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  • Junji Iwahara
Article

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 journalArticle

13 Scopus citations

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

73 Scopus citations

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 journalArticle

3 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 journalArticle

59 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 journalArticle

38 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 journalArticle

2 Scopus citations

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

7 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 journalArticle

3 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 journalArticle

30 Scopus citations

Dynamics of Ionic Interactions at Protein-Nucleic Acid Interfaces

Yu, B., Pettitt, B. M. & Iwahara, J., 2020, (Accepted/In press) In : Accounts of Chemical Research.

Research output: Contribution to journalArticle

Open Access

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 journalArticle

59 Scopus citations
14 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 journalArticle

32 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 journalArticle

2 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 journalArticle

14 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 journalArticle

11 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 journalArticle

3 Scopus citations
3 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 journalArticle

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 journalArticle

7 Scopus citations
49 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 journalArticle

4 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 journalArticle

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

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 journalArticle

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 journalArticle

7 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 journalArticle

41 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 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

20 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
Review article

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 journalReview article

6 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 journalReview article

27 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

11 Scopus citations