Interaction of human SRY protein with DNA: A molecular dynamics study

Proteins: Structure, Function and Genetics

Volumn 31, Issue 4, 1998, Pages 417-433

  Tang, Yun ^a   Nilsson, Lennart ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

Author keywords

DNA bending; DNAbinding proteins; High mobility group (HMG) box; Molecular dynamics; Sex determining region Y (SRY) protein

Indexed keywords

DNA BINDING PROTEIN; HIGH MOBILITY GROUP PROTEIN;

ARTICLE; DNA CONFORMATION; HUMAN; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; COMPUTER SIMULATION; DNA; DNA-BINDING PROTEINS; HUMANS; HYDROGEN BONDING; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEAR PROTEINS; PROTEIN BINDING; SEX-DETERMINING REGION Y PROTEIN; TRANSCRIPTION FACTORS;

EID: 0032101261     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19980601)31:4<417::AID-PROT8>3.0.CO;2-E     Document Type: Article

References (56)

1. Harrison, S.C. A structural taxonomy of DNA-binding domains. Nature 353:715-719, 1991.
2. Luisi, B. DNA-protein interaction at high resolution. In: "DNA-Protein: Structural Interactions." Lilley, D.M.J. (ed.). Oxford: IRL Press, 1995:1-48.
3. Sinclair, A.H., Berta, P., Palmer, M.S., Hawkins, J.R., Griffiths, B.L., Smith, M.J., Foster, J.W., Frischauf, A.-M., Lovell-Badge, R., Goodfellow, P.N. A gene from the human sex-determining region encodes a protein with homology to a conserved DNA-binding motif. Nature 346:240-244, 1990.
4. Werner, M.H., Huth, J.R., Gronenborn, A.M., Clore G.M. Molecular determinants of mammalian sex. Trends Biochem. Sci. 21:302-308, 1996.
5. Schafer, A.J., Goodfellow, P.N. Sex determination in humans. BioEssays 18:955-963, 1996.
6. Shah, V.C., Smart, V. Human chromosome Y and SRY. Cell Biol. Int. 20:3-6, 1996.
7. Ferrari, S., Harley, V.R., Pontiggia, A., Goodfellow, P.N., Lovell-Badge, R., Bianchi, M.E. SRY, like HMG1, recognizes sharp angles in DNA. EMBO J. 11:4497-4506, 1992.
8. van de Wetering, M., Clevers, H. Sequence-specific interaction of the HMG box proteins TCF-1 and SRY occurs within the minor groove of a Watson-Crick double helix. EMBO J. 11:3039-3044, 1992.
9. Whitfield, L.S., Lovell-Badge, R., Goodfellow, P.N. Rapid sequence evolution of the mammalian sex-determining gene SRY. Nature 364:713-715, 1993.
10. Pontiggia, A., Whitfield, S., Goodfellow, P.N., Lovell-Badge, R., Bianchi, M.E. Evolutionary conservation in the DNA-binding and -bending properties of HMG-boxes from SRY proteins of primates. Gene 154:277-280, 1995.
11. Sanchez, A., Bullejos, M., Burgos, M., Hera, C., Jimenez, R., Diaz de la Guardia, R. High sequence identity between the SRY HMG box from humans and insectivores. Mamm. Genome 7:536-538, 1996.
12. Tajima, T., Nakae, J., Shinohara, N., Fujieda, K. A novel mutation localized in the 3′ non-HMG box region of the SRY gene in 46X,Y gonadal dysgenesis. Hum. Mol. Genet. 3:1187-1189, 1994.
13. Hawkins, J.R. Sex determination. Hum. Mol. Genet. 3: 1463-1467, 1994.
14. Grosschedl, R., Giese, K., Pagel, J. HMG domain proteins: Architectural elements in the assembly of nucleoprotein structures. Trends Genet. 10:94-100, 1994.
15. Bianchi, M.E. The HMG-box domain. In: "DNA-Protein: Structural Interactions." Lilley, D.M.J. (ed.). Oxford: IRL Press, 1995:177-200.
