Iwahara Lab

Publications

We have published 97 papers, mainly on proteins, DNA, and their interactions.

  1. Iwahara, J. (2024) Transient helices with functional roles. Biophys J in press. [Pubmed]
  2. Wang, X., Yu, B., Sakurabayashi, S., Paz-Villatoro, J. M., Iwahara, J. (2024) Robust enzymatic production of DNA G-quadruplex, aptamer, DNAzyme, and other oligonucleotides: Applications for NMR. J Am Chem Soc 146, 1748-52. [Pubmed]
  3. Yu, B., Iwahara, J. (2024) Analyzing paramagnetic NMR data on target DNA search by proteins using a discrete-state kinetic model for translocation. Biopolymers 115, e23553. [Pubmed]
  4. Iwahara, J., Pettitt, B.M., Yu, B. (2023) Direct measurements of biomolecular electrostatics through experiments. Curr Opin Struct Biol 82, 102680. [Pubmed]
  5. Wang, X., Bigman, L., Greenblatt, H.M., Yu, B., Levy, Y., Iwahara, J. (2023) Negatively charged, intrinsically disordered regions can accelerate target search by DNA-binding proteins. Nucleic Acids Res 51, 4701-12. [Pubmed]
  6. Yu, B., Wang, X., Wang, T., Iwahara, J. (2023) DNA base order parameter determination without influence of chemical exchange. Methods 210, 1-9. [Pubmed]
  7. Yu, B., Wang, X., Iwahara, J. (2022) Measuring local electrostatic potentials around nucleic acids by paramagnetic NMR spectroscopy. J Phys Chem Lett 13, 10025-9. [Pubmed]
  8. Wang, X., Mayorga-Flores, M., Bien, K., Bailey, A.O., Iwahara, J. (2022) DNA-mediated proteolysis by neutrophil elastase enhances binding activities of the HMGB1 protein. J Biol Chem 298, 102577. [Pubmed]
  9. Wang, X., Yu, B., Iwahara, J. (2022) Slow rotational dynamics of cytosine NH2 groups in double-stranded DNA. Biochemistry 61, 1415-8. [Pubmed]
  10. Yu, B., Bien, K., Wang, T., Iwahara, J. (2022) Diffusion NMR-based comparison of electrostatic influences of DNA on various monovalent cations. Biophys J 121, 3562-70. [Pubmed]
  11. Chen, C., Yu, B., Yousefi, R., Iwahara, J., Pettitt, B.M. (2022) Assessment of the components of the electrostatic potential of proteins in solution: Comparing experiment and theory. J Phys Chem B 126, 4543-54. [Pubmed]
  12. Bigman, L.S., Iwahara, J., Levy, Y. (2022) Negatively charged disordered regions are prevalent and functionally important across proteomes. J Mol Biol 434, 167660. [Pubmed]
  13. Yu, B., Pletka, C.C., Iwahara, J. (2022) Protein electrostatics investigated through paramagnetic NMR for nonpolar groups. J Phys Chem B 125, 2196-202. [Pubmed]
  14. Yu, B., Bien, K.G., Pletka, C.C., Iwahara, J. (2022) Dynamics of cations around DNA and protein as revealed by 23Na diffusion NMR spectroscopy. Anal Chem 94, 2444-52. [Pubmed]
  15. Wang, X., Yu, B., Iwahara, J. (2021) Hindered rotations of protein asparagine/glutamine side-chain NH2 groups: Impact of hydrogen-bonding with DNA. J Phys Chem Lett 12, 11378-82. [Pubmed]
  16. Wang, X., Greenblatt, H.M., Bigman, L.S., Yu, B., Pletka, C.C., Levy, Y., Iwahara, J. (2021) Dynamic autoinhibition of the HMGB1 protein via electrostatic fuzzy interactions of intrinsically disordered regions. J Mol Biol 433 (18) 167122. [Pubmed]
  17. Yu, B., Pletka, C.C., Pettitt, B.M., Iwahara, J. (2021) De novo determination of near-surface electrostatic potentials by NMR. Proc Natl Acad Sci U S A 118 (25), e2104020118. [Pubmed]
  18. Yu, B., Iwahara, J. (2021) Experimental approaches for investigating ion atmospheres around nucleic acids and proteins. Comput Struct Biotechnol J 19, 2279-85. [Pubmed]
