Year |
Citation |
Score |
2021 |
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 Science : a Publication of the Protein Society. PMID 34107549 DOI: 10.1002/pro.4142 |
0.722 |
|
2020 |
Ilina TV, Xi Z, Brosenitsch T, Sluis-Cremer N, Ishima R. Large Multidomain Protein NMR: HIV-1 Reverse Transcriptase Precursor in Solution. International Journal of Molecular Sciences. 21. PMID 33333923 DOI: 10.3390/ijms21249545 |
0.311 |
|
2020 |
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 Science : a Publication of the Protein Society. PMID 33314454 DOI: 10.1002/pro.4013 |
0.768 |
|
2019 |
Xi Z, Wang Z, Sarafianos SG, Myshakina NS, Ishima R. Determinants of Active-Site Inhibitor Interaction with HIV-1 RNase H. Acs Infectious Diseases. PMID 31577424 DOI: 10.1021/Acsinfecdis.9B00300 |
0.416 |
|
2019 |
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 (London, England : 1993). PMID 31471129 DOI: 10.1016/J.Str.2019.08.004 |
0.333 |
|
2019 |
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. Journal of Biomolecular Nmr. PMID 31243634 DOI: 10.1007/S10858-019-00260-6 |
0.446 |
|
2019 |
Oda M, Xi Z, Inaba S, Slack RL, Ishima R. Binding thermodynamics of metal ions to HIV-1 ribonuclease H domain. Journal of Thermal Analysis and Calorimetry. 135: 2647-2653. PMID 30853849 DOI: 10.1007/S10973-018-7445-Y |
0.332 |
|
2018 |
Ilina TV, Slack RL, Elder JH, Sarafianos SG, Parniak MA, Ishima R. Effect of tRNA on the Maturation of HIV-Reverse Transcriptase. Journal of Molecular Biology. PMID 29751015 DOI: 10.1016/J.Jmb.2018.02.027 |
0.302 |
|
2018 |
Posner MG, Upadhyay A, Ishima R, Kalli AC, Harris G, Kremerskothen J, Sansom MSP, Crennell SJ, Bagby S. Distinctive phosphoinositide and Ca binding properties of normal and cognitive performance-linked variant forms of KIBRA C2 domain. The Journal of Biological Chemistry. PMID 29724824 DOI: 10.1074/Jbc.Ra118.002279 |
0.329 |
|
2018 |
Persons JD, Khan SN, Ishima R. An NMR strategy to detect conformational differences in a protein complexed with highly analogous inhibitors in solution. Methods (San Diego, Calif.). PMID 29656080 DOI: 10.1016/J.Ymeth.2018.04.005 |
0.762 |
|
2018 |
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. PMID 29457713 DOI: 10.1021/Acs.Biochem.7B01238 |
0.772 |
|
2018 |
Ishima R, Persons J, Khan S. Backbone 1H, 13C, and 15N Chemical Shift Assignments of HIV-1 Protease (Flap + mutant) bound to Darunavir Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr27377 |
0.398 |
|
2017 |
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, et al. A 2-hydroxyisoquinoline-1,3-dione active site RNase H inhibitor binds in multiple modes to HIV-1 reverse transcriptase. Antimicrobial Agents and Chemotherapy. PMID 28760905 DOI: 10.1128/Aac.01351-17 |
0.363 |
|
2017 |
Slack RL, Sharaf NG, Gronenborn AM, Ishima R. Structural Characteristics of the RNAse H Domain in HIV-1 Reverse Transcriptase Biophysical Journal. 112: 487a. DOI: 10.1016/J.Bpj.2016.11.2635 |
0.328 |
|
2016 |
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. The Journal of Physical Chemistry. B. 120: 12420-12431. PMID 27973819 DOI: 10.1021/Acs.Jpcb.6B08323 |
