全部 标题 作者
关键词 摘要

OALib Journal期刊
ISSN: 2333-9721
费用：99美元
投递稿件

查看量下载量

相关文章

更多...

What Is the Role of Motif D in the Nucleotide Incorporation Catalyzed by the RNA-dependent RNA Polymerase from Poliovirus?

DOI: 10.1371/journal.pcbi.1002851

Full-Text   Cite this paper   Add to My Lib

Abstract:

Poliovirus (PV) is a well-characterized RNA virus, and the RNA-dependent RNA polymerase (RdRp) from PV (3Dpol) has been widely employed as an important model for understanding the structure-function relationships of RNA and DNA polymerases. Many experimental studies of the kinetics of nucleotide incorporation by RNA and DNA polymerases suggest that each nucleotide incorporation cycle basically consists of six sequential steps: (1) an incoming nucleotide binds to the polymerase-primer/template complex; (2) the ternary complex (nucleotide-polymerase-primer/template) undergoes a conformational change; (3) phosphoryl transfer occurs (the chemistry step); (4) a post-chemistry conformational change occurs; (5) pyrophosphate is released; (6) RNA or DNA translocation. Recently, the importance of structural motif D in nucleotide incorporation has been recognized, but the functions of motif D are less well explored so far. In this work, we used two computational techniques, molecular dynamics (MD) simulation and quantum mechanics (QM) method, to explore the roles of motif D in nucleotide incorporation catalyzed by PV 3Dpol. We discovered that the motif D, exhibiting high flexibility in either the presence or the absence of RNA primer/template, might facilitate the transportation of incoming nucleotide or outgoing pyrophosphate. We observed that the dynamic behavior of motif A, which should be essential to the polymerase function, was greatly affected by the motions of motif D. In the end, through QM calculations, we attempted to investigate the proton transfer in enzyme catalysis associated with a few amino acid residues of motifs F and D.

