Kinetoplastid RNA editing ligases 1 and 2 exhibit different electrostatic properties

Journal of Molecular Modeling

Volumn 16, Issue 1, 2010, Pages 61-76

  Shaneh, Alireza ^a   Salavati, Reza ^a  

^a MCGILL UNIVERSITY   (Canada)

Author keywords

Editosome; Electrostatic potential energy; Homology modeling; Kinetoplastid RNA editing ligases; Poisson Boltzmann equation; RNA editing

Indexed keywords

KINETOPLASTID RNA EDITING LIGASE 1; KINETOPLASTID RNA EDITING LIGASE 2; LIGASE; UNCLASSIFIED DRUG;

ACIDITY; ALKALINITY; AMINO TERMINAL SEQUENCE; ARTICLE; BINDING AFFINITY; COMPUTER MODEL; ENZYME ANALYSIS; ENZYME BINDING; ENZYME STRUCTURE; ENZYME SUBSTRATE; ISOELECTRIC POINT; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; RNA EDITING;

AMINO ACID SEQUENCE; BINDING SITES; KINETOPLASTIDA; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; RNA EDITING; RNA LIGASE (ATP); SEQUENCE HOMOLOGY, AMINO ACID; STATIC ELECTRICITY; SUBSTRATE SPECIFICITY; TRYPANOSOMA;

KINETOPLASTIDA;

EID: 71349085267     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-009-0506-1     Document Type: Article

References (63)

