Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics.
Explicit solvent molecular dynamics simulations (in total almost 800 ns including locally enhanced sampling runs) were applied with different ion conditions and with two force fields (AMBER and CHARMM) to characterize typical geometries adopted by the flanking bases in the RNA kissing-loop complexes. We focus on flanking base positions in multiple x-ray and NMR structures of HIV-1 DIS kissing complexes and kissing complex from the large ribosomal subunit of Haloarcula marismortui. An initial x-ray open conformation of bulged-out bases in HIV-1 DIS complexes, affected by crystal packing, tends to convert to a closed conformation formed by consecutive stretch of four stacked purine bases. This is in agreement with those recent crystals where the packing is essentially avoided. We also observed variants of the closed conformation with three stacked bases, while nonnegligible populations of stacked geometries with bulged-in bases were detected, too. The simulation results reconcile differences in positions of the flanking bases observed in x-ray and NMR studies. Our results suggest that bulged-out geometries are somewhat more preferred, which is in accord with recent experiments showing that they may mediate tertiary contacts in biomolecular assemblies or allow binding of aminoglycoside antibiotics.
Réblová
Kamila
K
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
Fadrná
Eva
E
Sarzynska
Joanna
J
Kulinski
Tadeusz
T
Kulhánek
Petr
P
Ennifar
Eric
E
Koca
Jaroslav
J
Sponer
Jirí
J
D020029:Base Pairing / Q000235:genetics; D001665:Binding Sites; D003198:Computer Simulation; D019281:Dimerization; D015497:HIV-1 / Q000737:chemistry* / Q000235:genetics*; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry*; D024363:Transcription Initiation Site
D012367:RNA, Viral
Biophys J. 2006 Jul 15;91(2):626-38
16617077
RNA. 2006 Jul;12(7):1240-53
16682558
J Am Chem Soc. 2006 Jul 19;128(28):8992-3
16834346
Biochimie. 2006 Aug;88(8):1053-9
16905237
Proc Natl Acad Sci U S A. 2006 Sep 5;103(36):13380-5
16938834
Science. 2006 Sep 29;313(5795):1935-42
16959973
J Comput Aided Mol Des. 2006 May;20(5):263-79
17006738
Nucleic Acids Res. 2006;34(19):5361-8
17012271
Biopolymers. 2007 Feb 5;85(2):169-84
17080418
J Biomol Struct Dyn. 2007 Apr;24(5):471-9
17313192
Biophys J. 2007 Apr 15;92(8):2647-65
17259282
Biophys J. 2007 Jun 1;92(11):3817-29
17351000
Nucleic Acids Res. 2004;32(5):1666-77
15016910
Oligonucleotides. 2003;13(6):501-14
15025916
Biopolymers. 2004 Jun 15;74(3):177-88
15150793
Nat Rev Microbiol. 2004 Jun;2(6):461-72
15152202
Angew Chem Int Ed Engl. 2004 Jun 14;43(24):3177-82
15199571
Biophys J. 2004 Jul;87(1):227-42
15240460
Biophys J. 2004 Aug;87(2):800-11
15298889
Nucleic Acids Res. 2004;32(14):4269-80
15304564
Nucleic Acids Res. 2003 May 15;31(10):2671-82
12736317
Biophys J. 2003 Jun;84(6):3564-82
12770867
Biophys J. 2003 Jul;85(1):416-25