 References

[1]  Morrow CD, Warren B, Lentz MR (1987) Expression of enzymatically active poliovirus RNA-dependent RNA polymerase in Escherichia coli. Proc Natl Acad Sci USA 84: 6050–6054. doi: 10.1073/pnas.84.17.6050
[2]  Thompson AA, Peersen OB (2004) Structural basis for proteolysis-dependent activation of the poliovirus RNA-dependent RNA polymerase. EMBO J 23: 3462–3471. doi: 10.1038/sj.emboj.7600357
[3]  Love RA, Maegley KA, Yu X, Ferre RA, Lingardo LK, et al. (2004) The Crystal Structure of the RNA-Dependent RNA Polymerase from Human Rhinovirus: A Dual-Function Target for Common Cold Antiviral Therapy. Structure 12: 1533–1544. doi: 10.1016/j.str.2004.05.024
[4]  Ferrer-Orta C, Arias A, Perez-Luque R, Escarmís C, Domingo E, et al. (2004) Structure of Foot-and-Mouth Disease Virus RNA-dependent RNA Polymerase and Its Complex with a Template-Primer RNA. J Biol Chem 279: 47212–47221. doi: 10.1074/jbc.m405465200
[5]  Hansen JL, Long AM, Schultz SC (1997) Structure of the RNA-dependent RNA polymerase of Poliovirus. Structure 5: 1109–1122. doi: 10.1016/s0969-2126(97)00261-x
[6]  Crotty S, Cameron CE, Andino R (2001) RNA virus error catastrophe: Direct molecular test by using ribavirin. Proc Natl Acad Sci USA 98: 6895–6900. doi: 10.1073/pnas.111085598
[7]  Graci JD, Cameron CE (2006) Mechanisms of action of ribavirin against distinct viruses. Rev Med Virol 16: 37–48. doi: 10.1002/rmv.483
[8]  Graci JD, Harki DA, Korneeva VS, Edathil JP, Too K, et al. (2007) Lethal mutagenesis of poliovirus mediated by a mutagenic pyrimidine analogue. J Virol 81: 11256–11266. doi: 10.1128/jvi.01028-07
[9]  Campagnola G, Gong P, Peersen OB (2011) High-throughput screening identification of poliovirus RNA-dependent RNA polymerase inhibitors. Antiviral Res 91: 241–251. doi: 10.1016/j.antiviral.2011.06.006
[10]  Bruenn JA (1991) Relationships among the positive strand and double-strand RNA viruses as viewed through their RNA-dependent RNA polymerases. Nucleic Acids Res 19: 217–226. doi: 10.1093/nar/19.2.217
[11]  Castro C, Arnold JJ, Cameron CE (2005) Incorporation fidelity of the viral RNA-dependent RNA polymerase: a kinetic, thermodynamic and structural perspective. Virus Res 107: 141–149. doi: 10.1016/j.virusres.2004.11.004
[12]  Arnold JJ, Vignuzzi M, Stone JK, Andino R, Cameron CE (2005) Remote site control of an active site fidelity checkpoint in a viral RNA-dependent RNA polymerase. J Biol Chem 280: 25706–25716. doi: 10.1074/jbc.m503444200
[13]  Gong P, Peersen OB (2010) Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase. Proc Natl Acad Sci USA 107: 22505–22510. doi: 10.1073/pnas.1007626107
[14]  Moustafa IM, Shen H, Morton B, Colina CM, Cameron CE (2011) Molecular Dynamics Simulations of Viral RNA Polymerases Link Conserved and Correlated Motions of Functional Elements to Fidelity. J Mol Biol 410: 159–181. doi: 10.1016/j.jmb.2011.04.078
[15]  Arnold JJ, Cameron CE (2000) Poliovirus RNA-dependent RNA Polymerase (3Dpol.) Assembly of stable, elongation-competent complexes by using a symmetrical primer-template substrate (sym/sub). J Biol Chem 275: 5329–5339. doi: 10.1074/jbc.275.8.5329
[16]  Arnold JJ, Cameron CE (2004) Poliovirus RNA-Dependent RNA Polymerase (3Dpol): Pre-Steady-State Kinetic Analysis of Ribonucleotide Incorporation in the Presence of Mg2+. Biochemistry 43: 5126–5137. doi: 10.1021/bi035212y
[17]  Arnold JJ, Gohara DW, Cameron CE (2004) Poliovirus RNA-Dependent RNA Polymerase (3Dpol): Pre-Steady-State Kinetic Analysis of Ribonucleotide Incorporation in the Presence of Mn2+. Biochemistry 43: 5138–5148. doi: 10.1021/bi035213q
[18]  Gohara DW, Arnold JJ, Cameron CE (2004) Poliovirus RNA-Dependent RNA Polymerase (3Dpol): Kinetic, Thermodynamic, and Structural Analysis of Ribonucleotide Selection. Biochemistry 43: 5149–5158. doi: 10.1021/bi035429s
[19]  Pfeiffer JK, Kirkegaard K (2003) A single mutation in poliovirus RNA-dependent RNA polymerase confers resistance to mutagenic nucleotide analogs via increased fidelity. Proc Natl Acad Sci USA 100: 7289–7294. doi: 10.1073/pnas.1232294100
[20]  Vignuzzi M, Stone JK, Arnold JJ, Cameron CE, Andino R (2006) Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population. Nature 439: 344–348. doi: 10.1038/nature04388
[21]  Korneeva VS, Cameron CE (2007) Structure-function relationships of the viral RNA-dependent RNA polymerase: fidelity, replication speed, and initiation mechanism determined by a residue in the ribose-binding pocket. J Biol Chem 282: 16135–16145. doi: 10.1074/jbc.m610090200
[22]  Kuchta RD, Mizrahi V, Benkovic PA, Johnson KA, Benkovic SJ (1987) Kinetic mechanism of DNA polymerase I (Klenow). Biochemistry 26: 8410–8417. doi: 10.1021/bi00399a057
[23]  Eger BT, Kuchta RD, Carroll SS, Benkovic PA, Dahlberg ME, et al. (1991) Mechanism of DNA replication fidelity for three mutants of DNA polymerase I: Klenow fragment KF (exo+), KF (polA5), and KF (exo？). Biochemistry 30: 1441–1448. doi: 10.1021/bi00219a039
