The folding of knotted proteins: Insights from lattice simulations

Physical Biology

Volumn 7, Issue 1, 2010, Pages

  Faísca, Patrícia F N ^a   Travasso, Rui D M ^b   Charters, Tiago ^c   Nunes, Ana ^a,d   Cieplak, Marek ^e  

^a Centro de Fisica da Materia Condensada   (Portugal)

^b UNIVERSITY OF COIMBRA   (Portugal)

^c INSTITUTO SUPERIOR DE ENGENHARIA DE LISBOA   (Portugal)

^d UNIVERSITY OF LISBON   (Portugal)

^e INSTITUTE OF PHYSICS   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

LOTUS;

PROTEIN;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; KINETICS; MOLECULAR DYNAMICS; MONTE CARLO METHOD; PROTEIN FOLDING; THERMODYNAMICS;

KINETICS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MONTE CARLO METHOD; PROTEIN FOLDING; PROTEINS; THERMODYNAMICS;

EID: 77949803585     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/7/1/016009     Document Type: Article

References (46)

1. Mansfield M 1997 Fit to be tied Nat. Struct. Biol. 4 166-7
2. Koniaris K and Muthukumar M 1991 Knottedness in ring polymers Phys. Rev. Lett. 66 2211-4
3. Taylor W 2000 A deeply knotted structure and how it might fold Nature 406 916-9
4. Virnau P, Mirny M A and Kardar M A 2006 Intricate knots in proteins: function and evolution PloS Comput. Biol. 2 1074-9
5. King N P, Yeates E O and Yeates T O 2007 Identification of rare slipknots in proteins and their implications for stability and folding J. Mol. Biol. 373 153-66
6. Mansfield M 1994 Are there knots in proteins Nat. Struct. Biol. 1 213-4
7. Yeats T O, Norcross T S and King N P 2007 Knotted and topologically complex proteins as models for studying folding and stability Curr. Opin. Chem. Biol. 11 595-603
8. Mallam A L, Morris E L and Jackson S E 2008 Exploring knotting mechanisms in protein folding Proc. Natl Acad. Sci. USA 105 18740-5
9. Mallam A L, Onuoha S C and Jackson S E 2008 Knotted fusion proteins reveal unexpected possibilities in protein folding Mol. Cell 30 642-8
10. Taylor W 2007 Geometry knots and fold complexity: some new twists Comput. Biol. Chem. 31 151-62
11. Mallam A L and Jackson S E 2007 Probing nature's knots: the folding pathway of a knotted homodimeric protein J. Mol. Biol. 359 1420-36
12. Wallin S, Zeldovich K B and Shakhnovich E I 2007 Folding mechanics of a knotted protein J. Mol. Biol. 368 884-93
13. Sulkowska J I, Sulkowski P and Onuchic J 2008 Dodging the crisis of folding proteins with knots Proc. Natl Acad. Sci. USA 9 3119-24
14. Sulkowska J, Sulkowski P and Cieplak M 2008 Stabilizing effect of knots on proteins Proc. Natl Acad. Sci. USA 105 19714-9
15. Lua R C and Grosberg A Y 2006 Statistics of knots, geometry of conformations and evolution of proteins PloS Comput. Biol. 2 350-7
16. Sulkowska J I, Sulkowski P, Szymczak P and Cieplak M 2008 Tightening of knots in proteins Phys. Rev. Lett. 100 058106
17. Dzubiella J 2009 Sequence-specific size, structure, and stability of tight geometry knots Biophys. J. 96 19
18. Gō N and Taketomi H 1978 Respective roles of short- and long-range interactions in protein folding Proc. Natl Acad. Sci. 75 559-3
19. Metropolis N, Rosenbluth A W, Rosenbluth M N, Teller A H and Teller E 1953 Equation of state calculations by fast computing machines J. Chem. Phys. 21 1087-92
20. Landau D P and Binder K 2000 A Guide to Monte Carlo Simulations in Statistical Physics (Cambridge: Cambridge University Press)
21. Chan H S and Dill K A 1993 Energy landscapes and the collapse dynamics of homopolymers J. Chem. Phys. 99 2116-27
22. Chan H S and Dill K A 1994 Transition states and folding dynamics of proteins and heteropolymers J. Chem. Phys. 100 9238-57