12829496
Nucleic Acids Res. 2003 Dec 1;31(23):6942-52
14627827
Biophys J. 2003 Dec;85(6):3445-59
14645041
Chem Soc Rev. 2003 Nov;32(6):350-64
14671790
J Mol Biol. 2004 Jan 9;335(2):555-71
14672663
J Mol Model. 2004 Feb;10(1):60-8
14691674
Biophys J. 2005 May;88(5):3466-85
15722438
J Am Chem Soc. 2005 Oct 12;127(40):13906-18
16201812
Biophys J. 2005 Nov;89(5):2939-49
16100266
Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15854-9
16249344
J Biochem. 2005 Nov;138(5):583-92
16272570
Proc Natl Acad Sci U S A. 2004 Oct 12;101(41):14771-5
15465909
J Mol Biol. 1985 Jul 5;184(1):119-45
3897553
Proc Natl Acad Sci U S A. 1994 May 24;91(11):4945-9
8197162
Biochemistry. 1994 Nov 15;33(45):13464-74
7947755
J Biol Chem. 1995 Apr 7;270(14):8209-16
7713927
Biochemistry. 1996 Feb 6;35(5):1589-98
8634290
Biochemistry. 1996 Apr 16;35(15):5075-82
8664300
J Mol Graph. 1996 Feb;14(1):33-8, 27-8
8744570
J Virol. 1996 Sep;70(9):5902-8
8709210
J Biol Chem. 1996 Dec 27;271(52):33686-92
8969239
J Mol Biol. 1997 May 30;269(1):52-66
9193000
J Mol Biol. 1997 Jul 4;270(1):36-49
9231899
J Mol Biol. 1998 Mar 27;277(2):333-45
9514734
J Virol. 1998 May;72(5):3991-8
9557686
Nat Struct Biol. 1998 Jun;5(6):432-6
9628479
Structure. 1998 Aug 15;6(8):993-1005
9739090
J Biomol Struct Dyn. 1999 Feb;16(4):845-62
10217454
J Biomol Struct Dyn. 2005 Feb;22(4):425-39
15588106
J Mol Model. 2004 Dec;10(5-6):408-17
15597210
RNA. 2005 Feb;11(2):197-209
15659359
Structure. 1999 Nov 15;7(11):1439-49
10574792
J Mol Biol. 2000 Apr 14;297(5):1045-61
10764572
Curr Opin Struct Biol. 2000 Jun;10(3):311-7
10851190
Science. 2000 Aug 11;289(5481):905-20
10937989
Proc Natl Acad Sci U S A. 2000 Aug 15;97(17):9396-401
10931958
Nature. 2000 Sep 21;407(6802):327-39
11014182
Nature. 2000 Sep 21;407(6802):340-8
11014183
Biophys J. 2001 Jul;81(1):352-70
11423420
J Mol Biol. 2001 Nov 9;313(5):1073-91
11700064
Nat Struct Biol. 2001 Dec;8(12):1064-8
11702070
Cell. 2001 Nov 30;107(5):679-88
11733066
Biopolymers. 2000-2001;56(4):232-56
11754338
Biopolymers. 2000-2001;56(4):257-65
11754339
J Mol Biol. 2002 May 24;319(1):141-60
12051942
J Am Chem Soc. 2002 Oct 16;124(41):12154-64
12371855
J Biomol Struct Dyn. 2002 Dec;20(3):397-412
12437378
Nucleic Acids Res. 2003 Jan 15;31(2):629-38
12527771
J Biol Chem. 2003 Jan 24;278(4):2723-30
12435744
J Mol Biol. 2003 Feb 14;326(2):529-42
12559920
J Mol Biol. 2003 Apr 18;328(1):33-47
12683995
Nucleic Acids Res. 2003 May 15;31(10):2461-74
12736295
Science. 2005 Nov 4;310(5749):827-34
16272117
Biophys J. 2006 Jan 15;90(2):391-9
16239331
Nucleic Acids Res. 2006;34(1):343-52
16410614
J Mol Biol. 2006 Feb 24;356(3):771-82
16403527
Nucleic Acids Res. 2006;34(2):676-85
16452297
Nucleic Acids Res. 2006;34(2):697-708
16456030
Biophys J. 2006 Apr 1;90(7):2450-62
16399833
Nucleic Acids Res. 2006;34(8):2328-39
16679451
Structure. 2006 May;14(5):825-35
16698544
Biopolymers. 2006 Aug 5;82(5):504-20
16538608