Publications

65. D.D. Boehr. 2024. Allosteric functions and inhibitions: Structural Insights. Front. Mol. Biosci.

64. Mondal, S., Sarvari, G. and D.D. Boehr. 2023. Picornavirus 3C proteins intervene in host cell processes through proteolysis and interactions with RNA. Viruses, 15, 2413.

63. Yu, J. and D.D. Boehr. 2023. Regulatory mechanisms triggered by enzyme interactions with lipid membrane surfaces. Front. Mol. Biosci. 10, 1306483.

62. D’Amico, R.N. and D.D. Boehr. 2023.Allostery, engineering and inhibition of tryptophan synthase. Curr. Opin. Struct. Biol., 82, 102657.

61. Topakas, E., D.D. Boehr and R. Wohlgemuth. 2022. Biocatalysis in analysis and synthesis – past, present and future. Catalysts, 12, 1626.

60. Winston, D.S. and D.D. Boehr. 2022. Catalyst-based biomolecular logic gates. Catalysts, 12, 712.

59. Winston, D.S., S.D. Gorman and D.D. Boehr. 2022. Conformational transitions in yeast chorismate mutase important for allosteric regulation as identified by nuclear magnetic resonance spectroscopy. J. Mol. Biol., 434, 167531.

58. Winston, D.S. and D.D. Boehr. 2021. Allosteric and dynamic control of RNA-dependent RNA polymerase function and fidelity. Enzymes, 49, 149-193.

57. D’Amico, R.N., Y.K. Bosken, K.F. O’Rourke, A.M. Murray, W. Admasu, C.A. Chang and D.D. Boehr. 2021. Substitution of a surface-exposed residue involved in an allosteric network enhances tryptophan synthase function in cells. Front. Mol. Biosci., 8, 679915.

56. Winston, D.S. and D.D. Boehr. 2021. The picornavirus precursor 3CD has different conformational dynamics compared to 3Cpro and 3Dpol in functionally relevant regions. Viruses, 13, 442.

55. O’Rourke, K.F., R.N. D’Amico, D. Sahu and D.D. Boehr. 2021. Distinct conformational dynamics and allosteric networks in alpha tryptophan synthase during active catalysis. Protein Sci., 30, 543-557.

54. D’Amico, R.N., A.M. Murray and D.D. Boehr. 2020. Driving protein conformational cycles in physiology and disease: “Frustrated” amino acid interaction networks define dynamic energy landscapes: Amino acid interaction networks change progressively along alpha tryptophan synthase’s catalytic cycle. Bioessays, 42, e2000092.

53. Gorman, S.D., D.S. Winston, D.Sahu and D.D. Boehr. 2020. Different solvent and conformational entropy contributions to the allosteric activation and inhibition mechanisms of yeast chorismate mutase. Biochemistry, 59, 2528-2540.

52. Gorman, S.D., R.N. D’Amico, D.S. Winston and D.D. Boehr. 2019. Engineering allostery into proteins. Adv. Exp. Med. Biol., 1163, 359-384.

51. Boehr, A.K., J.J. Arnold, H.S. Oh, C.E. Cameron and D.D. Boehr. 2019. 2’-C-Methylated nucleotides terminate virus RNA synthesis by preventing active site closure of the viral RNA-dependent RNA polymerase. J. Biol. Chem., J. Biol. Chem., 294, 16897-16907.

50. Gorman, S.D. and D.D. Boehr. 2019. Energy and enzyme activity landscapes of yeast chorismate mutase at cellular concentrations of allosteric effectors. Biochemistry, 58, 4058-4069.

49. Shi, J., J.M. Perryman, X. Yang, X. Liu, D.M. Musser, A.K. Boehr, I.M. Moustafa, J.J. Arnold, C.E. Cameron and D.D. Boehr. 2019. Rational control of poliovirus RNA-dependent RNA polymerase fidelity by modulating motif-D loop conformational dynamics. Biochemistry, 58, 3735-3743.

48. O’Rourke, K.F., D. Sahu, Y.K. Bosken, R.N. D’Amico, C.A. Chang and D.D. Boehr. 2019. Coordinated network changes across the catalytic cycle of alpha tryptophan synthase. Structure, 27, 1405-1415.

