Coarse-grained biomolecular simulation with REACH: realistic extension algorithm via covariance Hessian.
Coarse-graining of protein interactions provides a means of simulating large biological systems. Here, a coarse-graining method, REACH, is introduced, in which the force constants of a residue-scale elastic network model are calculated from the variance-covariance matrix obtained from atomistic molecular dynamics (MD) simulation. In test calculations, the C(alpha)-atoms variance-covariance matrices are calculated from the ensembles of 1-ns atomistic MD trajectories in monomeric and dimeric myoglobin, and used to derive coarse-grained force constants for the local and nonbonded interactions. Construction of analytical model functions of the distance-dependence of the interresidue force constants allows rapid calculation of the REACH normal modes. The model force constants from monomeric and dimeric myoglobin are found to be similar in magnitude to each other. The MD intra- and intermolecular mean-square fluctuations and the vibrational density of states are well reproduced by the residue-scale REACH normal modes without requiring rescaling of the force constant parameters. The temperature-dependence of the myoglobin REACH force constants reveals that the dynamical transition in protein internal fluctuations arises principally from softening of the elasticity in the nonlocal interactions. The REACH method is found to be a reliable way of determining spatiotemporal protein motion without the need for expensive computations of long atomistic MD simulations.
Moritsugu
Kei
K
Center for Molecular Biophysics, University of Tennessee/Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Smith
Jeremy C
JC
D000465:Algorithms; D001703:Biophysics / Q000379:methods*; D003198:Computer Simulation; D030562:Databases, Protein; D019281:Dimerization; D004548:Elasticity; D008954:Models, Biological; D008956:Models, Chemical; D015233:Models, Statistical; D008968:Molecular Conformation; D009211:Myoglobin / Q000737:chemistry; D009991:Oscillometry; D012984:Software; D013696:Temperature; D013997:Time Factors
D009211:Myoglobin
Curr Opin Chem Biol. 1997 Dec;1(4):449-57
9667895
Science. 1991 Dec 13;254(5038):1598-603
1749933
Biophys J. 2006 May 15;90(10):3382-8
16500967
Science. 2000 Jun 2;288(5471):1604-7
10834833
J Phys Chem B. 2006 Nov 16;110(45):22842-52
17092036
Science. 1988 Mar 4;239(4844):1105-10
3125607
Proteins. 1999 Sep 1;36(4):425-35
10450084
Nucleic Acids Res. 2000 Jan 1;28(1):235-42
10592235
J Phys Chem B. 2006 Mar 23;110(11):5807-16
16539528
Biophys J. 2005 Jul;89(1):167-78
15879477
Phys Rev Lett. 2005 Nov 18;95(21):218103
16384188
Proc Natl Acad Sci U S A. 2005 Dec 27;102(52):18908-13
16354836
Phys Rev Lett. 2005 Nov 4;95(19):198103
16384030
Phys Rev Lett. 1989 Apr 17;62(16):1916-1919
10039803
Phys Rev Lett. 1996 Aug 26;77(9):1905-1908
10063201
Proteins. 2007 Mar 1;66(4):941-53
17154425
J Mol Biol. 2002 Jul 26;320(5):1011-24
12126621
J Chem Phys. 2006 Oct 21;125(15):151101
17059230
Biophys J. 2004 Jun;86(6):3846-54
15189881
Proteins. 1990;8(3):258-79
2281087
J Mol Biol. 1996 May 3;258(2):393-410
8627633
Proteins. 1999 Dec 1;37(4):654-67
10651280
Biophys J. 2006 Mar 1;90(5):1572-82
16361345
Curr Opin Struct Biol. 2005 Oct;15(5):586-92
16143512
Biophys J. 2003 Sep;85(3):1871-5
12944299
Proteins. 2006 Apr 1;63(1):197-209
16447281
Biophys J. 1999 Oct;77(4):2153-74
10512835
Protein Eng. 2001 Jan;14(1):1-6
11287673
Bioinformatics. 2005 Jul 1;21(13):2978-87
15860562
Proc Natl Acad Sci U S A. 1983 Jun;80(12):3696-700
6574507
J Mol Biol. 1985 Feb 5;181(3):423-47
2580101
Proc Natl Acad Sci U S A. 1985 Aug;82(15):4995-9
3860838
J Phys Chem B. 1998 Apr 30;102(18):3586-616
24889800
Comput Chem. 1995 Sep;19(3):241-6
7551557
Proteins. 1998 Nov 15;33(3):417-29
9829700
Fold Des. 1997;2(3):173-81
9218955
J Phys Chem B. 2005 Jun 23;109(24):12182-94
16852503
Q Rev Biophys. 1985 Aug;18(3):227-59
3916127
Annu Rev Biophys Biophys Chem. 1988;17:451-79
3293595
Phys Rev Lett. 2003 Nov 14;91(20):208106
14683404
Annu Rev Biophys Biomol Struct. 2001;30:211-43
11340059
Proc Natl Acad Sci U S A. 1990 Feb;87(4):1601-5
2304919
J Mol Biol. 1990 Nov 5;216(1):95-109
2231732
J Mol Biol. 2005 Jan 14;345(2):299-314
15571723
Proc Natl Acad Sci U S A. 1983 Nov;80(21):6571-5
6579545
Biophys J. 2007 Jun 15;92(12):4289-303
17400700
Biophys J. 2005 Sep;89(3):1455-63
15951386
Biophys J. 2002 Mar;82(3):1216-25
11867439
Methods Enzymol. 1994;239:657-700
7830601
Nature. 1989 Feb 23;337(6209):754-6
2918910