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  • Junji Iwahara
2015

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

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

Research output: Contribution to journalArticle

29 Scopus citations
2020

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 journalArticle

2015

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 journalArticle

14 Scopus citations
2018
2 Scopus citations
2020

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 journalArticle

1 Scopus citations
2015

A chemical approach for site-specific identification of NMR signals from protein side-chain NH<inf>3</inf><sup>+</sup> 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 journalArticle

13 Scopus citations
2013

NMR studies on the dynamics of hydrogen bonds and ion pairs involving lysine side chains of proteins

Zandarashvili, L., Esadze, A. & Iwahara, J., 2013, Biomolecular Spectroscopy: Advances from Integrating Experiments and Theory. Academic Press Inc., p. 37-80 44 p. (Advances in Protein Chemistry and Structural Biology; vol. 93).

Research output: Chapter in Book/Report/Conference proceedingChapter

22 Scopus citations
2016

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

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

Research output: Contribution to journalArticle

6 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 1 2017, In : Molecules. 22, 8, 1355.

Research output: Contribution to journalArticle

3 Scopus citations
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 journalArticle

6 Scopus citations
2014
49 Scopus citations
2013

Direct observation of the ion-pair dynamics at a protein-DNA interface by NMR spectroscopy

Anderson, K. M., Esadze, A., Manoharan, M., Brüschweiler, R., Gorenstein, D. G. & Iwahara, J., Mar 6 2013, In : Journal of the American Chemical Society. 135, 9, p. 3613-3619 7 p.

Research output: Contribution to journalArticle

48 Scopus citations
2018

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

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

Research output: Contribution to journalArticle

3 Scopus citations
2017

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 journalArticle

4 Scopus citations
2015

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 journalReview article

26 Scopus citations
2013

Speed-stability paradox in DNA-scanning by zinc-finger proteins

Iwahara, J. & Levy, Y., Jan 1 2013, In : Transcription. 4, 2, p. 58-61 4 p.

Research output: Contribution to journalArticle

Open Access
15 Scopus citations
2019
2020

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 journalArticle

1 Scopus citations
2017

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 journalArticle

10 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 journalArticle

72 Scopus citations
2018
3 Scopus citations
2019

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 journalArticle

2015

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

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

Research output: Contribution to journalArticle

29 Scopus citations
2016

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 journalArticle

37 Scopus citations

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 journalReview article

9 Scopus citations
2015

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 journalArticle

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 journalArticle

19 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 journalArticle

41 Scopus citations
2017

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 journalArticle

2 Scopus citations
2014
14 Scopus citations
2018

NMR-based investigations into target DNA search processes of proteins

Iwahara, J., Zandarashvili, L., Kemme, C. A. & Esadze, A., Jan 1 2018, (Accepted/In press) In : Methods.

Research output: Contribution to journalArticle

5 Scopus citations
2013

Real-time kinetics of high-mobility group box 1 (HMGB1) oxidation in extracellular fluids studied by in situ protein NMR spectroscopy

Zandarashvili, L., Sahu, D., Lee, K., Lee, Y. S., Singh, P., Rajarathnam, K. & Iwahara, J., Apr 26 2013, In : Journal of Biological Chemistry. 288, 17, p. 11621-11627 7 p.

Research output: Contribution to journalArticle

33 Scopus citations
2016

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 journalArticle

12 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 journalArticle

7 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 journalArticle

4 Scopus citations
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 journalArticle

58 Scopus citations