Knotted proteins: A tangled tale of Structural Biology
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[1] Sophie E Jackson,et al. Experimental detection of knotted conformations in denatured proteins , 2010, Proceedings of the National Academy of Sciences.
[2] Ronald C. Read,et al. The knot book: An elementary introduction to the mathematical theory of knots , 1997, Complex..
[3] José N Onuchic,et al. Knotting pathways in proteins. , 2013, Biochemical Society transactions.
[4] S. Jackson,et al. How do small single-domain proteins fold? , 1998, Folding & design.
[5] Anna L. Mallam,et al. How does a knotted protein fold? , 2009, The FEBS journal.
[6] R. Best,et al. Effects of interactions with the GroEL cavity on protein folding rates. , 2013, Biophysical journal.
[7] N R Cozzarelli,et al. Probability of DNA knotting and the effective diameter of the DNA double helix. , 1993, Proceedings of the National Academy of Sciences of the United States of America.
[8] Eugene I Shakhnovich,et al. Structural and energetic determinants of co-translational folding. , 2013, The Journal of chemical physics.
[9] Neil P King,et al. Protein stabilization in a highly knotted protein polymer. , 2011, Protein engineering, design & selection : PEDS.
[10] Vincent A Voelz,et al. Taming the complexity of protein folding. , 2011, Current opinion in structural biology.
[11] Peter Virnau,et al. Intricate Knots in Proteins: Function and Evolution , 2006, PLoS Comput. Biol..
[12] Enzo Orlandini,et al. The size of knots in polymers , 2009, Physical biology.
[13] M. M. Telo da Gama,et al. Native geometry and the dynamics of protein folding. , 2004, Biophysical chemistry.
[14] H. Chan,et al. Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding , 2008, Proceedings of the National Academy of Sciences.
[15] Sophie E Jackson,et al. Exploring knotting mechanisms in protein folding , 2008, Proceedings of the National Academy of Sciences.
[16] R. Jernigan,et al. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation , 1985 .
[17] R. Best,et al. Effect of interactions with the chaperonin cavity on protein folding and misfolding. , 2014, Physical chemistry chemical physics : PCCP.
[18] Shigeyuki Yokoyama,et al. An enzyme with a deep trefoil knot for the active-site architecture. , 2002, Acta crystallographica. Section D, Biological crystallography.
[19] J. Ponder,et al. Force fields for protein simulations. , 2003, Advances in protein chemistry.
[20] David E. Shaw,et al. Anton, A Special-Purpose Molecular Simulation Machine , 2011, Encyclopedia of Parallel Computing.
[21] P. Faísca,et al. How determinant is N-terminal to C-terminal coupling for protein folding? , 2015, Physical chemistry chemical physics : PCCP.
[22] Diogo Vila-Viçosa,et al. A Simulated Intermediate State for Folding and Aggregation Provides Insights into ΔN6 β2-Microglobulin Amyloidogenic Behavior , 2014, PLoS Comput. Biol..
[23] Peter G Wolynes,et al. P versus Q: structural reaction coordinates capture protein folding on smooth landscapes. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[24] Piotr Sułkowski,et al. Dodging the crisis of folding proteins with knots , 2009, Proceedings of the National Academy of Sciences.
[25] Sanne Abeln,et al. A Simple Lattice Model That Captures Protein Folding, Aggregation and Amyloid Formation , 2014, PloS one.
[26] Chih-Chieh Chen,et al. pKNOT v.2: the protein KNOT web server , 2012, Nucleic Acids Res..
[27] Cristian Micheletti,et al. Spontaneous knotting and unknotting of flexible linear polymers: equilibrium and kinetic aspects , 2013, 1304.3470.
[28] Pietro Faccioli,et al. The Role of Non-Native Interactions in the Folding of Knotted Proteins , 2012, PLoS Comput. Biol..
[29] A. Ikai,et al. The importance of being knotted: effects of the C‐terminal knot structure on enzymatic and mechanical properties of bovine carbonic anhydrase II 1 , 2002, FEBS letters.
