Transactions %D 2013 %T Knot localization in proteins. %A Rawdon, Eric J %A Millett, Kenneth C %A Joanna I. Sulkowska %A Stasiak, Andrzej %K Animals %K Humans %K Models, Molecular %K Protein Conformation %K Proteins %X 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. %B Biochemical Society Transactions %V 41 %P 538-41 %8 2013 Apr %G eng %N 2 %R 10.1042/BST20120329 %0 Journal Article %J Biochemical Society Transactions %D 2013 %T Knotting pathways in proteins. %A Joanna I. Sulkowska %A Noel, Jeffrey K %A Ramírez-Sarmiento, César A %A Rawdon, Eric J %A Millett, Kenneth C %A Onuchic, José N %K Animals %K Humans %K Protein Conformation %K Protein Engineering %K Protein Folding %K Proteins %K Thermodynamics %X Most proteins, in order to perform their biological function, have to fold to a compact native state. The increasing number of knotted and slipknotted proteins identified suggests that proteins are able to manoeuvre around topological barriers during folding. In the present article, we review the current progress in elucidating the knotting process in proteins. Although we concentrate on theoretical approaches, where a knotted topology can be unambiguously detected, comparison with experiments is also reviewed. Numerical simulations suggest that the folding process for small knotted proteins is composed of twisted loop formation and then threading by either slipknot geometries or flipping. As the size of the knotted proteins increases, particularly for more deeply threaded termini, the prevalence of traps in the free energy landscape also increases. Thus, in the case of longer knotted and slipknotted proteins, the folding mechanism is probably supported by chaperones. Overall, results imply that knotted proteins can be folded efficiently and survive evolutionary pressure in order to perform their biological functions. %B Biochemical Society Transactions %V 41 %P 523-7 %8 2013 Apr %G eng %N 2 %R 10.1042/BST20120342