23. Oliveberg M, Tan Y and Fersht A R 1995 Negative activation enthalpies in the kinetics of protein folding Proc. Natl Acad. Sci. USA 92 8926-9
24. Gutin A, Sali A, Abkevich V, Karplus M and Shakhnovich E I 1998 Temperature dependence of the folding rate in a simple protein model: search for a 'glass' transition J. Chem. Phys. 108 6466-83
25. Cieplak M, Hoang T X and Li M S 1999 Scaling of folding properties in simple models of proteins Phys. Rev. Lett. 83 1684-7
26. Faisca P F N and Ball R C 2002 Thermodynamic control and dynamical regimes in protein folding J. Chem. Phys. 116 7231-8
27. Plaxco K W, Simmons K T, Ruczinski I and Baker D 2000 Topology, stability, sequence and length: defining the determinants of two-state protein folding kinetics Biochemistry 39 11177-83
28. Adams C 2004 The Knot Book: An Elementary Introduction to the Mathematical Theory of Knot (Providence, RI: American Mathematical Society)
29. Liu Z and Chan H S 2008 Efficient chain moves for Monte Carlo simulations of a wormlike DNA model: excluded volume, supercoils, site juxtapositions, knots, and comparisons with random-flight and lattice models J. Chem. Phys. 128 145104
30. Millett K, Dobay A and Stasiak A 2005 Linear random knots and their scaling behavior Macromolecules 38 601-6
31. Kolesov G, Virnau P, Kardar M A and Mirny L A 2007 Protein knot server: detection of knots in protein structures Nucleic Acids Res. 35 W425-8
32. Lua R, Borovinskiy A L and Grosberg A Yu 2004 Fractal and statistical properties of large compact polymers: a computational study Polymer 45 717-31
33. Du R, Pande V S, Grosberg A Y, Tanaka T and Shakhnovich E S 1998 On the transition coordinate for protein folding J. Chem. Phys. 108 334-50
34. Hubner I A, Shimada J and Shakhnovich E I 2004 Commitment and nucleation in the protein G transition state J. Mol. Biol. 336 745-61
35. Travasso R D M, Faisca P F N and Gama M M T 2007 Nucleation phenomena in protein folding: the modulating role of protein sequence J. Phys.: Condens. Mater. 19 285212
36. Faisca P F N, Travasso R D M, Ball R C and Shakhnovich E I 2008 Identifying critical residues in protein folding: insights from Φ-value and Pfold analysis J. Chem. Phys. 129 095108
37. Hubner I A, Deeds E J and Shakhnovich E I 2006 Understanding ensemble protein folding at atomic detail Proc. Natl Acad. Sci. USA 103 17747-52
38. Abkevich V I, Gutin A M and Shakhnovich E I 1995 Impact of local and non-local interactions on thermodynamics and kinetics of protein folding J. Mol. Biol. 252 460-71
39. Shakhnovich E and Gutin A 1993 Engineering of stable and fast-folding sequences of model proteins Proc. Natl Acad. Sci. USA 90 7195-9
40. Makhatadze G I and Privalov P L 1995 Energetics of protein structure Adv. Protein Chem. 47 307-9
41. Faisca P F N and Plaxco K W 2006 Cooperativity and the origins of rapid, single-exponential kinetics Prot. Sci. 15 1608-18
42. Cieplak M and Hoang T X 2003 Universality classes in folding times of proteins Biophys. J. 84 475-88
43. Cieplak M, Hoang T X and Robbins M O 2002 Thermal folding and mechanical unfolding pathways of protein secondary structures Proteins: Funct., Struct. Genetics 49 104-13
44. Cieplak M and Sulkowska J I 2005 Thermal unfolding of proteins J. Chem. Phys. 123 194908
45. Kaya H and Chan H S 2005 Explicit-chain model of native-state hydrogen exchange: implications for event ordering and cooperativity in protein folding Proteins 58 31-44
46. Gosavi S, Chavez L L, Jennings P A and Onuchic J N 2006 Topological frustration and the folding of interleukin-1 beta J. Mol. Biol. 357 986-96