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Items: 1 to 20 of 74

1.

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

Kemme CA, Luu RH, Chen C, Pletka CC, Pettitt BM, Iwahara J.

J Phys Chem B. 2019 May 2;123(17):3706-3710. doi: 10.1021/acs.jpcb.9b03132. Epub 2019 Apr 18.

PMID:
30963768
2.

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

Nguyen D, Chen C, Pettitt BM, Iwahara J.

Methods Enzymol. 2019;615:285-332. doi: 10.1016/bs.mie.2018.08.017. Epub 2018 Sep 27.

PMID:
30638532
3.

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

Joseph PRB, Sawant KV, Iwahara J, Garofalo RP, Desai UR, Rajarathnam K.

Sci Rep. 2018 Aug 16;8(1):12289. doi: 10.1038/s41598-018-30697-y.

4.

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

Nguyen D, Iwahara J.

J Biomol NMR. 2018 May;71(1):45-51. doi: 10.1007/s10858-018-0189-y. Epub 2018 May 29.

5.

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

Iwahara J, Zandarashvili L, Kemme CA, Esadze A.

Methods. 2018 Sep 15;148:57-66. doi: 10.1016/j.ymeth.2018.05.004. Epub 2018 May 10. Review.

6.

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

Sepuru KM, Iwahara J, Rajarathnam K.

Analyst. 2018 Feb 7;143(3):635-638. doi: 10.1039/c7an01406f. Epub 2018 Jan 2.

7.

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

Nguyen D, Hoffpauir ZA, Iwahara J.

Biochemistry. 2017 Nov 7;56(44):5866-5869. doi: 10.1021/acs.biochem.7b00885.

8.

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

Sahu D, Iwahara J.

J Phys Chem B. 2017 Oct 19;121(41):9548-9556. doi: 10.1021/acs.jpcb.7b07779. Epub 2017 Oct 4.

9.

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 GLR, Volk DE, Iwahara J.

Molecules. 2017 Aug 15;22(8). pii: E1355. doi: 10.3390/molecules22081355.

10.

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

Kemme CA, Marquez R, Luu RH, Iwahara J.

Nucleic Acids Res. 2017 Jul 27;45(13):7751-7759. doi: 10.1093/nar/gkx387.

11.

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

Chattopadhyay A, Zandarashvili L, Luu RH, Iwahara J.

Biochemistry. 2016 Nov 29;55(47):6467-6474. Epub 2016 Nov 11.

12.

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.

J Phys Chem B. 2016 Oct 20;120(41):10679-10685. doi: 10.1021/acs.jpcb.6b08137. Epub 2016 Oct 10.

13.

Regulation of transcription factors via natural decoys in genomic DNA.

Kemme CA, Nguyen D, Chattopadhyay A, Iwahara J.

Transcription. 2016 Aug 7;7(4):115-20. doi: 10.1080/21541264.2016.1188873. Epub 2016 Jul 6. Review.

14.

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

Esadze A, Chen C, Zandarashvili L, Roy S, Pettitt BM, Iwahara J.

Nucleic Acids Res. 2016 Aug 19;44(14):6961-70. doi: 10.1093/nar/gkw531. Epub 2016 Jun 10.

15.

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

Nguyen D, Zandarashvili L, White MA, Iwahara J.

Chembiochem. 2016 Sep 2;17(17):1636-42. doi: 10.1002/cbic.201600265. Epub 2016 Jul 13.

16.

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

Zandarashvili L, Esadze A, Kemme CA, Chattopadhyay A, Nguyen D, Iwahara J.

J Phys Chem Lett. 2016 Mar 3;7(5):820-4. doi: 10.1021/acs.jpclett.6b00019. Epub 2016 Feb 22.

17.

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

Kemme CA, Esadze A, Iwahara J.

Biochemistry. 2015 Nov 10;54(44):6684-91. doi: 10.1021/acs.biochem.5b00967. Epub 2015 Nov 2.

18.

Physicochemical Properties of Ion Pairs of Biological Macromolecules.

Iwahara J, Esadze A, Zandarashvili L.

Biomolecules. 2015 Sep 30;5(4):2435-63. doi: 10.3390/biom5042435. Review.

19.

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

Zandarashvili L, Nguyen D, Anderson KM, White MA, Gorenstein DG, Iwahara J.

Biophys J. 2015 Sep 1;109(5):1026-37. doi: 10.1016/j.bpj.2015.07.032.

20.

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 CA, Levy Y, Iwahara J.

Proc Natl Acad Sci U S A. 2015 Sep 15;112(37):E5142-9. doi: 10.1073/pnas.1507726112. Epub 2015 Aug 31.

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