[24]  Zinnen S, Hsieh JC, Modrich P (1994) Misincorporation and mispaired primer extension by human immunodeficiency virus reverse transcriptase. J Biol Chem 269: 24195–24202.
[25]  Tsai YC, Johnson KA (2006) A new paradigm for DNA polymerase specificity. Biochemistry 45: 9675–9687. doi: 10.1021/bi060993z
[26]  Dunlap CA, Tsai MD (2002) Use of 2-aminopurine and tryptophan fluorescence as probes in kinetic analyses of DNA polymerase. Biochemistry 41: 11226–11235. doi: 10.1021/bi025837g
[27]  Henzler-Wildman KA, Kern D (2007) Dynamic personalities of proteins. Nature 450: 964–972. doi: 10.1038/nature06522
[28]  Henzler-Wildman KA, Lei M, Thai V, Kerns SJ, Karplus M, et al. (2007) A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450: 913–916. doi: 10.1038/nature06407
[29]  Boehr DD, Nussinov R, Wright PE (2009) The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol 5: 789–796. doi: 10.1038/nchembio.232
[30]  Ma B, Nussinov R (2010) Enzyme dynamics point to stepwise conformational selection in catalysis. Curr Opin Chem Biol 14: 652–659. doi: 10.1016/j.cbpa.2010.08.012
[31]  Cameron CE, Moustafa IM, Arnold JJ (2009) Dynamics: the missing link between structure and function of the viral RNA-dependent RNA polymerase. Curr Opin Struct Biol 19: 768–774. doi: 10.1016/j.sbi.2009.10.012
[32]  Steitz TA (1993) DNA- and RNA-dependent DNA polymerases. Curr Opin Struct Biol 3: 31–38. doi: 10.1016/0959-440x(93)90198-t
[33]  Steitz TA, Steitz JA (1993) A general two-metal-ion mechanism for catalytic RNA. Proc Natl Acad Sci USA 90: 6498–6502. doi: 10.1073/pnas.90.14.6498
[34]  Castro C, Smidansky E, Maksimchuk KR, Arnold JJ, Korneeva VS, et al. (2007) Two proton transfers in the transition state for nucleotidyl transfer catalyzed by RNA and DNA-dependent RNA and DNA polymerases. Proc Natl Acad Sci USA 104: 4267–4272. doi: 10.1073/pnas.0608952104
[35]  Castro C, Smidansky ED, Arnold JJ, Maksimchuk KR, Moustafa I, et al. (2009) Nucleic acid polymerses use a general acid for nucleotidyl transfer. Nature Structural and Molecular Biology 16: 212–218. doi: 10.1038/nsmb.1540
[36]  McCammon JA, Gelin BR, Karplus M (1977) Dynamics of folded proteins. Nature 267: 585–590. doi: 10.1038/267585a0
[37]  Karplus M, McCammon JA (2002) Molecular dynamics simulations of biomolecules. Nature Structural Biology 9: 646–652. doi: 10.1038/nsb0902-646
[38]  Mackerell AD (2004) Empirical force fields for biological macromolecules: overview and issues. J Comput Chem 25: 1584–1604. doi: 10.1002/jcc.20082
[39]  Mackerell AD (2005) Empirical Force Fields for Proteins: Current Status and Future Directions. Annual Reports in Computational Chemistry 1: 91–102. doi: 10.1016/s1574-1400(05)01007-8
[40]  DeLano WL (2002) The PyMOL molecular graphics system. San Carlos (California): DeLano Scientific. Available: http://www.pymol.org. Accessed 26 February 2007.
[41]  Case DA, Darden TA, Cheatham III TE, Simmerling CL, Wang J, et al.. (2008) AMBER 10. San Francisco: University of California.
[42]  Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79: 926–935. doi: 10.1063/1.445869
[43]  Berendsen HJ, Postma JPM, Van Gunsteren WF, Dinola A, Haak JR (1984) Molecular-Dynamics with coupling to an external bath. J Chem Phys 81: 3684–3690. doi: 10.1063/1.448118
[44]  Ryckaert JP, Ciccotti G, Berendsen HJC (1977) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23: 327–341. doi: 10.1016/0021-9991(77)90098-5
[45]  Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an N·log(N) method for Ewald sums in large systems. J Chem Phys 98: 10089–10092. doi: 10.1063/1.464397
[46]  Shao J, Tanner SW, Thompson N, Cheatham TE (2007) Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms. J Chem Theory Comput 3: 2312–2334. doi: 10.1021/ct700119m
[47]  Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, et al.. (2009) Gaussian 09, Revision A.1. Wallingford (Connecticut): Gaussian Inc.
[48]  Kortus MG, Kempf BJ, Haworth KG, Barton DJ, Peersen OB (2012) A Template RNA Entry Channel in the Fingers Domain of the Poliovirus Polymerase. J Mol Biol 417: 263–278. doi: 10.1016/j.jmb.2012.01.049
[49]  Yang X, Smidansky ED, Maksimchuk KR, Lum D, Welch JL, et al. (2012) Motif D of Viral RNA-Dependent RNA polymerases Determines Efficiency and Fidelity of Nucleotide Addition. Structure 20: 1519–1527. doi: 10.1016/j.str.2012.06.012
[50]  Mowat CG, Ruth Moysey R, Miles CS, Leys D, Doherty MK, et al. (2001) Kinetic and Crystallographic Analysis of the Key Active Site Acid/Base Arginine in a Soluble Fumarate Reductase. Biochemistry 40: 12292–12298. doi: 10.1021/bi011360h
[51]  Schlippe YVG, Hedstrom L (2005) A twisted base? The role of arginine in enzyme-catalyzed proton abstractions. Archives of Biochemistry and Biophysics 433: 266–278. doi: 10.1016/j.abb.2004.09.018
[52]  Michielssens S, Moors SLC, Froeyen M, Herdewijn P, Ceulemans A (2011) tructural basis for the role of LYS220 as proton donor for nucleotidyl transfer in HIV-1 reverse transcriptase. Biophys Chem 157: 1–6. doi: 10.1016/j.bpc.2011.03.009

Full-Text

Contact Us

service@oalib.com

QQ:3279437679

WhatsApp +8615387084133