Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM

Eisenmesser, 2002, Science, 295, 1520, 10.1126/science.1066176 Olsson, 2006, Chem. Rev., 106, 1737, 10.1021/cr040427e Warshel, 2006, Chem. Rev., 106, 3210, 10.1021/cr0503106 Garcia-Viloca, 2004, Science, 303, 186, 10.1126/science.1088172 Eisenmesser, 2005, Nature, 438, 117, 10.1038/nature04105 Daniel, 2003, Annu. Rev. Biohys. Biomol. Struct., 32, 69, 10.1146/annurev.biophys.32.110601.142445 Bruice, 2002, Acc. Chem. Res., 35, 139, 10.1021/ar0001665 Kraut, 2003, Annu. Rev. Biochem., 72, 517, 10.1146/annurev.biochem.72.121801.161617 Gao, 2006, Chem. Rev., 106, 3188, 10.1021/cr050293k Hammes-Schiffer, 2006, Annu. Rev. Biochem., 75, 519, 10.1146/annurev.biochem.75.103004.142800 Cech, 1981, Cell, 27, 487, 10.1016/0092-8674(81)90390-1 Kruger, 1982, Cell, 31, 147, 10.1016/0092-8674(82)90414-7 Guerriertakada, 1983, Cell, 35, 849, 10.1016/0092-8674(83)90117-4 Gilbert, 1986, Nature, 319, 618, 10.1038/319618a0 Cochrane, 2008, Acc. Chem. Res., 41, 1027, 10.1021/ar800050c Strobel, 2007, Curr. Opin. Chem. Biol., 11, 636, 10.1016/j.cbpa.2007.09.010 Walter, 2007, Mol. Cell, 28, 923, 10.1016/j.molcel.2007.12.001 Scott, 2007, Curr. Opin. Struct. Biol., 17, 280, 10.1016/j.sbi.2007.05.003 Bevilacqua, 2003, Biochemistry, 42, 2259, 10.1021/bi027273m Bevilacqua, 2006, Curr. Opin. Chem. Biol., 10, 455, 10.1016/j.cbpa.2006.08.014 Bevilacqua, 2008, Annu. Rev. Phys. Chem., 59, 79, 10.1146/annurev.physchem.59.032607.093743 Harris, 2008, Curr. Opin. Chem. Biol., 12, 626, 10.1016/j.cbpa.2008.10.005 McDowell, 2007, Biopolymers, 85, 169, 10.1002/bip.20620 Sponer, 2001, Biopolymers, 61, 3, 10.1002/1097-0282(2001)61:1<3::AID-BIP10048>3.0.CO;2-4 Warshel, 1976, J. Mol. Biol., 103, 227, 10.1016/0022-2836(76)90311-9 Truhlar, 1996, J. Phys. Chem., 100, 12771, 10.1021/jp953748q Pu, 2006, Chem. Rev., 106, 3140, 10.1021/cr050308e Klahn, 2005, J. Phys. Chem. B, 109, 15645, 10.1021/jp0521757 Banas, 2008, J. Phys. Chem. B, 112, 11177, 10.1021/jp802592z Radhakrishnan, 2007, Biophys. J., 93, 2391, 10.1529/biophysj.107.104661 Maseras, 1995, J. Comput. Chem., 16, 1170, 10.1002/jcc.540160911 Svensson, 1996, J. Chem. Phys., 105, 3654, 10.1063/1.472235 Froese, 1998, J. Am. Chem. Soc., 120, 1581, 10.1021/ja9728334 Vreven, 2003, J. Comput. Chem., 24, 760, 10.1002/jcc.10156 Vreven, 2003, Theor. Chem. Acc., 109, 125, 10.1007/s00214-002-0418-y Vreven, 2006, J. Chem. Theor. Comp., 2, 815, 10.1021/ct050289g Sponer, 2006 Sponer, 2007, Methods, 43, 278, 10.1016/j.ymeth.2007.02.004 1998 Zhao, 2005, J. Phys. Chem. A, 109, 2012, 10.1021/jp045141s Kendall, 1997, Theor. Chem. Acc., 97, 158, 10.1007/s002140050249 Werner, 2003, J. Chem. Phys., 118, 8149, 10.1063/1.1564816 Boys, 1970, Mol. Phys., 19, 553, 10.1080/00268977000101561 Min, 2008, J. Comput. Chem., 29, 1208, 10.1002/jcc.20880 Sponer, 2004, J. Am. Chem. Soc., 126, 10142, 10.1021/ja048436s Jurecka, 2003, J. Am. Chem. Soc., 125, 15608, 10.1021/ja036611j Sponer, 2006, Chem. Eur. J., 12, 2854, 10.1002/chem.200501239 