The exclusive effects of chaperonin on the behavior of proteins with 52 knot

The folding of proteins with a complex knot is still an unresolved question. Based on representative members of Ubiquitin C-terminal Hydrolases (UCHs) that contain the 52 knot in the native state, we explain how UCHs are able to unfold and refold in vitro reversibly within the structure-based model. In particular, we identify two, topologically different folding/unfolding pathways and corroborate our results with experiment, recreating the chevron plot. We show that confinement effect of chaperonin or weak crowding greatly facilitates folding, simultaneously slowing down the unfolding process of UCHs, compared with bulk conditions. Finally, we analyze the existence of knots in the denaturated state of UCHs. The results of the work show that the crowded environment of the cell should have a positive effect on the kinetics of complex knotted proteins, especially when proteins with deeper knots are found in this family.

[1]  Shang-Te Danny Hsu,et al.  The Knotted Protein UCH-L1 Exhibits Partially Unfolded Forms under Native Conditions that Share Common Structural Features with Its Kinetic Folding Intermediates. , 2016, Journal of molecular biology.

[2]  A I Jewett,et al.  Accelerated folding in the weak hydrophobic environment of a chaperonin cavity: creation of an alternate fast folding pathway. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Wim J. N. Meester,et al.  Structure of the Ubiquitin Hydrolase UCH-L3 Complexed with a Suicide Substrate* , 2005, Journal of Biological Chemistry.

[4]  I. Szleifer,et al.  MONTE CARLO SIMULATIONS OF CHAIN MOLECULES IN CONFINED ENVIRONMENTS , 1995 .

[5]  H. Nemoto,et al.  PGP 9 . 5 Methylation as a Marker for Metastatic Colorectal Cancer , 2009 .

[6]  D W Sumners,et al.  Knotting of random ring polymers in confined spaces. , 2006, The Journal of chemical physics.

[7]  K D Wilkinson,et al.  The neuron-specific protein PGP 9.5 is a ubiquitin carboxyl-terminal hydrolase. , 1989, Science.

[8]  Cristian Micheletti,et al.  Molecular Crowding Increases Knots Abundance in Linear Polymers , 2015 .

[9]  Ishtiaq Rehman,et al.  Human prostate cancer cells express neuroendocrine cell markers PGP 9.5 and chromogranin A , 2007, The Prostate.

[10]  J. Onuchic,et al.  Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins. , 2000, Journal of molecular biology.

[11]  K. Dill,et al.  Modeling the effects of mutations on the denatured states of proteins , 1992, Protein science : a publication of the Protein Society.

[12]  Hiroshi Nakayama,et al.  PGP9.5 overexpression in esophageal squamous cell carcinoma. , 2003, Hepato-gastroenterology.

[13]  Miguel A. Soler,et al.  Effects of knot type in the folding of topologically complex lattice proteins. , 2014, The Journal of chemical physics.

[14]  Szymon Niewieczerzal,et al.  Knotting and unknotting proteins in the chaperonin cage: Effects of the excluded volume , 2017, PloS one.

[15]  Carsten Kutzner,et al.  GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.

[16]  Neil P King,et al.  Protein stabilization in a highly knotted protein polymer. , 2011, Protein engineering, design & selection : PEDS.

[17]  Shang-Te Danny Hsu,et al.  The effect of Parkinson's-disease-associated mutations on the deubiquitinating enzyme UCH-L1. , 2011, Journal of molecular biology.

[18]  Miguel A. Soler,et al.  Steric confinement and enhanced local flexibility assist knotting in simple models of protein folding. , 2016, Physical chemistry chemical physics : PCCP.

[19]  Robert B. Best,et al.  Thermodynamics and kinetics of protein folding under confinement , 2008, Proceedings of the National Academy of Sciences.

[20]  Shoji Takada,et al.  How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: Molecular simulations , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[21]  Tetsuo Deguchi,et al.  A Statistical Study of Random Knotting Using the Vassiliev Invariants , 1994 .

[22]  Ryan L. Hayes,et al.  SMOG 2: A Versatile Software Package for Generating Structure-Based Models , 2016, PLoS Comput. Biol..

[23]  Antonio Suma,et al.  How to fold intricately: using theory and experiments to unravel the properties of knotted proteins. , 2016, Current opinion in structural biology.

[24]  Marek Cieplak,et al.  Stabilizing effect of knots on proteins , 2008, Proceedings of the National Academy of Sciences.

[25]  Shang-Te Danny Hsu,et al.  Folding analysis of the most complex Stevedore’s protein knot , 2016, Scientific Reports.

[26]  Pawel Dabrowski-Tumanski,et al.  In Search of Functional Advantages of Knots in Proteins , 2016, PloS one.

[27]  Marek Cieplak,et al.  Cotranslational folding of deeply knotted proteins , 2015, Journal of physics. Condensed matter : an Institute of Physics journal.

[28]  Rhonald C. Lua,et al.  Statistics of Knots, Geometry of Conformations, and Evolution of Proteins , 2006, PLoS Comput. Biol..

[29]  C. Chothia,et al.  The Packing Density in Proteins: Standard Radii and Volumes , 1999 .

[30]  Sophie E Jackson,et al.  Knot formation in newly translated proteins is spontaneous and accelerated by chaperonins. , 2012, Nature chemical biology.

[31]  K A Dill,et al.  Stabilization of proteins in confined spaces. , 2001, Biochemistry.

