Sequence dependencies of DNA deformability and hydration in the minor groove.
DNA deformability and hydration are both sequence-dependent and are essential in specific DNA sequence recognition by proteins. However, the relationship between the two is not well understood. Here, systematic molecular dynamics simulations of 136 DNA sequences that differ from each other in their central tetramer revealed that sequence dependence of hydration is clearly correlated with that of deformability. We show that this correlation can be illustrated by four typical cases. Most rigid basepair steps are highly likely to form an ordered hydration pattern composed of one water molecule forming a bridge between the bases of distinct strands, but a few exceptions favor another ordered hydration composed of two water molecules forming such a bridge. Steps with medium deformability can display both of these hydration patterns with frequent transition. Highly flexible steps do not have any stable hydration pattern. A detailed picture of this correlation demonstrates that motions of hydration water molecules and DNA bases are tightly coupled with each other at the atomic level. These results contribute to our understanding of the entropic contribution from water molecules in protein or drug binding and could be applied for the purpose of predicting binding sites.
Yonetani
Yoshiteru
Y
Computational Biology Group, Quantum Beam Science Directorate, Japan Atomic Energy Agency, Kyoto, Japan.
Kono
Hidetoshi
H
D001483:Base Sequence; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D017422:Sequence Analysis, DNA / Q000379:methods*; D014867:Water / Q000737:chemistry*
D014867:Water; D004247:DNA
Trends Biochem Sci. 2006 Oct;31(10):547-52
16920361
EMBO J. 1992 Jul;11(7):2695-705
1628628
Nucleic Acids Res. 2003 Sep 1;31(17):5108-21
12930962
Biochemistry. 2008 Feb 26;47(8):2325-38
18237194
Nucleic Acids Res. 2008 Apr;36(7):2379-94
18299282
Nucleic Acids Res. 1995 Sep 11;23(17):3385-92
7567447
Q Rev Biophys. 2001 Aug;34(3):269-324
11838235
J Mol Biol. 2007 Jan 5;365(1):1-9
17055530
Science. 1995 Aug 4;269(5224):656-63
7624794
J Mol Biol. 1997 Aug 15;271(2):244-57
9268656
J Mol Biol. 1989 Feb 20;205(4):787-91
2926825
Biophys J. 2000 May;78(5):2560-71
10777752
J Mol Biol. 1981 Sep 25;151(3):535-56
7338904
Biophys J. 1992 Sep;63(3):751-9
1384741
Nucleic Acids Res. 2008 Feb;36(2):376-86
18039704
Biochemistry. 2005 Jul 19;44(28):9785-94
16008363
Biophys J. 1998 Nov;75(5):2170-7
9788911
J Mol Biol. 2001 Oct 5;312(5):1037-49
11580248
J Mol Biol. 1999 Mar 5;286(4):1075-95
10047483
J Mol Biol. 1991 Jan 5;217(1):177-99
1988677
Nat Struct Biol. 1997 Aug;4(8):657-65
9253416
J Mol Biol. 2000 Jul 28;300(5):1113-31
10903858
Science. 1994 Jan 21;263(5145):348-55
8278807
J Mol Biol. 2002 Feb 1;315(5):1049-61
11827475
Biochemistry. 1998 Dec 1;37(48):16877-87
9836580
Proc Natl Acad Sci U S A. 1991 Jan 15;88(2):593-7
1988954
Biophys J. 2003 Nov;85(5):2872-83
14581192
J Mol Biol. 2000 Aug 18;301(3):643-63
10966775
Nature. 1998 Feb 12;391(6668):660-6
9490409
Biophys J. 1998 Jul;75(1):372-81
9649394
Science. 1994 Apr 29;264(5159):670
17737951
Biochemistry. 1991 Oct 22;30(42):10294-306
1718416
Biophys J. 2004 Dec;87(6):3799-813
15326025
Biochemistry. 1990 Jul 17;29(28):6551-61
2204415
J Am Chem Soc. 2005 Nov 23;127(46):16074-89
16287294
Nucleic Acids Res. 2007;35(18):6063-74
17766249
J Mol Biol. 2003 Mar 21;327(2):393-411
12628246
J Mol Biol. 1997 Apr 4;267(3):595-623
9126841
Annu Rev Biophys Biomol Struct. 2004;33:343-61
15139817
Biophys J. 2002 Jul;83(1):22-41
12080098
J Mol Biol. 2002 Oct 4;322(5):907-15
12367517
Biophys J. 1996 Jun;70(6):2857-66
8744323
Proc Natl Acad Sci U S A. 1998 Sep 15;95(19):11163-8
9736707