@article {387, title = {Knotting pathways in proteins.}, journal = {Biochemical Society Transactions}, volume = {41}, year = {2013}, month = {2013 Apr}, pages = {523-7}, abstract = {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.}, keywords = {Animals, Humans, Protein Conformation, Protein Engineering, Protein Folding, Proteins, Thermodynamics}, issn = {1470-8752}, doi = {10.1042/BST20120342}, author = {Joanna I. Sulkowska and Noel, Jeffrey K and Ram{\'\i}rez-Sarmiento, C{\'e}sar A and Rawdon, Eric J and Millett, Kenneth C and Onuchic, Jos{\'e} N} } @article {406, title = {Conservation of complex knotting and slipknotting patterns in proteins.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 Jun 26}, pages = {E1715-23}, abstract = {While analyzing all available protein structures for the presence of knots and slipknots, we detected a strict conservation of complex knotting patterns within and between several protein families despite their large sequence divergence. Because protein folding pathways leading to knotted native protein structures are slower and less efficient than those leading to unknotted proteins with similar size and sequence, the strict conservation of the knotting patterns indicates an important physiological role of knots and slipknots in these proteins. Although little is known about the functional role of knots, recent studies have demonstrated a protein-stabilizing ability of knots and slipknots. Some of the conserved knotting patterns occur in proteins forming transmembrane channels where the slipknot loop seems to strap together the transmembrane helices forming the channel.}, keywords = {Protein Conformation, Protein Folding, Proteins}, issn = {1091-6490}, doi = {10.1073/pnas.1205918109}, author = {Joanna I. Sulkowska and Rawdon, Eric J and Millett, Kenneth C and Onuchic, Jos{\'e} N and Stasiak, Andrzej} } @article {404, title = {Energy landscape of knotted protein folding.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, year = {2012}, month = {2012 Oct 30}, pages = {17783-8}, abstract = {Recent experiments have conclusively shown that proteins are able to fold from an unknotted, denatured polypeptide to the knotted, native state without the aid of chaperones. These experiments are consistent with a growing body of theoretical work showing that a funneled, minimally frustrated energy landscape is sufficient to fold small proteins with complex topologies. Here, we present a theoretical investigation of the folding of a knotted protein, 2ouf, engineered in the laboratory by a domain fusion that mimics an evolutionary pathway for knotted proteins. Unlike a previously studied knotted protein of similar length, we see reversible folding/knotting and a surprising lack of deep topological traps with a coarse-grained structure-based model. Our main interest is to investigate how evolution might further select the geometry and stiffness of the threading region of the newly fused protein. We compare the folding of the wild-type protein to several mutants. Similarly to the wild-type protein, all mutants show robust and reversible folding, and knotting coincides with the transition state ensemble. As observed experimentally, our simulations show that the knotted protein folds about ten times slower than an unknotted construct with an identical contact map. Simulated folding kinetics reflect the experimentally observed rollover in the folding limbs of chevron plots. Successful folding of the knotted protein is restricted to a narrow range of temperature as compared to the unknotted protein and fits of the kinetic folding data below folding temperature suggest slow, nondiffusive dynamics for the knotted protein.}, keywords = {Evolution, Molecular, Kinetics, Models, Molecular, Molecular Dynamics Simulation, Mutation, Protein Folding, Proteins}, issn = {1091-6490}, doi = {10.1073/pnas.1201804109}, author = {Joanna I. Sulkowska and Noel, Jeffrey K and Onuchic, Jos{\'e} N} } @article {409, title = {Slipknotting upon native-like loop formation in a trefoil knot protein.