Thermal effects in stretching of Go-like models of titin and secondary structures

Proteins: Structure, Function and Genetics

Volumn 56, Issue 2, 2004, Pages 285-297

  Cieplak, Marek ^a,b   Hoang, Trinh Xuan ^c,d   Robbins, Mark O ^b  

^a INSTITUTE OF PHYSICS   (Poland)

^b JOHNS HOPKINS UNIVERSITY   (United States)

^c ABDUS SALAM INTERNATIONAL CENTRE FOR THEORETICAL PHYSICS   (Italy)

^d INSTITUTE OF PHYSICS   (Viet Nam)

Author keywords

Go model; Mechanical stretching of proteins; Molecular dynamics; Protein folding; Titin

Indexed keywords

CONNECTIN;

ARTICLE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; TEMPERATURE;

COMPUTER SIMULATION; HUMANS; MODELS, MOLECULAR; MUSCLE PROTEINS; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN KINASES; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; TEMPERATURE;

JONES;

EID: 3042806394     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20081     Document Type: Article

References (49)

1. Labeit S, Barlow DP, Gautel M, Gibson T, Holt J, Hsieh CL, Francke U, Leonard K, Wardale J, Whiting A, Trinick J. A regular pattern of 2 types of 100-residue motif in the sequence of titin. Nature 1990;345:273-276.
2. Erickson HP. Stretching single protein molecules: titin is a weird spring. Science 1997;276:1090-1090.
3. Labeit S, Kolmerer B. Titins-giant proteins in charge of muscle ultrastructure and elasticity. Science 1995;270:293-296.
4. Linke WA, Ivemeyer M, Olivieri N, Kolmerer B, Ruegg JC, Labeit S. Towards a molecular understanding of the elasticity of titin. J Mol Biol 1996;261:62-71.
5. Granzier H, Helmes M, Trombitas K. Nonuniform elasticity of titin in cardiac myocytes: a study using immunoelectron microscopy and cellular mechanics. Biophys J 1996;70:430-442.
6. Improta S, Politou AS, Pastore A. Immunoglobulin-like modules from titin I-band: extensible components of muscle elasticity. Structure 1996;4:323-327.
7. Mayans O, Wuerges J, Gautel M, Wilmans M. Structural evidence for a possible role of reversible disulfide bridge formation in elasticity of the muscle protein titin. Structure 2001;9:331-340.
8. Pfuhl M, Pastore A. Tertiary structure of an Ig-like domain from a giant muscle protein titin: a new member of the I set. Structure 1995;3:391-401.
9. Muhle-Goll C, Pastore A, Nilges M. The 3D structure of a type I module from titin: a prototype of intracellular fibronectin type III domains. Structure 1998;6:1291-1302.
10. Wilmann M, Gautel M, Mayans O. Activation of calcium/calmodulin regulated kinases. Cell Mol Biol 2000;46:883-894.
11. Tskhovrebova L, Trinick K, Sleep JA, Simmons M. Elasticity and unfolding of single molecules of the giant muscle protein titin. Nature 1997;387:308-312.
12. Kellermayer MSZ, Smith SB, Granzier HL, Bustamante C. Folding-unfolding in single titin molecules characterized with laser tweezers. Science 1997;276:1112-1116.
13. Rief M, Gautel M, Oesterhelt F, Fernandez JM, Gaub HE. Reversible unfolding of individual titin immunoglobulin domains by AFM. Science 1997;276:1109-1112.
14. Marszalek PE, Lu H, Li HB, Carrion-Vazquez M, Oberhauser AF, Schulten K, Fernandez JM. Mechanical unfolding intermediates in titin modules. Nature 1999;402:100-103.
15. Carrion-Vasquez M, Oberhauser AF, Fowler SB, Marszalek PE, Broedel SE, Clarke J, Fernandez JM. Mechanical and chemical unfolding of a single protein: a comparison. Proc Natl Acad Sci USA 1999;96:3694-3699.
16. Oberhauser AF, Hansma PK, Carrion-Vazquez M, Fernandez JM. Stepwise unfolding of titin under force-clamp atomic force microscopy. Proc Natl Acad Sci USA 2001;98:468-472.
17. Oberhauser AF, Marszalek PE, Carrion-Vazquez M, Fernandez JM. Single protein misfolding events captured by atomic force microscopy. Nat Struct Biol 1999;6:1025-1028.
18. Smith BL, Schaeffer TE, Viani M, Thompson JB, Frederic NA, Kindt J, Belcher A, Stucky GD, Morse DE, Hansma PK. Molecular mechanistic origin of the toughness of natural adhesives, fibres and compsites. Nature 1999;399:761-763.
19. Brockwell DJ, Beddard GS, Clarkson J, Zinober RC, Blake AW, Trinick J, Olmsted PD, Smith DA, Radford SE. The effect of core destabilization on the mechanical resistance of 127. Biophys J 2002;83:458-472.
20. Zinober RC, Brockwell DJ, Beddard GS, Blake AW, Olmsted PD, Radford SE, Smith DA. Mechanically unfolding proteins: The effect of unfolding history and the supermolecular scaffold. Protein Sci 2002;11:2759-2765.