1. A Schnaufer GJ Domingo KD Stuart 2002 Natural and induced dyskinetoplastid trypanosomatids: how to live without mitochondrial DNA Int J Parasitol 32 9 1071 1084 10.1016/S0020-7519(02)00020-6 1:CAS:528: DC%2BD38XltFWjsL8%3D (Pubitemid 34761901)
2. KR Matthews 2005 The developmental cell biology of Trypanosoma brucei J Cell Sci 118 2 283 290 10.1242/jcs.01649 1:CAS:528:DC%2BD2MXhslymtbY%3D (Pubitemid 40277341)
3. Benne R (1993) RNA editing: the alteration of protein coding sequences of RNA. Horwood, New York
4. A Horvàth EA Berry DA Maslov 2000 Translation of the edited mRNA for Cytochrome b in Trypanosome Mitochondria Science 287 5458 1639 1640 10.1126/science.287.5458.1639 (Pubitemid 30127762)
5. A Horváth TG Kingan DA Maslov 2000 Detection of the mitochondrially encoded Cytochrome c oxidase subunit I in the Trypanosomatid Protozoan Leishmania tarentolae. Evidence for translation of unedited mRNA in the kinetoplast J Biol Chem 275 22 17160 17165 10.1074/jbc.M907246199 (Pubitemid 30398963)
6. B Blum N Bakalara L Simpson 1990 A model for RNA editing in kinetoplastid mitochondria: RNA molecules transcribed from maxicircle DNA provide the edited information Cell 60 189 198 10.1016/0092-8674(90)90735-W 1:CAS:528: DyaK3cXkvFahtbw%3D (Pubitemid 20055914)
7. L Simpson R Aphazizhev G Gao X Kang 2004 Mitochondrial proteins and complexes in Leishmania and Trypanosoma involved in U-insertion/deletion RNA editing RNA 10 2 159 170 10.1261/rna.5170704 1:CAS:528:DC%2BD2cXpsVSisw%3D%3D (Pubitemid 38129820)
8. J Lukeš H Hashimi A Zíková 2005 Unexplained complexity of the mitochondrial genome and transcriptome in kinetoplastid flagellates Curr Genet 48 5 277 299 10.1007/s00294-005-0027-0 (Pubitemid 41683417)
9. K Stuart K Schnaufer NL Ernst AK Panigrahi 2005 Complex management: RNA editing in trypanosomes Trends Biochem Sci 30 2 97 105 10.1016/j.tibs.2004.12. 006 1:CAS:528:DC%2BD2MXhtV2gsrY%3D (Pubitemid 40187302)
10. R Aphasizhev 2007 RNA editing Mol Biol 41 2 227 239 10.1134/ S0026893307020057 1:CAS:528:DC%2BD2sXksF2kt7c%3D (Pubitemid 46663966)
11. R Aphasizhev I Aphasizheva RE Nelson L Simpson 2003 A 100-kD complex of two RNA-binding proteins from mitochondria of Leishmania tarentolae catalyzes RNA annealing and interacts with several RNA editing components RNA 9 1 62 76 10.1261/rna.2134303 1:CAS:528:DC%2BD3sXhtFahs7o%3D (Pubitemid 36206303)
12. E Vondrušková J van den Burg A Zíková NL Ernst K Stuart R Benne J Lukeš 2005 RNA interference analyses suggest a transcript-specific regulatory role for mitochondrial RNA-binding Proteins MRP1 and MRP2 in RNA editing and other RNA processing in Trypanosoma brucei J Biol Chem 280 4 2429 2438 10.1074/jbc.M405933200 (Pubitemid 40189342)
13. M Schumacher E Karamooz A Zíková L Trantírek J Lukeš 2006 Crystal structures of T. brucei MRP1/MRP2 guide-RNA binding complex reveal RNA matchmaking mechanism Cell 126 4 701 711 10.1016/j.cell.2006. 06.047 1:CAS:528:DC%2BD28Xpt1aktbY%3D (Pubitemid 44255808)
14. AK Panigrahi SP Gygi NL Ernst RP Igo Jr SS Palazzo A Schnaufer DS Weston N Carmean R Salavati R Aebersold KD Stuart 2001 Association of two novel proteins, TbMP52 and TbMP48, with the Trypanosoma brucei RNA editing complex Mol Cell Biol 21 2 380 389 10.1128/MCB.21.2.380-389.2001 1:CAS:528: DC%2BD3MXhsFyht7g%3D (Pubitemid 32037359)