  19. Yu, B., Pletka, C.C., Iwahara, J. (2021) Quantifying and visualizing weak interactions between anions and proteins. Proc Natl Acad Sci U S A 118 (2), e2015879118. [Pubmed]
  20. Iwahara, J., Kolomeisky, A.B. (2021) Discrete-state stochastic kinetic models for target DNA search by proteins: Theory and experimental applications. Biophys Chem 269, 106521. [Pubmed]
  21. Yu, B., Pettitt, B.M., Iwahara, J. (2020) Dynamics of ionic interactions at protein-nucleic acid interfaces. Acc Chem Res 53, 1802-10. [Pubmed]
  22. Nepravishta, R., Pletka, C.C., Iwahara, J. (2020) Racemic phosphorothioate as a tool for NMR studies of protein-DNA complexes. J Biomol NMR 74, 421-9. [Pubmed]
  23. Yu, B., Pletka, C.C., Iwahara, J. (2020) NMR observation of intermolecular hydrogen bonds between protein tyrosine side-chain OH and DNA phosphate groups. J Phys Chem B 124, 1065-70. [Pubmed]
  24. Nepravishta, R., Yu, B., Iwahara, J. (2020) Hydrogen-exchange kinetics studied through analysis of self-decoupling of nuclear magnetic resonance. J Magn Reson 312, 106687. [Pubmed]
  25. Pletka, C.C., Nepravishta, R., Iwahara, J. (2020) Detecting counterion dynamics in DNA-protein association. Angew Chem Int Ed 59, 1465-8. [Pubmed]
  26. Yu, B., Pettitt, B.M., Iwahara, J. (2019) Experimental evidence of solvent-separated ion pairs as metastable states in electrostatic interactions of biological macromolecules.   J Phys Chem Lett 10, 7937-41. [Pubmed]
  27. Kemme, C.A., Luu, R.H., Chen, C., Pletka, C.C., Pettitt, B.M., Iwahara, J. (2019) The mobility of histidine side chains analyzed with 15N NMR relaxation and cross-correlation data: insight into zinc-finger - DNA interactions. J Phys Chem B 123, 3706-10. [PubMed]
  28. Nguyen, D., Chen, C., Pettitt, B.M., Iwahara, J. (2019) NMR methods for characterizing the basic side chains of proteins: electrostatic interactions, hydrogen bonds, and conformational dynamics. Methods Enzymol 615, 285-332. [ PubMed]
  29. Joseph, P.R.B., Sawant, K.V., Iwahara, J., Garofalo, R.O., Desai, U.R., Rarajathnam, K. (2018) Lysines and arginines play non-redundant roles in mediating chemokine-glycosaminoglycan interactions. Sci Rep 8, 12289. [PubMed]
  30. Iwahara, J., Zandarashvili, L., Kemme, C.A., Esadze, A. (2018) NMR-based investigations into target DNA search processes of proteins. Methods 148, 57-66. [PubMed]
  31. Nguyen, D., Iwahara, J. (2018) Impact of two-bond 15N-15N scalar couplings on 15N transverse relaxation measurements for arginine side chains of proteins. J Biomol NMR 71, 45-51. [PubMed]
  32. Sepuru, K.M., Iwahara, J., Rajarathnam, K. (2018) Direct detection of lysine side chain NH3+ in protein-heparin complexes using NMR spectroscopy. Analyst 143, 635-8. [PubMed]
  33. Nguyen, D., Hoffpauir, Z., Iwahara, J. (2017) Internal motions of basic side chains of the Antennapedia homeodomain in the free and DNA-bound states. Biochemistry 56, 5866-9. [PubMed]
  34. Sahu, D., Iwahara, J. (2017) Discrete-state kinetics model for NMR-based analysis of protein translocation on DNA at equilibrium. J Phys Chem B 121, 9548-56. [PubMed]
  35. Nguyen, D., Lokesh, G.L.R., Volk, D.E., Iwahara, J. (2017) A unique and simple approach to improve sensitivity in 15N NMR relaxation measurements for NH3+ groups: Application to a protein-DNA complex. Molecules 22, E1355. [PubMed]