0.361 |
|
2016 |
Sharaf NG, Ishima R, Gronenborn AM. Conformational plasticity of the NNRTI-binding pocket in HIV-1 reverse transcriptase - A fluorine NMR study. Biochemistry. PMID 27163463 DOI: 10.1021/Acs.Biochem.6B00113 |
0.428 |
|
2015 |
Ishima R. Effects of radiation damping for biomolecular NMR experiments in solution: a hemisphere concept for water suppression. Concepts in Magnetic Resonance. Part a, Bridging Education and Research. 44: 252-262. PMID 27524944 DOI: 10.1002/Cmr.A.21360 |
0.305 |
|
2015 |
Slack RL, Spiriti J, Ahn J, Parniak MA, Zuckerman DM, Ishima R. Structural integrity of the ribonuclease H domain in HIV-1 reverse transcriptase. Proteins. 83: 1526-38. PMID 26061827 DOI: 10.1002/Prot.24843 |
0.391 |
|
2014 |
Cai Y, Myint W, Paulsen JL, Schiffer CA, Ishima R, Kurt Yilmaz N. Drug Resistance Mutations Alter Dynamics of Inhibitor-Bound HIV-1 Protease. Journal of Chemical Theory and Computation. 10: 3438-3448. PMID 25136270 DOI: 10.1021/Ct4010454 |
0.762 |
|
2014 |
Sharaf NG, Poliner E, Slack RL, Christen MT, Byeon IJ, Parniak MA, Gronenborn AM, Ishima R. The p66 immature precursor of HIV-1 reverse transcriptase. Proteins. 82: 2343-52. PMID 24771554 DOI: 10.1002/Prot.24594 |
0.326 |
|
2014 |
Ishima R. A probe to monitor performance of ¹⁵N longitudinal relaxation experiments for proteins in solution. Journal of Biomolecular Nmr. 58: 113-22. PMID 24390467 DOI: 10.1007/S10858-013-9809-8 |
0.38 |
|
2014 |
Ishima R. CPMG relaxation dispersion. Methods in Molecular Biology (Clifton, N.J.). 1084: 29-49. PMID 24061914 DOI: 10.1007/978-1-62703-658-0_2 |
0.397 |
|
2012 |
Ilina T, Labarge K, Sarafianos SG, Ishima R, Parniak MA. Inhibitors of HIV-1 Reverse Transcriptase-Associated Ribonuclease H Activity. Biology. 1: 521-41. PMID 23599900 DOI: 10.3390/Biology1030521 |
0.346 |
|
2012 |
Cai Y, Yilmaz NK, Myint W, Ishima R, Schiffer CA. Differential Flap Dynamics in Wild-type and a Drug Resistant Variant of HIV-1 Protease Revealed by Molecular Dynamics and NMR Relaxation. Journal of Chemical Theory and Computation. 8: 3452-3462. PMID 23144597 DOI: 10.1021/Ct300076Y |
0.758 |
|
2012 |
Christen MT, Menon L, Myshakina NS, Ahn J, Parniak MA, Ishima R. Structural basis of the allosteric inhibitor interaction on the HIV-1 reverse transcriptase RNase H domain. Chemical Biology & Drug Design. 80: 706-16. PMID 22846652 DOI: 10.1111/Cbdd.12010 |
0.438 |
|
2012 |
Liriano MA, Varney KM, Wright NT, Hoffman CL, Toth EA, Ishima R, Weber DJ. Target binding to S100B reduces dynamic properties and increases Ca(2+)-binding affinity for wild type and EF-hand mutant proteins. Journal of Molecular Biology. 423: 365-85. PMID 22824086 DOI: 10.1016/J.Jmb.2012.07.011 |
0.312 |
|
2012 |
Myint W, Cai Y, Schiffer CA, Ishima R. Quantitative comparison of errors in 15N transverse relaxation rates measured using various CPMG phasing schemes. Journal of Biomolecular Nmr. 53: 13-23. PMID 22466935 DOI: 10.1007/S10858-012-9621-X |
0.726 |
|
2012 |
