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., Ishima, R., 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.
65. Sharaf NG, Ishima R, Gronenborn AM. Conformational Plasticity of theNNRTI-Binding Pocket in HIV-1 Reverse Transcriptase: A Fluorine Nuclear Magnetic Resonance Study. Biochemistry. 2016 Jul 19;55(28):3864-73.
66. Ishima R Effects of radiation damping for biomolecular NMR experiments in solution: a hemisphere concept for water suppression. Concepts Magn Reson Part A Bridg Educ Res. 2015 Sep;44A(5):252-262.
67. Karki I, Christen MT, Spiriti J, Slack RL, Oda M, Kanaori K, Zuckerman DM, Ishima, R. Entire-Dataset Analysis of NMR Fast-Exchange Titration Spectra: A Mg(2+) Titration Analysis for HIV-1 Ribonuclease H Domain. J Phys Chem B. 2016 Dec 15;120(49):12420-12431.
68. Kirby KA, Myshakina NA, Christen MT, Chen YL, Schmidt HA, Huber AD, Xi Z, Kim S, Rao RK, Kramer ST, Yang Q, Singh K, Parniak MA, Wang Z, Ishima R, Sarafianos SG. A 2-Hydroxyisoquinoline-1,3-Dione Active-Site RNase H Inhibitor Binds in Multiple Modes to HIV-1 Reverse Transcriptase. Antimicrob Agents Chemother. 2017 Sep 22;61(10).
69. Sharaf NG, Xi Z, Ishima R, Gronenborn AM. The HIV-1 p66 homodimeric RT exhibits different conformations in the binding-competent and -incompetent NNRTI site. Proteins. 2017 Dec;85(12):2191-2197.
70. Khan SN, Persons JD, Paulsen JL, Guerrero M, Schiffer CA, Kurt-Yilmaz N, Ishima R. Probing Structural Changes among Analogous Inhibitor-Bound Forms of HIV-1 Protease and a Drug-Resistant Mutant in Solution by Nuclear Magnetic Resonance. Biochemistry. 2018 Mar 13;57(10):1652-1662.
71. Persons JD, Khan SN, Ishima R. An NMR strategy to detect conformational differences in a protein complexed with highly analogous inhibitors in solution. Methods. 2018 Sep 15;148:9-18.
72. Ilina TV, Slack RL, Elder JH, Sarafianos SG, Parniak MA, Ishima R. Effect of tRNA on the Maturation of HIV-1 Reverse Transcriptase. J Mol Biol. 2018 Jun 22;430(13):1891-1900.
73. Posner MG, Upadhyay A, Ishima R, Kalli AC, Harris G, Kremerskothen J, Sansom MSP, Crennell SJ, Bagby S. Distinctive phosphoinositide- and Ca2+-binding properties of normal and cognitive performance-linked variant forms of KIBRA C2 domain. J Biol Chem. 2018 Jun 15;293(24):9335-9344.
74. Oda M, Xi Z, Inaba S, Slack RL, Ishima R. Binding thermodynamics of metal ions to HIV-1 ribonuclease H domain,” J Therm Anal Calorim 2019 Mar;135(5):2647-2653.
75. Ishima R, Kurt-Yilmaz N, Schiffer CA. NMR and MD studies combined to elucidate inhibitor and water interactions of HIV-1 protease and their modulations with resistance mutations, J Biomol NMR, 2019, 73, 365-74. PMID: 31243634.
76. Lu M, Ishima R, Polenova T, Gronenborn AM. 19F NMR Relaxation Studies of Fluorosubstituted Tryptophans, J Biomol NMR, 2019, 73, 401-9.. PMID: 31435857
77. Slack RL, Ilina TV, Xi Z, Giacobbi NS, Kawai G, Parniak MA, Sarafianos SG, Sluis Cremer N, Ishima R. Conformational Changes in HIV-1 Reverse Transcriptase that Facilitate Its Maturation, Structure, 2019, 27, 1581-93. PMID: 31471129
78. Xi, Z, Wang Z, Xi Z, Sarafianos SG, Myshakina, NS, Ishima R. Determinants of Active-Site Inhibitor Interaction with HIV1 RNase H, ACS Infectious Diseases, 2019, 5, 1963-74. PMID: 31577424
79. Ilina TV, Slack RL, Guerrero M, Ishima R. Effect of Lysyl-tRNA Synthetase on the Maturation of HIV-1 Reverse Transcriptase., ACS Omega, 2020, 5, 16619-27. PMID: 32685828
80. Khan SN, Persons JD, Guerrero M, Ilina TV, Oda M, Ishima R. A synergy of activity, stability, and inhibitor-interaction of HIV-1 protease mutants evolved under drug-pressure, Protein Sci, 2020 Dec. in press, PMID: 33314454
81. Xi Z, Liu X, Lin R, Persons JD, Ilina TV, Li W, Dimitrov DS, Ishima R. The reduced form of the antibody CH2 domain. Protein Sci, 2021, 30, 1895-1903, PMID: 34107549
82. Baek DS, Kim YJ, Vergara S, Conard A, Adams C, Calero G, Ishima R, Mellors JW, Dimitrov DS. A highly-specific fully-human antibody and CAR-T cells targeting CD66e/CEACAM5 are cytotoxic for CD66e-expressing cancer cells in vitro and in vivo, Cancer Lett, 2022. 525, 97-107. PMID: 34740610
83. Emert-Sedlak L. Moukha-Chafiq O, Shi H, Du S, Alvarado J, Pathak V, Tanner S, Hunter R, Nebane M, Chen L, Ilina T, Ishima R, Zhang S, Kuzmichev Y, Wonderlich E, Schader S, Augelli-Szafran C, Ptak R, Smithgall, T. Inhibitors of HIV-1 Nef-mediated activation of the myeloid Src-family kinase Hck block HIV-1 replication in macrophages and disrupt MHC-I downregulation, ACS Infectious Dis, 2022. 8(1), 91-105. PMID: 34985256
84. Xi Z, Ilina TV, Guerrero M, Fan L, Sluis-Cremer N, Wang YX, Ishima R. Relative domain orientation of the L289K HIV-1 reverse transcriptase monomer. Protein Sci. 2022. 31. E4307. PMID: 35481647
85. Sun Z, Chu X, Adams C, Ilina VT, Guerrero M, Lin G, Chen C, Dontcho J, Ishima R, Wei L, Mellors JW, Calero G, Dimitrov DS. Preclinical assessment of a novel human antibody VH domain targeting mesothelin as an antibody-drug conjugate. Mol Ther Oncolytics, 2023, 31, 100726.
Reviews:
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., Ishima, R., 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.
17. Ilina TV, Xi Z, Brosenitsch TA, Sluis-Cremer, N, Ishima R. (2020) Large multidomain protein NMR: HIV-1 reverse transcriptase precursor in solution, Int J Mol Sci, PMID: 33333923.
18. Ilina TV, Xi Z, Brosenitsch T, Sluis-Cremer N, Ishima R. Retroviral RNase H: Structure, mechanism, and inhibition., Enzymes. 2021;50:227-247. PMID: 34861939