  36. Kemme, C.A., Marquez, R., Luu, R.H., Iwahara, J. (2017) Potential role of DNA methylation as a facilitator of target search processes for transcription factors through interplay with methyl-CpG-binding proteins. Nucleic Acids Res 45, 7751-59. [PubMed]
  37. Chattopadhyay, A., Zandarashvili, L., Luu, R.H., Iwahara, J. (2016) Thermodynamic additivity for impacts of base-pair substitutions on association of the Egr-1 zinc-finger protein with DNA. Biochemistry 55, 6467-74. [PubMed]
  38. Chattopadhyay, A., Esadze, A., Roy, S., Iwahara, J. (2016) NMR scalar couplings across intermolecular hydrogen bonds between zinc-finger histidine side chains and DNA phosphate groups. J Phys Chem B 120, 10679-85. [PubMed]
  39. Nguyen, D., Zandarashvili, L., White, M.A., Iwahara, J. (2016) Stereospecific effects of oxygen-to-sulfur substitution in DNA phosphate on ion-pair dynamics and protein-DNA affinity. ChemBioChem 17, 1636-42. [PubMed]
  40. Esadze, A., Chen, C., Zandarashvili, L., Roy, S., Pettitt, B.M., Iwahara, J. (2016) Changes in conformational dynamics of basic side chains upon protein-DNA association. Nucleic Acids Res 44, 6961-70. [PubMed]
  41. Kemme, C.A., Nguyen, D., Chattopadhyay, A., Iwahara, J. (2016) Regulation of transcription factors via natural decoys in genomic DNA. Transcription 7, 115-20. [PubMed]
  42. Zandarashvili, L., Esadze, A., Kemme, C.A., Chattopadhyay, A., Nguyen, D., Iwahara, J. (2016) Residence times of molecular complexes in solution from NMR data of intermolecular hydrogen-bond scalar coupling. J Phys Chem Lett 7, 820-4. [PubMed]
  43. Kemme, C.A., Esadze, A., Iwahara, J. (2015) Influence of quasi-specific sites on kinetics of target DNA search by a sequence-specific DNA-binding protein. Biochemistry 54, 6684-91. [PubMed]
  44. Iwahara, J., Esadze, A., Zandarashvili, L. (2015) Physicochemical properties of ion pairs of biological macromolecules. Biomolecules 5, 2435-63. [PubMed]
  45. Zandarashvili, L., Esadze, A., Vuzman, D., Kemme, C.A., Levy, Y., Iwahara, J. (2015) Balancing between affinity and speed in target DNA search by zinc-finger proteins via modulation of dynamic conformational ensemble. Proc Natl Acad Sci U S A 112, E5142-9. [PubMed]
  46. Zandarashvili, L., Nguyen, D., Anderson, K.M., White, M.A., Gorenstein, D.G., Iwahara, J. (2015) Entropic enhancement of protein-DNA affinity by oxygen-to-sulfur substitution in DNA phosphate. Biophys J 109, 1026-37. [ PubMed]
  47. Chen, C., Esadze, A., Zandarashvili, L., Nguyen, D., Pettitt, B.M., Iwahara, J. (2015) Dynamic equilibria of short-range electrostatic interactions at molecular interfaces of protein-DNA complexes. J Phys Chem Lett 6, 2733-7. [ PubMed]
  48. Zandarashvili, L., White, M.A., Esadze, A., Iwahara, J. (2015) Structural impact of complete CpG methylation within target DNA on specific complex formation of the inducible transcription factor Egr-1. FEBS Lett 589, 1748-53. [ PubMed]
  49. Anderson, K.M., Nguyen, D., Esadze, A., Zandarashvili, L., Gorenstein, D.G., Iwahara, J. (2015) A chemical approach for site-specific identification of NMR signals from protein side-chain NH3+ groups forming intermolecular ion pairs in protein-nucleic acid complexes. J Biomol NMR 62, 1-5. [PubMed]
  50. Zandarashvili, L., Iwahara, J. (2015) Temperature dependence of internal motions of protein side-chain NH3+ groups: Insight into energy barriers for transient breakage of hydrogen bonds. Biochemistry 54, 538-45. [PubMed]