Ishima R. Recent developments in (15)N NMR relaxation studies that probe protein backbone dynamics. Topics in Current Chemistry. 326: 99-122. PMID 21898206 DOI: 10.1007/128_2011_212 |
0.415 |
|
2012 |
ISHIMA R. Current Progress in the NMR Relaxation Experiments to Detect Protein Dynamics Seibutsu Butsuri. 52: 242-245. DOI: 10.2142/Biophys.52.242 |
0.342 |
|
2011 |
Xu X, Ishima R, Ames JB. Conformational dynamics of recoverin's Ca2+-myristoyl switch probed by 15N NMR relaxation dispersion and chemical shift analysis. Proteins. 79: 1910-22. PMID 21465563 DOI: 10.1002/Prot.23014 |
0.346 |
|
2011 |
Webb C, Upadhyay A, Giuntini F, Eggleston I, Furutani-Seiki M, Ishima R, Bagby S. Structural features and ligand binding properties of tandem WW domains from YAP and TAZ, nuclear effectors of the Hippo pathway. Biochemistry. 50: 3300-9. PMID 21417403 DOI: 10.1021/Bi2001888 |
0.328 |
|
2011 |
Myint W, Gong Q, Ahn J, Ishima R. Characterization of sarcoplasmic reticulum Ca2+ ATPase nucleotide binding domain mutants using NMR spectroscopy. Biochemical and Biophysical Research Communications. 405: 19-23. PMID 21187073 DOI: 10.1016/J.Bbrc.2010.12.094 |
0.752 |
|
2011 |
Gong Q, Menon L, Ilina T, Miller LG, Ahn J, Parniak MA, Ishima R. Interaction of HIV-1 reverse transcriptase ribonuclease H with an acylhydrazone inhibitor. Chemical Biology & Drug Design. 77: 39-47. PMID 21114787 DOI: 10.1111/J.1747-0285.2010.01052.X |
0.387 |
|
2011 |
Liriano M, Varney KM, Ishima R, Weber DJ. Abstract 2328: 15N-backbone and side-chain dynamics of the mutant calcium-binding protein S100B D63N Cancer Research. 71: 2328-2328. DOI: 10.1158/1538-7445.Am2011-2328 |
0.385 |
|
2011 |
Menon L, Gong Q, Ahn J, Parniak MA, Ishima R. Structural Studies of RNase H Domain to Develop HIV-1 Reverse Transcriptase Inhibitors using Solution NMR Biophysical Journal. 100: 605a. DOI: 10.1016/J.Bpj.2010.12.3482 |
0.424 |
|
2010 |
Walsh JD, Meier K, Ishima R, Gronenborn AM. NMR studies on domain diffusion and alignment in modular GB1 repeats Biophysical Journal. 99: 2636-2646. PMID 20959105 DOI: 10.1016/J.Bpj.2010.08.036 |
0.312 |
|
2010 |
Yanamala N, Dutta A, Beck B, van Vliet B, van Fleet B, Hay K, Yazbak A, Ishima R, Doemling A, Klein-Seetharaman J. NMR-based screening of membrane protein ligands. Chemical Biology & Drug Design. 75: 237-56. PMID 20331645 DOI: 10.1111/J.1747-0285.2009.00940.X |
0.347 |
|
2010 |
Ishima R, Gong Q, Tie Y, Weber IT, Louis JM. Highly conserved glycine 86 and arginine 87 residues contribute differently to the structure and activity of the mature HIV-1 protease. Proteins. 78: 1015-25. PMID 19899162 DOI: 10.1002/Prot.22625 |
0.421 |
|
2010 |
Walsh JD, Meier K, Ishima R, Gronenborn AM. Diffusion and Alignment of Domain Repeats in Modular Proteins - A NMR Study Biophysical Journal. 98: 2-8. DOI: 10.1016/J.Bpj.2009.12.1292 |
0.343 |
|
2009 |
Louis JM, Ishima R, Aniana A, Sayer JM. Revealing the dimer dissociation and existence of a folded monomer of the mature HIV-2 protease. Protein Science : a Publication of the Protein Society. 18: 2442-53. PMID 19798742 DOI: 10.1002/Pro.261 |
