Structures during binding of cAMP receptor to promoter DNA: Promoter search slowed by non-specific sites

European Biophysics Journal

Volumn 41, Issue 5, 2012, Pages 415-424

  Porschke, Dietmar ^a  

^a MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

Author keywords

Bending; DNA binding; Electric dichroism; Kinetics; Pseudo sites; Stopped flow

Indexed keywords

BUFFER; CYCLIC AMP RECEPTOR; DNA;

ARTICLE; BINDING SITE; CHEMISTRY; CONFORMATION; ENZYME SPECIFICITY; KINETICS; METABOLISM; PROMOTER REGION; PROTEIN BINDING; TEMPERATURE;

BINDING SITES; BUFFERS; DNA; KINETICS; NUCLEIC ACID CONFORMATION; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; RECEPTORS, CYCLIC AMP; SUBSTRATE SPECIFICITY; TEMPERATURE;

EID: 84860273712     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00249-012-0791-y     Document Type: Article

References (53)

1. Arai M, Ito K, Inobe T, Nakao M, Maki K, Kamagata K, Kihara H, Amemiya Y, Kuwajima K (2002) Fast compaction of alphalactalbumin during folding studied by stopped-flow X-ray scattering. J Mol Biol 321(1):121-132. doi:10.1016/s0022- 2836 (02)00566-1 (Pubitemid 34948474)
2. Barkley MD (1981) Salt dependence of the kinetics of the lac repressor-operator interaction: role of non-operator deoxyribonucleic- acid in the association reaction. Biochemistry 20(13): 3833-3842
3. Berg OG, von Hippel PH (1988) Selection of DNA binding sites by regulatory proteins. II. The binding specificity of cyclic AMP receptor protein to recognition sites. J Mol Biol 200(4):709-723
4. Berg OG, Winter RB, von Hippel PH (1981) Diffusion-driven mechanisms of protein translocation on nucleic-acids.1. Models and theory. Biochemistry 20(24):6929-6948
5. Blazy B, Ullmann A (1986) Properties of cyclic AMP-independent catabolite gene activator proteins of Escherichia coli. J Biol Chem 261(25):11645-11649 (Pubitemid 17206084)
6. Diekmann S, Hillen W, Morgeneyer B, Wells RD, Porschke D (1982) Orientation relaxation of DNA restriction fragments and the internal mobility of the double helix. Biophys Chem 15(4): 263-270
7. Ebright RH, Ebright YW, Gunasekera A (1989) Consensus DNA site for the Escherichia coli catabolite gene activator protein (cap)- cap exhibits a 450-fold higher affinity for the consensus DNA site than for the Escherichia coli lac DNA site. Nucleic Acids Res 17(24):10295-10305 (Pubitemid 20012186)
8. Fic E, Polit A, Wasylewski Z (2006) Kinetic and structural studies of the allosteric conformational changes induced by binding of cAMP to the cAMP receptor protein from Escherichia coli. Biochemistry 45(2):373-380. doi:10.1021/bi051586a (Pubitemid 43100404)
9. Fic E, Bonarek P, Gorecki A, Kedracka-Krok S, Mikolajczak J, Polit A, Tworzydlo M, Dziedzicka-Wasylewska M, Wasylewski Z (2009) cAMP receptor protein from Escherichia coli as a model of signal transduction in proteins-a review. J Mol Microbiol Biotechnol 17(1):1-11. doi:10.1159/000178014
10. Fredericq E, Houssier C (1973) Electric dichroism and electric birefringence. Monographs on physical biochemistry. Clarendon Press, Oxford
11. Fried MG, Crothers DM (1984) Kinetics and mechanism in the reaction of gene regulatory proteins with DNA. J Mol Biol 172(3):263-282 (Pubitemid 14153857)
12. Ghosaini LR, Brown AM, Sturtevant JM (1988) Scanning calorimetric study of the thermal unfolding of catabolite activator protein from Escherichia coli in the absence and presence of cyclic mononucleotides. Biochemistry 27(14):5257-5261
13. Giraudpanis MJ, Toulme F, Blazy B, Maurizot JC, Culard F (1994) Fluorescence study on the nonspecific-binding of cyclic-AMP receptor protein to DNA-effect of pH. Biochimie 76(2):133-139 (Pubitemid 124007903)
