Specific DNA recognition by the Antp homeodomain: MD simulations of specific and nonspecific complexes

Proteins: Structure, Function and Genetics

Volumn 57, Issue 4, 2004, Pages 772-782

  Gutmanas, Aleksandras ^a   Billeter, Martin ^a  

^a UNIVERSITY OF GOTHENBURG   (Sweden)

Author keywords

DNA binding; Interface water; Molecular dynamics; Specific recognition; Transcription control

Indexed keywords

ANTENNAPEDIA PROTEIN; DNA; HOMEODOMAIN PROTEIN; MUTANT PROTEIN; UNCLASSIFIED DRUG; WATER;

ARTICLE; BINDING AFFINITY; DNA BINDING; DNA SEQUENCE; HYDROGEN BOND; HYDROPHOBICITY; MACROMOLECULE; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; MUTATION; NUCLEAR MAGNETIC RESONANCE; OPERATOR GENE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION; PROTEIN STRUCTURE; SIMULATION; X RAY CRYSTALLOGRAPHY;

ANTENNAPEDIA HOMEODOMAIN PROTEIN; BASE SEQUENCE; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DNA; MACROMOLECULAR SUBSTANCES; MUTATION; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; SUBSTRATE SPECIFICITY; TIME FACTORS; WATER;

EID: 10344241958     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20273     Document Type: Article

References (42)