47. O’Rourke, K.F., J.M. Axe, R.N. D’Amico, D. Sahu and D.D. Boehr. 2018. Millisecond timescale motions connect amino acid interaction networks in alpha tryptophan synthase. Front. Mol. Biosci., 5:92.

46. Boehr, D.D. 2018. NMR methods of characterizing biomolecular structural dynamics and conformational ensembles. Methods, 148, 1-3.

45. Gorman, S.D., D. Sahu, K.F. O’Rourke and D.D. Boehr. 2018. Assigning methyl resonances for protein solution-state NMR studies. Methods, 148, 88-99.

44. Boehr, D.D., R.N. D’Amico and K.F. O’Rourke. 2018. Engineered control of enzyme structural dynamics and function. 2018. Protein Sci., 27(4), 825-838.

43. Shengjuler, D., Y.M. Chan, S. Sun, I.M. Moustafa, Z.L. Li, D.W. Gohara, M. Buck, P.S. Cremer, D.D. Boehr and C.E. Cameron. 2017. The RNA-binding site of poliovirus 3C protein doubles as a phosphoinositide-binding domain. Structure, 25, 1875-1886.

42. Yang, X., X. Liu, D.M. Musser, I.M. Moustafa, J.J. Arnold, C.E. Cameron and D.D. Boehr. 2017. Triphosphate reorientation of the incoming nucleotide as a fidelity checkpoint in viral RNA-dependent RNA polymerases. J. Biol. Chem., 292, 3810-3826.

41. O’Rourke, K.F., A.M. Jelowiki and D.D. Boehr. 2016. Controlling active site loop dynamics in the (β/α)8 barrel enzyme indole-3-glycerol phosphate synthase. Catalysts, 6, 129.

40. O’Rourke, K.F., S.D. Gorman and D.D. Boehr. 2016. Biophysical and computational methods to analyze amino acid interaction networks in proteins. Comput. Struct. Biotechnol. J., 14, 245-251.

39. Chan, Y.M., I.M. Moustafa, J.J. Arnold, C.E. Cameron and D.D. Boehr. 2016. Long-range communication between different functional sites in the picornaviral 3C protein. Structure, 24, 509-517.

38. Liu, X., D.M. Musser, C.A. Lee, X. Yang, J.J. Arnold, C.E. Cameron and D.D. Boehr. 2015. Nucleobase but not sugar fidelity is maintained in the Sabin I RNA-dependent RNA polymerase. Viruses, 7, 5571-5586.

37. Van der Linden, L., L. Vives-Adrian, B. Selisko, C. Ferrer-Orta, X. Liu, K. Lanke, R. Ulferts, A.M. De Palma, F. Tanchis, N. Goris, D. Lefebvre, K. De Clercq, P. Leyssen, C. Lacroix, G. Purstinger, B. Coutard, B. Canard, D.D. Boehr, J.J. Arnold, C.E. Cameron, N. Verdaguer, J. Neyts and F.J. van Kuppeveld. 2015. The RNA template channel of the RNA-dependent RNA polymerase as a target for development of antiviral therapy of multiple genera within a virus family. PLOS Pathog., 11, e1004733.

36. Axe, J.M., K.F. O’Rourke, N.E. Kerstetter, E.M. Yezdimer, Y.M. Chan, A. Chasin and D.D. Boehr. 2015. Severing of a hydrogen bond disrupts amino acid networks in the catalytically active state of the alpha subunit of tryptophan synthase. Protein Sci., 24, 484-494.

35. Moustafa, I.M., V.K. Korboukh, J.J. Arnold, E.D. Smidansky, L.L. Marcotte, D.W.Gohara, X. Yang, M.A. Sainchez-Farrain, D. Filman, J.K. Maranas, D.D. Boehr, J.M. Hogle, C.M. Colina and C.E. Cameron. 2014. Structural dynamics as a contributor to error-prone replication by a RNA-dependent RNA polymerase. J. Biol. Chem., 289, 36229-36248.

34. Boehr, D.D., X. Liu and X. Yang. 2014. Targeting structural dynamics of the RNA-dependent RNA polymerase for anti-viral strategies. Curr. Opin. Virol., 9, 194-200.

