Abstract
Thermodynamics of protein folding refers to the stability measurements where structural changes of a given protein in the presence of a denaturing agent are monitored by spectroscopic or calorimetric techniques. In macroscopic point of view, protein stability represents the ratio of the population of its unfolded state to that of folded one in equilibrium condition, while in microscopic point of view, the stability is actually a net value from a combination of favorable and unfavorable contributions that affect the structural integrity of a protein molecule. In this manuscript, the principles and methodological aspects of thermodynamic studies and methods of data analysis as well as interpretation of the results are presented.
Graphical abstract
Similar content being viewed by others
Change history
21 December 2021
A Correction to this paper has been published: https://doi.org/10.1007/s00249-021-01586-6
References
Anfinsen CB (1973) Principles that govern the folding of protein chains. Science (80-) 181:223–230. https://doi.org/10.1126/science.181.4096.223
Ashraf GM, Greig NH, Khan TA et al (2014) Protein misfolding and aggregation in Alzheimer’s disease and type 2 diabetes mellitus. CNS Neurol Disord Drug Targets 13:1280–1293. https://doi.org/10.1158/1078-0432.CCR-15-0428.Bioactivity
Bruylants G, Wouters J, Michaux C (2005) Differential scanning calorimetry in life science: thermodynamics, stability, molecular recognition and application in drug design. Curr Med Chem 12:2011–2020
Bryan PN (1995) Methods m molecular biology. Humana Press Inc, New York
Chen B, Schellman JA (1989) Low-temperature unfolding of a mutant of phage T4 lysozyme. 1. Equilibrium studies. Biochemistry 28:685–691. https://doi.org/10.1021/bi00428a041
Consalvi V, Chiaraluce R, Giangiacomo L et al (2000) Thermal unfolding and conformational stability of the recombinant domain II of glutamate dehydrogenase from the hyperthermophile Thermotoga maritima. Protein Eng 13:501–507. https://doi.org/10.1093/protein/13.7.501
Dill KA (1990) Dominant forces in protein folding. Biochemistry 29:7133–7155. https://doi.org/10.1021/bi00483a001
Ebrahimi M, Mohseni A, Khalifeh K et al (2017) Evolutionary conservation of EF-hand ΙΙ loop in aequorin: priority of intensity to decay rate in bioluminescence emission. Arch Biochem Biophys 634:29–37. https://doi.org/10.1016/j.abb.2017.09.018
Eyring H (1935) The activated complex and the absolute rate of chemical reactions. Chem Rev 17:65–77. https://doi.org/10.1021/cr60056a006
Fersht AR, Matouschek A, Bycroft M, Kellis JT, Serrano L (1991) Physical-organic molecular biology: pathway and stability of protein folding. Pure Appl Chem 63:187–194. https://doi.org/10.1098/rstb.1991.0046
Freire E (1995) Thermal denaturation methods in the study of protein folding. Methods Enzymol 259:144–168
Gianni S, Camilloni C, Giri R et al (2014) Understanding the frustration arising from the competition between function, misfolding, and aggregation in a globular protein. Proc Natl Acad Sci 111:14141–14146. https://doi.org/10.1073/pnas.1405233111
Gill P, Moghadam TT, Ranjbar B (2010) Differential scanning calorimetry techniques: applications in biology and nanoscience. J Biomol Tech 21:167–193
Goldenzweig A, Fleishman S (2018) Principles of protein stability and their application in computational design. Annu Rev Biochem. https://doi.org/10.1146/annurev-biochem-062917-012102
Gómez J, Hilser VJ, Xie D, Freire E (1995) The heat capacity of proteins. Proteins Struct Funct Bioinform 22:404–412. https://doi.org/10.1002/prot.340220410
