Thermal denaturation of the apo-cyclic AMP receptor protein and noncovalent interactions between its domains

Molecules and Cells

Volumn 26, Issue 1, 2008, Pages 61-66

  Won, Hyung Sik ^a   Seo, Min Duk ^b   Ko, Hyun Suk ^a   Choi, Wahn Soo ^a   Lee, Bong Jin ^b  

^a Konkuk University   (South Korea)

^b Seoul National University   (South Korea)

Author keywords

Allostery; Circular dichroism; Cyclic AMP receptor protein; Differential scanning calorimetry; Fluorescence spectroscopy; Interdomain interaction; Thermal denaturation

Indexed keywords

APOLIPOPROTEIN; CYCLIC AMP; CYCLIC AMP RECEPTOR; RECOMBINANT DNA; APOPROTEIN; CYCLIC AMP BINDING PROTEIN;

ARTICLE; CALORIMETRY; CIRCULAR DICHROISM; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DIFFERENTIAL SCANNING CALORIMETRY; FLUORESCENCE ANALYSIS; MOLECULAR PROBE; NONHUMAN; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN DENATURATION; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN ISOLATION; PROTEIN STRUCTURE; RECEPTOR BINDING; THERMODYNAMICS; ALLOSTERISM; CHEMISTRY; ESCHERICHIA COLI; GENETICS; METABOLISM; PROTEIN BINDING; PROTEIN TERTIARY STRUCTURE;

ENTEROBACTERIACEAE;

ALLOSTERIC REGULATION; APOPROTEINS; CALORIMETRY, DIFFERENTIAL SCANNING; CIRCULAR DICHROISM; CYCLIC AMP; CYCLIC AMP RECEPTOR PROTEIN; ESCHERICHIA COLI; PROTEIN BINDING; PROTEIN DENATURATION; PROTEIN STRUCTURE, TERTIARY; THERMODYNAMICS;

EID: 53449085848     PISSN: 10168478     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (41)

