Refolding the engrailed homeodomain: structural basis for the accumulation of a folding intermediate.
The ultrafast folding pathway of the engrailed homeodomain has been exceptionally well characterized by experiment and simulation. Helices II and III of the three-helix bundle protein form the native helix-turn-helix motif as an on-pathway intermediate within a few microseconds. The slow step is then the proper docking of the helices in approximately 15 mus. However, there is still the unexplained puzzle of why helix docking is relatively slow, which is part of the more general question as to why rearrangements of intermediates occur slowly. To address this problem, we performed 46 all-atom molecular dynamics refolding simulations in explicit water, for a total of 15 micros of simulation time. The simulations started from an intermediate state structure that was generated in an unfolding simulation at 498 K and was then quenched to folding-permissive temperatures. The protein refolded successfully in only one of the 46 simulations, and in that case the refolding pathway mirrored the unfolding pathway at high temperature. In the 45 simulations in which the protein did not fully fold, nonnative salt bridges trapped the protein, which explains why the protein folds relatively slowly from the intermediate state.
McCully
Michelle E
ME
Biomolecular Structure and Design Program, Department of Bioengineering, University of Washington, Seattle, Washington, USA.
Beck
David A C
DA
Fersht
Alan R
AR
Daggett
Valerie
V
D056004:Molecular Dynamics Simulation; D017510:Protein Folding; D058849:Protein Refolding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D044366:Transition Temperature; D014867:Water / Q000737:chemistry
D011506:Proteins; D014867:Water
J Comput Chem. 2004 Oct;25(13):1605-12
15264254
Biophys J. 2010 Jun 2;98(11):2671-81
20513412
Biophys J. 2007 Nov 15;93(10):3382-91
17978165
Biophys J. 2008 Mar 1;94(5):1622-9
18024496
Nature. 2003 Feb 20;421(6925):863-7
12594518
J Mol Biol. 1996 Mar 29;257(2):412-29
8609633
Protein Sci. 1994 Oct;3(10):1779-87
7849596
Biochemistry. 2005 Jan 18;44(2):609-16
15641786
Nature. 2005 Oct 13;437(7061):1053-6
16222301
Nature. 2010 Feb 4;463(7281):685-8
20130652
J Mol Biol. 1971 Feb 14;55(3):379-400
5551392
Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13286-91
14595026
Cell. 2008 Jun 27;133(7):1277-89
18585360
J Mol Biol. 2003 Nov 7;333(5):977-91
14583194
Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Nov;72(5 Pt 1):051919
16383657
Proc Natl Acad Sci U S A. 2007 May 29;104(22):9272-7
17517666
J Mol Biol. 2004 Aug 20;341(4):1109-24
15328620
Proc Natl Acad Sci U S A. 1994 Oct 25;91(22):10430-4
7937969
J Mol Biol. 1999 Jul 2;290(1):283-304
10388573
Biochemistry. 2008 Jul 8;47(27):7079-89
18553935
Biopolymers. 1983 Dec;22(12):2577-637
6667333
J Mol Biol. 2007 Feb 16;366(2):677-86
17174331
J Mol Biol. 1996 Mar 29;257(2):430-40
8609634
Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14122-5
12388785
Methods. 2004 Sep;34(1):112-20
15283920
Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17747-52
17095606
Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15486-91
14671331
J Biomol NMR. 2008 Mar;40(3):189-202
18274703
Q Rev Biophys. 2007 Nov;40(4):287-326
18405419
Proc Natl Acad Sci U S A. 2000 Dec 5;97(25):13518-22
11087839