Kohn, 1965, Phys. Rev., 140, 1133, 10.1103/PhysRev.140.A1133 Koch, 2001 Zhao, 2008, Acc. Chem. Res., 41, 157, 10.1021/ar700111a Lynch, 2001, J. Phys. Chem. A, 105, 2936, 10.1021/jp004262z Lynch, 2000, J. Phys. Chem. A, 104, 4811, 10.1021/jp000497z Zhao, 2008, Theor. Chem. Acc., 120, 215, 10.1007/s00214-007-0310-x Car, 1985, Phys. Rev. Lett., 55, 2471, 10.1103/PhysRevLett.55.2471 Carloni, 2002, Acc. Chem. Res., 35, 455, 10.1021/ar010018u Dal Peraro, 2007, Curr. Opin. Struct. Biol., 17, 149, 10.1016/j.sbi.2007.03.018 VandeVondele, 2005, Comput. Phys. Commun., 167, 103, 10.1016/j.cpc.2004.12.014 Elstner, 2001, J. Chem. Phys., 114, 5149, 10.1063/1.1329889 Jurecka, 2007, J. Comput. Chem., 28, 555, 10.1002/jcc.20570 Grimme, 2004, J. Comput. Chem., 25, 1463, 10.1002/jcc.20078 Nam, 2007, J. Chem. Theor. Comp., 3, 486, 10.1021/ct6002466 Elstner, 1998, Phys. Rev. B, 58, 7260, 10.1103/PhysRevB.58.7260 Yang, 2008, J. Chem. Theor. Comp., 4, 2067, 10.1021/ct800330d Warshel, 1991 Higashi, 2008, J. Chem. Theor. Comp., 4, 790, 10.1021/ct800004y Mackerell, 2004, J. Comput. Chem., 25, 1584, 10.1002/jcc.20082 Cornell, 1995, J. Am. Chem. Soc., 117, 5179, 10.1021/ja00124a002 Cheatham, 1999, J. Biomol. Struct. Dyn., 16, 845, 10.1080/07391102.1999.10508297 Wang, 2000, J. Comput. Chem., 21, 1049, 10.1002/1096-987X(200009)21:12<1049::AID-JCC3>3.0.CO;2-F Perez, 2007, Biophys. J., 92, 3817, 10.1529/biophysj.106.097782 Varnai, 2004, Nucleic Acids Res., 32, 4269, 10.1093/nar/gkh765 Perez, 2008, Nucleic Acids Res., 36, 2379, 10.1093/nar/gkn082 Perez, 2007, J. Am. Chem. Soc., 129, 14739, 10.1021/ja0753546 Krasovska, 2006, Biophys. J., 91, 626, 10.1529/biophysj.105.079368 Reblova, 2006, Biopolymers, 82, 504, 10.1002/bip.20503 Spackova, 2006, Nucleic Acids Res., 34, 697, 10.1093/nar/gkj470 Foloppe, 2000, J. Comput. Chem., 21, 86, 10.1002/(SICI)1096-987X(20000130)21:2<86::AID-JCC2>3.0.CO;2-G MacKerell, 2000, J. Comput. Chem., 21, 105, 10.1002/(SICI)1096-987X(20000130)21:2<105::AID-JCC3>3.0.CO;2-P Pan, 2003, Nucleic Acids Res., 31, 7131, 10.1093/nar/gkg941 Reblova, 2007, Biophys. J., 93, 3932, 10.1529/biophysj.107.110056 Sarzynska, 2008, Biopolymers, 89, 732, 10.1002/bip.21001 Fadrna, 2007, J. Biomol. Struct. Dyn., 24, 709 Fadrna, 2004, Biophys. J., 87, 227, 10.1529/biophysj.103.034751 Rhodes, 2006, Proc. Natl. Acad. Sci. USA, 103, 13380, 10.1073/pnas.0605090103 Ditzler, 2009, RNA, 15, 560, 10.1261/rna.1416709 Krasovska, 2005, J. Mol. Biol., 351, 731, 10.1016/j.jmb.2005.06.016 Gresh, 2003, J. Phys. Chem. B, 107, 8669, 10.1021/jp022659s Sponer, 2000, J. Phys. Chem. B, 104, 7535, 10.1021/jp001711m Cheatham, 2000, Annu. Rev. Phys. Chem., 51, 435, 10.1146/annurev.physchem.51.1.435 Chu, 2008, Curr. Opin. Chem. Biol., 12, 619, 10.1016/j.cbpa.2008.10.010 Razga, 2006, Structure, 14, 825, 10.1016/j.str.2006.02.012 Auffinger, 2000, J. Mol. Biol., 300, 1113, 10.1006/jmbi.2000.3894 Auffinger, 2007, J. Chem. Theor. Comp., 3, 1851, 10.1021/ct700143s Degreve, 1999, J. Chem. Phys., 111, 5150, 10.1063/1.479783 