1. Angulo, J.A., and Krakow, J.S. (1985). Effect of deoxyribopolymers and ribopolymers on the sensitivity of the cyclic-AMP receptor protein of Escherichia coli to proteolytic attack. Arch. Biochem. Biophys. 236, 11-16.
2. Benoff, B., Yang, H., Lawson, C.L., Parkinson, G., Liu, J., Blatter, E., Ebright, Y.W., Berman, H.M., and Ebright, R.H. (2002). Structural basis of transcription activation: the CAP-αCTD-DNA complex. Science 297, 1562-1566.
3. Blandamer, M.J., Briggs, B., Cullis, P.M., Jackson, A.P., Maxwell, A., and Reece, R.J. (1994). Domain structures of Escherichia coli DNA gyrase as revealed by differential scanning calorimetry. Biochemistry 33, 7510-7516.
4. Blaszczyk, U., and Wasylewski, Z. (2003). Interaction of cAMP receptor protein from Escherichia coli with cAMP and DNA studied by differential scanning calorimetry. J. Prot. Chem. 22, 285-293.
5. Botsford, J.L., and Harman, J.G. (1992). Cyclic AMP in prokaryotes. Microbiol. Rev. 56, 100-122.
6. Byrne, M.P., and Stites, W.E. (2007). Thermal denaturations of staphylococcal nuclease wild-type and mutants monitored by fluorescence and circular dichroism are similar: lack of evidence for other than a two state thermal denaturation. Biophys. Chem. 125, 490-496.
7. Cheng, X., Gonzalez, M.L., and Lee, J.C. (1993). Energetics of intersubunit and intrasubunit interactions of Escherichia coli adenosine cyclic 3′,5′-phosphate receptor protein. Biochemistry 32, 8130-8139.
8. Chu, S.Y., Tordova, M., Gilliland, G.L., Gorshkova, I., Shi, Y., Wang, S., and Schwarz, F.P. (2001). The structure of the T127L/S128A mutant of cAMP receptor protein facilitates promoter site binding. J. Biol. Chem. 276, 11230-11236.
9. Clore, G.M., and Gronenborn, A.M. (1982). Proton nuclear magnetic resonance study of the histidine residues of the Escherichia coli adenosine cyclic 3′,5′-phosphate receptor protein. Biochemistry 21, 4048-4053.
10. den Blaauwen, T., van der Wolk, J.P.W., van der Does, C., van Wely, K.H.M., and Driessen, A.J.M. (1999). Thermodynamics of nucleotide binding to NBS-I of the Bacillus subtilis preprotein translocase subunit SecA. FEBS Lett. 458, 145-150.
11. Eun, S.-Y., Jang, H.-K., Han, S.-K., Ryu, P.-D., Lee, B.-J., Han, K.-H., and Kim, S.-J. (2006). A helix-induced oligomeric transition of gaegurin 4, an antimicrobial peptide isolated from a Korean frog. Mol. Cells 21, 229-236.
12. Ghosaini, L.R., Brown, A.M., and Sturtevant, J.M. (1998). Scanning calorimetric study of the thermal unfolding of catabolite activator protein from Escherichia coli in the absence and presence of cyclic mononucleotides. Biochemistry 27, 5257-5261.
13. Gronenborn, A.M., and Clore, G.M. (1986). Overproduction of the cyclic AMP receptor protein of Escherichia coli and expression of the engineered C-terminal DNA-binding domain. Biochem. J. 236, 643-649.
14. Harman, J.G. (2001) Allosteric regulation of the cAMP receptor protein. Biochim. Biophys. Acta 1547, 1-17.
15. Heyduk, T., Lee, J.C., Ebright, Y.W., Blatter, E.E., Zhou, Y., and Ebright, R.H. (1993). CAP interacts with RNA polymerase in solution in the absence of promoter DNA. Nature 364, 548-549.
16. Hollands, K., Busby, S.J.W., and Lloyd, G.S. (2007). New targets for the cyclic AMP receptor protein in the Escherichia coli K-12 genome. FEMS Microbiol. Lett. 274, 89-94.
17. Johnson, C.R., Morin, P.E., Arrowsmith, C.H., and Freire, E. (1995). Thermodynamic analysis of the structural stability of the tetrameric oligomerization domain of p53 tumor suppressor. Biochemistry 34, 5309-5316.
18. Kolb, A., Busby, S., Buc, H., Garges, S., and Adhya, S. (1993). Transcriptional regulation by cAMP and its receptor protein. Annu. Rev. Biochem. 62, 749-795.
19. Krupakar, J., Swaminathan, C.P., Das, P.K., Surolia, A., and Podder, S.K. (1999). Calorimetric studies on the stability of the ribosome-inactivating protein abrin II: effects of pH and ligand binding. Biochem. J. 338, 273-279.
20. Lawson, C.L., Swigon, D., Murakami, K.S., Darst, S.A., Berman, H.M., and Ebright, R.H. (2004). Catabolite activator protein: DNA binding and transcription activation. Curr. Opin. Struct. Biol. 14, 10-20.