[30] E I Shakhnovich,et al. Specific nucleus as the transition state for protein folding: evidence from the lattice model. , 1994, Biochemistry.
[31] Sophie E Jackson,et al. Folding studies on a knotted protein. , 2005, Journal of molecular biology.
[32] Stefan Wallin,et al. Coupled folding-binding in a hydrophobic/polar protein model: impact of synergistic folding and disordered flanks. , 2012, Biophysical journal.
[33] E. Shakhnovich,et al. Non‐native interactions play an effective role in protein folding dynamics , 2010, Protein science : a publication of the Protein Society.
[34] V. Pande. Understanding protein folding using Markov state models. , 2014, Advances in experimental medicine and biology.
[35] Frank Noé,et al. An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation , 2014, Advances in Experimental Medicine and Biology.
[36] J. Richardson. beta-Sheet topology and the relatedness of proteins. , 1977, Nature.
[37] José N Onuchic,et al. Backtracking on the folding landscape of the β-trefoil protein interleukin-1β? , 2008, Proceedings of the National Academy of Sciences.
[38] Neil P King,et al. Knotted and topologically complex proteins as models for studying folding and stability. , 2007, Current opinion in chemical biology.
[39] A. Horwich,et al. The crystal structure of the asymmetric GroEL–GroES–(ADP)7 chaperonin complex , 1997, Nature.
[40] Michele Vendruscolo,et al. Validity of Gō models: comparison with a solvent-shielded empirical energy decomposition. , 2002, Biophysical journal.
[41] Y. Sugita,et al. Replica-exchange molecular dynamics method for protein folding , 1999 .
[42] Sophie E Jackson,et al. Mechanistic insights into the folding of knotted proteins in vitro and in vivo. , 2015, Journal of molecular biology.
[43] Matthias Rief,et al. Tightening the knot in phytochrome by single-molecule atomic force microscopy. , 2008, Biophysical journal.
[44] A. Irbäck,et al. Aggregate geometry in amyloid fibril nucleation. , 2013, Physical review letters.
[45] Luigi Delle Site,et al. A pH-dependent coarse-grained model for peptides , 2012, 1212.4312.
[46] I. Coluzza. Constrained versus unconstrained folding free-energy landscapes , 2015 .
[47] D. Landau,et al. Efficient, multiple-range random walk algorithm to calculate the density of states. , 2000, Physical review letters.
[48] Gustavo Caetano-Anollés,et al. Evolutionary Optimization of Protein Folding , 2013, PLoS Comput. Biol..
[49] Joan-Emma Shea,et al. Coarse-grained models for protein aggregation. , 2011, Current opinion in structural biology.
[50] Miguel A. Soler,et al. Effects of knot type in the folding of topologically complex lattice proteins. , 2014, The Journal of chemical physics.
[51] P. Faísca,et al. The nucleation mechanism of protein folding: a survey of computer simulation studies , 2009, Journal of physics. Condensed matter : an Institute of Physics journal.
[52] Neil P King,et al. Identification of rare slipknots in proteins and their implications for stability and folding. , 2007, Journal of molecular biology.
[53] P. Faísca,et al. Why Do Protein Folding Rates Correlate with Metrics of Native Topology? , 2012, PloS one.
[54] Andreas Bracher,et al. Molecular chaperones in protein folding and proteostasis , 2011, Nature.
[55] Pietro Faccioli,et al. Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field , 2013, PLoS Comput. Biol..
[56] Miguel A. Soler,et al. How Difficult Is It to Fold a Knotted Protein? In Silico Insights from Surface-Tethered Folding Experiments , 2012, PloS one.
[57] Peter Virnau,et al. Protein knot server: detection of knots in protein structures , 2007, Nucleic Acids Res..
[58] Stefan Wallin,et al. Smooth functional transition along a mutational pathway with an abrupt protein fold switch. , 2014, Biophysical journal.
