Rieko Ishima

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Effect of the active site D25N mutation on the structure, stability, and ligand binding of the mature HIV-1 protease
    Jane M Sayer
    Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
    J Biol Chem 283:13459-70. 2008
  2. ncbi Extending the range of amide proton relaxation dispersion experiments in proteins using a constant-time relaxation-compensated CPMG approach
    Rieko Ishima
    Molecular Structural Biology Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892 4307, USA
    J Biomol NMR 25:243-8. 2003
  3. ncbi Carbonyl carbon transverse relaxation dispersion measurements and ms-micros timescale motion in a protein hydrogen bond network
    Rieko Ishima
    Molecular Structural Biology Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland 20892 4307, USA
    J Biomol NMR 29:187-98. 2004
  4. ncbi Error estimation and global fitting in transverse-relaxation dispersion experiments to determine chemical-exchange parameters
    Rieko Ishima
    Molecular Structural Biology Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892 4307, USA
    J Biomol NMR 32:41-54. 2005
  5. ncbi Solution structure of the mature HIV-1 protease monomer: insight into the tertiary fold and stability of a precursor
    Rieko Ishima
    Molecular Structural Biology Unit, NIDCR, National Institutes of Health, Bethesda, Maryland 20892 4307, USA
    J Biol Chem 278:43311-9. 2003
  6. pmc Revealing the dimer dissociation and existence of a folded monomer of the mature HIV-2 protease
    John M Louis
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892 0520, USA
    Protein Sci 18:2442-53. 2009
  7. pmc Engineered human antibody constant domains with increased stability
    Rui Gong
    Protein Interactions Group, CCRNP, CCR, National Institutes of Health, Frederick, Maryland 21702, USA
    J Biol Chem 284:14203-10. 2009
  8. ncbi HIV-1 protease: structure, dynamics, and inhibition
    John M Louis
    Laboratory of Chemical Physics, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Adv Pharmacol 55:261-98. 2007
  9. pmc Rapid structural fluctuations of the free HIV protease flaps in solution: relationship to crystal structures and comparison with predictions of dynamics calculations
    DARON I FREEDBERG
    Molecular Structural Biology Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland 20892, USA
    Protein Sci 11:221-32. 2002
  10. ncbi Accuracy of optimized chemical-exchange parameters derived by fitting CPMG R2 dispersion profiles when R2(0a) not = R2(0b)
    Rieko Ishima
    Molecular Structural Biology Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892 4307, USA
    J Biomol NMR 34:209-19. 2006