16. Weir, H.M., Kraulis, P.J., Hill, C.S., Raine, A.R.C., Laue, E.D., Thomas, J.O. Structure of the HMG box motif in B-domain of HMG1. EMBO J. 12:1311-1319, 1993.
17. Read, C.M., Cary, P.D., Crane-Robinson, C., Driscoll, P.C., Norman, D.G. Solution structure of a DNA-binding domain from HMG1. Nucleic Acids Res. 21:3427-3436, 1993.
18. Hardman, C.H., Broadhurst, R.W., Raine, A.R.C., Grasser, K.D., Thomas, J.O., Laue, E.D. Structure of the A-domain of HMG1 and its interaction with DNA as studied by heteronuclear three- and four-dimensional NMR spectroscopy. Biochemistry 34:16596-16607, 1995.
19. Jones, D.N.M., Searles, M.A., Shaw, G.L., Churchill, M.E.A., Ner, S.S., Keeler, J., Travers, A.A., Neuhaus, D. The solution structure and dynamics of the DNA-binding domain of HMG-D from Drosophila melanogaster. Structure 2:609-627, 1994.
20. van Houte, L.P.A., Chuprina, V.P., van der Wetering, M., Boelens, R., Kaptein, R., Clevers, H. Solution structure of the sequence-specific HMG box of the lymphocyte transcriptional activator Sox-4. J. Biol. Chem. 270:30516-30524, 1995.
21. Werner, M.H., Huth, J.R., Gronenborn, A.M., Clore, G.M. Molecular basis of human 46X, Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex. Cell 81:705-714, 1995.
22. King, C.-Y., Weiss, M.A. The SRY high-mobility-group box recognizes DNA by partial intercalation in the minor groove: A topological mechanism of sequence specificity. Proc. Natl. Acad. Sci. USA 90:11990-11994, 1993.
23. Haqq, C.M., King, C.-Y., Ukiyama, E., Falsafi, S., Haqq, T.N., Donahoe, P.K., Weiss, M.A. Molecular basis of mammalian sexual determination: Activation of Müllerian inhibiting substance gene expression by SRY. Science 266:1494-1500, 1994.
24. Love, J.J., Li, X., Case, D.A., Giese, K., Grosschedl, R., Wright, P.E. Structural basis for DNA bending by the architectural transcription factor LEF-1. Nature 376:791-795, 1995.
25. Harley, V.R., Jackson, D.I., Hextall, P.J., Hawkins, J.R., Berkovitz, G.D., Sockanathan, S., Lovell-Badge, R., Goodfellow, P.N. DNA binding activity of recombinant SRY from normal males and XY females. Science 255:453-456, 1992.
26. Pontiggia, A., Rimini, R., Harley, V.R., Goodfellow, P.N., Lovell-Badge, R., Bianchi, M.E. Sex-reversing mutations affect the architecture of SRY-DNA complexes. EMBO J. 13:6115-6124, 1994.
27. Rimini, R., Pontiggia, A., Spada, F., Ferrari, S., Harley, V.R., Goodfellow, P.N., Bianchi, M.E. Interaction of normal and mutant SRY proteins with DNA. Phil. Trans. R. Soc. Lond. B 350:215-220, 1995.
28. Peters, R., King, C.-Y., Ukiyama, E., Falsafi, S., Donahoe, P.K., Weiss, M.A. An SRY mutation causing human sex reversal resolves a general mechanism of structure-specific DNA recognition: Application to the four-way DNA junction. Biochemistry 34:4569-4576, 1995.
29. Karplus, M., Petsko, G.A. Molecular dynamics simulations in biology. Nature 347:631-639, 1990.
30. van Gunsteren, W.F., Berendsen, H.J.C. Computer simulation of molecular dynamics: Methodology, applications, and perspectives in chemistry. Angew. Chem. Int. Ed. Engl. 29:992-1023, 1990.
31. Brooks C.L. III Methodological advances in molecular dynamics simulations of biological systems. Curr. Opin. Struct. Biol. 5:211-215, 1995.
32. Schwabe, J.W.R. The role of water in protein-DNA interactions. Curr. Opin. Struct. Biol. 7:126-134, 1997.
33. Levitt, M., Park, B.H. Water: Now you see it, now you don't. Structure 1:223-226, 1993.