  51. Esadze, A., Kemme, C.A., Kolomeisky, A.B., Iwahara, J. (2014) Positive and negative impacts of nonspecific sites during target location by a sequence-specific DNA-binding protein: origin of the optimal search at physiological ionic strength. Nucleic Acids Res 42, 7039-46. [PubMed]
  52. Esadze, A., Iwahara, J. (2014) Stopped-flow fluorescence kinetic study of protein sliding and intersegment transfer in the target DNA search process. J Mol Biol 426, 230-44. [PubMed]
  53. Esadze, A., Zandarashvili, L., Iwahara, J. (2014) Effective strategy to assign 1H-15N heteronuclear correlation NMR signals from lysine side-chain NH3+ groups of proteins at low temperature. J Biomol NMR 60, 23-7. [PubMed]
  54. Anderson, K.M., Esadze, A., Manoharan, M., Brüschweiler, R., Gorenstein, D.G., Iwahara, J. (2013) Direct observation of the ion-pair dynamics at a protein-DNA interface by NMR spectroscopy. J Am Chem Soc 135, 3613-9. [ PubMed]
  55. Zandarashvili, L., Esadze, A., Iwahara, J. (2013) NMR studies on the dynamics of hydrogen bonds and ion pairs involving lysine side chains of proteins. Adv Protein Chem Struct Biol 93, 37-80. [PubMed]
  56. Zandarashvili, L., Sahu, D., Lee, K., Lee, Y.S., Singh, P., Rajarathnam, K., Iwahara, J. (2013) Real-time kinetics of high-mobility group box 1 oxidation in extracellular fluids studied by in situ protein NMR spectroscopy. J Biol Chem 288, 11621-7. [PubMed]
  57. Iwahara, J., Levy Y. (2013) Speed-stability paradox in DNA-scanning by zinc-finger proteins. Transcription 4, 58-61. [PubMed]
  58. Zandarashvili, L, Vuzman, D, Esadze, A, Takayama, Y, Sahu, D, Levy, Y, Iwahara, J. (2012) Asymmetrical roles of zinc fingers in dynamic DNA-scanning process by the inducible transcription factor Egr-1. Proc Natl Acad Sci U S A 109, E1724-32. [PubMed]
  59. Zandarashvili, L., Li, D.W., Wang, T., Brüschweiler, R., Iwahara, J. (2011) Signature of mobile hydrogen bonding of lysine side-chains from long range 15N-13C scalar J-couplings and computation. J Am Chem Soc 133, 9192-5. [PubMed]
  60. Esadze, A., Li, D.W., Wang, T., Brüschweiler, R., Iwahara, J. (2011) Dynamics of lysine side-chain amino groups in a protein studied by heteronuclear 1H-15N NMR spectroscopy. J Am Chem Soc 133, 909-19. [PubMed]
  61. Iwahara, J., Clore, G.M. (2010) Structure-independent analysis of the breadth of the positional distribution of disordered groups in macromolecules from order parameters for long variable-length vectors using NMR paramagnetic relaxation enhancement. J Am Chem Soc 132, 13346-56. [PubMed]
  62. Takayama, Y., Sahu, D., Iwahara, J. (2010) NMR studies of translocation of the Zif268 protein between its target DNA sites.Biochemistry 49, 7998-8005. [PubMed]
  63. Clore, G.M., Iwahara, J. (2009) Theory, practice and applications of paramagnetic relaxation enhancement for the characterization of low-population states of biological macromolecules and their complexes. Chem Rev 109, 4108-39. [ PubMed]
  64. Sahu, D., Debnath, P., Takayama, Y., Iwahara, J. (2008) Redox properties of the A-domain of the HMGB1 protein. FEBS Lett 582, 3973-8. [PubMed]
  65. Takayama, Y., Castaneda, C.A., Chimenti, M., Garcia-Moreno, B., Iwahara, J. (2008) Direct evidence for deprotonation of a lysine side-chain buried in the hydrophobic core of a protein. J Am Chem Soc 130, 6714-5. [PubMed]
  66. Takayama, Y., Sahu, D., Iwahara, J. (2008) Observing in-phase single-quantum 15N multiplets for NH2/NH3+ groups with two-dimensional heteronuclear correlation spectroscopy. J Magn Reson 194, 313-6. [PubMed]