14. Gomez-Hens A, Perez-Bendito D (1991) The stopped-flow technique in analytical-chemistry. Anal Chim Acta 242(2):147-177
15. Gorecki A, Kepys B, Bonarek P, Wasylewski Z (2009) Kinetic studies of cAMP-induced propagation of the allosteric signal in the cAMP receptor protein from Escherichia coli with the use of site-directed mutagenesis. Int J Biol Macromol 44(3):262-270. doi:10.1016/j.ijbiomac.2008.12.015
16. Gorman J, Greene EC (2008) Visualizing one-dimensional diffusion of proteins along DNA. Nat Struct Mol Biol 15(8):768-774. doi: 10.1038/Nsmb.1441
17. Grillo I (2009) Applications of stopped-flow in SAXS and SANS. Curr Opin Colloid Interface Sci 14(6):402-408. doi:10.1016/ j.cocis.2009.04.005
18. Guiso N, Blazy B (1980) Regulatory aspects of the cyclic amp receptor protein in Escherichia coli K-12. Biochem Biophys Res Commun 94(1):278-283
19. Halford SE, Marko JF (2004) How do site-specific DNA-binding proteins find their targetsč Nucleic Acids Res 32(10):3040-3052. doi:10.1093/nar/gkh624 (Pubitemid 39022995)
20. Hiller DA, Fogg JM, Martin AM, Beechem JM, Reich NO, Perona JJ (2003) Simultaneous DNA binding and bending by EcoRV endonuclease observed by real-time fluorescence. Biochemistry 42(49):14375-14385. doi:10.1021/Bi035520w (Pubitemid 37531983)
21. Kahn JD, Crothers DM (1998) Measurement of the DNA bend angle induced by the catabolite activator protein using Monte Carlo simulation of cyclization kinetics. J Mol Biol 276(1):287-309 (Pubitemid 28085424)
22. Kapanidis AN, Ebright YW, Ludescher RD, Chan S, Ebright RH (2001) Mean DNA bend angle and distribution of DNA bend angles in the CAP-DNA complex in solution. J Mol Biol 312(3):453-468. doi:10.1006/jmbi.2001.4976 (Pubitemid 32928117)
23. Kleinschmidt C, Tovar K, Hillen W, Porschke D (1988) Dynamics of repressor operator recognition-the Tn10-encoded tetracycline resistance control. Biochemistry 27(4):1094-1104
24. Kolb A, Busby S, Buc H, Garges S, Adhya S (1993) Transcriptional regulation by cAMP and its receptor protein. Ann Rev Biochem 62:749-795 (Pubitemid 23237887)
25. Kuzmic P (1996) Program DYNAFIT for the analysis of enzyme kinetic data: application to HIV proteinase. Anal Biochem 237(2):260-273 (Pubitemid 26177089)
26. Kuznetsov SV, Sugimura S, Vivas P, Crothers DM, Ansari A (2006) Direct observation of DNA bending/unbending kinetics in complex with DNA-bending protein IHF. Proc Natl Acad Sci USA 103(49):18515-18520. doi:10.1073/pnas. 0608394103 (Pubitemid 44913442)
27. Lin SH, Lee JC (2002) Communications between the high-affinity cyclic nucleotide binding sites in E. coli cyclic AMP receptor protein: effect of single site mutations. Biochemistry 41(39): 11857-11867
28. Lin SH, Lee JC (2003) Determinants of DNA bending in the DNAcyclic AMP receptor protein complexes in Escherichia coli. Biochemistry 42(17):4809-4818. doi:10.1021/bi027259c?
29. Parkinson G, Wilson C, Gunasekera A, Ebright YW, Ebright RE, Berman HM (1996) Structure of the CAP-DNA complex at 2.5 angstrom resolution: a complete picture of the protein-DNA interface. J Mol Biol 260(3):395-408 (Pubitemid 26254119)
30. Passner JM, Steitz TA (1997) The structure of a CAP-DNA complex having two cAMP molecules bound to each monomer. Proc Natl Acad Sci USA 94(7):2843-2847 (Pubitemid 127634966)
31. Pendergrast PS, Ebright YW, Ebright RH (1994) High-specificity DNA cleavage agent-design and application to kilobase and megabase DNA substrates. Science 265(5174):959-962 (Pubitemid 24281494)
32. Popovych N, Tzeng SR, Tonelli M, Ebright RH, Kalodimos CG (2009) Structural basis for cAMP-mediated allosteric control of the catabolite activator protein. Proc Natl Acad Sci USA 106(17):6927-6932
33. Porschke D (1984) Dynamics of DNA condensation. Biochemistry 23(21):4821-4828