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, year = {2010}, month = {2010 Aug 31}, pages = {15403-8}, abstract = {Protein knots and slipknots, mostly regarded as intriguing oddities, are gradually being recognized as significant structural motifs. Recent experimental results show that knotting, starting from a fully extended polypeptide, has not yet been observed. Understanding the nucleation process of folding knots is thus a natural challenge for both experimental and theoretical investigation. In this study, we employ energy landscape theory and molecular dynamics to elucidate the entire folding mechanism. The full free energy landscape of a knotted protein is mapped using an all-atom structure-based protein model. Results show that, due to the topological constraint, the protein folds through a three-state mechanism that contains (i) a precise nucleation site that creates a correctly twisted native loop (first barrier) and (ii) a rate-limiting free energy barrier that is traversed by two parallel knot-forming routes. The main route corresponds to a slipknot conformation, a collapsed configuration where the C-terminal helix adopts a hairpin-like configuration while threading, and the minor route to an entropically limited plug motion, where the extended terminus is threaded as through a needle. Knot formation is a late transition state process and results show that random (nonspecific) knots are a very rare and unstable set of configurations both at and below folding temperature. Our study shows that a native-biased landscape is sufficient to fold complex topologies and presents a folding mechanism generalizable to all known knotted protein topologies: knotting via threading a native-like loop in a preordered intermediate.}, keywords = {Algorithms, Archaea, Archaeal Proteins, Crystallization, Databases, Protein, Models, Molecular, Molecular Dynamics Simulation, Protein Conformation, Protein Folding, Protein Multimerization, Protein Structure, Secondary, Protein Structure, Tertiary, Thermodynamics}, issn = {1091-6490}, doi = {10.1073/pnas.1009522107}, author = {Noel, Jeffrey K and Joanna I. Sulkowska and Onuchic, Jos{\'e} N} } @article {410, title = {A Stevedore{\textquoteright}s protein knot.}, journal = {PLoS Comput Biol}, volume = {6}, year = {2010}, month = {2010 Apr}, pages = {e1000731}, abstract = {Protein knots, mostly regarded as intriguing oddities, are gradually being recognized as significant structural motifs. Seven distinctly knotted folds have already been identified. It is by and large unclear how these exceptional structures actually fold, and only recently, experiments and simulations have begun to shed some light on this issue. In checking the new protein structures submitted to the Protein Data Bank, we encountered the most complex and the smallest knots to date: A recently uncovered alpha-haloacid dehalogenase structure contains a knot with six crossings, a so-called Stevedore knot, in a projection onto a plane. The smallest protein knot is present in an as yet unclassified protein fragment that consists of only 92 amino acids. The topological complexity of the Stevedore knot presents a puzzle as to how it could possibly fold. To unravel this enigma, we performed folding simulations with a structure-based coarse-grained model and uncovered a possible mechanism by which the knot forms in a single loop flip.}, keywords = {Databases, Protein, Hydrolases, Molecular Dynamics Simulation, Protein Conformation, Protein Folding}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1000731}, author = {B{\"o}linger, Daniel and Joanna I. Sulkowska and Hsu, Hsiao-Ping and Mirny, Leonid A and Kardar, Mehran and Onuchic, Jos{\'e} N and Virnau, Peter} } @article {411, title = {Jamming proteins with slipknots and their free energy landscape.}, journal = {Phys Rev Lett}, volume = {103}, year = {2009}, month = {2009 Dec 31}, pages = {268103}, abstract = {Theoretical studies of stretching proteins with slipknots reveal a surprising growth of their unfolding times when the stretching force crosses an intermediate threshold. This behavior arises as a consequence of the existence of alternative unfolding routes that are dominant at different force ranges. The existence of an intermediate, metastable configuration where the slipknot is jammed is responsible for longer unfolding times at higher forces. Simulations are performed with a coarse-grained model with further quantification using a refined description of the geometry of the slipknots. The simulation data are used to determine the free energy landscape of the protein, which supports recent analytical predictions.}, keywords = {Protein Conformation, Protein Folding, Proteins, Thermodynamics, Time Factors}, issn = {1079-7114}, author = {Joanna I. Sulkowska and Su{\l}kowski, Piotr and Onuchic, Jos{\'e} N} }