1. Härd T. NMR studies of protein-nucleic acid complexes: structures, solvation, dynamics and coupled protein folding. Q Rev Biophys 1999;32:57-98.
2. Burley SK, Kamada K. Transcription factor complexes. Curr Opin Struct Biol 2002;12:225-230.
3. Branden C, Tooze J. Introduction to protein structure. New York: Garland; 1999.
4. Janin J. Wet and dry interfaces: the role of solvent in protein-protein and protein-DNA recognition. Struct Fold Des 1999;7: R277-R279.
5. Nikolov DB, Chen H, Halay ED, Hoffman A, Roeder RG, Burley SK. Crystal structure of a human TATA box-binding protein/ TATA element complex. Proc Natl Acad Sci USA 1996;93:4862-4867.
6. Billeter M. Homeodomain-type DNA recognition. Prog Biophys Mol Biol 1996;66:211-225.
7. Wolberger C. Homeodomain interactions. Curr Opin Struct Biol 1996;6:62-68.
8. Otwinowski Z, Schevitz RW, Zhang RG, Lawson CL, Joachimiak A, Marmorstein RQ, Luisi BF, Sigler PB. Crystal structure of trp repressor/operator complex at atomic resolution. Nature 1988;335:321-329.
9. Zhang H, Zhao D, Revington M, Lee W, Jia X, Arrowsmith C, Jardetzky O. The solution structures of the trp repressor-operator DNA complex. J Mol Biol 1994;238:592-614.
10. Wolberger C. Multiprotein-DNA complexes in transcriptional regulation. Annu Rev Biophys Biomol Struct 1999;28:29-56.
11. Choo Y, Isalan M. Advances in zinc finger engineering. Curr Opin Struct Biol 2000;10:411-416.
12. Gehring WJ. Homeo boxes in the study of development. Science 1987;236:1245-1252.
13. Qian YQ, Billeter M, Otting G, Müller M, Gehring WJ, Wüthrich K. The structure of the Antennapedia homeodomain determined by NMR spectroscopy in solution: comparison with prokaryotic repressors. Cell 1989;59:573-580.
14. Gehring WJ, Qian YQ, Billeter M, Furukubo-Tokunaga K, Schier AF, Resendez-Perez D, Affolter M, Otting G, Wüthrich K. Homeodomain-DNA recognition. Cell 1994;78:211-223.
15. Tucker-Kellogg L, Rould MA, Chambers KA, Ades SE, Sauer RT, Pabo CO. Engrailed (Gln50→Lys) homeodomain-DNA complex at 1.9 Å resolution: structural basis for enhanced affinity and altered specificity. Structure 1997;5:1047-1054.
16. Fraenkel E, Rould MA, Chambers KA, Pabo CO. Engrailed homeodomain-DNA complex at 2.2 Å resolution: a detailed view of the interface and comparison with other engrailed structures. J Mol Biol 1998;284:351-361.
17. Grant RA, Rould MA, Klemm JD, Pabo CO. Exploring the role of glutamine 50 in the homeodomain-DNA interface: crystal structure of engrailed (Gln50→Ala) complex at 2.0 Å. Biochemistry 2000;39:8187-8192.
18. Koizumi K, Lintas C, Nirenberg M, Maeng JS, Ju JH, Mack JW, Gruschus JM, Odenwald WF, Ferretti JA. Mutations that affect the ability of the vnd/NK-2 homeoprotein to regulate gene expression: transgenic alterations and tertiary structure. Proc Natl Acad Sci USA 2003;100:3119-3124.
19. Billeter M, Qian YQ, Otting G, Müller M, Gehring W, Wüthrich K. Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex. J Mol Biol 1993;234:1084-1093.
20. Fernandez C, Szyperski T, Billeter M, Ono A, Iwai H, Kainosho M, Wüthrich K. Conformational changes of the BS2 operator DNA upon complex formation with the Antennapedia homeodomain studied by NMR with 13C/15N-labeled DNA. J Mol Biol 1999;292:609-617.
21. Fraenkel E, Pabo CO. Comparison of X-ray and NMR structures for the Antennapedia homeodomain-DNA complex. Nat Struct Biol 1998;5:692-697.
22. Percival-Smith A, Müller M, Affolter M, Gehring WJ. The interaction with DNA of wild-type and mutant fushi tarazu homeodomains. EMBO J 1990;9:3967-3974 [Corrigendum. EMBO J 1992;11:382].
23. Percival-Smith A, Müller M, Affolter M, Gehring WJ. The interaction with DNA of wild-type and mutant fushi tarazu homeodomains. EMBO J 1990;9:3967-3974 [Corrigendum. EMBO J 1992;11:382].
24. Ades SE, Sauer RT. Differential DNA-binding specificity of the engrailed homeodomain: the role of residue 50. Biochemistry 1994;33:9187-9194.
25. Ades SE, Sauer RT. Specificity of minor-groove and major-groove interactions in a homeodomain-DNA complex. Biochemistry 1995;34:14601-14608.
26. Hirsch JA, Aggarwal AK. Structure of the even-skipped homeodomain complexed to AT-rich DNA: new perspectives on homeodomain specificity. EMBO J 1995;14:6280-6291.
27. Qian YQ, Otting G, Billeter M, Müller M, Gehring W, Wüthrich K. Nuclear magnetic resonance spectroscopy of a DNA complex with the uniformly 13C-labeled Antennapedia homeodomain and structure determination of the DNA-bound homeodomain. J Mol Biol 1993;234:1070-1083.
28. Billeter M, Güntert P, Luginbühl P, Wüthrich K. Hydration and DNA recognition by homeodomains. Cell 1996;85:1057-1065.
29. Duan Y, Kollman PA. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 1998;282:740-744.
30. Cheatham TE III, Kollman PA. Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution. J Mol Biol 1996;259:434-444.
31. Hansson T, Oostenbrink C, van Gunsteren WF. Molecular dynamics simulations. Curr Opin Struct Biol 2002;12:190-196.
32. Duan J, Nilsson L. The role of residue 50 and hydration water molecules in homeodomain DNA recognition. Eur Biophys J 2002;31:306-316.
33. Koradi R, Billeter M, Wüthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 1996;14:51-55.
34. Case DA, Pearlman DA, Caldwell JW, Cheatham III TE, Ross WS, Simmerling CL, Darden TA, Merz KM, Stanton RV, Cheng AL, Vincent JJ, Crowley M, Fergusson DM, Radmer EJ, Seibel GL, Singh UC, Weiner PK, Kollman PA. AMBER 5. San Francisco: University of California; 1997.
35. Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, Debolt S, Ferguson D, Seibel G, Kollman P. Amber, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules. Comp Phys Comm 1995;91:1-41.
36. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A 2nd generation force-field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995;117:5179-5197.
37. Berendsen HJC, Postma JPM, van Gunsteren WF, Dinola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684-3690.
38. Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of Cartesian equations of motion of a system with constraints-molecular dynamics of N-alkanes. J Comp Phys 1977;23:327-341.
39. Darden T, York D, Pedersen L. Particle mesh Ewald-an N · Log(N) method for Ewald sums in large systems. J Chem Phys 1993;98:10089-10092.
40. Andersen HC. Molecular-dynamics simulations at constant pressure and-or temperature. J Chem Phys 1980;72:2384-2393.
41. Harvey SC, Tan RKZ, Cheatham TE. The flying ice cube: velocity rescaling in molecular dynamics leads to violation of energy equipartition. J Comput Chem 1998;19:726-740.
42. Schwabe JW. The role of water in protein-DNA interactions. Curr Opin Struct Biol 1997;7:126-134.