0.471 |
|
2009 |
Myint W, Ishima R. Chemical exchange effects during refocusing pulses in constant-time CPMG relaxation dispersion experiments. Journal of Biomolecular Nmr. 45: 207-16. PMID 19618276 DOI: 10.1007/S10858-009-9344-9 |
0.719 |
|
2009 |
Xiao X, Feng Y, Vu BK, Ishima R, Dimitrov DS. A large library based on a novel (CH2) scaffold: identification of HIV-1 inhibitors. Biochemical and Biophysical Research Communications. 387: 387-92. PMID 19615335 DOI: 10.1016/J.Bbrc.2009.07.044 |
0.368 |
|
2009 |
Vu BK, Walsh JD, Dimitrov DS, Ishima R. Dynamics of antibody domains studied by solution NMR. Methods in Molecular Biology (Clifton, N.J.). 525: 533-43, xv. PMID 19252840 DOI: 10.1007/978-1-59745-554-1_29 |
0.367 |
|
2009 |
Myint W, Gong Q, Ishima R. Practical aspects of 15N CPMG transverse relaxation experiments for proteins in solution Concepts in Magnetic Resonance Part a: Bridging Education and Research. 34: 63-75. DOI: 10.1002/Cmr.A.20133 |
0.734 |
|
2008 |
Miklóssy G, Tözsér J, Kádas J, Ishima R, Louis JM, Bagossi P. Novel macromolecular inhibitors of human immunodeficiency virus-1 protease. Protein Engineering, Design & Selection : Peds. 21: 453-61. PMID 18480092 DOI: 10.1093/Protein/Gzn022 |
0.383 |
|
2008 |
Sayer JM, Liu F, Ishima R, Weber IT, Louis JM. Effect of the active site D25N mutation on the structure, stability, and ligand binding of the mature HIV-1 protease. The Journal of Biological Chemistry. 283: 13459-70. PMID 18281688 DOI: 10.1074/Jbc.M708506200 |
0.412 |
|
2008 |
Jee J, Ishima R, Gronenborn AM. Characterization of specific protein association by15N CPMG relaxation dispersion NMR: The GB1A34F monomer-dimer equilibrium Journal of Physical Chemistry B. 112: 6008-6012. PMID 18004837 DOI: 10.1021/Jp076094H |
0.401 |
|
2008 |
Ishima R, Louis JM. A diverse view of protein dynamics from NMR studies of HIV-1 protease flaps. Proteins. 70: 1408-15. PMID 17894346 DOI: 10.1002/Prot.21632 |
0.402 |
|
2007 |
Chang SL, Hinck AP, Ishima R. Model-free analysis for large proteins at high magnetic field strengths. Journal of Biomolecular Nmr. 38: 315-24. PMID 17593525 DOI: 10.1007/S10858-007-9171-9 |
0.337 |
|
2007 |
Louis JM, Ishima R, Torchia DA, Weber IT. HIV-1 protease: structure, dynamics, and inhibition. Advances in Pharmacology (San Diego, Calif.). 55: 261-98. PMID 17586318 DOI: 10.1016/S1054-3589(07)55008-8 |
0.434 |
|
2007 |
Ishima R, Torchia DA, Louis JM. Mutational and structural studies aimed at characterizing the monomer of HIV-1 protease and its precursor. The Journal of Biological Chemistry. 282: 17190-9. PMID 17412697 DOI: 10.1074/Jbc.M701304200 |
0.449 |
|
2007 |
Gong Q, Ishima R. 15N-{1H} NOE experiment at high magnetic field strengths. Journal of Biomolecular Nmr. 37: 147-57. PMID 17225068 DOI: 10.1007/S10858-006-9125-7 |
0.323 |
|
2005 |
Ishima R, Torchia DA. Error estimation and global fitting in transverse-relaxation dispersion experiments to determine chemical-exchange parameters. Journal of Biomolecular Nmr. 32: 41-54. PMID 16041482 DOI: 10.1007/S10858-005-3593-Z |
