Research Topics

Publication List

Selected Articles:

38. Ishima, R. and Torchia, D. A. (2006) Accuracy of optimized chemical-exchange parameters derived by fitting CPMG R2 dispersion profiles when R20a ≠ R20b, J. Biomol. NMR, 34, 209-219.

39. Gong, Q. & Ishima, R. (2007) 15N-{1H} NOE experiment at high magnetic field strengths. J. Biomol. NMR, 37, 147-157.

40. Ishima, R., Torchia, D. A., and Louis, J. M. (2007) Mutational and structural studies aimed at characterizing the monomer of HIV-1 protease and its precursor.  J. Biol. Chem. 282, 17190-17199.

41. Chang, S. L., Hinck, A. P., Ishima, R. (2007) “Model-free analysis for large proteins at high magnetic field strengths” J. Biomol. NMR, 38, 315-324.

42.  Louis, J. M. and Ishima, R. (2007) “A diverse view of protein dynamics from NMR studies of HIV-1 protease flaps”, Proteins, 70, 1408-1415

43.  Jee, J.G., Ishima, R., & Gronenborn, A.M. (2008) “Characterization of specific protein association by 15N CPMG relaxation dispersion NMR: the GB1A34F monomer-dimer equilibrium.”, J. Phys. Chem. B., 112, 6008-6012.

44. Sayer, J.M.,. Liu, F., Ishima, R., Weber, I.T. & Louis, J. M. (2008) “Effect of the active-site D25N mutation on the structure, stability, and ligand binding of the mature HIV-1 protease”. J. Biol. Chem. 283, 13459-13457.

45. Miklóssy, G., Tözsér, G., Kádas, J., Ishima, R.,  Louis, J. M., and Bagossi, P.  (2008)  Novel macromolecular inhibitors of HIV-1 protease, Protein Eng Des Sel.  21, 453-61

46. Myint, W. Gong, Q., &   Ishima, R. (2009) Practical aspects of 15N CPMG transverse relaxation experiments for proteins in solution. Concepts in Magnetic Resonance, A34, 63-75

47. Gong, R., Vu, B. K., Feng, Y., Prieto, D. A., Dyba, M. A.. Walsh, J. D., Prabakaran, P., Veenstra, T. D., Tarasov, S. G., Ishima, R., Dimitrov, D. S. (2009) Engineered Human antibody constant domains with increased stability. J. Biol. Chem., 284, 14203-14210.

48. Xiao, X., Feng, Y., Vu, B. ,  Ishima, R., Dimitrov, D. S. (2009) A large library based on a novel (CH2) scaffold: Identification on HIV-1 inhibitors. Biochem. Biophys. Res. Commu., 387, 387-392.

49. Myint, W., & Ishima, R. (2009) Chemical exchange effects during refocusing pulses in constant-time CPMG relaxation dispersion experiments, J. Biomol NMR, 45, 207-216.

50. Ishima, R., Gong, Q., Tie, Y., Weber, I.T., & Louis, J.M. (2009) Highly conserved glycine 86 and arginine 87 residues contribute differently to the structure and activity of the mature HIV-1 protease, Proteins, 78(4):1015-25.

51. Louis, J.M., Ishima, R., Aniana, A., & Sayer, J. M. (2009) Revealing the Dimer Dissociation and Existence of a Folded Monomer of the Mature HIV-2 Protease, Protein Sci., 18, 2442-2453.

52. Walsh, J.D., Meier, K., Ishima, R., & Gronenborn, A. M. (2010) NMR Studies on Domain Diffusion and Alignment in Modular GB1 Repeats, Biophys J. 99, 2636-46.

53. Gong, Q., Menon, L., Ilina, T., Miller, L.G., Ahn, J., Parniak, M.A., & Ishima, R. (2011) Interaction of HIV-1 Reverse Transcriptase Ribonuclease H with an Acylhydrazone Inhibitor, Chemical Biology & Drug Design, 77, 39-47.

54. Myint, W., Gong, Q., Ahn, J., & Ishima, R. (2011) Characterization of Sarcoplasmic Reticulum Ca2+ ATPase Nucleotide Binding Domain Mutants using NMR spectroscopy, Biochem Biophys Res Commun, 405, 19-23.