33. Axe, J.M., E.M. Yezdimer, K.F. O’Rourke, N.E. Kerstetter, W. You, C.E. Chang and D.D. Boehr. 2014. Amino acid networks in a (β/α)8 barrel enzyme change during catalytic turnover. J. Am. Chem. Soc., 136, 6818-6821.

32. Boehr, D.D. 2014. The ins and outs of viral RNA polymerase translocation. J. Mol. Biol., 426, 1373-1376.

31. Zaccardi, M.J., K.F. O’Rourke, E.M. Yezdimer, L.J. Loggia, S. Woldt and D.D. Boehr. 2014. Loop-loop interactions govern multiple steps in indole-3-glycerol phosphate synthase catalysis. Protein Sci., 23, 302-311.

30. Liu, X., X. Yang, C.A. Lee, I.M. Moustafa, E.D. Smidansky, D. Lum, J.J. Arnold, C.E. Cameron and D.D. Boehr. 2013. Vaccine-derived mutation in motif D of poliovirus RNA-dependent RNA polymerase lowers nucleotide incorporation fidelity. J. Biol. Chem., 288, 32753-32765.

29. Zaccardi, M.J., E.M. Yezdimer and D.D. Boehr. 2013. Functional identification of the general acid and base in the dehydration step of indole-3-glycerol phosphate synthase catalysis. J. Biol. Chem., 288, 26350-26356.

28. Boehr, D.D., J.J. Arnold, I.M. Moustafa and C.E. Cameron. 2013. Structure, dynamics and fidelity of RNA-dependent RNA polymerases. Nucleic Acids and Molecular Biology, 30, 309-333.

27. Boehr, D.D., J.R. Schnell, D. McElheny, S.H. Bae, B.M. Duggan, S.J. Benkovic, H.J. Dyson and P.E. Wright. 2013. A distal mutation perturbs dynamic amino acid networks in dihydrofolate reductase. Biochemistry, 52, 4605-4619.

26. Axe, J.M. and D.D. Boehr. 2013. Long-range interactions in the alpha subunit of tryptophan synthase help to coordinate ligand binding, catalysis and substrate channeling. J. Mol. Biol., 425, 1527-1545.

25. Yang, X., E.D. Smidansky, K.R. Maksimchuk, D. Lum, J.L. Welch, J.J. Arnold, C.E. Cameron and D.D. Boehr. 2012. Motif D of viral RNA-dependent RNA polymerases determines efficiency and fidelity of nucleotide addition. Structure, 20, 1519-1527.

24. Weikl, T.R. and D.D. Boehr. 2012. Conformational selection and induced changes along the catalytic cycle of Escherichia.coli dihydrofolate reductase. Proteins, 80, 2369-2383.

23. Zaccardi, M.J., O. Mannweiler and D.D. Boehr. 2012. Differences in the catalytic mechanisms of mesophilic and thermophilic indole-3-glycerol phosphate synthase enzymes at their adaptive temperatures. Biochem. Biophys. Res. Comm., 418, 324-329.

22. D.D. Boehr. 2011. Promiscuity in protein-RNA interactions: Conformational ensembles facilitate molecular recognition in the spliceosome: Conformational diversity in U2AF(65) facilitates binding to diverse RNA sequences. Bioessays, 34, 174-180.

21. Yang, X., J.L. Welch, Arnold, J.J. and D.D. Boehr. 2010. Long-range interaction networks in the function and fidelity of poliovirus RNA-dependent RNA polymerase studied by nuclear magnetic resonance. Biochemistry, 49, 9361-9371.

20. Boehr, D.D., D. McElheny, H.J. Dyson and P.E. Wright. 2010. Millisecond timescale fluctuations in dihydrofolate reductase are exquisitely sensitive to the bound ligands. PNAS, 107, 1373-1378.

19. Boehr, D.D. During transitions proteins make fleeting bonds. 2009. Cell, 139, 1049-1051.

18. Boehr, D.D., R. Nussinov and P.E. Wright. 2009. The role of dynamic conformational ensembles in biomolecular recognition. Nat. Chem. Biol., 5, 789-796.

17. Boehr, D.D. and P.E. Wright. 2008. How do proteins interact? Science, 320, 1429-1430.

16. Boehr, D.D., H.J. Dyson and P.E. Wright. 2008. Conformational relaxation following hydride transfer plays a limiting role in dihydrofolate reductase catalysis. Biochemistry, 47, 9227-9233.

