Abstract
The conformational stability of dimeric globular proteins can be measured by equilibrium denaturation studies in solvents such as guanidine hydrochloride or urea. Many dimeric proteins denature with a 2-state equilibrium transition, whereas others have stable intermediates in the process. For those proteins showing a single transition of native dimer to denatured monomer, the conformational stabilities, delta Gu (H2O), range from 10 to 27 kcal/mol, which is significantly greater than the conformational stability found for monomeric proteins. The relative contribution of quaternary interactions to the overall stability of the dimer can be estimated by comparing delta Gu (H2O) from equilibrium denaturation studies to the free energy associated with simple dissociation in the absence of denaturant. In many cases the large stabilization energy of dimers is primarily due to the intersubunit interactions and thus gives a rationale for the formation of oligomers. The magnitude of the conformational stability is related to the size of the polypeptide in the subunit and depends upon the type of structure in the subunit interface. The practical use, interpretation, and utility of estimation of conformational stability of dimers by equilibrium denaturation methods are discussed.
Full Text
The Full Text of this article is available as a PDF (938.8 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Aceto A., Caccuri A. M., Sacchetta P., Bucciarelli T., Dragani B., Rosato N., Federici G., Di Ilio C. Dissociation and unfolding of Pi-class glutathione transferase. Evidence for a monomeric inactive intermediate. Biochem J. 1992 Jul 1;285(Pt 1):241–245. doi: 10.1042/bj2850241. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Banik U., Saha R., Mandal N. C., Bhattacharyya B., Roy S. Multiphasic denaturation of the lambda repressor by urea and its implications for the repressor structure. Eur J Biochem. 1992 May 15;206(1):15–21. doi: 10.1111/j.1432-1033.1992.tb16896.x. [DOI] [PubMed] [Google Scholar]
- Barrick D., Baldwin R. L. Stein and Moore Award address. The molten globule intermediate of apomyoglobin and the process of protein folding. Protein Sci. 1993 Jun;2(6):869–876. doi: 10.1002/pro.5560020601. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Blackburn M. N., Noltmann E. A. Evidence for an intermediate in the denaturation and assembly of phosphoglucose isomerase. Arch Biochem Biophys. 1981 Nov;212(1):162–169. doi: 10.1016/0003-9861(81)90355-6. [DOI] [PubMed] [Google Scholar]
- Borchert T. V., Abagyan R., Jaenicke R., Wierenga R. K. Design, creation, and characterization of a stable, monomeric triosephosphate isomerase. Proc Natl Acad Sci U S A. 1994 Feb 15;91(4):1515–1518. doi: 10.1073/pnas.91.4.1515. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bowie J. U., Sauer R. T. Equilibrium dissociation and unfolding of the Arc repressor dimer. Biochemistry. 1989 Sep 5;28(18):7139–7143. doi: 10.1021/bi00444a001. [DOI] [PubMed] [Google Scholar]
- Bowie J. U., Sauer R. T. Identifying determinants of folding and activity for a protein of unknown structure. Proc Natl Acad Sci U S A. 1989 Apr;86(7):2152–2156. doi: 10.1073/pnas.86.7.2152. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Brayer G. D., McPherson A. Refined structure of the gene 5 DNA binding protein from bacteriophage fd. J Mol Biol. 1983 Sep 15;169(2):565–596. doi: 10.1016/s0022-2836(83)80065-5. [DOI] [PubMed] [Google Scholar]
- Carter P. J., Winter G., Wilkinson A. J., Fersht A. R. The use of double mutants to detect structural changes in the active site of the tyrosyl-tRNA synthetase (Bacillus stearothermophilus). Cell. 1984 Oct;38(3):835–840. doi: 10.1016/0092-8674(84)90278-2. [DOI] [PubMed] [Google Scholar]
- Chothia C., Finkelstein A. V. The classification and origins of protein folding patterns. Annu Rev Biochem. 1990;59:1007–1039. doi: 10.1146/annurev.bi.59.070190.005043. [DOI] [PubMed] [Google Scholar]
