Simulation of the thermodynamics of folding and unfolding of the Trp-cage mini-protein TC5b using different combinations of force fields and solvation models

Science China Chemistry

Volumn 53, Issue 1, 2010, Pages 196-201

  Duan, Lili ^b   Mei, Ye ^a   Li, Yongle ^c   Zhang, Qinggang ^b   Zhang, Dawei ^d   Zhang, John Zenghui ^a,e  

^a EAST CHINA NORMAL UNIVERSITY   (China)

^b SHANDONG NORMAL UNIVERSITY   (China)

^c NANJING UNIVERSITY   (China)

^d Nanyang Technological University   (Singapore)

^e NEW YORK UNIVERSITY   (United States)

Author keywords

Folding and unfolding; Implicit solvation; Melting curve; Replica exchange; TC5b; Trp cage

Indexed keywords

AMBER FORCE-FIELD; EXPERIMENTAL VALUES; FORCE FIELDS; GENERALIZED BORN MODELS; IMPLICIT SOLVATION; MELTING CURVES; MELTING TEMPERATURES; MOLECULAR DYNAMICS SIMULATIONS; SIMULATION TIME; SOLVATION MODELS; THERMODYNAMIC PROFILES;

BIOLOGY; MELTING POINT; METAL MELTING; MOLECULAR DYNAMICS; PROTEINS; SYNTHESIS (CHEMICAL); THERMODYNAMIC PROPERTIES;

SOLVATION;

EID: 76449085514     PISSN: 16747291     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11426-009-0196-7     Document Type: Article

References (36)