34. Nilsson, L. Protein-DNA interactions. In: "The Encyclopedia of Computational Chemistry." Schleyer, P.v.R. (ed.). New York: John Wiley & Sons, 1998 (in press).
35. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., Karplus, M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4:187-217, 1983.
36. MacKerell, A.D. Jr., Wiorkiewicz-Kuczera, J., Karplus, M. An all-atom empirical energy function for the simulation of nucleic acids. J. Am. Chem. Soc. 117:11946-11975, 1995.
37. Jorgensen, W.L., Chandraseklar, J., Madura, J.D., Impey, R.W., Klein, M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935, 1983.
38. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Mayer, E.F., Brice, J.M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., Tasumi, M. The protein data bank. A computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542, 1977.
39. Brünger, A., Karplus, M. Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison. Proteins 4:148-156, 1988.
40. van Gunsteren, W.F., Berendsen, H.J.C. Algorithms for macromolecular dynamics and constraint dynamics. Mol. Phys. 34:1311-1327, 1977.
41. Brooks, C.L. III, Karplus, M. Deformable stochastic boundaries in molecular dynamics. J. Chem. Phys. 79:6312-6325, 1983.
42. McDonald, I.K., Thornton, J.M. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238:777-793, 1994.
43. Arnott, S., Hukins, D.W.L. Refinement of the structure of B-DNA and implications for the analysis of X-ray diffraction data from fibres of biopolymers. J. Mol. Biol. 81:93-105, 1973.
44. QUANTA 3.3, Burlington, MA: Molecular Simulation Inc., 1992.
45. Lee, B., Richards, F.M. The interpretation of protein structures: Estimation of static accessibility. J. Mol. Biol. 55:379-400, 1971.
46. Werner, M.H., Bianchi, M.E., Gronenborn, A.M., Clore, G.M. NMR spectroscopic analysis of the DNA conformation induced by the human testis determining factor SRY. Biochemistry 34:11998-12004, 1995.
47. Lebrun, A., Shakked, Z., Lavery, R. Local DNA stretching mimics the distortion caused by the TATA box-binding protein. Proc. Natl. Acad. Sci. USA 94:2993-2998, 1997.
48. Balaeff, A., Churchill, M.E.A., Schulten, K. Structure prediction of a complex between the chromosomal protein HMG-D and DNA. Proteins 30:113-135, 1998.
49. Delcourt, S.G., Blake, R.D. Stacking energies in DNA. J. Biol. Chem. 266:15160-15169, 1991.
50. Harley, V.R., Lovell-Badge, R., Goodfellow, P.N. Definition of a consensus DNA binding site for SRY. Nucleic Acids Res. 22:1500-1501, 1994.
51. Juo, Z.S., Chiu, T.K., Leiberman, P.M., Baikalov, I., Berk, A.J., Dickerson, R.E. How proteins recognize the TATA box. J. Mol. Biol. 261:239-254, 1996.
52. Werner, M.H., Gronenborn, A.M., Clore, G.M. Intercalation, DNA kinking, and the control of transcription. Science 271:778-784, 1996.
53. Feig, M., Pettitt, M. Experiment vs force fields: DNA conformation from molecular dynamics simulations. J. Phys. Chem. B 101:7361-7363, 1997.
54. Hartmann, B., Lavery, R. DNA structural forms. Q. Rev. Biophys. 29:309-368, 1996.
55. Elcock, A.H., McCammon, J.A. The low dielectric interior of proteins was sufficient to cause major structural changes in DNA on association. J. Am. Chem. Soc. 118:3787-3788, 1996.
56. Kraulis, P.J. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:946-950, 1991.