[59] Lukasz Goldschmidt,et al. Structure and folding of a designed knotted protein , 2010, Proceedings of the National Academy of Sciences.
[60] Marek Cieplak,et al. Molecular dynamics of folding of secondary structures in Go-type models of proteins , 1999, cond-mat/9911488.
[61] Rhonald C. Lua,et al. Statistics of Knots, Geometry of Conformations, and Evolution of Proteins , 2006, PLoS Comput. Biol..
[62] Marc L. Mansfield,et al. Fit to be tied , 1997, Nature Structural Biology.
[63] José N Onuchic,et al. Slipknotting upon native-like loop formation in a trefoil knot protein , 2010, Proceedings of the National Academy of Sciences.
[64] Jeffrey K Noel,et al. Energy landscape of knotted protein folding , 2012, Proceedings of the National Academy of Sciences.
[65] Karl F Freed,et al. De novo prediction of protein folding pathways and structure using the principle of sequential stabilization , 2012, Proceedings of the National Academy of Sciences.
[66] J. Onuchic,et al. Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L. , 2003, Journal of molecular biology.
[67] E. Shakhnovich,et al. Assessing the Effect of Loop Mutations in the Folding Space of β2-Microglobulin with Molecular Dynamics Simulations , 2013, International journal of molecular sciences.
[68] Diwakar Shukla,et al. To milliseconds and beyond: challenges in the simulation of protein folding. , 2013, Current opinion in structural biology.
[69] Eugene I. Shakhnovich,et al. Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus , 2000, Nature Structural Biology.
[70] Muthukumar,et al. Knottedness in ring polymers. , 1991, Physical review letters.
[71] Sophie E Jackson,et al. Untangling the folding mechanism of the 52‐knotted protein UCH‐L3 , 2009, The FEBS journal.
[72] Hiroyuki Hori,et al. Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme. , 2004, Structure.
[73] K. Dill. Theory for the folding and stability of globular proteins. , 1985, Biochemistry.
[74] D. Yee,et al. Principles of protein folding — A perspective from simple exact models , 1995, Protein science : a publication of the Protein Society.
[75] K. Dill,et al. Protein folding in the landscape perspective: Chevron plots and non‐arrhenius kinetics , 1998, Proteins.
[76] Stefan Wallin,et al. The folding mechanics of a knotted protein. , 2006, Journal of molecular biology.
[77] Akos Dobay,et al. Linear Random Knots and Their Scaling Behavior , 2005 .
[78] Carl Troein,et al. Mutation-induced fold switching among lattice proteins. , 2011, The Journal of chemical physics.
[79] J. M. Sanchez-Ruiz,et al. Protein kinetic stability. , 2010, Biophysical chemistry.
[80] William R. Taylor,et al. A deeply knotted protein structure and how it might fold , 2000, Nature.
[81] Juan Liu,et al. Respective roles of short-and long-range interactions in protein folding , 2004, Wuhan University Journal of Natural Sciences.
[82] H. Chan,et al. Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: how adequate is native-centric topological modeling? , 2002, Journal of molecular biology.
[83] Raffaello Potestio,et al. Knotted vs. Unknotted Proteins: Evidence of Knot-Promoting Loops , 2010, PLoS Comput. Biol..
[84] Youngchang Kim,et al. The active site of the SET domain is constructed on a knot , 2002, Nature Structural Biology.
[85] V. Pande,et al. Absolute comparison of simulated and experimental protein-folding dynamics , 2002, Nature.
[86] L. Mirny,et al. Evolutionary conservation of the folding nucleus. , 2000, Journal of molecular biology.
[87] P. Virnau,et al. Sequence determines degree of knottedness in a coarse-grained protein model. , 2015, Physical review letters.
[88] Sophie E Jackson,et al. Probing nature's knots: the folding pathway of a knotted homodimeric protein. , 2006, Journal of molecular biology.
[89] V. Pande,et al. On the transition coordinate for protein folding , 1998 .