1. J.W. Neidigh R.M. Fesinmeyer N.H. Andersen 2002 Designing a 20-residue protein Nat Struct Biol 107 425 430 10.1038/nsb798 1:CAS:528: DC%2BD38XjvFOms7g%3D (Pubitemid 34568786)
2. L. Qiu S.A. Pabit A.E. Roitberg S.J. Hagen 2002 Smaller and faster: the 20-residue trp-cage protein folds in 4 μs J Am Chem Soc 124 12952 12953 10.1021/ja0279141 1:CAS:528:DC%2BD38Xnsl2hsrk%3D (Pubitemid 35247099)
3. G.V. Nikiforovich N.H. Andersen R.M. Fesinmeyer C. Frieden 2003 Possible locally driven folding pathways of TC5b, a 20-residue protein Proteins: Struct Funct Genet 52 292 302 10.1002/prot.10409 1:CAS:528:DC%2BD3sXlsFahtLk%3D (Pubitemid 36828952)
4. S. Chowdhury M.C. Lee G. Xiong Y. Duan 2003 Ab initio folding simulation of the trp-cage mini-protein approaches NMR resolution J Mol Biol 327 711 717 10.1016/S0022-2836(03)00177-3 1:CAS:528:DC%2BD3sXhvFersr0%3D (Pubitemid 36300811)
5. C. Simmerling B. Strockbine A.E. Roitberg 2002 All-atom structure prediction and folding simulations of a stable protein J Am Chem Soc 124 11258 11259 10.1021/ja0273851 1:CAS:528:DC%2BD38XmsFWjsr8%3D
6. C.D. Snow B. Zagrovic V.S. Pande 2002 The trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations J Am Chem Soc 124 14548 14549 10.1021/ja028604l 1:CAS:528:DC%2BD38XoslSnsr4%3D (Pubitemid 35425023)
7. J.W. Pitera W. Swope 2003 Understanding folding and design: replica-exchange simulations of "trp-cage" miniproteins Proc Natl Acad Sci USA 100 7587 7592 10.1073/pnas.1330954100 1:CAS:528:DC%2BD3sXlt1Wrurc%3D (Pubitemid 36760013)
8. R.H. Zhou 2003 Trp-cage: folding free energy landscape in explicit water Proc Natl Acad Sci USA 100 13280 13285 10.1073/pnas.2233312100 1:CAS:528:DC%2BD3sXptFOis78%3D (Pubitemid 37444733)
9. D. Paschek H. Nymeyer A.E. García 2007 Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water J Struct Biol 157 524 533 10.1016/j.jsb.2006.10.031 1:CAS:528:DC%2BD2sXisVCnsr8%3D (Pubitemid 46321518)
10. A. Schug T. Herges W. Wenzel 2003 Reproducible protein folding with the stochastic tunneling method Phys Rev Lett 91 158102 158105 10.1103/PhysRevLett. 91.158102 1:CAS:528:DC%2BD3sXotVOlsLc%3D
11. M.S. Shell R. Ritterson K.A. Dill 2008 A test on peptide folding of AMBER force fields with implicit solvation J Phys Chem B 112 6878 6886 10.1021/jp800282x 1:CAS:528:DC%2BD1cXls1Oitb4%3D
12. K. Hukushima K. Nemoto 1996 Exchange Monte Carlo method and application to spin glass simulations J Phys Soc 65 1604 1608 10.1143/JPSJ.65.1604 1:CAS:528:DyaK28XktFagt7c%3D (Pubitemid 126456584)
13. U.H.E. Hansmann 1997 Parallel tempering algorithm for conformational studies of biological molecules Chem Phys Lett 281 140 150 10.1016/S0009- 2614(97)01198-6 1:CAS:528:DyaK2sXotFWktr4%3D
14. Y. Sugita Y. Okamoto 1999 Replica-exchange molecular dynamic method for protein folding Chem Phys Lett 314 141 151 10.1016/S0009-2614(99)01123-9 1:CAS:528:DyaK1MXotVKrsLc%3D
15. R.H. Zhou B.J. Berne 2002 Can a continuum solvent model reproduce the free energy landscape for β-hairpin folding in water? Proc Natl Acad Sci USA 99 12777 12782 10.1073/pnas.142430099 1:CAS:528:DC%2BD38XnvFGhsLg%3D
16. D.R. Roe V. Hornak C. Simmerling 2005 Folding cooperativity in a three-stranded β-sheet model J Mol Biol 352 370 381 10.1016/j.jmb.2005.07. 036 1:CAS:528:DC%2BD2MXpslylt7o%3D (Pubitemid 41207788)
17. W. Zhang C. Wu Y. Duan 2005 Convergence of replica exchange molecular dynamics J Chem Phys 123 154105 10.1063/1.2056540 1:CAS:528:DC%2BD2MXhtFKlsrrE
18. D. Sindhikara Y. Meng A.E. Roitberg 2008 Exchange frequency in replica exchange molecular dynamics J Chem Phys 128 024103 10.1063/1.2816560 1:CAS:528:DC%2BD1cXosVKksQ%3D%3D
19. M.C. Tesi E.J.J. van Rensburg E. Orlandini S.G. Whittington 1996 Monte Carlo study of the interacting self-avoiding walk model in three dimensions J Stat Phys 82 155 181 10.1007/BF02189229 (Pubitemid 126330155)
