Find Research outputs

Search results

• 2015

  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

• 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
• 2019

  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
• 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
• 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

  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

• 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
• 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

• 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
• 2014

  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
• 2015

  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

• 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

• 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
• 2019

  NMR Methods for Characterizing the Basic Side Chains of Proteins: Electrostatic Interactions, Hydrogen Bonds, and Conformational Dynamics

  Nguyen, D., Chen, C., Pettitt, B. M. & Iwahara, J., Jan 1 2019, Methods in Enzymology. Wand, A. J. (ed.). Academic Press Inc., p. 285-332 48 p. (Methods in Enzymology; vol. 615).

  Research output: Chapter in Book/Report/Conference proceeding › Chapter

  • Coulomb interactions
  • Hydrogen bonds
  • Nuclear magnetic resonance
  • Static Electricity
  • Hydrogen

• 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
• 2015

  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