Nuclear Magnetic Resonance Analysis of Protein-DNA Interactions

Overview

Journal J R Soc Interface

Specialties Biology
Biomedical Engineering
Biophysics

Date 2011 Mar 11

PMID 21389020

Citations 17

Authors

S Campagne

V Gervais

A Milon

Affiliations

Soon will be listed here.

Abstract

Recent methodological and instrumental advances in solution-state nuclear magnetic resonance have opened up the way to investigating challenging problems in structural biology such as large macromolecular complexes. This review focuses on the experimental strategies currently employed to solve structures of protein-DNA complexes and to analyse their dynamics. It highlights how these approaches can help in understanding detailed molecular mechanisms of target recognition.

Citing Articles

Polymer-Nanodiscs as a Novel Alignment Medium for High-Resolution NMR-Based Structural Studies of Nucleic Acids.

Krishnarjuna B, Ravula T, Faison E, Tonelli M, Zhang Q, Ramamoorthy A Biomolecules. 2022; 12(11).

PMID: 36358983 PMC: 9687133. DOI: 10.3390/biom12111628.

Nucleic acid-protein interfaces studied by MAS solid-state NMR spectroscopy.

Aguion P, Marchanka A, Carlomagno T J Struct Biol X. 2022; 6:100072.

PMID: 36090770 PMC: 9449856. DOI: 10.1016/j.yjsbx.2022.100072.

Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology.

Saran R, Wang Y, Li I Sensors (Basel). 2020; 20(24).

PMID: 33302459 PMC: 7764255. DOI: 10.3390/s20247019.

Protein Side-Chain-DNA Contacts Probed by Fast Magic-Angle Spinning NMR.

Lacabanne D, Boudet J, Malar A, Wu P, Cadalbert R, Salmon L J Phys Chem B. 2020; 124(49):11089-11097.

PMID: 33238710 PMC: 7734624. DOI: 10.1021/acs.jpcb.0c08150.

Racemic phosphorothioate as a tool for NMR investigations of protein-DNA complexes.

Nepravishta R, Pletka C, Iwahara J J Biomol NMR. 2020; 74(8-9):421-429.

PMID: 32683519 PMC: 7511421. DOI: 10.1007/s10858-020-00333-x.

References

Takahashi H, Nakanishi T, Kami K, Arata Y, Shimada I . A novel NMR method for determining the interfaces of large protein-protein complexes. Nat Struct Biol. 2000; 7(3):220-3. DOI: 10.1038/73331. View

van Dijk M, Bonvin A . Pushing the limits of what is achievable in protein-DNA docking: benchmarking HADDOCK's performance. Nucleic Acids Res. 2010; 38(17):5634-47. PMC: 2943626. DOI: 10.1093/nar/gkq222. View

de Vries S, van Dijk M, Bonvin A . The HADDOCK web server for data-driven biomolecular docking. Nat Protoc. 2010; 5(5):883-97. DOI: 10.1038/nprot.2010.32. View

Lipsitz R, Tjandra N . Residual dipolar couplings in NMR structure analysis. Annu Rev Biophys Biomol Struct. 2004; 33:387-413. DOI: 10.1146/annurev.biophys.33.110502.140306. View

Schwieters C, Suh J, Grishaev A, Ghirlando R, Takayama Y, Clore G . Solution structure of the 128 kDa enzyme I dimer from Escherichia coli and its 146 kDa complex with HPr using residual dipolar couplings and small- and wide-angle X-ray scattering. J Am Chem Soc. 2010; 132(37):13026-45. PMC: 2955445. DOI: 10.1021/ja105485b. View

Boisbouvier J, Bryce D, Oneil-Cabello E, Nikonowicz E, Bax A . Resolution-optimized NMR measurement of (1)D(CH), (1)D(CC) and (2)D(CH) residual dipolar couplings in nucleic acid bases. J Biomol NMR. 2005; 30(3):287-301. DOI: 10.1007/s10858-005-1846-5. View

Grishaev A, Ying J, Canny M, Pardi A, Bax A . Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data. J Biomol NMR. 2008; 42(2):99-109. PMC: 2597493. DOI: 10.1007/s10858-008-9267-x. View

Garvie C, Wolberger C . Recognition of specific DNA sequences. Mol Cell. 2001; 8(5):937-46. DOI: 10.1016/s1097-2765(01)00392-6. View

Cuniasse P, Sowers L, Eritja R, Kaplan B, Goodman M, Cognet J . Abasic frameshift in DNA. Solution conformation determined by proton NMR and molecular mechanics calculations. Biochemistry. 1989; 28(5):2018-26. DOI: 10.1021/bi00431a009. View

10.

van Dijk M, van Dijk A, Hsu V, Boelens R, Bonvin A . Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility. Nucleic Acids Res. 2006; 34(11):3317-25. PMC: 1500871. DOI: 10.1093/nar/gkl412. View

11.

Fried M, Crothers D . Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res. 1981; 9(23):6505-25. PMC: 327619. DOI: 10.1093/nar/9.23.6505. View

12.

McAteer K, Aceves-Gaona A, Michalczyk R, Buchko G, Isern N, Silks L . Compensating bends in a 16-base-pair DNA oligomer containing a T(3)A(3) segment: A NMR study of global DNA curvature. Biopolymers. 2004; 75(6):497-511. DOI: 10.1002/bip.20168. View

13.

Ko S, Yu E, Shin J, Yoo H, Tanaka T, Kim W . Solution structure of the DNA binding domain of rice telomere binding protein RTBP1. Biochemistry. 2009; 48(5):827-38. DOI: 10.1021/bi801270g. View

14.

Falb M, Amata I, Gabel F, Simon B, Carlomagno T . Structure of the K-turn U4 RNA: a combined NMR and SANS study. Nucleic Acids Res. 2010; 38(18):6274-85. PMC: 2952850. DOI: 10.1093/nar/gkq380. View

15.

Kalodimos C, Bonvin A, Salinas R, Wechselberger R, Boelens R, Kaptein R . Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain. EMBO J. 2002; 21(12):2866-76. PMC: 126071. DOI: 10.1093/emboj/cdf318. View

16.

Wells M, Tidow H, Rutherford T, Markwick P, Jensen M, Mylonas E . Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain. Proc Natl Acad Sci U S A. 2008; 105(15):5762-7. PMC: 2311362. DOI: 10.1073/pnas.0801353105. View

17.

Cai S, Zhu L, Zhang Z, Chen Y . Determination of the three-dimensional structure of the Mrf2-DNA complex using paramagnetic spin labeling. Biochemistry. 2007; 46(17):4943-50. PMC: 2527749. DOI: 10.1021/bi061738h. View

18.

Panne D, Maniatis T, Harrison S . Crystal structure of ATF-2/c-Jun and IRF-3 bound to the interferon-beta enhancer. EMBO J. 2004; 23(22):4384-93. PMC: 526468. DOI: 10.1038/sj.emboj.7600453. View

19.

Pretto D, Tsutakawa S, Brosey C, Castillo A, Chagot M, Smith J . Structural dynamics and single-stranded DNA binding activity of the three N-terminal domains of the large subunit of replication protein A from small angle X-ray scattering. Biochemistry. 2010; 49(13):2880-9. PMC: 2847624. DOI: 10.1021/bi9019934. View

20.

Farjon J, Boisbouvier J, Schanda P, Pardi A, Simorre J, Brutscher B . Longitudinal-relaxation-enhanced NMR experiments for the study of nucleic acids in solution. J Am Chem Soc. 2009; 131(24):8571-7. PMC: 2846706. DOI: 10.1021/ja901633y. View