Green RF Jr, Pace CN (1974) Urea and guanidine hydrochloride denaturation of ribonuclease, lysozyme, α-chymotrypsin, and β-lactoglobulin. J Biol Chem 249:5388–5393
Griko YV, Privalov PL, Sturtevant JM, Venyaminov SY (1988a) Cold denaturation of staphylococcal nuclease. Proc Natl Acad Sci. 85:3343–3347. https://doi.org/10.1073/pnas.85.10.3343
Griko YV, Privalov PL, Venyaminov SY, Kutyshenko VP (1988b) Thermodynamic study of the apomyoglobin structure. J Mol Biol 202:127–138. https://doi.org/10.1016/0022-2836(88)90525-6
Griko YV, Makhatadze GI, Privalov PL, Hartley RW (1994) Thermodynamics of barnase unfolding. Protein Sci 3:669–676. https://doi.org/10.1002/pro.5560030414
Hartl FU (2017) Protein misfolding diseases. Annu Rev Biochem 86:21–26
Jacobson T, Priya S, Sharma SK et al (2017) Cadmium causes misfolding and aggregation of cytosolic proteins in yeast. Mol Cell Biol 37:e00490-16. https://doi.org/10.1128/MCB.00490-16
Jarabak J, Seeds AE, Talalay P (1966) Reversible cold inactivation of a 17β-hydroxysteroid dehydrogenase of human placenta: protective effect of glycerol. Biochemistry 5:1269–1279. https://doi.org/10.1021/bi00868a021
Johnson CM (2013) Differential scanning calorimetry as a tool for protein folding and stability. Arch Biochem Biophys 531:100–109. https://doi.org/10.1016/j.abb.2012.09.008
Lazaridis T, Karplus M (2003) Thermodynamics of protein folding: a microscopic view. Biophys Chem 100:367–395. https://doi.org/10.1016/S0301-4622(02)00293-4
Lee JC, Timasheff SN (1974) Partial specific volumes and interactions with solvent components of proteins in guanidine hydrochloride. Biochemistry 13:257–265. https://doi.org/10.1007/BF02702747
Lepock JR (1997) Protein denaturation during heat shock. Adv Mol Cell Biol 19:223–259
Lewit-Bentley A, Réty S (2000) EF-hand calcium-binding proteins. Curr Opin Struct Biol 10:637–643. https://doi.org/10.1016/S0959-440X(00)00142-1
Makhatadze GI, Privalov PL (1990) Heat capacity of proteins. I. Partial molar heat capacity of individual amino acid residues in aqueous solution: hydration effect. J Mol Biol 213:375–384. https://doi.org/10.1016/S0022-2836(05)80197-4
Makhatadze GI, Privalov PL (1995) Energetics of protein structure. Adv Protein Chem 47:307–425. https://doi.org/10.1016/S0065-3233(08)60548-3
Malmendal A, Linse S, Evenäs J et al (1999) Battle for the EF-hands: magnesium-calcium interference in calmodulin. Biochemistry 38:11844–11850. https://doi.org/10.1021/bi9909288
Masi M (2009) Thermodynamic systems and state functions. In: Carra S (ed) Fundamentals of chemistry. EOLSS, Abu Dhabi, pp 371–410
Masino L, Martin S, Bayley P (2000) Ligand binding and thermodynamic stability of a multidomain protein, calmodulin. Protein Sci 9:1519–1529. https://doi.org/10.1110/ps.9.8.1519
Matouschek A, Kellis JT Jr, Serrano L, Fersht AR (1989) Mapping the transition state and pathway of protein folding by protein engineering. Nature 340:122
McGrath BM, Walsh G (2006) Directory of therapeutic enzymes. Taylor & Francis, Boca Raton
Midic U, Oldfield CJ, Keith AK et al (2009) Protein disorder in the human diseasome: unfoldomics of human genetic diseases. BMC Genom 10:1–24. https://doi.org/10.1186/1471-2164-10-S1-S12
Moradi K, Shirdel SA, Shamsi M et al (2017) Investigating the structural and functional features of representative recombinants of chondroitinase ABC I. Enzyme Microb Technol. https://doi.org/10.1016/j.enzmictec.2017.08.006
Moreau KL, King JA (2012) Protein misfolding and aggregation in cataract disease and prospects for prevention. Trends Mol Med 18:273–282. https://doi.org/10.1016/j.molmed.2012.03.005