0.339 |
|
2004 |
Ravindranath HH, Chen LS, Zeichner-David M, Ishima R, Ravindranath RM. Interaction between the enamel matrix proteins amelogenin and ameloblastin. Biochemical and Biophysical Research Communications. 323: 1075-83. PMID 15381109 DOI: 10.1016/J.Bbrc.2004.08.207 |
0.324 |
|
2004 |
Ishima R, Baber J, Louis JM, Torchia DA. Carbonyl carbon transverse relaxation dispersion measurements and ms-micros timescale motion in a protein hydrogen bond network. Journal of Biomolecular Nmr. 29: 187-98. PMID 15014232 DOI: 10.1023/B:Jnmr.0000019249.50306.5D |
0.362 |
|
2003 |
Ishima R, Torchia DA, Lynch SM, Gronenborn AM, Louis JM. Solution structure of the mature HIV-1 protease monomer: insight into the tertiary fold and stability of a precursor. The Journal of Biological Chemistry. 278: 43311-9. PMID 12933791 DOI: 10.1074/Jbc.M307549200 |
0.416 |
|
2003 |
Katoh E, Louis JM, Yamazaki T, Gronenborn AM, Torchia DA, Ishima R. A solution NMR study of the binding kinetics and the internal dynamics of an HIV-1 protease-substrate complex. Protein Science : a Publication of the Protein Society. 12: 1376-85. PMID 12824484 DOI: 10.1110/Ps.0300703 |
0.44 |
|
2003 |
Ishima R, Torchia DA. Extending the range of amide proton relaxation dispersion experiments in proteins using a constant-time relaxation-compensated CPMG approach. Journal of Biomolecular Nmr. 25: 243-8. PMID 12652136 DOI: 10.1023/A:1022851228405 |
0.384 |
|
2003 |
Louis JM, Ishima R, Nesheiwat I, Pannell LK, Lynch SM, Torchia DA, Gronenborn AM. Revisiting monomeric HIV-1 protease. Characterization and redesign for improved properties. The Journal of Biological Chemistry. 278: 6085-92. PMID 12468541 DOI: 10.1074/Jbc.M209726200 |
0.438 |
|
2003 |
Torchia DA, Ishima R. Molecular structure and dynamics of proteins in solution: Insights derived from high-resolution NMR approaches Pure and Applied Chemistry. 75: 1371-1381. DOI: 10.1351/Pac200375101371 |
0.361 |
|
2002 |
Freedberg DI, Ishima R, Jacob J, Wang YX, Kustanovich I, Louis JM, Torchia DA. Rapid structural fluctuations of the free HIV protease flaps in solution: relationship to crystal structures and comparison with predictions of dynamics calculations. Protein Science : a Publication of the Protein Society. 11: 221-32. PMID 11790832 DOI: 10.1110/Ps.33202 |
0.406 |
|
2001 |
Ishima R, Louis JM, Torchia DA. Optimized labeling of 13CHD2 methyl isotopomers in perdeuterated proteins: potential advantages for 13C relaxation studies of methyl dynamics of larger proteins. Journal of Biomolecular Nmr. 21: 167-71. PMID 11727980 DOI: 10.1023/A:1012482426306 |
0.307 |
|
2001 |
Ishima R, Ghirlando R, Tözsér J, Gronenborn AM, Torchia DA, Louis JM. Folded monomer of HIV-1 protease. The Journal of Biological Chemistry. 276: 49110-6. PMID 11598128 DOI: 10.1074/Jbc.M108136200 |
0.423 |
|
2001 |
Ishima R, Petkova AP, Louis JM, Torchia DA. Comparison of methyl rotation axis order parameters derived from model-free analyses of (2)H and (13)C longitudinal and transverse relaxation rates measured in the same protein sample. Journal of the American Chemical Society. 123: 6164-71. PMID 11414851 DOI: 10.1021/Ja0104711 |
