Publications

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82. Green KD, Punetha A, Hou C, Garneau-Tsodikova S* and Tsodikov OV*. (2019) Probing the robustness of inhibitors of tuberculosis aminoglycoside resistance enzyme Eis by mutagenesis. ACS Infect. Dis., 5, 1772-1778.

81. Hou C, Rohr J*, Parkin S* and Tsodikov OV*. (2019) How mithramycin stereochemistry dictates its structure and DNA binding function. MedChemComm, 10, 735-741. (* co-corresponding authors)

80. Mori S#, Pang AH#, Thamban Chandrika N, Garneau-Tsodikova S* and Tsodikov OV*. (2019) Unusual substrate and halide versatility of phenolic halogenase PltM. Nat. Commun., 10, 1255. (# first co-authors, * co-corresponding authors)

79. Hou C and Tsodikov OV. (2019) Utilizing guanine coordinated Zn2+ to determine DNA crystal structures by single-wavelength anomalous diffraction. Acta Cryst. D., 75, 32-40

78. Holbrook SYL, Gentry MS, Tsodikov OV* and Garneau-Tsodikova S*. (2018) Nucleoside triphosphate cosubstrates control the substrate profile and efficiency of aminoglycoside 3'-O-phosphotransferase type IIa. MedChemComm, 9, 1332-1339. (* co-corresponding authors)

77. Pang AH, Obiero JM, Kulczyk AW, Sviripa VM and Tsodikov OV. (2018) A crystal structure of coil 1B of vimentin in the filamentous form provides a model of a high-order assembly of a vimentin filament. FEBS J., 285, 2888-2899.

76. Ngo HX, Green KD,  Gajadeera C, Willby MJ, Holbrook SYL, Hou C, Garzan A, Mayhoub AS, Posey JE*, Tsodikov OV* and Garneau-Tsodikova S*. (2018) Potent 1,2,4-triazino[5,6b]indole-3-thioether inhibitors of the kanamycin resistance enzyme Eis from Mycobacterium tuberculosis. ACS Infect. Dis., 41030-1040. (* co-corresponding authors)

75. Hou C, Biswas T and Tsodikov OV. (2018) Structures of the catalytic domain of bacterial primase DnaG in complexes with DNA provide insight into key priming events. Biochemistry, 57, 2084-2093.

74. Mori S#, Pang AH#, Lundy TA, Garzan A, Tsodikov OV* and Garneau-Tsodikova S*. (2018) Structural basis for backbone N-methylation by an interrupted adenylation domain. Nat. Chem. Biol., 14, 428-430. (# first co-authors, * co-corresponding authors)

73. Green KD, Biswas T, Pang AH, Willby MJ, Reed MS, Stuchlik O, Pohl J, Posey JE, Tsodikov OV* and Garneau-Tsodikova S*. (2018) Acetylation by Eis and deacetylation by Rv1151c of Mycobacterium tuberculosis HupB: biochemical and structural insight. Biochemistry, 57, 781-790. (* co-corresponding authors)

72. Thamban Chandrika N, Shrestha SK, Ngo HX, Tsodikov OV, Howard KC and Garneau-Tsodikova S. (2018) Alkylated piperazines and piperazine-azole hybrids as antifungal agents. J. Med. Chem., 61158-173.

71. Mori S, Garzan A, Tsodikov OV and Garneau-Tsodikova S. (2017) Deciphering Nature's intricate way of N,S-dimethylating L-cysteine: sequential action of two bifunctional adenylation domainsBiochemistry, 566087-6097.

70. Garzan A#, Willby MJ#, Ngo HX, Gajadeera C, Green KD, Holbrook SYL, Hou C, Posey JE*, Tsodikov OV* and Garneau-Tsodikova S*. (2017) Combating Eis-mediated kanamycin resistance of M. tuberculosis by novel pyrrolo[1,5-a]pyrazine-based Eis inhibitors. ACS Infect. Dis., 3, 302-309. (# first co-authors, * co-corresponding authors)

69. Pang AH, Garneau-Tsodikova S and Tsodikov OV. (2017) In vitro assays to identify antibiotics targeting DNA metabolism. Methods Mol. Biol., 1520, 175-200.