15. LN Rusché CE Huang KJ Piller M Hemann E Wirtz B Sollner-Webb 2001 The two RNA ligases of the Trypanosoma brucei RNA editing complex: cloning the essential band IV gene and identifying the band V gene Mol Cell Biol 21 4 979 989 10.1128/MCB.21.4.979-989.2001 (Pubitemid 32114948)
16. MT McManus M Shimamura J Grams SL Hajduk 2001 Identification of candidate mitochondrial RNA editing ligases from Trypanosoma brucei RNA 7 2 167 175 10.1017/S1355838201002072 1:CAS:528:DC%2BD3MXitlSlu78%3D (Pubitemid 33590500)
17. J Cruz-Reyes AG Zhelonkina CE Huang B Sollner-Webb 2002 Distinct functions of two RNA ligases in active Trypanosoma brucei RNA editing complexes Mol Cell Biol 22 13 4652 4660 10.1128/MCB.22.13.4652-4660.2002 1:CAS:528:DC%2BD38Xks1yrsbo%3D (Pubitemid 34620401)
18. EA Worthey A Schnaufer IS Mian K Stuart R Salavati 2003 Comparative analysis of editosome proteins in trypanosomatids Nucl Acids Res 31 22 6392 6408 10.1093/nar/gkg870 1:CAS:528:DC%2BD3sXptVCjtr4%3D (Pubitemid 37508743)
19. SS Palazzo AK Panigrahi RP Igo Jr R Salavati K Stuart 2003 Kinetoplastid RNA editing ligases: complex association, characterization, and substrate requirements Mol Biochem Parasito 127 2 161 167 10.1016/S0166-6851(02)00333-X 1:CAS:528:DC%2BD3sXisV2ltbs%3D (Pubitemid 36369691)
20. G Gao AM Simpson X Kang K Rogers M Nebohacova F Li L Simpson 2005 Functional complementation of Trypanosoma brucei RNA in vitro editing with recombinant RNA ligase Proc Natl Acad Sci U S A 102 13 4712 4717 10.1073/pnas.0500553102 1:CAS:528:DC%2BD2MXjt1Oiu70%3D (Pubitemid 40471519)
21. A Schnaufer AK Panigrahi B Panicucci RP Igo Jr R Salavati K Stuart 2001 An RNA ligase essential for RNA editing and survival of the bloodstream form of Trypanosoma brucei Science 291 5511 2159 2162 10.1126/science.1058655 1:CAS:528:DC%2BD3MXitFCltb8%3D (Pubitemid 32224448)
22. CE Huang J Cruz-Reyes AG Zhelonkina S O'Hearn E Wirtz B Sollner-Webb 2001 Roles for ligases in the RNA editing complex of Trypanosoma brucei: band IV is needed for U-deletion and RNA repair The EMBO J 20 17 4694 4703 10.1093/emboj/20.17.4694 1:CAS:528:DC%2BD3MXnt1Cmt7g%3D (Pubitemid 32848623)
23. M Drozdz SS Palazzo R Salavati J O'Rear C Clayton K Stuart 2002 TbMP81 is required for RNA editing in Trypanosoma brucei EMBO J 21 7 1791 1799 10.1093/emboj/21.7.1791 1:CAS:528:DC%2BD38XjtVOgtLg%3D (Pubitemid 34614635)
24. G Gao L Simpson 2003 Is the Trypanosoma brucei REL1 RNA ligase specific for U-deletion RNA editing, and is the REL2 RNA ligase specific for U-insertion editing? J Biol Chem 278 30 27570 27574 10.1074/jbc.M303317200 1:CAS:528:DC%2BD3sXlsFKktrs%3D (Pubitemid 36899942)
25. J Deng A Schnaufer R Salavati KD Stuart GJ Hol 2004 High resolution crystal structure of a key editosome enzyme from Trypanosoma brucei: RNA editing ligase 1 J Mol Biol 343 3 601 613 10.1016/j.jmb.2004.08.041 1:CAS:528:DC%2BD2cXot1Wrt70%3D (Pubitemid 39311608)
26. A Schnaufer NL Ernst SS Palazzo J O'Rear R Salavati K Stuart 2003 Separate insertion and deletion subcomplexes of the Trypanosoma brucei RNA editing complex Mol Cell 12 2 307 319 10.1016/S1097-2765(03)00286-7 1:CAS:528:DC%2BD3sXnt12qt7g%3D (Pubitemid 37238918)
27. AG Murzin 1993 OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences EMBO J 12 3 861 867 1:CAS:528:DyaK3sXit1ymtLc%3D
28. AJ Doherty SW Suh 2000 Structural and mechanistic conservation in DNA ligases Nucleic Acids Res 28 21 4051 4058 10.1093/nar/28.21.4051 1:CAS:528:DC%2BD3cXovFKrurY%3D