Collaborators

Detail Information

Publications20

  1. pmc Effect of the active site D25N mutation on the structure, stability, and ligand binding of the mature HIV-1 protease
    Jane M Sayer
    Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
    J Biol Chem 283:13459-70. 2008
    ..DRV by a factor of approximately 10(6) relative to PR.DRV. These results suggest that interactions mediated by the catalytic Asp residues make a major contribution to the tight binding of DRV to PR...
  2. ncbi Extending the range of amide proton relaxation dispersion experiments in proteins using a constant-time relaxation-compensated CPMG approach
    Rieko Ishima
    Molecular Structural Biology Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892 4307, USA
    J Biomol NMR 25:243-8. 2003
    ..We also compare the relative merits of (1)H versus (15)N transverse relaxation measurements and note the benefits of using a perdeuterated protein to measure the relaxation dispersion of both spin types...
  3. ncbi Carbonyl carbon transverse relaxation dispersion measurements and ms-micros timescale motion in a protein hydrogen bond network
    Rieko Ishima
    Molecular Structural Biology Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland 20892 4307, USA
    J Biomol NMR 29:187-98. 2004
    ....
  4. ncbi Error estimation and global fitting in transverse-relaxation dispersion experiments to determine chemical-exchange parameters
    Rieko Ishima
    Molecular Structural Biology Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892 4307, USA
    J Biomol NMR 32:41-54. 2005
    ..10%, was of marginal significance according to the F-test...
  5. ncbi Solution structure of the mature HIV-1 protease monomer: insight into the tertiary fold and stability of a precursor
    Rieko Ishima
    Molecular Structural Biology Unit, NIDCR, National Institutes of Health, Bethesda, Maryland 20892 4307, USA
    J Biol Chem 278:43311-9. 2003
    ..Knowledge of the protease monomer structure and critical features of its dimerization may aid in the screening and design of compounds that target the protease prior to its maturation from the Gag-Pol precursor...
  6. pmc Revealing the dimer dissociation and existence of a folded monomer of the mature HIV-2 protease
    John M Louis
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892 0520, USA
    Protein Sci 18:2442-53. 2009
    ..Use of SMR and NMR with PR2 facilitates probing for potential inhibitors that restrict protein folding and/or dimerization and, thus, may provide insights for the future design of inhibitors to circumvent drug resistance...
  7. pmc Engineered human antibody constant domains with increased stability
    Rui Gong
    Protein Interactions Group, CCRNP, CCR, National Institutes of Health, Frederick, Maryland 21702, USA
    J Biol Chem 284:14203-10. 2009
    ....
  8. ncbi HIV-1 protease: structure, dynamics, and inhibition
    John M Louis
    Laboratory of Chemical Physics, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Adv Pharmacol 55:261-98. 2007
  9. pmc Rapid structural fluctuations of the free HIV protease flaps in solution: relationship to crystal structures and comparison with predictions of dynamics calculations
    DARON I FREEDBERG
    Molecular Structural Biology Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland 20892, USA
    Protein Sci 11:221-32. 2002
    ..These results are compared with theoretical predictions of flap dynamics and the possible biological significance of the sub-ns time scale dynamics of the flap tips is discussed...
  10. ncbi Accuracy of optimized chemical-exchange parameters derived by fitting CPMG R2 dispersion profiles when R2(0a) not = R2(0b)
    Rieko Ishima
    Molecular Structural Biology Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892 4307, USA
    J Biomol NMR 34:209-19. 2006
    ..A theoretical analysis using the Carver-Richards equation explains these results, and yields simple, general equations for estimating the magnitudes of the errors in the optimized parameters, as a function of (R2(0a) - R2(0b))...
  11. ncbi Revisiting monomeric HIV-1 protease. Characterization and redesign for improved properties
    John M Louis
    Laboratory of Chemical Physics, National Institute Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Biol Chem 278:6085-92. 2003
    ..This extends the target area of current inhibitors, all of which bind across the active site formed by both subunits in the active dimer...
  12. pmc Dynamics of antibody domains studied by solution NMR
    Bang K Vu
    NCI Frederick, National Institutes of Health, Frederick, MD, USA
    Methods Mol Biol 525:533-43, xv. 2009
    ..Here, we describe a protocol that was used to study the dynamics of an antibody domain in solution using NMR. We describe protein preparation for NMR studies, NMR sample optimization, signal assignments, and dynamics experiments...
  13. ncbi 15N-{1H} NOE experiment at high magnetic field strengths
    Qingguo Gong
    Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA15260, USA
    J Biomol NMR 37:147-57. 2007
    ..We also discuss ranges of rotational correlation times and proton spin-flip rate, in which the NOE values can be corrected by the equations...
  14. pmc Novel macromolecular inhibitors of human immunodeficiency virus-1 protease
    Gabriella Miklossy
    Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen, PO Box 6, Debrecen H 4012, Hungary
    Protein Eng Des Sel 21:453-61. 2008
    ..In cell culture experiments, infectivity of viral particles containing PR(RER) protein was reduced by 82%, at mutant to wild-type infective DNA ratio of 2:1...
  15. pmc A solution NMR study of the binding kinetics and the internal dynamics of an HIV-1 protease-substrate complex
    Etsuko Katoh
    Biochemistry Department, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305 8602, Japan
    Protein Sci 12:1376-85. 2003
    ..Flap dynamics of the protease-substrate complex are compared with those of protease-inhibitor complexes, and the implications of these results for substrate-binding models are discussed...
  16. ncbi Characterization of specific protein association by 15N CPMG relaxation dispersion NMR: the GB1(A34F) monomer-dimer equilibrium
    JunGoo Jee
    Department of Structural Biology, University of Pittsburgh School of Medicine, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15260, USA
    J Phys Chem B 112:6008-12. 2008
    ....
  17. ncbi A diverse view of protein dynamics from NMR studies of HIV-1 protease flaps
    Rieko Ishima
    Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
    Proteins 70:1408-15. 2008
    ..For the first time, we show that the tips of the flaps in the unliganded protease dimer interact with each other in solution. Accordingly, we discuss the consistency of the simulations with the model derived from all experimental data...
  18. ncbi Model-free analysis for large proteins at high magnetic field strengths
    Shou Lin Chang
    Institute of Bioinformatics and Structural Biology, Department of Life Science, National Tsing Hua University, Hsinchu 30055, Taiwan
    J Biomol NMR 38:315-24. 2007
    ..Here, we quantitatively estimate the errors introduced by the use of the simplified spectral density in model-free analysis for large proteins at high magnetic field strength...
  19. ncbi Mutational and structural studies aimed at characterizing the monomer of HIV-1 protease and its precursor
    Rieko Ishima
    Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
    J Biol Chem 282:17190-9. 2007
    ....
  20. ncbi Interaction between the enamel matrix proteins amelogenin and ameloblastin
    Hanumanth H Ravindranath
    Center for Craniofacial Molecular Biology, University of Southern California, 2250 Alcazar Street, Los Angeles, CA 90033, USA
    Biochem Biophys Res Commun 323:1075-83. 2004
    ..Dosimetry and Scatchard analyses showed the specific interaction between ATMP and ameloblastin, suggesting that amelogenin may interact with ameloblastin to form a heteromolecular assembly...