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• Article

  Asymmetrical roles of zinc fingers in dynamic DNA-scanning process by the inducible transcription factor Egr-1

  Zandarashvili, L., Vuzman, D., Esadze, A., Takayama, Y., Sahu, D., Levy, Y. & Iwahara, J., Jun 26 2012, In: Proceedings of the National Academy of Sciences of the United States of America. 109, 26, p. E1724-E1732

  Research output: Contribution to journal › Article › peer-review

  • Zinc Fingers
  • Transcription Factors
  • DNA
  • Kinetics
  • Mutant Proteins
  76 Scopus citations

• Changes in conformational dynamics of basic side chains upon protein-DNA association

  Esadze, A., Chen, C., Zandarashvili, L., Roy, S., Pettitt, B. M. & Iwahara, J., Aug 19 2016, In: Nucleic acids research. 44, 14, p. 6961-6970 10 p.

  Research output: Contribution to journal › Article › peer-review

  • DNA
  • Lysine
  • Arginine
  • Proteins
  • Entropy
  41 Scopus citations

• Detecting Counterion Dynamics in DNA–Protein Association

  Pletka, C. C., Nepravishta, R. & Iwahara, J., Jan 20 2020, In: Angewandte Chemie - International Edition. 59, 4, p. 1465-1468 4 p.

  Research output: Contribution to journal › Article › peer-review

  • Ions
  • DNA
  • Nuclear magnetic resonance spectroscopy
  • Positive ions
  • Nuclear magnetic resonance
  3 Scopus citations

• Dynamics of ionic interactions at protein-nucleic acid interfaces

  Yu, B., Pettitt, B. M. & Iwahara, J., Sep 15 2020, In: Accounts of Chemical Research. 53, 9, p. 1802-1810 9 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Nucleic Acids
  • Ions
  • Proteins
  • Cations
  • Macromolecules
  3 Scopus citations

• Dynamics of lysine side-chain amino groups in a protein studied by heteronuclear ¹H-¹⁵N NMR spectroscopy

  Esadze, A., Li, D. W., Wang, T., Brüschweiler, R. & Iwahara, J., Feb 2 2011, In: Journal of the American Chemical Society. 133, 4, p. 909-919 11 p.

  Research output: Contribution to journal › Article › peer-review

  • Nuclear magnetic resonance spectroscopy
  • Proton Magnetic Resonance Spectroscopy
  • Lysine
  • Proteins
  • Magnetic Resonance Spectroscopy
  60 Scopus citations

• Effective strategy to assign ¹H-¹⁵N heteronuclear correlation NMR signals from lysine side-chain NH<inf>3</inf> ⁺ groups of proteins at low temperature

  Esadze, A., Zandarashvili, L. & Iwahara, J., 2014, In: Journal of Biomolecular NMR. 60, 1, p. 23-27 5 p.

  Research output: Contribution to journal › Article › peer-review

  • Biomolecular Nuclear Magnetic Resonance
  • Nuclear magnetic resonance
  • Lysine
  • Temperature
  • Pair Bond
  16 Scopus citations

• Experimental Evidence of Solvent-Separated Ion Pairs as Metastable States in Electrostatic Interactions of Biological Macromolecules

  Yu, B., Pettitt, B. M. & Iwahara, J., Dec 19 2019, In: Journal of Physical Chemistry Letters. 10, 24, p. 7937-7941 5 p.

  Research output: Contribution to journal › Article › peer-review

  • Coulomb interactions
  • Macromolecules
  • macromolecules
  • metastable state
  • Ions
  2 Scopus citations

• Hydrogen-exchange kinetics studied through analysis of self-decoupling of nuclear magnetic resonance

  Nepravishta, R., Yu, B. & Iwahara, J., Mar 2020, In: Journal of Magnetic Resonance. 312, 106687.

  Research output: Contribution to journal › Article › peer-review

  • Nuclear magnetic resonance
  • Hydrogen
  • decoupling
  • Magnetic Resonance Spectroscopy
  • nuclear magnetic resonance
  1 Scopus citations

• Mobility of Histidine Side Chains Analyzed with ¹⁵ N NMR Relaxation and Cross-Correlation Data: Insight into Zinc-Finger-DNA Interactions

  Kemme, C. A., Luu, R. H., Chen, C., Pletka, C. C., Pettitt, B. M. & Iwahara, J., May 2 2019, In: Journal of Physical Chemistry B. 123, 17, p. 3706-3710 5 p.

  Research output: Contribution to journal › Article › peer-review

  • histidine
  • Nuclear magnetic resonance
  • Histidine
  • Zinc
  • DNA
  1 Scopus citations

• NMR Observation of Intermolecular Hydrogen Bonds between Protein Tyrosine Side-Chain OH and DNA Phosphate Groups

  Yu, B., Pletka, C. C. & Iwahara, J., Feb 13 2020, In: Journal of Physical Chemistry B. 124, 6, p. 1065-1070 6 p.