29. RE Amaro RV Swift JA McCammon 2007 Functional and structural insights revealed by molecular dynamics simulations of an essential RNA editing ligase in Trypanosoma brucei PLoS Negl Trop Dis 1 2 e68 10.1371/journal.pntd.0000068 (Pubitemid 352024652)
30. X Kang G Gao K Rogers AM Falick S Zhou L Simpson 2006 Reconstitution of full-round uridine-deletion RNA editing with three recombinant proteins Proceedings of the National Academy of Sciences 103 38 13944 13949 10.1073/pnas.0604476103 1:CAS:528:DC%2BD28XhtVCqs7vI (Pubitemid 44452962)
31. HM Berman J Westbrook Z Feng G Gilliland TN Bhat H Weissig IN Shindyalov PE Bourne 2000 The protein data bank Nucleic Acids Res 28 1 235 242 10.1093/nar/28.1.235 1:CAS:528:DC%2BD3cXhvVKjt7w%3D
32. LJ Henderson 1908 Concerning the relationship between the strength of acids and their capacity to preserve neutrality Am J Physiol 21 4 173 179 1:CAS:528:DyaD1cXmt1Cl
33. KA Hasselbalch 1917 Die Berechnung der Wasserstoffzahl des Blutes aus der freien und gebunden Kohlensäure desselben, und die Sauerstoffbindung des Blutes als Funktion der Wasserstoffzahl Biochemische Zeitschrift 78 112 144
34. JB Olmsted 1986 Microtubule-associated proteins Annu Rev Cell Biol 2 1 421 457 10.1146/annurev.cb.02.110186.002225 1:CAS:528:DyaL2sXksFOktg%3D%3D
35. GS Bloom SA Endow 1994 Motor proteins. 1: kinesins Protein Profile 1 10 1059 1116 1:CAS:528:DyaK2MXltlCmu74%3D
36. SF Altschul TL Madden AA Schaffer J Zhang Z Zhang W Miller DJ Lipman 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res 25 17 3389 3402 10.1093/nar/25.17.3389 1:CAS:528:DyaK2sXlvFyhu7w%3D (Pubitemid 27359211)
37. S Henikoff JG Henikoff 1992 Amino acid substitution matrices from protein blocks Proc Natl Acad Sci U S A 89 22 10915 10919 10.1073/pnas.89.22.10915 1:CAS:528:DyaK3sXjsFCgsQ%3D%3D
38. RC Edgar 2004 MUSCLE: a multiple sequence alignment method with reduced time and space complexity BMC Bioinformatics 5 1 113 10.1186/1471-2105-5-113 (Pubitemid 40195393)
39. CD Michener RR Sokal 1957 A quantitative approach to a problem in classification Evolution 11 2 130 162 10.2307/2406046
40. Sneath PHA, Sokal RB (1973) Numerical taxonomy: the principles and practice of numerical classification. W.H. Freeman, San Francisco
41. C Notredame DG Higgins J Heringa 2000 T-Coffee: a novel method for fast and accurate multiple sequence alignment J Mol Biol 302 1 205 217 10.1006/jmbi.2000.4042 1:CAS:528:DC%2BD3cXmtVGntr8%3D (Pubitemid 30694431)
42. K Katoh K Misawa K Kuma T Miyata 2002 MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform Nucleic Acids Res 30 14 3059 3066 10.1093/nar/gkf436 1:CAS:528:DC%2BD38XlslOqu7s%3D
43. A Šali TL Blundell 1993 Comparative protein modelling by satisfaction of spatial restraints J Mol Biol 234 3 779 815 10.1006/jmbi.1993. 1626 (Pubitemid 24007801)
44. MY Shen A Šali 2006 Statistical potential for assessment and prediction of protein structures Protein Sci 15 11 2507 2524 10.1110/ps.062416606 1:CAS:528:DC%2BD28XhtFygsrfO (Pubitemid 44771688)
45. R Lüthy JU Bowie D Eisenberg 1992 Assessment of protein models with three-dimensional profiles Nature 356 6364 83 85 10.1038/356083a0
46. W Kabsch C Sander 1983 Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 12 2577 2637 10.1002/bip.360221211 1:CAS:528:DyaL2cXkslegtQ%3D%3D
47. I Klapper R Hagstrom R Fine K Sharp B Honig 1986 Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification Proteins: Structure, Function, and Genetics 1 1 47 59 10.1002/prot.340010109 1:CAS:528:DyaL2sXhsFWisw%3D%3D (Pubitemid 17073401)