34. Porschke D (1991) Persistence length and bending dynamics of DNA from electrooptical measurements at high salt concentrations. Biophys Chem 40(2):169-179
35. Porschke D (1998) Time-resolved analysis of macromolecular structures during reactions by stopped-flow electrooptics. Biophys J 75(1):528-537 (Pubitemid 28311844)
36. Porschke D (2007) The nature of ''unusual'' electro-optical transients observed for DNA. Colloid Surface B 56(1-2):44-49. doi: 10.1016/j.colsurfb.2006. 11.020 (Pubitemid 46476853)
37. Porschke D (2010) Allosteric control of promoter DNA bending by cyclic AMP Receptor and cyclic AMP. Biochemistry 49(26): 5553-5559. doi:10.1021/Bi100542f
38. Porschke D (2011) Electric birefringence at small angles from crossed position: enhanced sensitivity and special effects. J Phys Chem B 115(14):4177-4183. doi:10.1021/Jp111240e
39. Porschke D, Antosiewicz JM (2007) Quantitative molecular electrooptics: macromolecular structures and their dynamics in solution. In: Stoylov SP, Stoimenova MV (eds) Molecular and colloidal electro-optics. CRC, Boca Raton, pp 59-107
40. Porschke D, Jung M (1985) The conformation of single stranded oligonucleotides and of oligonucleotide-oligopeptide complexes from their rotation relaxation in the nanosecond time range. J Biomol Struct Dyn 2(6):1173-1184 (Pubitemid 15030018)
41. Revzin A, von Hippel PH (1977) Direct measurement of association constants for binding of Escherichia coli lac repressor to nonoperator DNA. Biochemistry 16(22):4769-4776 (Pubitemid 8220964)
42. Richter PH, Eigen M (1974) Diffusion controlled reaction-rates in spheroidal geometry-application to repressor-operator association and membrane-bound enzymes. Biophys Chem 2(3):255-263
43. Riggs AD, Bourgeois S, Cohn M (1970) Lac repressor-operator interaction.3. Kinetic studies. J Mol Biol 53(3):401-417
44. Schultz SC, Shields GC, Steitz TA (1991) Crystal structure of a CAPDNA complex: The DNA is bent by 90-. Science 253(5023): 1001-1007 (Pubitemid 21917242)
45. Sharma H, Yu SN, Kong JL, Wang JM, Steitz TA (2009) Structure of apo-CAP reveals that large conformational changes are necessary for DNA binding. Proc Natl Acad Sci USA 106(39): 16604-16609. doi:10.1073/pnas.0908380106
46. Sugimura S, Crothers DM (2006) Stepwise binding and bending of DNA by Escherichia coli integration host factor. Proc Natl Acad Sci USA 103(49):18510-18514. doi:10.1073/pnas.0608337103 (Pubitemid 44913441)
47. Tims HS, Widom J (2007) Stopped-flow fluorescence resonance energy transfer for analysis of nucleosome dynamics. Methods 41(3):296-303. doi:10.1016/j.ymeth.2007.01.001
48. Tworzydlo M, Polit A, Mikolajczak J, Wasylewski Z (2005) Fluorescence quenching and kinetic studies of conformational changes induced by DNA and cAMP binding to cAMP receptor protein from Escherichia coli. FEBS J 272(5):1103-1116. doi: 10.1111/j.1742.4658.2005.04540.x
49. Van Nuland NAJ, Forge V, Balbach J, Dobson CM (1998) Real-time NMR studies of protein folding. Acc Chem Res 31(11):773-780 (Pubitemid 128474544)
50. von Hippel PH, Berg OG (1989) Facilitated target location in biological-systems. J Biol Chem 264(2):675-678
51. Weber IT, Steitz TA (1984) A model for the non-specific binding of catabolite gene activator protein to DNA. Nucleic Acids Res 12(22):8475-8487
52. Winter RB, Berg OG, von Hippel PH (1981) Diffusion-driven mechanisms of protein translocation on nucleic-acids. 3. The Escherichia coli lac repressor-operator interaction: kinetic measurements and conclusions. Biochemistry 20(24):6961-6977 (Pubitemid 12185949)
53. Zubay G (1980) The isolation and properties of CAP, the catabolite gene activator. Methods Enzymol 65:856-877