21. Cieplak M, Hoang TX, Robbins MO. Folding and stretching in a Go-like model of titin, Proteins 2002;49:114-124.
22. Lu H, Isralewitz B, Krammer A, Vogel V, Schulten K. Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. Biophys J 1998;75:662-671.
23. Lu H, Schulten K. Steered molecular dynamics simulation of conformational changes of immunoglobulin domain I27 interprete atomic force microscopy observations. Chem Phys 1999;247:141-153.
24. Fowler SB, Best RB, Toca Herrera JL, Rutherford TJ, Steward A, Paci E, Karplus M, Clarke J. Mechanical unfolding of a titin Ig domain: structure of unfolding intermediate revealed by combining AFM, molecular dynamics simulations, NMR and protein engineering. J Mol Biol 2002;322:841-849.
25. Abe H, Go N. Noninteracting local-structure model of folding and unfolding transition in globular proteins: II. Application to two-dimensional lattice proteins. Biopolymers 1981;20:1013-1031.
26. Takada S. Go-ing for the prediction of protein folding mechanism. Proc Natl Acad Sci USA 1999;96:11698-11700.
27. Cieplak M, Hoang TX, Robbins MO. Thermal folding and mechanical unfolding pathways of protein secondary structures. Proteins 2002;49:104-113.
28. Doi M, Edwards SF. The theory of polymer dynamics. Oxford University Press; Oxford, UK: 1989.
29. Marko JF, Siggia ED. Stretching DNA. Macromolecules 1995;28: 8759-8770.
30. Hoang TX, Cieplak M. Molecular dynamics of folding of secondary structures in Go-like models of proteins. J Chem Phys 2000;112: 6851-6862.
31. Hoang TX, Cieplak M. Sequencing of folding events in Go-like proteins. J Chem Phys 2001;113:8319-8328.
32. Cieplak M, Hoang TX. Kinetics non-optimality and vibrational stability of proteins. Proteins 2001;44:20-25.
33. Cieplak M, Hoang TX. Universality classes in folding times of proteins. Biophys J 2003;84:475-488.
34. Tsai J, Taylor R, Chothia C, Gerstein M. The packing density in proteins: standard radii and volumes. J Mol Biol 1999;290:253-266.
35. Cieplak M, Hoang TX. The range of contact interactions and the kinetics of the Go models of proteins. Int J Mod Phys C 2002;13: 1231-1242 and http://arxiv.org/abs/cond-mat/0206299
36. Bernstein FC, Koetzle TF, Williams GJB, Meyer Jr. EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542.
37. Streyer L. Biochemistry. 4th edition. New York: W. H. Freeman; 1995.
38. Grest GS, Kremer K. Molecular dynamics simulation for polymers in the presence of a heat bath. Phys Rev A 1986;33:3628-3631.
39. Veitshans T, Klimov D, Thirumalai D. Protein folding kinetics: time scales, pathways and energy landscapes in terms of sequence-dependent properties. Folding Des 1997;2:1-22.
40. Williams PM, Fowler SB, Best RB, Toca-Herrera JL, Scott KA, Steward A, Clarke J. Hidden complexity in the mechanical properties of titin. Nature 2003;422:446-449.
41. Clementi C, Nymeyer H, Onuchic JN. Topological and energetic factors: what determines the structural details of the transition state ensemble and "on-route" intermediates for protein folding?: an investigation for small globular proteins. J Mol Biol 2000;298: 937-953.
42. Cieplak M, Hoang TX, Robbins MO. Stretching of proteins in the entropic limit. Phys Rev E 2004;69, 011912.
43. Cieplak M, Hoang TX, Li MS. Scaling of folding properties in simple models of proteins. Phys Rev Lett 1999;83:1684-1687.
44. Paci E, Karplus M. Unfolding proteins by external forces and temperature: the importance of topology and energetics. Proc Natl Acad Sci USA 2000;97:6521-6526.
45. Fowler SB, Clarke J. Mapping the folding pathway of animmunoglobulin domain: structural detail from the phi value analysis and movement of the transition state. Structure 2001;9:355-366.
46. Best RB, Fowler SB, Herrera JLT, Steward A, Paci E, Clarke J. Mechanical unfolding of a titin Ig domain: structure of transition state revealed by combining atomic force microscopy, protein engineering and molecular dynamics simulations. J Mol Biol 2003;330:867-877.
47. Yang G, Cecconi C, Baase WA, Vetter IR, Breyer WA, Haack JA, Matthews BW, Dahlquist FW, Bustamante C. Solid-state synthesis and mechanical unfolding of polymers of T4 lysozyme. Proc Nat Acad Sci USA 2000;97:139-144.
48. Makarov D, Hansma PK, Metiu H. Kinetic Monte Carlo simulation of titin unfolding. J Chem Phys 2001;114:9663-9673.
49. Evans E. Probing the relation between force-lifetime-and chemistry in single molecular bonds. Annu Rev Biophys Biomol Struct 2001;30:105-128.