68. Garzan A, Willby MJ, Green KD, Gajadeera CS, Hou C, Tsodikov OV*, Posey JE* and Garneau-Tsodikova S*. (2016) Sulfonamide-based inhibitors of aminoglycoside acetyltransferase Eis abolish resistance to kanamycin in Mycobacterium tuberculosis. J. Med. Chem., 5910619-10628. (* co-corresponding authors)

67. Garzan A, Willby MJ, Green KD, Tsodikov OV, Posey JE* and Garneau-Tsodikova S*. (2016) Discovery and optimization of two Eis inhibitor families as kanamycin adjuvants against drug-resistant M. tuberculosisACS Med. Chem. Lett., 71219-1221. (* co-corresponding authors)

66. Pang AH#, Garzan A#, Larsen MJ, McQuade TJ, Garneau-Tsodikova S* and Tsodikov OV*. (2016) Discovery of allosteric and selective inhibitors of inorganic pyrophosphatase from Mycobacterium tuberculosisACS Chem. Biol., 113084-3092. (# first co-authors, * co-corresponding authors)

65. Hou C, Weidenbach S, Cano KE, Wang Z, Mitra P, Ivanov DN*, Rohr J* and Tsodikov OV*. (2016) Structures of mithramycin analogues bound to DNA and implications for targeting transcription factor FLI1Nucleic Acids Res., 44,  8990-9004. (* co-corresponding authors)

64. Willby MJ, Green KD, Gajadeera CS, Hou C, Tsodikov OV*, Posey JE* and Garneau-Tsodikova S*. (2016) Potent inhibitors of acetyltransferase Eis overcome kanamycin resistance in Mycobacterium tuberculosis. ACS Chem. Biol., 11, 1639-1646. (* co-corresponding authors)

63. Meyer P, Socias S, Key J, Ransey E, Tjon EC, Buschiazzo A, Lei M, Botka C, Withrow J, Neau DB, Rajashankar K, Anderson KS, Baxter R, Blacklow S, Boggon T, Bonvin A, Borek D, Brett T, Caflisch A, Chang C-I, Chazin W, Corbett KD, Cosgrove M, Crosson S, Dhe-Paganon S, Di Cera E, Drennan C, Eck M, Eichman B, Fan Q, Ferre-D'Amare A, Fraser JS, Fromme JC, Garcia K, Gaudet R, Gong P, Harrison S, Heldwein E, Jia Z, Keenan R, Kruse A, Kvansakul M, McLellan J, Modis Y, Nam Y, Otwinowski Z, Pai EF, Pereira PJB, Petosa C, Raman CS, Rapoport T, Roll-Mecak A, Rosen M, Rudenko G, Schlessinger J, Schwartz T, Shamoo Y, Sondermann H, Tao Y, Tolia N, Tsodikov OV, Westover KD, Wu H, Foster I, Maia F, Gonen T, Kirchhausen T, Diederichs K, Crosas M and Sliz P. (2016) Data publication with the structural biology data grid supports live analysis. Nat. Commun., 7, 10882.

62. Weidenbach S, Hou C, Chen J-M, Tsodikov OV* and Rohr J*. (2016) Dimerization and DNA recognition rules of mithramycin and its analogues. J. Inorg. Biochem., 156, 40-47. (* co-corresponding authors)

61. Hou C and Tsodikov OV. (2015) Structural basis for dimerization and DNA binding of transcription factor FLI1. Biochemistry54, 7365-7374.

60. Sviripa VM, Burikhanov R, Obiero JM, Yuan Y, Nickell JR, Dwoskin LP, Zhan C, Liu C, Tsodikov OV*, Rangnekar VM* and Watt DS*. (2015) Par-4 secretion: Stoichiometry of 3-Arylquinone binding to vimentin. Org. Biomol. Chem., 14, 74-84. (* co-corresponding authors)

59. Pang AH, Garneau-Tsodikova S and Tsodikov OV. (2015) Crystal structure of halogenase PltA from the pyoluteorin biosynthetic pathway. J. Struct. Biol., 192, 347-357.