  67. Sahu, D., Clore, G.M., Iwahara, J. (2007) TROSY-based z-Exchange Spectroscopy: Application to the determination of the activation energy for intermolecular protein translocation between specific sites on different DNA molecules. J Am Chem Soc 129, 13232-7. [PubMed]
  68. Clore, G.M., Tang, C., Iwahara, J. (2007) Elucidating transient macromolecular interactions using paramagnetic relaxation enhancement, Curr Opin Struct Biol 17, 603-16. [PubMed]
  69. Iwahara, J., Jung, Y.S., Clore, G.M. (2007) Heteronuclear NMR spectroscopy for lysine NH3 in proteins: Unique effect of water-exchange on 15N transverse relaxation. J Am Chem Soc 129, 2971-80. [PubMed]
  70. Suh, J.Y., Iwahara, J., Clore, G.M. (2007) Intramolecular domain-domain association / dissociation and phosphoryl transfer in the mannitol transporter of Escherichia coli are not coupled. Proc Natl Acad Sci. U S A 104, 3153-8. [ PubMed]
  71. Kobayashi, N., Iwahara, J., Koshiba, S., Tomizawa, T., Tochio, N., Güntert, P., Kigawa, T., Yokoyama, S. (2007) KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies. J Biomol NMR 39, 31-52. [PubMed]
  72. Iwahara J., Tang C, Clore GM (2007) Practical aspects of 1H transverse paramagnetic relaxation enhancement measurements on macromolecules. J Magn Reson 184, 185-93. [PubMed]
  73. Iwahara, J. Clore GM. (2006) Sensitivity improvement for correlations involving arginine side-chain Ne/He resonances in multi-dimensional NMR experiments using broadband 15N 180° pulses. J Biomol NMR 36, 251-7. [ PubMed]
  74. Tang C, Iwahara, J. Clore GM. (2006) Visualization of transient encounter complexes in protein-protein association. Nature 444, 383-6. [PubMed]
  75. Iwahara, J. Zweckstetter M, Clore GM. (2006) NMR structural and kinetic characterization of a homeodomain diffusing and hopping on nonspecific DNA. Proc Natl Acad Sci U S A 103, 15062-7. [PubMed]
  76. Iwahara, J. Clore GM. (2006) Detecting transient intermediates in macromolecular binding by paramagneticNMR. Nature 440, 1227-30. [PubMed]
  77. Iwahara, J. Clore GM. (2006) Direct observation of enhanced translocation of a homeodomain between DNA cognate sites by NMR exchange spectroscopy. J Am Chem Soc 128, 404-5. [PubMed]
  78. Tang C, Iwahara, J. Clore GM. (2005) Accurate determination of leucine and valine side-chain conformations using U-[15N/13C/2H]/[1H-(methine/methyl)-Leu/Val] isotope labeling, NOE pattern recognition, and methine Cγ-Hγ/Cβ-Hβ residual dipolar couplings: application to the 34-kDa enzyme IIAchitobiose. J Biomol NMR 33, 105-21. [PubMed]
  79. Iwahara, J. Peterson RD, Clubb RT. (2005) Compensating increases in protein backbone flexibility occur when the Dead ringer AT-rich interaction domain (ARID) binds DNA: a nitrogen-15 relaxation study. Protein Sci 14, 1140-50. [ PubMed]
  80. Iwahara, J. Schwieters CD, Clore GM. (2004) Characterization of nonspecific protein-DNA interactions by 1H paramagnetic relaxation enhancement. J Am Chem Soc 126, 12800-8. [PubMed]
  81. Iwahara, J. Schwieters CD, Clore GM. (2004) Ensemble approach for NMR structure refinement against 1H paramagnetic relaxation enhancement data arising from a flexible paramagnetic group attached to a macromolecule. J Am Chem Soc 126, 5879-96. [PubMed]