0.325 |
|
2001 |
Ishima R, Louis JM, Torchia DA. Characterization of two hydrophobic methyl clusters in HIV-1 protease by NMR spin relaxation in solution. Journal of Molecular Biology. 305: 515-21. PMID 11152609 DOI: 10.1006/Jmbi.2000.4321 |
0.323 |
|
2000 |
Ishima R, Torchia DA. Protein dynamics from NMR. Nature Structural Biology. 7: 740-3. PMID 10966641 DOI: 10.1038/78963 |
0.389 |
|
2000 |
Ishima R, Louis JM, Torchia DA. Transverse13C Relaxation of CHD2Methyl Isotopmers To Detect Slow Conformational Changes of Protein Side Chains [J. Am. Chem. Soc.1999,121, 11589−11590]. Journal of the American Chemical Society. 122: 548-548. DOI: 10.1021/Ja995542Z |
0.32 |
|
1999 |
Ishima R, Torchia DA. Estimating the time scale of chemical exchange of proteins from measurements of transverse relaxation rates in solution. Journal of Biomolecular Nmr. 14: 369-72. PMID 10526408 DOI: 10.1023/A:1008324025406 |
0.325 |
|
1999 |
Ishima R, Freedberg DI, Wang YX, Louis JM, Torchia DA. Flap opening and dimer-interface flexibility in the free and inhibitor-bound HIV protease, and their implications for function. Structure (London, England : 1993). 7: 1047-55. PMID 10508781 DOI: 10.1016/S0969-2126(99)80172-5 |
0.456 |
|
1999 |
Tomomori C, Tanaka T, Dutta R, Park H, Saha SK, Zhu Y, Ishima R, Liu D, Tong KI, Kurokawa H, Qian H, Inouye M, Ikura M. Solution structure of the homodimeric core domain of Escherichia coli histidine kinase EnvZ Nature Structural Biology. 6: 729-734. PMID 10426948 DOI: 10.1038/11495 |
0.344 |
|
1999 |
Ishima R, Louis JM, Torchia DA. Transverse 1H cross relaxation in 1H-15N correlated 1H CPMG experiments. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 137: 289-92. PMID 10053163 DOI: 10.1006/Jmre.1998.1672 |
0.337 |
|
1999 |
Ishima R, Louis JM, Torchia DA. Transverse 13C relaxation of CHD2 methyl isotopmers to detect slow conformational changes of protein side chains [12] Journal of the American Chemical Society. 121: 11589-11590. DOI: 10.1021/Ja992836B |
0.302 |
|
1998 |
Hayashi F, Ishima R, Liu D, Tong KI, Kim S, Reinberg D, Bagby S, Ikura M. Human general transcription factor TFIIB: Conformational variability and interaction with VP16 activation domain Biochemistry. 37: 7941-7951. PMID 9609687 DOI: 10.1021/Bi9801098 |
0.363 |
|
1998 |
Ishima R, Wingfield PT, Stahl SJ, Kaufman JD, Torchia DA. Using amide 1H and 15N transverse relaxation to detect millisecond time-scale motions in perdeuterated proteins: Application to HIV-1 protease Journal of the American Chemical Society. 120: 10534-10542. DOI: 10.1021/Ja981546C |
0.413 |
|
1995 |
Ishima R, Yamasaki K, Saito M, Nagayama K. Spectral densities of nitrogen nuclei in Escherichia coli ribonuclease HI obtained by 15N NMR relaxation and molecular dynamics Journal of Biomolecular Nmr. 6: 217-220. PMID 8589610 DOI: 10.1007/Bf00211786 |
0.345 |
|
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