A Single Interfacial Point Mutation Rescues Solution Structure Determination of the Complex of HMG-D with a DNA Bulge

Overview

Journal Chembiochem

Specialty Biochemistry

Date 2024 Aug 15

PMID 39145407

Authors

Guy R Hill

Ji-Chun Yang

Laura E Easton

Rachel Cerdan

Stephen H McLaughlin

Katherine Stott

Andrew A Travers

David Neuhaus

Affiliations

Soon will be listed here.

Abstract

Broadening of signals from atoms at interfaces can often be a limiting factor in applying solution NMR to the structure determination of complexes. Common contributors to such problems include exchange between free and bound states and the increased molecular weight of complexes relative to the free components, but another cause that can be more difficult to deal with occurs when conformational dynamics within the interface takes place at an intermediate rate on the chemical shift timescale. In this work we show how a carefully chosen mutation in the protein HMG-D rescued such a situation, making possible high-resolution structure determination of its complex with a dA bulge DNA ligand designed to mimic a natural DNA bend, and thereby revealing a new spatial organization of the complex.

References

Case D, Cheatham 3rd T, Darden T, Gohlke H, Luo R, Merz Jr K . The Amber biomolecular simulation programs. J Comput Chem. 2005; 26(16):1668-88. PMC: 1989667. DOI: 10.1002/jcc.20290. View

Allain F, YEN Y, Masse J, Schultze P, Dieckmann T, Johnson R . Solution structure of the HMG protein NHP6A and its interaction with DNA reveals the structural determinants for non-sequence-specific binding. EMBO J. 1999; 18(9):2563-79. PMC: 1171337. DOI: 10.1093/emboj/18.9.2563. View

Churchill M, Jones D, Glaser T, HEFNER H, Searles M, Travers A . HMG-D is an architecture-specific protein that preferentially binds to DNA containing the dinucleotide TG. EMBO J. 1995; 14(6):1264-75. PMC: 398206. DOI: 10.1002/j.1460-2075.1995.tb07110.x. View

Love J, Li X, Case D, Giese K, Grosschedl R, Wright P . Structural basis for DNA bending by the architectural transcription factor LEF-1. Nature. 1995; 376(6543):791-5. DOI: 10.1038/376791a0. View

Murphy E, Zhurkin V, Louis J, Cornilescu G, Clore G . Structural basis for SRY-dependent 46-X,Y sex reversal: modulation of DNA bending by a naturally occurring point mutation. J Mol Biol. 2001; 312(3):481-99. DOI: 10.1006/jmbi.2001.4977. View

Payet D, Travers A . The acidic tail of the high mobility group protein HMG-D modulates the structural selectivity of DNA binding. J Mol Biol. 1997; 266(1):66-75. DOI: 10.1006/jmbi.1996.0782. View

Sherman F, Stewart J, Tsunasawa S . Methionine or not methionine at the beginning of a protein. Bioessays. 1985; 3(1):27-31. DOI: 10.1002/bies.950030108. View

Cerdan R, Payet D, Yang J, Travers A, Neuhaus D . HMG-D complexed to a bulge DNA: an NMR model. Protein Sci. 2001; 10(3):504-18. PMC: 2374130. DOI: 10.1110/ps.35501. View

Dow L, Jones D, Wolfe S, Verdine G, Churchill M . Structural studies of the high mobility group globular domain and basic tail of HMG-D bound to disulfide cross-linked DNA. Biochemistry. 2000; 39(32):9725-36. DOI: 10.1021/bi000723v. View

10.

Laskowski R, Rullmannn J, MacArthur M, Kaptein R, Thornton J . AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR. 1996; 8(4):477-86. DOI: 10.1007/BF00228148. View

11.

Voong C, Goodrich J, Kugel J . Interactions of HMGB Proteins with the Genome and the Impact on Disease. Biomolecules. 2021; 11(10). PMC: 8533419. DOI: 10.3390/biom11101451. View

12.

Iwahara J, Wojciak J, Clubb R . Improved NMR spectra of a protein-DNA complex through rational mutagenesis and the application of a sensitivity optimized isotope-filtered NOESY experiment. J Biomol NMR. 2001; 19(3):231-41. DOI: 10.1023/a:1011296112710. View

13.

Wishart D, Bigam C, Yao J, Abildgaard F, Dyson H, Oldfield E . 1H, 13C and 15N chemical shift referencing in biomolecular NMR. J Biomol NMR. 1995; 6(2):135-40. DOI: 10.1007/BF00211777. View

14.

Schwieters C, Kuszewski J, Tjandra N, Clore G . The Xplor-NIH NMR molecular structure determination package. J Magn Reson. 2003; 160(1):65-73. DOI: 10.1016/s1090-7807(02)00014-9. View

15.

Lorenz M, Hillisch A, Payet D, Buttinelli M, Travers A, Diekmann S . DNA bending induced by high mobility group proteins studied by fluorescence resonance energy transfer. Biochemistry. 1999; 38(37):12150-8. DOI: 10.1021/bi990459+. View

16.

Werner M, Huth J, Gronenborn A, Clore G . Molecular basis of human 46X,Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex. Cell. 1995; 81(5):705-14. DOI: 10.1016/0092-8674(95)90532-4. View

17.

Ner S, Churchill M, Searles M, Travers A . dHMG-Z, a second HMG-1-related protein in Drosophila melanogaster. Nucleic Acids Res. 1993; 21(18):4369-71. PMC: 310074. DOI: 10.1093/nar/21.18.4369. View

18.

Hommel U, Harvey T, Driscoll P, Campbell I . Human epidermal growth factor. High resolution solution structure and comparison with human transforming growth factor alpha. J Mol Biol. 1992; 227(1):271-82. DOI: 10.1016/0022-2836(92)90697-i. View

19.

Murphy 4th F, Sweet R, Churchill M . The structure of a chromosomal high mobility group protein-DNA complex reveals sequence-neutral mechanisms important for non-sequence-specific DNA recognition. EMBO J. 1999; 18(23):6610-8. PMC: 1171724. DOI: 10.1093/emboj/18.23.6610. View

20.

Stros M . HMGB proteins: interactions with DNA and chromatin. Biochim Biophys Acta. 2010; 1799(1-2):101-13. DOI: 10.1016/j.bbagrm.2009.09.008. View