58. Pratt AC, Dewage SW, Pang AH, Biswas T, Barnard-Britson S, Cisneros GA* and Tsodikov OV*. (2015) Structural and computational dissection of the catalytic mechanism of the inorganic pyrophosphatase from Mycobacterium tuberculosis. J. Struct Biol., 192, 76-87. (* co-corresponding authors)

57. Yatchang MF, LeVine H, Green KD, Tsodikov OV and Garneau-Tsodikova S. (2015) Effects of structural modifications on the metal binding, anti-amyloid activity and cholinesterase inhibitory activity of chalcones. Org. Biomol. Chem., 13, 9418-9426.

56. Tsodikov OV*, Hou C, Walsh CT and Garneau-Tsodikova S*. (2015) Crystal structure of O-methyltransferase CalO6 from the calicheamicin biosynthetic pathway: a case of challenging structure determination at low resolution. BMC Struct. Biol., 15, 13. (* co-corresponding authors)

55. Green KD, Biswas T, Chang C, Wu R, Chen W, Janes BK, Chalupska D, Gornicki P, Hanna PC, Tsodikov OV, Joachimiak A and Garneau-Tsodikova S. (2015) Biochemical and structural analysis of an Eis family aminoglycoside acetyltransferase from Bacillus anthracis. Biochemistry, 54, 3197-3206.

54. Leggas D and Tsodikov OV. (2015) Determination of small crystal structures from a minimum set of diffraction intensities by homotopy continuation. Acta Crystallogr. A (Foundations of Crystallography), 71, 319-324.

53. Chen J-M, Hou C, Wang G, Tsodikov OV* and Rohr J*. (2015) Structural insight into MtmC, a bifunctional ketoreductase-methyltransferase involved in the assembly of the mithramycin trisaccharide chain. Biochemistry, 54, 2481-2489. (* co-corresponding authors)

52. Gajadeera CS, Zhang X, Wei Y* and Tsodikov OV*. (2015) Structure of inorganic pyrophosphatase from Staphylococcus aureus reveals conformational flexibility of the active site. J. Struct. Biol., 189, 81-86. (* co-corresponding authors)

51. Gajadeera C#, Willby M#, Green KD, Shaul P, Fridman M, Garneau-Tsodikova S*, Posey JE* and Tsodikov OV*. (2015) Antimycobacterial activity of DNA intercalator inhibitors of Mycobacterium tuberculosis primase DnaG. J. Antibiot., 68, 153-157. (# first co-authors, * co-corresponding authors)

50. Sviripa VM, Zhang W, Balia AG, Tsodikov OV, Nickell JR, Gizard F, Yu T, Lee EY, Dwoskin LP, Liu C and Watt DS. (2014) 2',6'-dihalostyrylanilines, pyridines and pyrimidines for the inhibition of the catalytic subunit of methionine S-adenosyltransferase-2 (MAT2A). J. Med. Chem., 57, 6083-6091.

49. De-Donatis GM, Zhao Z, Wang S, Huang LP, Schwartz C, Tsodikov OV, Zhang H, Haque F and Guo P. (2014) Finding of widespread viral and bacterial revolution dsDNA translocation motors distinct from rotation motors by channel chirality and size. Cell Biosci. 4:30.

48. Al-Asadi A, Leggas D and Tsodikov OV. (2014) Ambiguity of structure determination from a minimum of diffraction intensities. Acta Crystallogr. A (Foundations of Crystallography), 70, 354-357.

47. Tsodikov OV*, Green KD and Garneau-Tsodikova S*. (2014) A random sequential mechanism of aminoglycoside acetylation by Mycobacterium tuberculosis Eis protein. PLoS One, 9, e92370. (* co-corresponding authors)

46. Biswas T*, Green KD, Garneau-Tsodikova S and Tsodikov OV*. (2013) Discovery of inhibitors of Bacillus anthracis primase DnaG. Biochemistry, 52, 6905-6910. (* co-corresponding authors)

45. Guinn EJ#, Kontur WS#, Tsodikov OV#, Shkel I and Record MT Jr. (2013) Probing the protein folding mechanism using solutes and heat capacity changes. Proc. Natl. Acad. Sci. U. S. A., 110, 16784-16789. (# first co-authors) Related commentary: Revealing what gets buried first in protein folding, by Tobin Sosnick and Michael Baxa.