Chen, 2007, J. Phys. Chem. B, 111, 11884, 10.1021/jp0765392 Joung, 2008, J. Phys. Chem. B, 112, 9020, 10.1021/jp8001614 Aqvist, 1990, J. Phys. Chem., 94, 8021, 10.1021/j100384a009 Smith, 1994, J. Chem. Phys., 100, 3757, 10.1063/1.466363 Aqvist, 1994, J. Phys. Chem., 98, 8253, 10.1021/j100084a049 Ennifar, 2003, Nucleic Acids Res., 31, 2671, 10.1093/nar/gkg350 Reblova, 2003, Nucleic Acids Res., 31, 6942, 10.1093/nar/gkg880 Auffinger, 2004, Structure, 12, 379, 10.1016/j.str.2004.02.015 Ke, 2007, Structure, 15, 281, 10.1016/j.str.2007.01.017 Morokuma, 2006, J. Chem. Theor. Comp., 2, 1317, 10.1021/ct600135b Wei, 2007, J. Phys. Chem. B, 111, 1514, 10.1021/jp070120u Bunton, 1958, J. Chem. Soc., 3574, 10.1039/jr9580003574 Bunton, 1960, J. Chem. Soc., 3293, 10.1039/jr9600003293 Laio, 2002, J. Phys. Chem. B, 106, 7300, 10.1021/jp0143138 Helgaker, 1990, Chem. Phys. Lett., 173, 145, 10.1016/0009-2614(90)80068-O Uggerud, 1992, J. Am. Chem. Soc., 114, 4265, 10.1021/ja00037a033 Laio, 2002, J. Chem. Phys., 116, 6941, 10.1063/1.1462041 Schlegel, 2001, J. Chem. Phys., 114, 9758, 10.1063/1.1372182 Schlegel, 2002, J. Chem. Phys., 117, 8694, 10.1063/1.1514582 Iyengar, 2001, J. Chem. Phys., 115, 10291, 10.1063/1.1416876 M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, J.A. Montgomery, Jr., T. Vreven, K.N. Kudin, J. C. Burant, J.M. Millam, S.S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G.A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J.E. Knox, H.P. Hratchian, J.B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, P.Y. Ayala, K. Morokuma, G.A. Voth, P. Salvador, J.J. Dannenberg, V.G. Zakrzewski, S. Dapprich, A.D. Daniels, M. C. Strain, O. Farkas, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J.V. Ortiz, Q. Cui, A.G. Baboul, S. Clifford, J. Cioslowski, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R.L. Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, M. Challacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W. Wong, C. Gonzalez, J.A. Pople, Gaussian 03, Gaussian, Inc., Wallingford CT, 2004. Herbert, 2004, J. Chem. Phys., 121, 11542, 10.1063/1.1814934 Iyengar, 2002, Isr. J. Chem., 42, 191, 10.1560/GLW2-8NVQ-4N6T-6C92 Henkelman, 2000, J. Chem. Phys., 113, 9978, 10.1063/1.1323224 Fischer, 1992, Chem. Phys. Lett., 194, 252, 10.1016/0009-2614(92)85543-J Iannuzzi, 2003, Phys. Rev. Lett., 90, 10.1103/PhysRevLett.90.238302 Muller, 2002, J. Chem. Phys., 116, 897, 10.1063/1.1427722 Ciccotti, 2000, J. Mol. Liq., 89, 1, 10.1016/S0167-7322(00)90001-1 Ciccotti, 2004, Mol. Simul., 30, 787, 10.1080/0892702042000270214 Torrie, 1977, J. Comput. Phys., 23, 187, 10.1016/0021-9991(77)90121-8 Kumar, 1992, J. Comput. Chem., 13, 1011, 10.1002/jcc.540130812 Sprik, 1998, J. Chem. Phys., 109, 7737, 10.1063/1.477419 Salehi-Ashtiani, 2006, Science, 313, 1788, 10.1126/science.1129308 Fedor, 2005, Nat. Rev. Mol. Cell Biol., 6, 399, 10.1038/nrm1647 Doudna, 2005, Nat. Struct. Mol. Biol., 12, 395, 10.1038/nsmb932 Been, 2006, Curr. Top. Microbiol. Immunol., 307, 