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• 2018

  Direct detection of lysine side chain NH₃⁺ in protein-heparin complexes using NMR spectroscopy

  Sepuru, K. M., Iwahara, J. & Rajarathnam, K., Feb 7 2018, In: Analyst. 143, 3, p. 635-638 4 p.

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

  • Chemical shift
  • Heparin
  • Nuclear magnetic resonance spectroscopy
  • Lysine
  • nuclear magnetic resonance
  7 Scopus citations

• Impact of two-bond ¹⁵N–¹⁵N scalar couplings on ¹⁵N transverse relaxation measurements for arginine side chains of proteins

  Nguyen, D. & Iwahara, J., May 1 2018, In: Journal of Biomolecular NMR. 71, 1, p. 45-51 7 p.

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

  • Arginine
  • Modulation
  • Nuclear magnetic resonance
  • Proteins
  • Quenching
  3 Scopus citations

• Lysines and Arginines play non-redundant roles in mediating chemokine-glycosaminoglycan interactions

  Joseph, P. R. B., Sawant, K. V., Iwahara, J., Garofalo, R. P., Desai, U. R. & Rajarathnam, K., Dec 1 2018, In: Scientific reports. 8, 1, 12289.

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

  • Glycosaminoglycans
  • Lysine
  • Chemokines
  • Arginine
  • Neutrophils
  3 Scopus citations

• NMR-based investigations into target DNA search processes of proteins

  Iwahara, J., Zandarashvili, L., Kemme, C. A. & Esadze, A., Sep 15 2018, In: Methods. 148, p. 57-66 10 p.

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

  • Nuclear magnetic resonance
  • DNA
  • DNA Repair Enzymes
  • Proteins
  • Nuclear magnetic resonance spectroscopy
  9 Scopus citations
• 2017

  A unique and simple approach to improve sensitivity in ¹⁵N-NMR relaxation measurements for NH₃⁺ groups: Application to a protein-DNA complex

  Nguyen, D., Lokesh, G. L. R., Volk, D. E. & Iwahara, J., Aug 2017, In: Molecules. 22, 8, 1355.

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

  • Nuclear magnetic resonance
  • Lysine
  • deoxyribonucleic acid
  • proteins
  • nuclear magnetic resonance
  4 Scopus citations

• Discrete-State Kinetics Model for NMR-Based Analysis of Protein Translocation on DNA at Equilibrium

  Sahu, D. & Iwahara, J., Oct 19 2017, In: Journal of Physical Chemistry B. 121, 41, p. 9548-9556 9 p.

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

  • Nuclear magnetic resonance
  • DNA
  • Proteins
  • deoxyribonucleic acid
  • proteins
  4 Scopus citations

• Internal Motions of Basic Side Chains of the Antennapedia Homeodomain in the Free and DNA-Bound States

  Nguyen, D., Hoffpauir, Z. A. & Iwahara, J., Nov 7 2017, In: Biochemistry. 56, 44, p. 5866-5869 4 p.

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

  • DNA
  • Molecular recognition
  • Nuclear magnetic resonance spectroscopy
  • Hydrogen bonds
  • Thymine
  13 Scopus citations

• Potential role of DNA methylation as a facilitator of target search processes for transcription factors through interplay with methyl-CpG-binding proteins

  Kemme, C. A., Marquez, R., Luu, R. H. & Iwahara, J., Jul 1 2017, In: Nucleic acids research. 45, 13, p. 7751-7759 9 p.

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

  • DNA Methylation
  • Carrier Proteins
  • Transcription Factors
  • Methyl CpG Binding Domain
  • CpG Islands
  5 Scopus citations
• 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

  Anderson, K. M., Nguyen, D., Esadze, A., Zandrashvili, L., Gorenstein, D. G. & Iwahara, J., Jun 1 2015, In: Journal of Biomolecular NMR. 62, 1, p. 1-5 5 p., 9909.

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

  • Nuclear magnetic resonance
  • Nucleic Acids
  • Ions
  • Phosphates
  • Proteins
  13 Scopus citations

• Balancing between affinity and speed in target DNA search by zinc-finger proteins via modulation of dynamic conformational ensemble

  Zandarashvili, L., Esadze, A., Vuzman, D., Kemme, C. A., Levy, Y. & Iwahara, J., Sep 15 2015, In: Proceedings of the National Academy of Sciences of the United States of America. 112, 37, p. E5142-E5149

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

  • Zinc Fingers
  • Gene Editing
  • DNA-Binding Proteins
  • DNA
  • Kinetics
  63 Scopus citations

• Dynamic equilibria of short-range electrostatic interactions at molecular interfaces of protein-DNA complexes

  Chen, C., Esadze, A., Zandarashvili, L., Nguyen, D., Pettitt, B. M. & Iwahara, J., Jul 16 2015, In: Journal of Physical Chemistry Letters. 6, 14, p. 2733-2737 5 p.

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

  • Coulomb interactions
  • DNA
  • Ions
  • Proteins
  • deoxyribonucleic acid
  31 Scopus citations

• Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate

  Zandarashvili, L., Nguyen, D., Anderson, K. M., White, M. A., Gorenstein, D. G. & Iwahara, J., Sep 2 2015, In: Biophysical journal. 109, 5, p. 1026-1037 12 p.

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

  • Sulfur
  • Phosphates
  • Oxygen
  • DNA
  • Crystallography
  34 Scopus citations

• Influence of quasi-specific sites on kinetics of target DNA search by a sequence-specific DNA-binding protein

  Kemme, C. A., Esadze, A. & Iwahara, J., Nov 10 2015, In: Biochemistry. 54, 44, p. 6684-6691 8 p.

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

  • DNA-Binding Proteins
  • Kinetics
  • DNA
  • Transcription Factors
  • calf thymus DNA
  16 Scopus citations

• Physicochemical properties of ion pairs of biological macromolecules

  Iwahara, J., Esadze, A. & Zandarashvili, L., 2015, In: Biomolecules. 5, 4, p. 2435-2463 29 p., A11.

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

  • Macromolecules
  • Physicochemical properties
  • Ions
  • Chemical Phenomena
  • Crystal structure
  28 Scopus citations

• Structural impact of complete CpG methylation within target DNA on specific complex formation of the inducible transcription factor Egr-1

  Zandarashvili, L., White, M. A., Esadze, A. & Iwahara, J., Jul 3 2015, In: FEBS Letters. 589, 15, p. 1748-1753 6 p., 37178.

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

  • Methylation
  • Transcription Factors
  • Crystal structure
  • DNA
  • Cytosine
  23 Scopus citations

• Temperature dependence of internal motions of protein side-chain NH₃⁺ groups: Insight into energy barriers for transient breakage of hydrogen bonds

  Zandarashvili, L. & Iwahara, J., Jan 20 2015, In: Biochemistry. 54, 2, p. 538-545 8 p.

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

  • Energy barriers
  • Hydrogen bonds
  • Hydrogen
  • Temperature
  • Proteins
  20 Scopus citations
• 2014

  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

• 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., Jun 17 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

• 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
• 2012

  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
• 2011

  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

• 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