44. Diehl RC, Guinn E, Capp MW, Tsodikov OV and Record MT Jr. (2013) Quantifying additive interactions of the osmolyte proline with individual groups of proteins: comparisons with urea and glycine betaine, interpretation of m-values. Biochemistry, 52, 5997-6010.

43. Houghton JL#, Biswas T#, Chen W, Tsodikov OV* and Garneau-Tsodikova S*. (2013) Chemical and structural insights into the regioversatility of the aminoglycoside acetyltransferase Eis. ChemBioChem. 16, 2127-2135. (# first co-authors, * co-corresponding authors)

42. Larrouy-Maumus G#, Biswas T#, Hunt DM, Kelly G, Tsodikov OV* and de Carvalho LPS*. (2013) Discovery of a glycerol 3-phosphate phosphatase reveals glycerophospholipid polar head recycling in Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. U. S. A., 110, 11320-11325. (# first co-authors, * co-corresponding authors)

41. Small JL, O'Donoghue AJ, Boritsch EC, Tsodikov OV, Knudsen GM, Vandal O, Craik CS and Ehrt S. (2013) Substrate specificity of MarP, a periplasmic protease required for resistance to acid and oxidative stress in Mycobacterium tuberculosis. J. Biol. Chem., 288, 12489-12499.

40. Furman R, Biswas, T, Danhart EM, Foster MP, Tsodikov OV and Artsimovitch I. (2013) DksA2, a zinc-independent structural analog of the transcription factor DksA. FEBS Lett., 587, 614-619.

39. Furman R, Tsodikov OV, Wolf YI and Artsimovitch I. (2013) An insertion in the catalytic trigger loop gates the secondary channel of RNA polymerase. J. Mol. Biol., 425, 82-93.

38. Biswas T, Resto-Roldan E, Sawyer SK, Artsimovitch I and Tsodikov OV. (2013) A novel non-radioactive primase-pyrophosphatase activity assay and its application to the discovery of inhibitors of Mycobacterium tuberculosis primase DnaG. Nucleic Acids Res., 41, e56.

37. Malik S, Willby M, Sikes D, Tsodikov OV and Posey JE. (2012) New insights into fluoroquinolone resistance in Mycobacterium tuberculosis: functional genetic analysis of gyrA and gyrB mutations. PLoS One, 7, e39754.

36. Chen W, Green KD, Tsodikov OV and Garneau-Tsodikova S. (2012) Aminoglycoside multiacetylating activity of the Enhanced Intracellular Survival protein from Mycobacterium smegmatis and its inhibition. Biochemistry, 51, 4959-4967.

35. Biswas T#, Houghton JL#, Garneau-Tsodikova S* and Tsodikov OV*. (2012) The structural basis for substrate versatility of chloramphenicol acetyltransferase CATI. Protein Sci., 21, 520-530. (# first co-authors, * co-corresponding authors)

34. Al-Asadi A, Chudin E, Tsodikov OV. (2012) Enumeration of one-dimensional crystal structures obtained from a minimum of diffraction intensities. Acta Crystallogr. A (Foundations of Crystallography), 68, 313-318.

33. Chen W, Biswas T (first co-author), Porter VR, Tsodikov OV*, Garneau-Tsodikova S*. (2011) Unusual regioversatility of acetyltransferase Eis, a cause of drug resistance in XDR-TB. Proc. Natl. Acad. Sci. U. S. A., 108, 9804-9808. (* co-corresponding authors)

32. Tsodikov OV*, Biswas T*. (2011) Structural and thermodynamic signatures of DNA recognition by Mycobacterium tuberculosis DnaA. J. Mol. Biol., 410, 461-476. (* co-corresponding authors)

31. Shkel I, Lee HS, Tsodikov OV. (2011) Conditional ambiguity of one-dimensional crystal structures determined from a minimum of diffraction intensity data. Acta Crystallogr. A (Foundations of Crystallography), 67, 292-296.