[90] Marc L. Mansfield,et al. Are there knots in proteins? , 1994, Nature Structural Biology.
[91] Lidia Prieto,et al. Thermodynamics of Go-type models for protein folding. , 2005, The Journal of chemical physics.
[92] Sophie E Jackson,et al. Knot formation in newly translated proteins is spontaneous and accelerated by chaperonins. , 2012, Nature chemical biology.
[93] Rui D M Travasso,et al. The folding of knotted proteins: insights from lattice simulations , 2010, Physical biology.
[94] F. Ding,et al. Ab initio folding of proteins with all-atom discrete molecular dynamics. , 2008, Structure.
[95] C. Adams. Tales of Topology. (Book Reviews: The Knot Book. An Elementary Introduction to the Mathematical Theory of Knots.) , 1994 .
[96] P. Faísca,et al. The protein folding transition state: insights from kinetics and thermodynamics. , 2010, The Journal of chemical physics.
[97] Henri Orland,et al. Absence of knots in known RNA structures , 2015, Proceedings of the National Academy of Sciences.
[98] Robert B. Best,et al. Thermodynamics and kinetics of protein folding under confinement , 2008, Proceedings of the National Academy of Sciences.
[99] E I Shakhnovich,et al. Identification of a conserved aggregation-prone intermediate state in the folding pathways of Spc-SH3 amyloidogenic variants. , 2012, Journal of molecular biology.
[100] J. P. Garrahan,et al. The limited role of nonnative contacts in the folding pathways of a lattice protein. , 2008, Journal of molecular biology.
[101] Joanna I. Sulkowska,et al. Knotting a Protein in Explicit Solvent , 2014 .
[102] Eric J. Rawdon,et al. KnotProt: a database of proteins with knots and slipknots , 2014, Nucleic Acids Res..
[103] Joseph A. Bank,et al. Supporting Online Material Materials and Methods Figs. S1 to S10 Table S1 References Movies S1 to S3 Atomic-level Characterization of the Structural Dynamics of Proteins , 2022 .
[104] E I Shakhnovich,et al. Robustness of atomistic Gō models in predicting native-like folding intermediates. , 2012, The Journal of chemical physics.
[105] J. Richardson,et al. β-Sheet topology and the relatedness of proteins , 1977, Nature.
[106] Marek Cieplak,et al. Stabilizing effect of knots on proteins , 2008, Proceedings of the National Academy of Sciences.
[107] K. Dill,et al. The Protein-Folding Problem, 50 Years On , 2012, Science.
[108] Marta Enciso,et al. A refined hydrogen bond potential for flexible protein models. , 2010, The Journal of chemical physics.
[109] Sophie E Jackson,et al. A comparison of the folding of two knotted proteins: YbeA and YibK. , 2007, Journal of molecular biology.
[110] Miguel A. Soler,et al. Effects of Knots on Protein Folding Properties , 2013, PloS one.
[111] Eric J. Rawdon,et al. Conservation of complex knotting and slipknotting patterns in proteins , 2012, Proceedings of the National Academy of Sciences.
[112] F. Hartl,et al. Converging concepts of protein folding in vitro and in vivo , 2009, Nature Structural &Molecular Biology.
[113] Michele Vendruscolo,et al. Prediction of aggregation-prone regions in structured proteins. , 2008, Journal of molecular biology.
[114] J Günter Grossmann,et al. Knotted fusion proteins reveal unexpected possibilities in protein folding. , 2008, Molecular cell.
[115] Gerhard Hummer,et al. Native contacts determine protein folding mechanisms in atomistic simulations , 2013, Proceedings of the National Academy of Sciences.
[116] Stuart G. Whittington,et al. Entanglement complexity of self-avoiding walks , 1992 .
[117] Joanna I. Sulkowska,et al. A Stevedore's Protein Knot , 2010, PLoS Comput. Biol..
[118] Jianyin Shao,et al. Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms. , 2007, Journal of chemical theory and computation.