20. M. Feig J. Karanicolas C.L. Brooks 2004 MMTSB tool set: Enhanced sampling and multiscale modeling methods for applications in structural biology J Mol Graphics Modell 22 377 395 10.1016/j.jmgm.2003.12.005 1:CAS:528: DC%2BD2cXjt1Shur4%3D (Pubitemid 38510304)
21. A.E. García K.Y. Sanbonmatsu 2001 Exploring the energy landscape of a β-hairpin in explicit solvent Proteins: Struct Funct Genet 42 345 354 10.1002/1097-0134(20010215)42:3<345::AID-PROT50>3.0.CO;2-H (Pubitemid 32107759)
22. A.E. García K.Y. Sanbonmatsu 2002 α-Helical stabilization by side chain shielding of backbone hydrogen bonds Proc Natl Acad Sci USA 99 2782 2787 10.1073/pnas.042496899 1:CAS:528:DC%2BD38Xit1Crt7s%3D (Pubitemid 34240538)
23. J. Karanicolas C.L. Brooks 2003 The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: Lessons for protein design? Proc Natl Acad Sci USA 100 3954 3959 10.1073/pnas.0731771100 1:CAS:528:DC%2BD3sXivFSqtb4%3D (Pubitemid 36418138)
24. B.S. Kinnear M.F. Jarrold U.H.E. Hansmann 2004 All-atom generalized-ensemble simulations of small proteins J Mol Graphics Modell 22 397 403 10.1016/j.jmgm.2003.12.006 1:CAS:528:DC%2BD2cXjt1Shur8%3D (Pubitemid 38510305)
25. S. Jang E. Kim Y. Pak 2006 Free energy surfaces of miniproteins with a β β α motif: replica exchange molecular dynamics simulation with an implicit solvation model Proteins: Struct Funct Bioinf 62 663 671 10.1002/prot.20771 1:CAS:528:DC%2BD28XhsVGrurY%3D (Pubitemid 43191253)
26. Y. Sugita A. Kitao Y. Okamoto 2000 Multidimensional replica exchange method for free-energy calculations J Chem Phys 113 6042 6051 10.1063/1.1308516 1:CAS:528:DC%2BD3cXntFSrt7w%3D (Pubitemid 30969886)
27. R.H. Zhou B.J. Berne R. Germain 2001 The free energy landscape for β-hairpin folding in explicit water Proc Natl Acad Sci USA 98 14931 14936 10.1073/pnas.201543998 1:CAS:528:DC%2BD38Xptlyi (Pubitemid 34013947)
28. G.D. Hawkins C.J. Cramer D.G. Truhlar 1995 Pairwise solute descreening of solute charges from a dielectric medium Chem Phys Lett 246 122 129 10.1016/0009-2614(95)01082-K 1:CAS:528:DyaK2MXpsV2mt74%3D
29. V. Tsui D.A. Case 2001 Theory and applications of the generalized Born solvation model in macromolecular simulations Biopolymers 56 275 291 10.1002/1097-0282(2000)56:4<275::AID-BIP10024>3.0.CO;2-E 1:STN:280:DC%2BD38%2FntVSlsA%3D%3D
30. A. Onufriev D. Bashford D.A. Case 2004 Exploring native states and large-scale conformational changes with a modified generalized Born model Proteins: Struct Funct Bioinf 55 383 394 10.1002/prot.20033 1:CAS:528: DC%2BD2cXjtFKhs78%3D (Pubitemid 38437495)
31. J.R. Weiser P.S. Shenkin W.C. Still 1999 Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO) J Comput Chem 20 217 230 10.1002/(SICI)1096-987X(19990130)20:2<217::AID-JCC4>3.0.CO;2-A 1:CAS:528:DyaK1MXltVCltQ%3D%3D
32. J.P. Ryckaert G. Ciccotti H.J.C. Berendsen 1977 Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes J Comput Phys 23 327 341 10.1016/0021-9991(77)90098-5 1:CAS:528:DyaE2sXktVGhsL4%3D
33. J. Zhang M. Qin W. Wang 2006 Folding mechanism of β-hairpins studied by replica exchange molecular simulations Proteins: Struct Funct Bioinf 62 672 685 10.1002/prot.20813 1:CAS:528:DC%2BD28XhsVGrurc%3D (Pubitemid 43191254)
34. D. van der Spoel M.M. Seibert 2006 Protein folding kinetics and thermodynamics from atomistic simulations Phys Rev Lett 96 238102 10.1103/PhysRevLett.96.238102 1:CAS:528:DC%2BD28XmtVKqtLc%3D (Pubitemid 43909363)
35. H. Lei C. Wu H. Liu Y. Duan 2007 Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations Proc Natl Acad Sci USA 104 4925 4930 10.1073/pnas.0608432104 1:CAS:528:DC%2BD2sXjvFKitbs%3D (Pubitemid 47186153)
36. J. Chen W. Im C.L. Brooks III 2006 Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field J Am Chem Soc 128 3728 3736 10.1021/ja057216r 1:CAS:528:DC%2BD28XhvVequ7g%3D