- Chothia C., Wodak S., Janin J. Role of subunit interfaces in the allosteric mechanism of hemoglobin. Proc Natl Acad Sci U S A. 1976 Nov;73(11):3793–3797. doi: 10.1073/pnas.73.11.3793. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Clark A. C., Sinclair J. F., Baldwin T. O. Folding of bacterial luciferase involves a non-native heterodimeric intermediate in equilibrium with the native enzyme and the unfolded subunits. J Biol Chem. 1993 May 25;268(15):10773–10779. [PubMed] [Google Scholar]
- Darke P. L., Jordan S. P., Hall D. L., Zugay J. A., Shafer J. A., Kuo L. C. Dissociation and association of the HIV-1 protease dimer subunits: equilibria and rates. Biochemistry. 1994 Jan 11;33(1):98–105. doi: 10.1021/bi00167a013. [DOI] [PubMed] [Google Scholar]
- De Francesco R., Pastore A., Vecchio G., Cortese R. Circular dichroism study on the conformational stability of the dimerization domain of transcription factor LFB1. Biochemistry. 1991 Jan 8;30(1):143–147. doi: 10.1021/bi00215a021. [DOI] [PubMed] [Google Scholar]
- Dirr H. W., Reinemer P. Equilibrium unfolding of class pi glutathione S-transferase. Biochem Biophys Res Commun. 1991 Oct 15;180(1):294–300. doi: 10.1016/s0006-291x(05)81291-4. [DOI] [PubMed] [Google Scholar]
- Fernando T., Royer C. A. Unfolding of trp repressor studied using fluorescence spectroscopic techniques. Biochemistry. 1992 Jul 28;31(29):6683–6691. doi: 10.1021/bi00144a007. [DOI] [PubMed] [Google Scholar]
- Gittelman M. S., Matthews C. R. Folding and stability of trp aporepressor from Escherichia coli. Biochemistry. 1990 Jul 31;29(30):7011–7020. doi: 10.1021/bi00482a009. [DOI] [PubMed] [Google Scholar]
- Grant S. K., Deckman I. C., Culp J. S., Minnich M. D., Brooks I. S., Hensley P., Debouck C., Meek T. D. Use of protein unfolding studies to determine the conformational and dimeric stabilities of HIV-1 and SIV proteases. Biochemistry. 1992 Oct 6;31(39):9491–9501. doi: 10.1021/bi00154a023. [DOI] [PubMed] [Google Scholar]
- Herold M., Kirschner K. Reversible dissociation and unfolding of aspartate aminotransferase from Escherichia coli: characterization of a monomeric intermediate. Biochemistry. 1990 Feb 20;29(7):1907–1913. doi: 10.1021/bi00459a035. [DOI] [PubMed] [Google Scholar]
- Jaenicke R. Folding and association of proteins. Prog Biophys Mol Biol. 1987;49(2-3):117–237. doi: 10.1016/0079-6107(87)90011-3. [DOI] [PubMed] [Google Scholar]
- Janin J., Miller S., Chothia C. Surface, subunit interfaces and interior of oligomeric proteins. J Mol Biol. 1988 Nov 5;204(1):155–164. doi: 10.1016/0022-2836(88)90606-7. [DOI] [PubMed] [Google Scholar]
- Kim P. S., Baldwin R. L. Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding. Annu Rev Biochem. 1982;51:459–489. doi: 10.1146/annurev.bi.51.070182.002331. [DOI] [PubMed] [Google Scholar]
- Leistler B., Herold M., Kirschner K. Collapsed intermediates in the reconstitution of dimeric aspartate aminotransferase from Escherichia coli. Eur J Biochem. 1992 Apr 15;205(2):603–611. doi: 10.1111/j.1432-1033.1992.tb16818.x. [DOI] [PubMed] [Google Scholar]
- Liang H., Sandberg W. S., Terwilliger T. C. Genetic fusion of subunits of a dimeric protein substantially enhances its stability and rate of folding. Proc Natl Acad Sci U S A. 1993 Aug 1;90(15):7010–7014. doi: 10.1073/pnas.90.15.7010. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Liang H., Terwilliger T. C. Reversible denaturation of the gene V protein of bacteriophage f1. Biochemistry. 1991 Mar 19;30(11):2772–2782. doi: 10.1021/bi00225a006. [DOI] [PubMed] [Google Scholar]
- Lim W. A., Farruggio D. C., Sauer R. T. Structural and energetic consequences of disruptive mutations in a protein core. Biochemistry. 1992 May 5;31(17):4324–4333. doi: 10.1021/bi00132a025. [DOI] [PubMed] [Google Scholar]
- Mann C. J., Royer C. A., Matthews C. R. Tryptophan replacements in the trp aporepressor from Escherichia coli: probing the equilibrium and kinetic folding models. Protein Sci. 1993 Nov;2(11):1853–1861. doi: 10.1002/pro.5560021107. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Matsumura M., Becktel W. J., Matthews B. W. Hydrophobic stabilization in T4 lysozyme determined directly by multiple substitutions of Ile 3. Nature. 1988 Aug 4;334(6181):406–410. doi: 10.1038/334406a0. [DOI] [PubMed] [Google Scholar]