  Research output: Contribution to journal › Article › peer-review

  • tyrosine
  • Hydrogen bonds
  • Nuclear magnetic resonance
  • Phosphates
  • hydrogen bonds
  2 Scopus citations

• NMR Scalar Couplings across Intermolecular Hydrogen Bonds between Zinc-Finger Histidine Side Chains and DNA Phosphate Groups

  Chattopadhyay, A., Esadze, A., Roy, S. & Iwahara, J., Oct 20 2016, In: Journal of Physical Chemistry B. 120, 41, p. 10679-10685 7 p.

  Research output: Contribution to journal › Article › peer-review

  • histidine
  • Hydrogen bonds
  • Nuclear magnetic resonance
  • Phosphates
  • Histidine
  7 Scopus citations

• 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

  Esadze, A., Kemme, C. A., Kolomeisky, A. B. & Iwahara, J., 2014, In: Nucleic acids research. 42, 11, p. 7039-7046 8 p.

  Research output: Contribution to journal › Article › peer-review

  • DNA-Binding Proteins
  • Osmolar Concentration
  • Zinc Fingers
  • Kinetics
  • DNA
  51 Scopus citations

• Racemic phosphorothioate as a tool for NMR investigations of protein-DNA complexes

  Nepravishta, R., Pletka, C. C. & Iwahara, J., Sep 1 2020, In: Journal of Biomolecular NMR. 74, 8-9, p. 421-429 9 p.

  Research output: Contribution to journal › Article › peer-review

  • Nuclear magnetic resonance
  • DNA
  • Chemical shift
  • Phosphates
  • Proteins
  1 Scopus citations

• Residence Times of Molecular Complexes in Solution from NMR Data of Intermolecular Hydrogen-Bond Scalar Coupling

  Zandarashvili, L., Esadze, A., Kemme, C. A., Chattopadhyay, A., Nguyen, D. & Iwahara, J., Mar 3 2016, In: Journal of Physical Chemistry Letters. 7, 5, p. 820-824 5 p.

  Research output: Contribution to journal › Article › peer-review

  • Hydrogen bonds
  • Nuclear magnetic resonance
  • hydrogen bonds
  • nuclear magnetic resonance
  • decoupling
  12 Scopus citations

• Signature of mobile hydrogen bonding of lysine side chains from long-range ¹⁵N-¹³C scalar J-couplings and computation

  Zandarashvili, L., Li, D. W., Wang, T., Brüschweiler, R. & Iwahara, J., Jun 22 2011, In: Journal of the American Chemical Society. 133, 24, p. 9192-9195 4 p.

  Research output: Contribution to journal › Article › peer-review

  • Hydrogen bonds
  • Hydrogen Bonding
  • Hydrogen
  • Lysine
  • Molecular Dynamics Simulation
  29 Scopus citations

• Stereospecific Effects of Oxygen-to-Sulfur Substitution in DNA Phosphate on Ion Pair Dynamics and Protein–DNA Affinity

  Nguyen, D., Zandarashvili, L., White, M. A. & Iwahara, J., Sep 2 2016, In: ChemBioChem. p. 1636-1642 7 p.

  Research output: Contribution to journal › Article › peer-review

  • Sulfur
  • Substitution reactions
  • Phosphates
  • Ions
  • Oxygen
  8 Scopus citations

• Stopped-flow fluorescence kinetic study of protein sliding and intersegment transfer in the target DNA search process

  Esadze, A. & Iwahara, J., Jan 9 2014, In: Journal of Molecular Biology. 426, 1, p. 230-244 15 p.

  Research output: Contribution to journal › Article › peer-review

  • Fluorescence
  • Kinetics
  • DNA
  • Zinc Fingers
  • Proteins
  42 Scopus citations

• Thermodynamic Additivity for Impacts of Base-Pair Substitutions on Association of the Egr-1 Zinc-Finger Protein with DNA

  Chattopadhyay, A., Zandarashvili, L., Luu, R. H. & Iwahara, J., Nov 29 2016, In: Biochemistry. 55, 47, p. 6467-6474 8 p.

  Research output: Contribution to journal › Article › peer-review

  • Thermodynamics
  • Zinc Fingers
  • Base Pairing
  • Free energy
  • Substitution reactions
  5 Scopus citations
• Review article

  Regulation of transcription factors via natural decoys in genomic DNA

  Kemme, C. A., Nguyen, D., Chattopadhyay, A. & Iwahara, J., Aug 7 2016, In: Transcription. 7, 4, p. 115-120 6 p.

  Research output: Contribution to journal › Review article › peer-review

  • Transcription Factors
  • DNA
  • Genes
  14 Scopus citations