47 Perrotta, 1999, Science, 286, 123, 10.1126/science.286.5437.123 Nakano, 2000, Science, 287, 1493, 10.1126/science.287.5457.1493 Das, 2005, Nat. Chem. Biol., 1, 45, 10.1038/nchembio703 Ke, 2004, Nature, 429, 201, 10.1038/nature02522 Ferre-D’Amare, 1998, Nature, 395, 567, 10.1038/26912 Koo, 2008, 92 Liu, 2007, J. Phys. Chem. B, 111, 439, 10.1021/jp064292n Buzayan, 1986, Nucleic Acids Res., 14, 9729, 10.1093/nar/14.24.9729 Buzayan, 1988, Nucleic Acids Res., 16, 4009, 10.1093/nar/16.9.4009 van Tol, 1990, Nucleic Acids Res., 18, 1971, 10.1093/nar/18.8.1971 Walter, 1998, Curr. Opin. Chem. Biol., 2, 24, 10.1016/S1367-5931(98)80032-X Fedor, 2000, J. Mol. Biol., 297, 269, 10.1006/jmbi.2000.3560 Kuzmin, 2005, J. Mol. Biol., 349, 989, 10.1016/j.jmb.2005.04.005 Cottrell, 2007, J. Biol. Chem., 282, 13498, 10.1074/jbc.M700451200 Rupert, 2002, Science, 298, 1421, 10.1126/science.1076093 Torelli, 2007, RNA, 13, 1052, 10.1261/rna.510807 Macelrevey, 2008, RNA, 14, 1600, 10.1261/rna.1055308 Torelli, 2008, Biochem. Biophys. Res. Commun., 371, 154, 10.1016/j.bbrc.2008.04.036 Pinard, 2001, EMBO J., 20, 6434, 10.1093/emboj/20.22.6434 Kuzmin, 2004, J. Mol. Biol., 340, 233, 10.1016/j.jmb.2004.04.067 Rupert, 2001, Nature, 410, 780, 10.1038/35071009 Salter, 2006, Biochemistry, 45, 686, 10.1021/bi051887k Lebruska, 2002, Chem. Biol., 9, 465, 10.1016/S1074-5521(02)00130-8 Gao, 1998, J. Phys. Chem. A, 102, 4714, 10.1021/jp9809890 Nam, 2008, RNA, 14, 1501, 10.1261/rna.863108 Nam, 2008, J. Am. Chem. Soc., 130, 4680, 10.1021/ja0759141 Forster, 1987, Cell, 50, 9, 10.1016/0092-8674(87)90657-X Scott, 1999, Q. Rev. Biophys., 32, 241, 10.1017/S003358350000353X Martick, 2008, Nature, 454, 899, 10.1038/nature07117 Pley, 1994, Nature, 372, 68, 10.1038/372068a0 Scott, 1995, Cell, 81, 991, 10.1016/S0092-8674(05)80004-2 Wedekind, 1998, Annu. Rev. Biophys. Biomol. Struct., 27, 475, 10.1146/annurev.biophys.27.1.475 Blount, 2005, Annu. Rev. Biophys. Biomol. Struct., 34, 415, 10.1146/annurev.biophys.34.122004.184428 Martick, 2008, Chem. Biol., 15, 332, 10.1016/j.chembiol.2008.03.010 Nelson, 2008, RNA, 14, 605, 10.1261/rna.912608 Leclerc, 2006, J. Phys. Chem. B, 110, 3395, 10.1021/jp053835a Lee, 2007, J. Chem. Theor. Comp., 3, 325, 10.1021/ct6003142 Torres, 2003, J. Am. Chem. Soc., 125, 9861, 10.1021/ja021451h Lee, 2008, J. Am. Chem. Soc., 130, 3053, 10.1021/ja076529e Boero, 2007, J. Phys. Condens. Matter, 19, 365217, 10.1088/0953-8984/19/36/365217 Ban, 2000, Science, 289, 905, 10.1126/science.289.5481.905 Nissen, 2000, Science, 289, 920, 10.1126/science.289.5481.920 Trobro, 2005, Proc. Natl. Acad. Sci. USA, 102, 12395, 10.1073/pnas.0504043102 Trobro, 2006, Biochemistry, 45, 7049, 10.1021/bi0605383 Trobro, 2007, Mol. Cell, 27, 758, 10.1016/j.molcel.2007.06.032 Trobro, 2008, Biochemistry, 47, 4898, 10.1021/bi8001874 Sharma, 2005, Biochemistry, 44, 11307, 10.1021/bi0509806 Aqvist, 1993, Chem. Rev., 93, 2523, 10.1021/cr00023a010 Sievers, 2004, Proc. Natl. Acad. Sci. USA, 101, 12397, 10.1073/pnas.0402488101