55. Xu, X., Ishima, R.+, & Ames, J.B. + (2011) Conformational Dynamics of Recoverin’s Ca2+-myristoyl Switch Probed by 15N NMR Relaxation Dispersion and Chemical Shift Analysis, Proteins, 79. 1910-22. (co-corresponding authors)

56. Webb, C., Upadhyay, A., Giuntini, F., Eggleston, I., Furutani-Seiki, M., Ishima, R. & Bagby, S. (2011) Structural features and ligand binding properties of tandem WW domains from YAP and TAZ, nuclear effectors of the Hippo pathway. Biochemistry, 50, 3300-9.

57. Myint, W., Cai, Y., Schiffer, C. & Ishima, R. (2012) Quantitative comparison of errors in 15N transverse relaxation rates measured using various CPMG phasing schemes. J Biomol NMR, 53, 13-23.

58. Cai, Y., Yilmaz, N.K., Myint, W., Ishima, R. & Schiffer, C. (2012) Differential Flap Dynamics in Wild-type and a Drug Resistant Variant of HIV-1 Protease Revealed by Molecular Dynamics and NMR Relaxation. J Chem. Theory Comput. 8, 3452-62

59. Liriano,  M.A., Varney, K.M., Wright, N.T., Hoffman, C.L.,  Toth, E.A., IshimaR., and Weber, D.J. (2012) Target binding to S100B reduces dynamic properties and increases Ca2+-binding affinity for wild type and EF-hand mutant proteins. J Mol Biol. 423, 365-85

60. Christen1, M.T., Menon, L., Myshakina, N.A., Ahn, J., Parniak, M.A. & Ishima, R. (2012) Structural Basis of the Allosteric Inhibitor Interaction on the HIV-1 Reverse Transcriptase RNase H domain. Chemical Biology & Drug Design, 80, 706-16

61. Ishima, R. (2014) A probe to monitor performance of 15N longitudinal relaxation experiments for proteins in solution, J Biomol NMR, 58, 113-22.

62. Cai, Y., Myint, W., Paulsen, J., Schiffer, C., Ishima, R. & Yilmaz, N.K. (2014) Drug Resistance Mutations Alter Dynamics of Inhibitor-Bound HIV-1 Protease. J Chem Theory Comput. 8, 3452-62.

63. Sharaf, N.G, Poliner, E., Slack, R.L., Christen, M.T., Byeon, I.J., Parniak, M.A., Gronenborn, A.M. & Ishima, R. (2014) The p66 immature precursor of HIV-1 reverse transcriptase, Proteins, 80, 706-16.

64. Slack, R.L., Spiriti, J., Ahn, J. Parniak. A.M., Zuckerman, D.M. & Ishima, R. (2015) Structural Integrity of the Ribonuclease H domain in HIV-1 Reverse Transcriptase. Proteins, 83, 1526-38.

65. Sharaf, N.G., Ishima, R. & Gronenborn A.M. (2016) Conformational Plasticity of the NNRTI-Binding Pocket in HIV-1 Reverse Transcriptase: A Fluorine Nuclear Magnetic Resonance Study. Biochemistry, 55, 3864-73.

66. Ishima, R. (2016) Effects of radiation damping for biomolecular NMR experiments in solution: a hemisphere concept for water suppression. Concepts in Magnetic Resonance, 44A, 252-262.

67. Karki, I., Christen, M. T., Spiriti, J., Slack, R.L., Oda, M., Kanaori, K., Zuckerman, D.M. & Ishima, R. (2016) Entire-Dataset Analysis of NMR Fast-Exchange Titration Spectra: A Mg2+ Titration Analysis for HIV-1 Ribonuclease H Domain. J Phys Chem B, 120, 12420-31.

68. Kirby K.A., Myshakina N.A., Christen M.T., Chen Y.L., Schmidt H.A., Huber A.D., Xi Z., Kim S., Rao R.K., Kramer S.T., Yang Q., Singh K., Parniak M.A., Wang Z., Ishima, R. & Sarafianos S.G. (2017) A 2-Hydroxyisoquinoline-1,3-Dione Active-Site RNase H Inhibitor Binds in Multiple Modes to HIV-1 Reverse Transcriptase. Antimicrob Agents Chemother. 61(10). pii: e01351-17.