[32]  Pietro Faccioli,et al.  The Role of Non-Native Interactions in the Folding of Knotted Proteins: Insights from Molecular Dynamics Simulations , 2013, Biomolecules.

[33]  José N Onuchic,et al.  Slipknotting upon native-like loop formation in a trefoil knot protein , 2010, Proceedings of the National Academy of Sciences.

[34]  Narayanan Eswar,et al.  Protein structure modeling with MODELLER. , 2008, Methods in molecular biology.

[35]  Joanna I. Sulkowska,et al.  Knotting a Protein in Explicit Solvent , 2014 .

[36]  Kenji Hibi,et al.  PGP9.5 methylation as a marker for metastatic colorectal cancer. , 2008, Anticancer research.

[37]  Joanna I. Sulkowska,et al.  A Stevedore's Protein Knot , 2010, PLoS Comput. Biol..

[38]  Jozef H. Przytycki,et al.  Invariants of links of Conway type , 1988, 1610.06679.

[39]  Eric J. Rawdon,et al.  KnotProt: a database of proteins with knots and slipknots , 2014, Nucleic Acids Res..

[40]  Sophie E Jackson,et al.  Characterization of the Folding of a 52-Knotted Protein Using Engineered Single-Tryptophan Variants. , 2016, Biophysical journal.

[41]  Xi-Zhong Shen,et al.  High expression of UCH37 is significantly associated with poor prognosis in human epithelial ovarian cancer , 2014, Tumor Biology.

[42]  Stefan Wallin,et al.  The folding mechanics of a knotted protein. , 2006, Journal of molecular biology.

[43]  Jun Wang,et al.  Folding behavior of chaperonin‐mediated substrate protein , 2005, Proteins.

[44]  René Bernards,et al.  A Genomic and Functional Inventory of Deubiquitinating Enzymes , 2005, Cell.

[45]  Xijia Miao,et al.  Gene expression changes during HPV‐mediated carcinogenesis: A comparison between an in vitro cell model and cervical cancer , 2008, International journal of cancer.

[46]  Rieko Setsuie,et al.  The functions of UCH-L1 and its relation to neurodegenerative diseases , 2007, Neurochemistry International.

[47]  Kenneth C. Millett,et al.  A new polynomial invariant of knots and links , 1985 .

[48]  D W Sumners,et al.  Simulations of knotting in confined circular DNA. , 2008, Biophysical journal.

[49]  Joan-Emma Shea,et al.  Reconciling theories of chaperonin accelerated folding with experimental evidence , 2009, Cellular and Molecular Life Sciences.

[50]  Shoji Takada,et al.  Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2ouf-knot , 2012, Proceedings of the National Academy of Sciences.

[51]  Shinzaburo Noguchi,et al.  High expression of ubiquitin carboxy‐terminal hydrolase‐L1 and ‐L3 mRNA predicts early recurrence in patients with invasive breast cancer , 2006, Cancer science.

[52]  Vijay S Pande,et al.  Protein folding under confinement: A role for solvent , 2007, Proceedings of the National Academy of Sciences.

[53]  A. Nakao,et al.  PGP9.5 as a prognostic factor in pancreatic cancer. , 2000, Clinical cancer research : an official journal of the American Association for Cancer Research.

[54]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[55]  Juan J de Pablo,et al.  Confinement effects on the thermodynamics of protein folding: Monte Carlo simulations. , 2006, Biophysical journal.

[56]  Eric J. Rawdon,et al.  Conservation of complex knotting and slipknotting patterns in proteins , 2012, Proceedings of the National Academy of Sciences.

[57]  Shang-Te Danny Hsu,et al.  Backbone assignments of the 26 kDa neuron-specific ubiquitin carboxyl-terminal hydrolase L1 (UCH-L1) , 2010, Biomolecular NMR assignments.

[58]  A. Pühler,et al.  Molecular systems biology , 2007 .

[59]  Kenneth C. Millett,et al.  A LOAD BALANCED ALGORITHM FOR THE CALCULATION OF THE POLYNOMIAL KNOT AND LINK INVARIANTS , 1991 .

[60]  Aakrosh Ratan,et al.  Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2 ouf-knot , 2012 .

[61]  Marek Cieplak,et al.  Selection of optimal variants of Gō-like models of proteins through studies of stretching. , 2008, Biophysical journal.

[62]  José N Onuchic,et al.  Knotting pathways in proteins. , 2013, Biochemical Society transactions.

[63]  Shang-Te Danny Hsu,et al.  Entropic stabilization of a deubiquitinase provides conformational plasticity and slow unfolding kinetics beneficial for functioning on the proteasome , 2017, Scientific Reports.

[64]  Piotr Sułkowski,et al.  Dodging the crisis of folding proteins with knots , 2009, Proceedings of the National Academy of Sciences.

[65]  Matthias Rief,et al.  Knotting and unknotting of a protein in single molecule experiments , 2016, Proceedings of the National Academy of Sciences.

[66]  A. Sali,et al.  Statistical potential for assessment and prediction of protein structures , 2006, Protein science : a publication of the Protein Society.

[67]  Everett A Lipman,et al.  Single-molecule spectroscopy of protein folding in a chaperonin cage , 2010, Proceedings of the National Academy of Sciences.

[68]  T Takano,et al.  PGP9.5 mRNA could contribute to the molecular-based diagnosis of medullary thyroid carcinoma. , 2004, European journal of cancer.

[69]  Sophie E Jackson,et al.  Untangling the folding mechanism of the 52‐knotted protein UCH‐L3 , 2009, The FEBS journal.