30. Biswas T, Small J, Vandal O, Odaira T, Deng H, Ehrt S*, Tsodikov OV*. (2010) Structural insight into serine protease Rv3671c that protects M. tuberculosis from oxidative and acidic stress. Structure, 18, 1353-1363. (*co-corresponding authors)

29. Biswas T, Tsodikov OV. (2010) An easy-to-use tool for planning and modeling a calorimetric titration. Anal. Biochem. 406, 91-93.

28. Biswas T, Zolova OE, Lombo F, de la Calle F, Salas JA, Tsodikov OV*, Garneau-Tsodikova S*. (2010) A new scaffold of an old protein fold ensures binding to the bisintercalator thiocoraline. J. Mol. Biol., 397, 495-507. (*co-corresponding authors)

27. Orelli B, McClendon TB, Tsodikov OV, Ellenberger T, Niedernhofer LJ, Scharer OD. (2010) The XPA-binding domain of ERCC1 is required for nucleotide excision repair but not other DNA repair pathways. J. Biol. Chem., 285, 3705-3712.

26. Biswas T, Yi L, Aggarwal P, Wu J, Rubin JR, Stuckey JA, Woodard RW*, Tsodikov OV*. (2009) The tail of KdsC: Conformational changes control the activity of a haloacid dehalogenase superfamily phosphatase. J. Biol. Chem., 284, 30594-30603. (*co-corresponding authors)

25. Biswas T, Pero JM, Joseph GC, Tsodikov OV. (2009) DNA-dependent ATPase activity of bacterial XPB helicases. Biochemistry, 48, 2839-2848.

24. Garneau-Tsodikova SG, Shkel IA, Tsodikov OV. (2009) Exact and user-friendly kinetic analysis of the two-step rapid equilibrium Michaelis-Menten mechanism. Anal. Biochem., 387, 276-279.

23. McQuade TJ, Shallop AD, Sheoran A, DelProposto JE, Tsodikov OV, Garneau-Tsodikova S. (2009) A non-radioactive high-throughput assay for screening and characterization of adenylation domains for nonribosomal peptide combinatorial biosynthesis. Anal. Biochem., 386, 244-250.

22. Bagwell CE, Bhat S, Hawkins GM, Smith BW, Biswas T, Hoover TR, Saunders E, Han CS, Tsodikov OV, Shimkets LJ. (2008) Survival in nuclear waste, extreme resistance, and potential applications gleaned from the genome sequence of Kineococcus radiotolerans SRS30216. PLoS One, 3M, e3878.

21. Biswas T, Tsodikov OV. (2008) Hexameric ring structure of the N-terminal domain of Mycobacterium tuberculosis DnaB helicase. FEBS J., 275, 3064-3071.

20. Tsodikov OV, Ivanov D (first co-author), Orelli B, Staresincic L, Shoshani I, Oberman R, Scharer OD, Wagner G, Ellenberger T. (2007) Structural basis for the recruitment of ERCC1-XPF to nucleotide excision repair complexes by XPA. EMBO J., 26, 4768-76.

19. Ivanov D, Tsodikov OV (first co-author), Kasanov J, Ellenberger T, Wagner G, Collins T. (2007) Domain-swapped dimerization of the HIV-1 capsid C-terminal domain. Proc. Natl. Acad. Sci. U. S. A., 104, 4353-8.

18. Pascal JM, Tsodikov OV, Hura GL, Song W, Cotner EA, Classen S, Tomkinson AE, Tainer JA, Ellenberger T. (2006) A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA. Mol. Cell., 24, 279-91.

17. Tsodikov OV, Enzlin JH, Scharer OD, Ellenberger T. (2005) Crystal structure and DNA binding functions of ERCC1, a subunit of the DNA structure-specific endonuclease XPF-ERCC1. Proc. Natl. Acad. Sci. U. S. A., 102, 11236-41.

16. Cox JM, Tsodikov OV, Cox MM. (2005) Organized unidirectional waves of ATP hydrolysis within a RecA filament. PLoS Biology, 3, 231-243.

15. Saecker RM, Tsodikov OV, Capp MW, Record MT Jr. (2003) Rapid quench mixing to quantify kinetics of steps in association of Escherichia coli RNA polymerase with promoter DNA. Methods Enzymol., 370, 535-546.