15. Boehr, D.D., D. McElheny, H.J. Dyson and P.E. Wright. 2006. The dynamic energy landscape of dihydrofolate reductase catalysis. Science, 313, 1638-1642.

14. Boehr, D.D., H.J. Dyson and P.E. Wright. 2006. An NMR perspective on enzyme dynamics. Chem. Rev., 106, 3055-3079.

13. Boehr, D.D., A.R. Farley, F.J. LaRonde, T.R. Murdock, G.D. Wright and J.R. Cox. 2005. Establishing the principles of recognition in the adenine-binding region of an aminoglycoside antibiotic kinase [APH(3’)-IIIa]. Biochemistry, 44, 12445-12453.

12. Boehr, D.D., I. Moore. and G.D. Wright. 2005. Aminoglycoside Resistance Mechanisms. In Frontiers in Antibiotic Resistance A Tribute to Stuart B. Levy, D.G. White, M.N. Alekshum, P.F. McDermott, Eds., Blackwell. pp. 85-100.

11. Boehr, D.D., D.M. Daigle and G.D. Wright. 2004. Domain-domain interactions in the aminoglycoside antibiotic resistance enzyme AAC(6′)-APH(2″). Biochemistry 43: 9846-9855.

10. Draker, K.A., D.D. Boehr, N.H. Elowe, T.J. Noga and G.D. Wright. 2003. Functional annotation of putative aminoglycoside antibiotic modifying proteins in Mycobacterium tuberculosis H37Rv. J. Antibiot. 56: 135-142.

9. Boehr, D.D., K.A. Draker, K. Koteva, M. Bains, R.E. Hancock and G.D. Wright. 2003. Broad-spectrum peptide inhibitors of aminoglycoside antibiotic resistance enzymes. Chem. Biol. 10: 189-196.

8. Boehr, D.D., S.I. Jenkins and G.D. Wright. 2003. The molecular basis of the expansive substrate specificity of the antibiotic resistance enzyme aminoglycoside acetyltransferase-6′-aminoglycoside phosphotransferase-2″. The role of ASP-99 as an active site base important for acetyl transfer. J. Biol. Chem. 278: 12873-12880.

7. Boehr, D.D., K.A. Draker and G.D. Wright. 2003. Aminoglycoside and aminocyclitols in Antibiotic and Chemotherapy: Anti-infective agents and their use in therapy. (Eds. Finch, R.G., Greenwood, D., Norrby, S.R. and Whitley, R.J.) Churchill Livingstone, Edingburgh, 155-184.

6. Boehr, D.D., A.R. Farley, G.D. Wright and J.R. Cox. 2002. Analysis of the pi-pi stacking interactions between the aminoglycoside antibiotic kinase APH(3′)-IIIa and its nucleotide ligands. Chem. Biol. 9: 1209-1217.

5. Thompson, P.R., D.D. Boehr, A.M. Berghuis and G.D. Wright. 2002. Mechanism of aminoglycoside antibiotic kinase APH(3′)-IIIa: role of the nucleotide positioning loop. Biochemistry 41: 7001-7007.

4. Boehr, D.D., W.S. Lane and G.D. Wright. 2001. Active site labeling of the gentamicin resistance enzyme AAC(6′)-APH(2″) by the lipid kinase inhibitor wortmannin. Chem. Biol. 8: 791-800.

3. Boehr, D.D., P.R. Thompson and G.D. Wright. 2001. Molecular mechanism of aminoglycoside antibiotic kinase APH(3′)-IIIa: roles of conserved active site residues. J. Biol. Chem. 276: 23929-23936.

2. Sucheck, S.J., A.L. Wong, K.M. Koeller, D.D. Boehr, K.A. Draker, P. Sears, G.D. Wright and C.H. Wong. 2000. Design of bifunctional antibiotics that target bacterial rRNA and inhibit resistance-causing enzymes. J. Am. Chem. Soc. 122:5230-5231.

1. Weselake, R.J., E.C. Kazala, K. Cianflone, D.D. Boehr, C.K. Middleton, C.D. Rennie, A. Laroche, I. Recnik. 2000. Human acylation stimulating protein enhances triacylglycerol biosynthesis in plant microsomes. FEBS Lett. 481: 189-192.