Temperature and urea induced denaturation of the TRP-cage mini protein TC5b: A simulation study consistent with experimental observations.
The effects of temperature and urea denaturation (6M urea) on the dominant structures of the 20-residue Trp-cage mini-protein TC5b are investigated by molecular dynamics simulations of the protein at different temperatures in aqueous and in 6M urea solution using explicit solvent degrees of freedom and the GROMOS force-field parameter set 45A3. In aqueous solution at 278 K, TC5b is stable throughout the 20 ns of MD simulation and the trajectory structures largely agree with the NMR-NOE atom-atom distance data available. Raising the temperature to 360 K and to 400 K, the protein denatures within 22 ns and 3 ns, showing that the denaturation temperature is well below 360 K using the GROMOS force field. This is 40-90 K lower than the denaturation temperatures observed in simulations using other much used protein force fields. As the experimental denaturation temperature is about 315 K, the GROMOS force field appears not to overstabilize TC5b, as other force fields and the use of continuum solvation models seem to do. This feature may directly stem from the GROMOS force-field parameter calibration protocol, which primarily involves reproduction of condensed phase thermodynamic quantities such as energies, densities, and solvation free energies of small compounds representative for protein fragments. By adding 6M urea to the solution, the onset of denaturation is observed in the simulation, but is too slow to observe a particular side-chain side-chain contact (Trp6-Ile4) that was experimentally observed to be characteristic for the denatured state. Interestingly, using temperature denaturation, the process is accelerated and the experimental data are reproduced.
Gattin
Z
Z
Swiss Federal Institute of Technology, ETH, Zürich, Switzerland.
Riniker
S
S
Hore
P J
PJ
Mok
K H
KH
van Gunsteren
W F
WF
D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D011489:Protein Denaturation; D011994:Recombinant Proteins / Q000737:chemistry*; D013696:Temperature; D013816:Thermodynamics; D014508:Urea / Q000737:chemistry*
D010455:Peptides; D011994:Recombinant Proteins; C476389:TC5b protein, synthetic; C508725:Trp-cage peptide; D014508:Urea
Nat Struct Biol. 2002 Jun;9(6):425-30
11979279
Biochemistry. 2001 Nov 6;40(44):13188-200
11683627
J Am Chem Soc. 2005 Aug 10;127(31):10943-50
16076200
J Am Chem Soc. 2005 Jun 22;127(24):8606-7
15954761
Nature. 2007 May 3;447(7140):106-9
17429353
J Mol Biol. 2003 Mar 28;327(3):711-7
12634063
J Am Chem Soc. 2002 Nov 6;124(44):12952-3
12405814
Proteins. 2003 Aug 1;52(2):292-302
12833552
J Am Chem Soc. 2004 Feb 18;126(6):1849-57
14871118
Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12491-6
15314214
Proteins. 2007;69 Suppl 8:3-9
17918729
Angew Chem Int Ed Engl. 2001 Jan 19;40(2):351-355
29712400
Proc Natl Acad Sci U S A. 2005 Nov 15;102(46):16650-5
16269542
Proteins. 2001;Suppl 5:2-7
11835476
Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):905-21
9757107
Curr Opin Struct Biol. 2008 Apr;18(2):149-53
18280138
Proteins. 1999 Sep 1;36(4):542-55
10450095
Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13280-5
14581616
Biophys J. 2005 Aug;89(2):842-57
15908578
Proc Natl Acad Sci U S A. 2003 Jun 24;100(13):7587-92
12808142
J Am Chem Soc. 2002 Dec 11;124(49):14548-9
12465960
J Chem Phys. 2004 Dec 1;121(21):10748-56
15549960
Biopolymers. 1983 Dec;22(12):2577-637
6667333
J Comput Chem. 2004 Oct;25(13):1656-76
15264259
J Comput Chem. 2005 Dec;26(16):1719-51
16211540
Chem Rev. 2006 May;106(5):1559-88
16683745
J Am Chem Soc. 2002 Sep 25;124(38):11258-9
12236726
J Struct Biol. 2007 Mar;157(3):524-33
17293125
J Am Chem Soc. 2004 Mar 24;126(11):3398-9
15025447
Proteins. 1999 Feb 15;34(3):269-80
10024015