14. Saecker RM, Tsodikov OV (first co-author), McQuade KL, Schlax PE, Capp MW, Record MT Jr. (2002) Kinetic studies and structural models of the association of E. coli σ70 RNA polymerase with the λPR promoter: Large scale conformational changes in forming the kinetically significant intermediates. J. Mol. Biol., 319, 649-671.

13. Tsodikov OV*, Record MT Jr, Sergeev YV. (2002) Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature. J. Comp. Chem., 23, 600-609(* corresponding author)

12. Tsujikawa L, Tsodikov OV, deHaseth PL. (2002) Interaction of RNA polymerase with forked DNA: evidence for two kinetically significant intermediates on the pathway to the final complex. Proc. Natl. Acad. Sci. U. S. A., 99, 3493-3498.

11. Shkel IA, Tsodikov OV, Record MT Jr. (2002) Asymptotic solution of the cylindrical nonlinear Poisson-Boltzmann equation at low salt concentration: Analytic expressions for surface potential and preferential interaction coefficient. Proc. Natl. Acad. Sci. U. S. A., 99, 2597-2602.

10. Tsodikov OV, Holbrook JA, Shkel IA, Record MT Jr. (2001) Analytic binding isotherms describing competitive interactions of a protein ligand with specific and nonspecific sites on the same DNA oligomer. Biophys. J., 81, 1960-1969.

9. Holbrook JA, Tsodikov OV, Saecker RM, Record MT Jr. (2001) Specific and non-specific interactions of integration host factor with DNA: Thermodynamic evidence for disruption of multiple IHF surface salt-bridges coupled to DNA binding. J. Mol. Biol., 310, 379-401.

8. Shkel IA, Tsodikov OV, Record MT Jr. (2000) Complete asymptotic solution of cylindrical and spherical Poisson-Boltzmann equations at experimental salt concentrations. J. Phys. Chem. B., 104, 5161-5170.

7. Tsodikov OV, Saecker RM, Melcher SE, Levandoski MM, Frank DE, Capp MW, Record MT Jr. (1999) Wrapping of flanking non-operator DNA in lac repressor-operator complexes: Implications for DNA looping. J. Mol. Biol., 294, 639-655.

6. Arenson TA, Tsodikov OV, Cox MM. (1999) Quantitative analysis of kinetics of end-dependent disassembly of RecA filaments from ssDNA. J. Mol. Biol., 288, 391-401.

5. Tsodikov OV, Record MT Jr. (1999) General method of analysis of kinetic equations for multistep reversible mechanisms in the signe-exponential regime: Application to kinetics of open complex formation between Eσ70 RNA polymerase and λPR promoter DNA. Biophys. J., 76, 1320-1329.

4. Craig ML, Tsodikov OV, McQuade KL, Schlax PE, Capp MW, Saecker RM, Record MT Jr. (1998) DNA footprints of the two kinetically significant intermediates in formation of an RNA polymerase-promoter open complex: Evidence that interactions with start site and downstream DNA induce sequential conformational changes in polymerase and DNA. J. Mol. Biol., 283, 741-756.

3. Tsodikov OV, Craig ML, Saecker RM, Record MT Jr. (1998) Quantitative analysis of multiple-hit footprinting studies to characterize DNA conformational changes in protein-DNA complexes: Application to DNA opening by Eσ70 RNA polymerase. J. Mol. Biol., 283, 757-769.

2. Frank DE, Saecker RM, Bond JP, Capp MW, Tsodikov OV, Melcher SE, Levandoski MM, Record MT Jr. (1997) Thermodynamics of the interactions of lac repressor with variants of the symmetric lac operator: Effect of converting a consensus site to a non-specific site. J. Mol. Biol., 267, 1186-120.

1. Levandoski MM, Tsodikov OV, Frank DE, Melcher SE, Saecker RM, Record MT Jr. (1996) Cooperative and anticooperative effects in binding of the first and second plasmid Osym operators to a LacI tetramer: Evidence for contributions of non-operator DNA binding by wrapping and looping. J. Mol. Biol., 260, 697-717.