69. Sharaf N.G., Xi Z., Ishima, R. & Gronenborn A.M. (2017) The HIV-1 p66 homodimeric RT exhibits different conformations in the binding-competent and -incompetent NNRTI site. Proteins, 85, 2191-7.

70. Khan, S.N., Persons, J.D., Paulsen, J.L., Guerrero, M,. Schiffer, C.A., Kurt-Yilmaz, N. & Ishima, R. (2018) Probing Structural Changes among Analogous Inhibitor-Bound Forms of HIV-1 Protease and a Drug-Resistant Mutant in Solution by Nuclear Magnetic Resonance. Biochemistry, 57, 1652-62.

71. Persons, J.D., Khan, S.N. & Ishima, R. (2018) An NMR strategy to detect conformational differences in a protein complexed with highly analogous inhibitors in solution. Methods. pii: S1046-2023(18)30014-8.

72. Ilina, T.V., Skack, R.L. Elder, J.H., Sarafianos, S.G., Parniak, M.A. & Ishima, R. (2018) Effect of tRNA on the maturation of HIV-reverse transcriptase. J Mol Biol., 430, 1891-1900.

73. Posner M.G., Upadhyay A., Ishima R., Kalli A.C., Harris G., Kremerskothen J., Sansom M.S.P., Crennell S.J. & Bagby S. (2018) Distinctive phosphoinositide- and Ca2+-binding properties of normal and cognitive performance-linked variant forms of KIBRA C2 domain. J Biol Chem, 293, 9335-44.


6. Louis, J. M., Torchia, D. A., Ishima, R. & Weber, I. T. (2007) HIV-1 protease: structure, dynamics and inhibition.  In: HIV-1: Molecular Biology and Pathogenetics, Adv. Pharmacol. Vol.55, 261-298,  Ed. Jeang, K.T., Elsevier.

7. Vu, B.K., Walsh, J., Dimitrov, D., and Ishima, R. (2009) Dynamics of domain antibodies studied by solution NMR.  In, Therapeutic Antibodies: Methods and Protocols (Methods in Molecular Biology), Ed. Dimitrov, A.S. Chapter 29, Humana Press.

8. Yanamala, N., Dutta, A., Bec, B., van Fleet, B., Hay, K., Yazbak, A., IshimaR., Doemling A., & Klein-Seetharaman, J. (2009) NMR-based screening of membrane protein ligands, Chemical Biology & Drug Design, 75, 237-56.

9. Ishima, R. Short entry of “Relaxation Dispersion” in Encyclopedia of Biophysics  (2010), Ed. Roberts. G., Springer.

10. Ishima, R. (2011) Recent Developments in 15N NMR Relaxation Studies that Probe Protein Backbone Dynamics, Chapt 5, Topics in Current Chemistry, Ed. Zhu, G., Springer-Verlag Berlin Heidelberg (in press).

11. Ishima, R. (2012) Current progress in the NMR relaxation experiments to detect protein dynamics (in Japanese), Biophysics (The Biophysical Society of Japan), 52, 242-245.

12. Ilina, T., Labarge, K., Sarafianos, S.G., Ishima, R. & Parniak, P.A. (2012) Inhibitors of HIV-1 reverse transcriptase-associated ribonuclease H activity, Biology, 1, 521-41.

13. Ishima, R. (2013) CPMG Relaxation dispersion experiment. In, Protein Dynamics (Methods in Molecular Biology), Ed. Dennis Livesay, Humana Press. 1084, Chapter 2.

14. Ishima, R. (2014) CPMG Relaxation dispersion experiment. In, Protein Dynamics (Methods in Molecular Biology), Ed. Dennis Livesay, Humana Press. 1084, Chapter 2.

15. Ishima, R. (2015) Protein-inhibitor interaction studies using NMR, in e-Book Series on Application of NMR Spectroscopy in “Molecular Identification”, edited by Prof. Atta-ur-Rahman, FRS and Dr. M. Iqbal Choudhary, Bentham Science Publishers.

16. Ishima, R. & Bagby, S. (2016) Protein dynamics revealed by CPMG dispersion in Modern Magnetic Resonance, 2nd edition, Springer. 1-17.