48. MK Gilson B Honig 1988 Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis Proteins: Structure, Function, and Genetics 4 1 7 18 10.1002/prot.340040104 1:CAS:528:DyaL1MXitVOnuw%3D%3D
49. A Nicholls B Honig 1991 A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation J Comp Chem 12 4 435 445 10.1002/jcc.540120405 1:CAS:528:DyaK3MXisFCgtr0%3D
50. W Rocchia E Alexov B Honig 2001 Extending the applicability of the nonlinear Poisson-Boltzmann equation: multiple dielectric constants and multivalent ions J of Phys l Chem B 105 28 6754 6754 10.1021/jp012279r 1:CAS:528:DC%2BD3MXksFelsbY%3D (Pubitemid 35339047)
51. TA Halgren 1996 Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94 J Comp Chem 17 5 & 6 490 519 10.1002/(SICI)1096-987X(199604)17:5/6<490::AID-JCC1>3.0.CO;2-P 1:CAS:528:DyaK28XhvVGmsbk%3D
52. TA Halgren 1996 Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions J Comp Chem 17 5 & 6 520 552 10.1002/(SICI)1096-987X(199604)17:5/6<520::AID-JCC2>3.0.CO;2-W 1:CAS:528:DyaK28XhvVGmsbY%3D
53. TA Halgren 1996 Merck molecular force field. III. Molecular geometries and vibrational frequencies for MMFF94 J Comp Chem 17 5 & 6 553 586 10.1002/(SICI)1096-987X(199604)17:5/6<553::AID-JCC3>3.0.CO;2-T 1:CAS:528:DyaK28XhvVGmsbc%3D
54. TA Halgren RB Nachbar 1996 Merck molecular force field. IV. Conformational energies and geometries for MMFF94 J Comp Chem 17 5 & 6 587 615 1:CAS:528:DyaK28XhvVGmtr4%3D
55. TA Halgren 1996 Merck molecular force field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules J Comp Chem 17 5 & 6 616 641 10.1002/(SICI)1096-987X(199604)17:5/6<616::AID- JCC5>3.0.CO;2-X 1:CAS:528:DyaK28XhvVGmtr8%3D
56. TA Halgren 1999 MMFF VI. MMFF94s option for energy minimization studies J Comp Chem 20 7 720 729 10.1002/(SICI)1096-987X(199905)20:7<720::AID- JCC7>3.0.CO;2-X 1:CAS:528:DyaK1MXjtVSlsrc%3D
57. TA Halgren 1999 MMFF VII. Characterization of MMFF94, MMFF94s, and other widely available force fields for conformational energies and for intermolecular-interaction energies and geometries J Comp Chem 20 7 730 748 10.1002/(SICI)1096-987X(199905)20:7<730::AID-JCC8>3.0.CO;2-T 1:CAS:528:DyaK1MXjtVSls7s%3D
58. N Blomberg RR Gabdoulline M Nilges RC Wade 1999 Classification of protein sequences by homology modeling and quantitative analysis of electrostatic similarity Proteins: Str, Function and Genetics 37 379 387 10.1002/(SICI)1097- 0134(19991115)37:3<379::AID-PROT6>3.0.CO;2-K 1:CAS:528:DyaK1MXntFOjsb0%3D (Pubitemid 29519728)
59. RC Wade RR Gabdoulline F DeRienzo 2001 Protein interaction property similarity analysis Int J Quant Chem 83 122 127 10.1002/qua.1204 1:CAS:528:DC%2BD3MXjsVCgsro%3D
60. RC Wade RR Gabdoulline F DeRienzo 2007 qPIPSA: relating enzymatic kinetic parameters and interaction fields BMC Bioinformatics 8 373 10.1186/1471-2105-8- 373
61. Richter S, Wenzel A, Stein M, Gabdoulline RR, Wade RC (2008) webPIPSA: a web server for the comparison of protein interaction properties. Nucleic Acid Res,Web server early access, 36:W276Crossed D signW280
62. EE Hodgkin WG Richards 1987 Molecular similarity based on electrostatic potential and electric field Int J Quant Chem Quant Biol Symp 14 105 110 10.1002/qua.560320814 1:CAS:528:DyaL1cXktlOgsrc%3D
63. T Kortemme DE Kim D Baker 2004 Computational alanine scanning of protein-protein interfaces Sci STKE 2004 219 pl2 10.1126/stke.2192004pl2