- Matthews C. R. Effect of point mutations on the folding of globular proteins. Methods Enzymol. 1987;154:498–511. doi: 10.1016/0076-6879(87)54092-7. [DOI] [PubMed] [Google Scholar]
- Matthews C. R. Pathways of protein folding. Annu Rev Biochem. 1993;62:653–683. doi: 10.1146/annurev.bi.62.070193.003253. [DOI] [PubMed] [Google Scholar]
- McDonald N. Q., Lapatto R., Murray-Rust J., Gunning J., Wlodawer A., Blundell T. L. New protein fold revealed by a 2.3-A resolution crystal structure of nerve growth factor. Nature. 1991 Dec 5;354(6352):411–414. doi: 10.1038/354411a0. [DOI] [PubMed] [Google Scholar]
- Mei G., Rosato N., Silva N., Jr, Rusch R., Gratton E., Savini I., Finazzi-Agrò A. Denaturation of human Cu/Zn superoxide dismutase by guanidine hydrochloride: a dynamic fluorescence study. Biochemistry. 1992 Aug 18;31(32):7224–7230. doi: 10.1021/bi00147a003. [DOI] [PubMed] [Google Scholar]
- Milla M. E., Sauer R. T. P22 Arc repressor: folding kinetics of a single-domain, dimeric protein. Biochemistry. 1994 Feb 8;33(5):1125–1133. doi: 10.1021/bi00171a011. [DOI] [PubMed] [Google Scholar]
- Monera O. D., Shaw G. S., Zhu B. Y., Sykes B. D., Kay C. M., Hodges R. S. Role of interchain alpha-helical hydrophobic interactions in Ca2+ affinity, formation, and stability of a two-site domain in troponin C. Protein Sci. 1992 Jul;1(7):945–955. doi: 10.1002/pro.5560010713. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Morjana N. A., McKeone B. J., Gilbert H. F. Guanidine hydrochloride stabilization of a partially unfolded intermediate during the reversible denaturation of protein disulfide isomerase. Proc Natl Acad Sci U S A. 1993 Mar 15;90(6):2107–2111. doi: 10.1073/pnas.90.6.2107. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Mossing M. C., Sauer R. T. Stable, monomeric variants of lambda Cro obtained by insertion of a designed beta-hairpin sequence. Science. 1990 Dec 21;250(4988):1712–1715. doi: 10.1126/science.2148648. [DOI] [PubMed] [Google Scholar]
- Murphy K. P., Freire E. Thermodynamics of structural stability and cooperative folding behavior in proteins. Adv Protein Chem. 1992;43:313–361. doi: 10.1016/s0065-3233(08)60556-2. [DOI] [PubMed] [Google Scholar]
- Narhi L. O., Rosenfeld R., Wen J., Arakawa T., Prestrelski S. J., Philo J. S. Acid-induced unfolding of brain-derived neurotrophic factor results in the formation of a monomeric "a state". Biochemistry. 1993 Oct 12;32(40):10819–10825. doi: 10.1021/bi00091a037. [DOI] [PubMed] [Google Scholar]
- Nicosia A., Monaci P., Tomei L., De Francesco R., Nuzzo M., Stunnenberg H., Cortese R. A myosin-like dimerization helix and an extra-large homeodomain are essential elements of the tripartite DNA binding structure of LFB1. Cell. 1990 Jun 29;61(7):1225–1236. doi: 10.1016/0092-8674(90)90687-a. [DOI] [PubMed] [Google Scholar]
- Pabo C. O., Sauer R. T., Sturtevant J. M., Ptashne M. The lambda repressor contains two domains. Proc Natl Acad Sci U S A. 1979 Apr;76(4):1608–1612. doi: 10.1073/pnas.76.4.1608. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pace C. N. Conformational stability of globular proteins. Trends Biochem Sci. 1990 Jan;15(1):14–17. doi: 10.1016/0968-0004(90)90124-t. [DOI] [PubMed] [Google Scholar]
- Pace C. N. Determination and analysis of urea and guanidine hydrochloride denaturation curves. Methods Enzymol. 1986;131:266–280. doi: 10.1016/0076-6879(86)31045-0. [DOI] [PubMed] [Google Scholar]
- Pace C. N., Laurents D. V., Thomson J. A. pH dependence of the urea and guanidine hydrochloride denaturation of ribonuclease A and ribonuclease T1. Biochemistry. 1990 Mar 13;29(10):2564–2572. doi: 10.1021/bi00462a019. [DOI] [PubMed] [Google Scholar]
- Pace N. C., Tanford C. Thermodynamics of the unfolding of beta-lactoglobulin A in aqueous urea solutions between 5 and 55 degrees. Biochemistry. 1968 Jan;7(1):198–208. doi: 10.1021/bi00841a025. [DOI] [PubMed] [Google Scholar]