21. Lee, C.-J., Won, H.-S., Kim, J.-M., Lee, B.-J., and Kang, S.-O. (2007). Molecular domain organization of BldD, an essential transcriptional regulator for developmental process of Streptomyces coelicolor A3(2). Proteins 68, 344-352.
22. 13C-carbonyl NMR. J. Biochem. 130, 57-61.
23. Lee, Y.-H., Won, H.-S., Lee, M.-H., and Lee, B.-J. (2002). Effects of salt and nickel ion on the conformational stability of Bacillus pasteurii UreE. FEBS Lett. 522, 135-140.
24. Li, J., Cheng, X., and Lee, J.C. (2002). Structure and dynamics of the modular halves of Escherichia coli cyclic AMP receptor protein. Biochemistry 41, 14771-14778.
25. Orlov, V.N., Rostkova, E.V., Nikolaeva, O.P., Drachev, V.A., Gusev, N.B., and Levitsky, D.I. (1998). Thermally induced chain exchange of smooth muscle tropomyosin dimers studied by differential scanning calorimetry. FEBS Lett. 433, 241-244.
26. Pabo, C.O., Sauer, R.T., Sturtevant, J.M., and Ptashne, M. (1979). The λ repressor contains two domains. Proc. Natl. Acad. Sci. USA 76, 1608-1612.
27. Parkinson, G., Wilson, C., Gunasekera, A., Ebright, Y.W., Ebright, R.E., and Berman, H.M. (1996). Structure of the CAP-DNA complex at 2.5 angstroms resolution: a complete picture of the protein-DNA recognition. J. Mol. Biol. 260, 395-408.
28. Passner, J.M., and Steitz, T.A. (1997). The structure of a CAP-DNA complex having two cAMP molecules bound to each monomer. Proc. Natl. Acad. Sci. USA 94, 2843-2847.
29. Passner, J.M., Schultz, S.C., and Steitz, T.A. (2000). Modeling the cAMP-induced allosteric transition using the crystal structure of CAP-cAMP at 2.1 ̊resolution. J. Mol. Biol. 304, 847-859.
30. Popovych, N., Sun, S., Ebright, R.H., and Kalodimos, C.G. (2006). Dynamically driven protein allostery. Nat. Struct. Mol. Biol. 13, 831-838.
31. Privalov, P.L. (1982). Stability of proteins: proteins which do not present a single cooperative system. Adv. Protein Chem. 35, 1-104.
32. Rodger, A., and Nordén, B. (1997). Circular dichroism of biomolecules. In Circular Dichroism and Linear Dichroism (Oxford, UK: Oxford University Press), pp. 15-32.
33. Schultz, S.C., Shields, G.C., and Steitz, T.A. (1991). Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science 253, 1001-1007.
34. Sreerama, N., and Woody, R.W. (2000). Circular dichroism of peptides and proteins. In Circular Dichroism: Principles and Applications, N. Berova, K. Nakanishi, and R.W. Woody, 2nd eds. (New York, USA: WILEY-VCH), pp. 601-620.
35. Weber, I.T., and Steitz, T.A. (1987). Structure of a complex of catabolite gene activator protein and cyclic AMP refined at 2.5 ̊ resolution. J. Mol. Biol. 198, 311-326.
36. Wenk, M., Jaenicke, R., and Mayr, E.-M. (1998). Kinetic stabilization of a modular protein by domain interactions. FEBS Lett. 438, 127-130.
37. Won, H.-S., Yamazaki, T., Lee, T.-W., Yoon, M.-K., Park, S.-H., Kyogoku, Y., and Lee, B.-J. (2000). Structural understanding of the allosteric conformational change of cyclic AMP receptor protein by cyclic AMP binding. Biochemistry 45, 13953-13962.
38. Won, H.-S., Lee, T.-W., Park, S.-H., and Lee, B.-J. (2002). Stoichiometry and structural effect of the cyclic nucleotide binding to cyclic AMP receptor protein. J. Biol. Chem. 277, 11450-11455.
39. Won, H.-S., Jung, S.-J., Kim, H.E., Seo, M.-D., and Lee, B.-J. (2004a). Systematic peptide engineering and structural characterization to search for the shortest antimicrobial peptide analogue of gaegurin 5. J. Biol. Chem. 279, 14784-14791.
40. Won, H.-S., Kim, S.S., Jung, S.-J., Son, W.-S., Lee, B., and Lee, B.-J. (2004b). Structure-activity relationships of antimicrobial peptides from the skin of Rana esculenta inhabiting in Korea. Mol. Cells 17, 469-476.
41. Zaiss, K., and Jaenicke, R. (1999). Thermodynamic study of phosphoglycerate kinase from Thermotogia maritima and its isolated domains: reversible thermal unfolding monitored by differential scanning calorimetry and circular dichroism spectroscopy. Biochemistry 38, 4633-4639.