  82. Iwahara, J. Anderson DE, Murphy EC, Clore GM. (2003) EDTA-derivatized deoxythymidine as a tool for rapid determination of protein binding polarity to DNA by intermolecular paramagnetic relaxation enhancement. J Am Chem Soc 125, 6634-5. [PubMed]
  83. Sam MD, Papagiannis CV, Connolly KM, Corselli L, Iwahara, J. Lee J, Phillips M, Wojciak JM, Johnson RC, Clubb RT. (2002) Regulation of directionality in bacteriophage lambda site-specific recombination: structure of the Xis protein. J Mol Biol 324, 791-805. [PubMed]
  84. Kikuchi J, Iwahara, J. Kigawa T, Murakami Y, Okazaki T, Yokoyama S. (2002) Solution structure determination of the two DNA-binding domains in the Schizosaccharomyces pombe Abp1 protein by a combination of dipolar coupling and diffusion anisotropy restraints. J Biomol NMR 22, 333-47. [PubMed]
  85. Iwahara, J. Iwahara M, Daughdrill GW, Ford J, Clubb RT. (2002) The structure of the Dead ringer-DNA complex reveals how AT-rich interaction domains (ARIDs) recognize DNA. EMBO J 21, 1197-209. [PubMed]
  86. Tanaka Y, Nureki O, Kurumizaka H, Fukai S, Kawaguchi S, Ikuta M, Iwahara, J. Okazaki T, Yokoyama S. (2001) Crystal structure of the CENP-B protein-DNA complex: the DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA. EMBO J 20, 6612-8. [PubMed]
  87. Iwahara, J. Wojciak JM, Clubb RT. (2001) An efficient NMR experiment for analyzing sugar-puckering in unlabeled DNA: Application to the 26-kDa dead ringer-DNA complex. J Magn Reson 153, 262-6. [PubMed]
  88. Ilangovan U, Ton-That H, Iwahara, J. Schneewind O, Clubb RT. (2001) Structure of sortase, the transpeptidase that anchors proteins to the cell wall of Staphylococcus aureus. Proc Natl Acad Sci U S A 98, 6056-61. [PubMed]
  89. Ilangovan U, Iwahara, J. Ton-That H, Schneewind O, Clubb RT. (2001) Assignment of the 1H, 13C and 15N signals of Sortase. J Biomol NMR19, 379-80. [PubMed]
  90. Iwahara, J. Wojciak JM, Clubb RT. (2001) Improved NMR spectra of a protein-DNA complex through rational mutagenesis and the application of a sensitivity optimized isotope-filtered NOESY experiment. J Biomol NMR 19, 231-41. [ PubMed]
  91. Wojciak JM, Iwahara, J. Clubb RT. (2001) The Mu repressor-DNA complex contains an immobilized 'wing' within the minor groove. Nat Struct Biol 8, 84-90. [PubMed]
  92. Iwahara, J. Clubb RT. (1999) Solution structure of the DNA binding domain from Dead ringer, a sequence-specific AT-rich interaction domain (ARID). EMBO J 18, 6084-94. [PubMed]
  93. Iwahara, J. Clubb RT. (1999) 1H, 13C, 15N resonance assignments of the AT-rich interaction domain form the Dead Ringer protein. J Biomol NMR 15, 85-6. [PubMed]
  94. Koshiba S, Kigawa T, Iwahara, J. Kikuchi A, Yokoyama S. (1999) Solution structure of the Eps15 homology domain of a human POB1 (partner of RalBP1). FEBS Lett 442, 138-42. [PubMed]
  95. Iwahara, J. Kigawa T, Kitagawa K, Masumoto H, Okazaki T, Yokoyama S. (1998) A helix-turn-helix structure unit in human centromere protein B (CENP-B). EMBO J 17, 827-37. [PubMed]
  96. Ito Y, Yamasaki K, Iwahara, J. Terada T, Kamiya A, Shirouzu M, Muto Y, Kawai G, Yokoyama S, Laue ED, Walchli M, Shibata T, Nishimura S, Miyazawa T. (1997) Regional polysterism in the GTP-bound form of the human c-Ha-Ras protein. Biochemistry 36, 9109-19. [PubMed]
  97. Ishima R, Iwahara, J. Yokoyama S, Nagayama K. (1996) Gaussian Spectral-Density Function for Protein Internal Motions. J Magn Reson B 111, 281-4. [PubMed]

    98. Citation Information
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