- Pakula A. A., Sauer R. T. Amino acid substitutions that increase the thermal stability of the lambda Cro protein. Proteins. 1989;5(3):202–210. doi: 10.1002/prot.340050303. [DOI] [PubMed] [Google Scholar]
- Peng X., Jonas J., Silva J. L. Molten-globule conformation of Arc repressor monomers determined by high-pressure 1H NMR spectroscopy. Proc Natl Acad Sci U S A. 1993 Mar 1;90(5):1776–1780. doi: 10.1073/pnas.90.5.1776. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Privalov P. L., Gill S. J. Stability of protein structure and hydrophobic interaction. Adv Protein Chem. 1988;39:191–234. doi: 10.1016/s0065-3233(08)60377-0. [DOI] [PubMed] [Google Scholar]
- Privalov P. L., Griko YuV, Venyaminov SYu, Kutyshenko V. P. Cold denaturation of myoglobin. J Mol Biol. 1986 Aug 5;190(3):487–498. doi: 10.1016/0022-2836(86)90017-3. [DOI] [PubMed] [Google Scholar]
- Privalov P. L., Potekhin S. A. Scanning microcalorimetry in studying temperature-induced changes in proteins. Methods Enzymol. 1986;131:4–51. doi: 10.1016/0076-6879(86)31033-4. [DOI] [PubMed] [Google Scholar]
- Privalov P. L. Stability of proteins: small globular proteins. Adv Protein Chem. 1979;33:167–241. doi: 10.1016/s0065-3233(08)60460-x. [DOI] [PubMed] [Google Scholar]
- Raumann B. E., Rould M. A., Pabo C. O., Sauer R. T. DNA recognition by beta-sheets in the Arc repressor-operator crystal structure. Nature. 1994 Feb 24;367(6465):754–757. doi: 10.1038/367754a0. [DOI] [PubMed] [Google Scholar]
- Reece L. J., Nichols R., Ogden R. C., Howell E. E. Construction of a synthetic gene for an R-plasmid-encoded dihydrofolate reductase and studies on the role of the N-terminus in the protein. Biochemistry. 1991 Nov 12;30(45):10895–10904. doi: 10.1021/bi00109a013. [DOI] [PubMed] [Google Scholar]
- Sacchetta P., Aceto A., Bucciarelli T., Dragani B., Santarone S., Allocati N., Di Ilio C. Multiphasic denaturation of glutathione transferase B1-1 by guanidinium chloride. Role of the dimeric structure on the flexibility of the active site. Eur J Biochem. 1993 Aug 1;215(3):741–745. doi: 10.1111/j.1432-1033.1993.tb18087.x. [DOI] [PubMed] [Google Scholar]
- Sandberg W. S., Terwilliger T. C. Engineering multiple properties of a protein by combinatorial mutagenesis. Proc Natl Acad Sci U S A. 1993 Sep 15;90(18):8367–8371. doi: 10.1073/pnas.90.18.8367. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Santoro M. M., Bolen D. W. A test of the linear extrapolation of unfolding free energy changes over an extended denaturant concentration range. Biochemistry. 1992 May 26;31(20):4901–4907. doi: 10.1021/bi00135a022. [DOI] [PubMed] [Google Scholar]
- Silva J. L., Silveira C. F., Correia Júnior A., Pontes L. Dissociation of a native dimer to a molten globule monomer. Effects of pressure and dilution on the association equilibrium of arc repressor. J Mol Biol. 1992 Jan 20;223(2):545–555. doi: 10.1016/0022-2836(92)90669-b. [DOI] [PubMed] [Google Scholar]
- Steif C., Weber P., Hinz H. J., Flossdorf J., Cesareni G., Kokkinidis M. Subunit interactions provide a significant contribution to the stability of the dimeric four-alpha-helical-bundle protein ROP. Biochemistry. 1993 Apr 20;32(15):3867–3876. doi: 10.1021/bi00066a005. [DOI] [PubMed] [Google Scholar]
- Tanford C. Protein denaturation. Adv Protein Chem. 1968;23:121–282. doi: 10.1016/s0065-3233(08)60401-5. [DOI] [PubMed] [Google Scholar]
- Thompson K. S., Vinson C. R., Freire E. Thermodynamic characterization of the structural stability of the coiled-coil region of the bZIP transcription factor GCN4. Biochemistry. 1993 Jun 1;32(21):5491–5496. doi: 10.1021/bi00072a001. [DOI] [PubMed] [Google Scholar]
- Timasheff S. N. Water as ligand: preferential binding and exclusion of denaturants in protein unfolding. Biochemistry. 1992 Oct 20;31(41):9857–9864. doi: 10.1021/bi00156a001. [DOI] [PubMed] [Google Scholar]
- Timm D. E., de Haseth P. L., Neet K. E. Comparative equilibrium denaturation studies of the neurotrophins: nerve growth factor, brain-derived neurotrophic factor, neurotrophin 3, and neurotrophin 4/5. Biochemistry. 1994 Apr 19;33(15):4667–4676. doi: 10.1021/bi00181a602. [DOI] [PubMed] [Google Scholar]