Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field

PLoS Computational Biology

Volumn 9, Issue 3, 2013, Pages

  a Beccara, Silvio ^a   Škrbić, Tatjana ^a   Covino, Roberto ^b,c   Micheletti, Cristian ^d   Faccioli, Pietro ^b,c  

^a FONDAZIONE BRUNO KESSLER   (Italy)

^b UNIVERSITY OF TRENTO   (Italy)

^c INFN TIFPA   (Italy)

^d IOM CNR LABORATORIO TASC   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID INTERACTIONS; AMINO-ACIDS; ATOMISTIC SIMULATIONS; ATOMISTICS; FOLDING PATHWAY; FOLDINGS; FORCEFIELDS; NATIVE TOPOLOGY; NATIVE-CENTRIC MODELS; REACTION PATHWAYS;

PROTEINS;

KNOTTED PROTEIN MJ0366; PEPTIDES AND PROTEINS; UNCLASSIFIED DRUG;

ARTICLE; BETA SHEET; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; CRYSTAL STRUCTURE; DOMINANT REACTION PATHWAY; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR MODEL; PHYSICAL PHENOMENA; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN KNOTTING; PROTEIN STRUCTURE; PROTEIN UNFOLDING; REALISTIC ATOMISTIC FORCE FIELD; STRUCTURE ANALYSIS;

EID: 84876001589     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003002     Document Type: Article

References (38)

1. Yeates TO, Norcross TS, King NP, (2007) Knotted and topologically complex proteins as models for studying folding and stability. Curr Opin Chem Biol 11: 595-603.
2. Taylor WR, (2007) Protein knots and fold complexity: some new twists. Comput Biol Chem 31: 151-162.
3. Mallam AL, (2009) How does a knotted protein fold? FEBS J 276: 365-375.
4. Virnau P, Mallam A, Jackson S, (2011) Structures and folding pathways of topologically knotted proteins. J Phys Condens Matter 23: 033101-033101.
5. Lua RC, Grosberg AY, (2006) Statistics of knots, geometry of conformations, and evolution of proteins. PLoS Comput Biol 2: e45.
6. Potestio R, Micheletti C, Orland H, (2010) Knotted vs. unknotted proteins: evidence of knotpromoting loops. PLoS Comput Biol 6: e100864.
7. Eriksson AE, Jones TA, Liljas A, (1988) Refined structure of human carbonic anhydrase II at 2.0 A resolution. Proteins 4: 274-282.
8. Mansfield ML, (1994) Are there knots in proteins? Nat Struct Biol 1: 213-214.
9. King NP, Jacobitz AW, Sawaya MR, Goldschmidt L, Yeates TO, (2010) Structure and folding of a designed knotted protein. Proc Natl Acad Sci U S A 107: 20732-20737.
10. Mallam AL, Jackson SE, (2012) Knot formation in newly translated proteins is spontaneous and accelerated by chaperonins. Nat Chem Biol 8: 147-153.
11. Sulkowska JI, Sulkowski P, Onuchic J, (2009) Dodging the crisis of folding proteins with knots. Proc Natl Acad Sci U S A 106: 3119-3124.
12. Noel JK, Sulkowska JI, Onuchic JN, (2010) Slipknotting upon native-like loop formation in a trefoil knot protein. Proc Natl Acad Sci U S A 107: 15403-15408.
13. Wallin S, Zeldovich KB, Shakhnovich EI, (2007) The folding mechanics of a knotted protein. J Mol Biol 368: 884-893.
14. Škrbić T, Micheletti C, Faccioli P, (2012) The role of non-native interactions in the folding of knotted proteins. PLoS Comput Biol 8: e1002504.
15. Wang J, Cieplak P, Kollman P, (2000) How well does a restrained electrostatic potential (resp) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 21: 1049.
16. Beccara S, Škrbić T, Covino R, Faccioli P, (2012) Dominant folding pathways of a WW domain. Proc Natl Acad Sci U S A 109: 2330-2335.
17. Shaw DE, Maragakis P, Lindorff-Larsen K, Piana S, Dror RO, et al. (2010) Atomic-Level Characterization of the Structural Dynamics of Proteins. Science 330: 341-346.
18. Paci E, Karplus M, (1999) Forced unfolding of fibronectin type 3 modules: An analysis by biased molecular dynamics simulations. J Mol Biol 288: 441-459.
19. Camilloni C, Broglia RA, Tiana G, (2011) Hierarchy of folding and unfolding events of protein G, CI2, and ACBP from explicit-solvent simulations. J Chem Phys 134: 045105-045105.
20. Faccioli P, Sega M, Pederiva F, Orland H, (2006) Dominant pathways in protein folding. Phys Rev Lett 97: 108101-108101.
21. Sega M, Faccioli P, Pederiva F, Garberoglio G, Orland H, (2007) Quantitative protein dynamics from dominant folding pathways. Phys Rev Lett 99: 118102-118102.
22. Autieri E, Faccioli P, Sega M, Pederiva F, Orland H, (2009) Dominant reaction pathways in highdimensional systems. J Chem Phys 130: 064106-064106.
23. Mazzola G, Beccara SA, Faccioli P, Orland H, (2011) Fluctuations in the ensemble of reaction pathways. J Chem Phys 134: 164109-164109.
24. Krivov SV, (2011) The free energy landscape analysis of protein (fip35) folding dynamics. The journal of physical chemistry B 115: 12315-24.
25. Bölinger D, Sulkowska JI, Hsu HP, Mirny LA, Kardar M, et al. (2010) A stevedore's protein knot. PLoS Comput Biol 6: e1000731.
26. Hess B, Kutzner C, van der Spoel D, Lindahl E, (2008) Gromacs 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theor Comput 4: 435-447.
27. Onufriev A, Bashford D, Case DA, (2004) Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins 55: 383-394.
28. Schaefer M, Bartels C, Karplus M, (1998) Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model. J Mol Biol 284: 835-848.
29. Kim YC, Hummer G, (2008) Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding. J Mol Biol 375: 1416-1433.
30. Best RB, Hummer G, (2010) Coordinate-dependent diffusion in protein folding. Proc Natl Acad Sci U S A 107: 1088-1093.
31. Karanicolas J, Brooks CL, (2004) Integrating folding kinetics and protein function: biphasic kinetics and dual binding specificity in a WW domain. Proc Natl Acad Sci U S A 101: 3432-3437.
32. Quake SR, (1995) Fast Monte Carlo algorithms for knotted polymers. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 52: 1176-1180.
33. Kremer K, Binder K, (1988) Simulation of lattice models for macromolecules. Comput Phys Rep 7: 259-310.
34. Jorgensen W, Tirado-Rives J, (1996) Monte Carlo vs molecular dynamics for conformational sampling. J Phys Chem 100: 14508-14513.
35. Sulkowska JI, Noel JK, Onuchic JN, (2012) Energy landscape of knotted protein folding. Proc Natl Acad Sci U S A 109: 17783-8.
36. Tubiana L, Orlandini E, Micheletti C, (2011) Probing the entanglement and locating knots in ring polymers: a comparative study of different arc closure schemes. Progress of Theoretical Physics Supplement 191: 192-204.
37. Tubiana L, Orlandini E, Micheletti C, (2011) Multiscale entanglement in ring polymers under spherical confinement. Phys Rev Lett 107: 188302-188302.
38. Humphrey W, Dalke A, Schulten K, (1996) VMD: visual molecular dynamics. J Mol Graph 14: 33-38.