A directed essential dynamics simulation of peptide folding.
We present a directed essential dynamics (DED) method for peptide and protein folding. DED is a molecular dynamics method based on the essential dynamics sampling and the principal component analysis. The main idea of DED is to use principal component analysis to determine the direction of the most active collective motion of peptides at short intervals of time (20 fs) during the folding process and then add an additional force along it to adjust the folding direction. This method can make the peptides avoid being trapped in the local minima for a long time and enhance the sampling efficiency in conformational space during the simulation. An S-peptide with 15 amino acids is used to demonstrate the DED method. The results show that DED can lead the S-peptide to fold quickly into the native state, whereas traditional molecular dynamics needs more time to do this.
Chen
Changjun
C
Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
Xiao
Yi
Y
Zhang
Linsen
L
D001703:Biophysics / Q000379:methods*; D003198:Computer Simulation; D006860:Hydrogen Bonding; D008958:Models, Molecular; D015233:Models, Statistical; D008962:Models, Theoretical; D010455:Peptides / Q000737:chemistry*; D025341:Principal Component Analysis; D011487:Protein Conformation; D017510:Protein Folding; D013696:Temperature; D013816:Thermodynamics; D013997:Time Factors
D010455:Peptides
Methods. 1998 Mar;14(3):318-28
9571087
J Mol Biol. 2002 Sep 6;322(1):189-203
12215424
Proteins. 1995 Oct;23(2):177-86
8592699
J Mol Biol. 1993 Jun 5;231(3):825-39
8515453
J Biomol Struct Dyn. 1996 Feb;13(4):615-25
8906882
Proc Natl Acad Sci U S A. 2000 Dec 5;97(25):13614-8
11095708
Proc Natl Acad Sci U S A. 2002 May 14;99(10):6719-24
11983864
Biochemistry. 1991 Apr 23;30(16):3864-71
2018759
Biochemistry. 1996 Oct 22;35(42):13681-8
8885848
Proteins. 1994 Sep;20(1):68-84
7824524
Nat Struct Biol. 1995 Oct;2(10):852-5
7552708
Annu Rev Biophys Biomol Struct. 2001;30:361-96
11340064
J Biotechnol. 2000 May 26;79(3):193-203
10867180
Science. 1995 Jul 21;269(5222):393-6
7618103
Proteins. 1993 Dec;17(4):412-25
8108382
Proc Natl Acad Sci U S A. 1995 Feb 28;92(5):1282-6
7877968
J Mol Biol. 2001 May 25;309(1):299-313
11491298
Biophys J. 2001 Jan;80(1):505-15
11159421
Proc Natl Acad Sci U S A. 1999 Aug 3;96(16):9062-7
10430895
Protein Sci. 2001 Jul;10(7):1403-14
11420442
Proc Natl Acad Sci U S A. 1992 Sep 15;89(18):8721-5
1528885
Proc Natl Acad Sci U S A. 1992 Jul 1;89(13):5937-41
1631077
Science. 1998 Oct 23;282(5389):740-4
9784131
Proteins. 1995 Mar;21(3):167-95
7784423
J Mol Biol. 2001 Oct 12;313(1):151-69
11601853
Proc Natl Acad Sci U S A. 1983 Jun;80(12):3696-700
6574507
Curr Opin Struct Biol. 1999 Apr;9(2):164-9
10322205
Biophys J. 2003 Nov;85(5):2865-71
14581191
J Phys Chem B. 1998 Apr 30;102(18):3586-616
24889800
Proteins. 1995 May;22(1):45-54
7675786
Biochemistry (Mosc). 1999 Dec;64(12):1408-17
10648965
Proteins. 2000 Sep 1;40(4):637-61
10899787
Phys Rev Lett. 1992 Apr 27;68(17):2696-2699
10045464
Proc Natl Acad Sci U S A. 1993 Aug 1;90(15):7195-9
8346235
Biophys J. 2003 Jun;84(6):3583-93
12770868
Proteins. 2001 Feb 1;42(2):256-68
11119650
Proc Natl Acad Sci U S A. 1983 Nov;80(21):6571-5
6579545
Protein Eng. 1998 Oct;11(10):891-900
9862208