Myers JK, Nick Pace C, Martin Scholtz J (1995) Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding. Protein Sci 4:2138–2148. https://doi.org/10.1002/pro.5560041020
Nojima H, Hon-nam K, Shima T, Nodal H (1978) Reversible thermal unfolding of thermostable cytochrome c-552. J Mol Biol 122:33–42
Pace CN (1975) The stability of globular proteins. Crit Rev Biochem 3:1–43. https://doi.org/10.1021/bi00889a005
Pace CN (1986) Determination and analysis of urea and guanidine hydrochloride denaturation curves. Methods Enzymol 131:266–280
Pace CN, Shaw KL (2000) Linear extrapolation method of analyzing solvent denaturation curves. Proteins Suppl 4:1–7. https://doi.org/10.1002/1097-0134(2000)41:4+%3c1:AID-PROT10%3e3.0.CO;2-2
Pace CN, Tanford C (1968) Thermodynamics of the unfolding of, β-lactoglobulin a in aqueous urea solutions between 5 and 55″. Biochemistry 7:198–208
Pace CN, Laurents DV, Thomson JA (1990) pH dependence of the urea and guanidine hydrochloride denaturation of ribonuclease A and ribonuclease Tl. Biochemistry 29:2564–2572. https://doi.org/10.1021/bi00462a019
Pace CN, Scholtz JM, Grimsley GR (2014) Forces stabilizing proteins. FEBS Lett 588:2177–2184. https://doi.org/10.1021/nl061786n.Core-Shell
Poklar N, Vesnaver G (2000) Thermal denaturation of proteins studied by UV spectroscopy. J Chem Educ 77:380. https://doi.org/10.1021/ed077p380
Polaina J, MacCabe AP (eds) (2007) Industrial enzymes structure, function and applications. Springer, Berlin
Prakash V, Loucheux C, Scheufele S et al (1981) Interactions of proteins with solvent components in 8 m urea. Arch Biochem Biophys 210:455–464. https://doi.org/10.1016/0003-9861(81)90209-5
Privalov PL (1979) Stability of proteins: small globular proteins. Adv Protein Chem 33:167–241. https://doi.org/10.1016/S0065-3233(08)60460-X
Privalov PL (1990) Cold denaturation of protein. Crit Rev Biochem Mol Biol 25:281–306. https://doi.org/10.3109/10409239009090612
Privalov PL (2015) Microcalorimetry of macromolecules: the physical basis of biological structures structures. J Solut Chem 44:1141–1161. https://doi.org/10.1007/s10953-015-0337-x
Privalov PL, Crane-Robinson C (2018) Forces maintaining the DNA double helix and its complexes with transcription factors. Prog Biophys Mol Biol 135:30–48. https://doi.org/10.1016/j.pbiomolbio.2018.01.007
Privalov PL, Dragan AI (2007) Microcalorimetry of biological macromolecules. Biophys Chem 126:16–24. https://doi.org/10.1016/j.bpc.2006.05.004
Privalov PL, Khechinashvili NN (1974) A thermodynamic approach to the problem of stabilization of globular protein structure: a calorimetric study. J Mol Bid 86:665–684. https://doi.org/10.1016/0022-2836(74)90188-0
Privalov PL, Makhatadze GI (1990) Heat capacity of proteins II. Partial molar heat capacity of the unfolded polypeptide chain of proteins: protein unfolding effects. J Mol Biol 213:385–391. https://doi.org/10.1016/S0022-2836(05)80198-6
Privalov PL, Potekhin SA (1986) Scanning microcalorimetry in studying temperature-induced changes in proteins. Methods Enzymol 131:4–51. https://doi.org/10.1016/0076-6879(86)31033-4
Privalov PL, Griko YV, Venyaminov SY, Kutyshenko VP (1986) Cold denaturation of myoglobin. J Mol Biol 190:487–498. https://doi.org/10.1016/0022-2836(86)90017-3
Razvi A, Scholtz JM (2006) A thermodynamic comparison of HPr proteins from extremophilic organisms. Biochemistry 45:4084–4092. https://doi.org/10.1021/bi060038+
Santoro MM, Bolen DW (1988) Unfolding free-energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesylfonyl alpha-chymotrypsin using different denaturants. Biochemistry 27:8063–8068. https://doi.org/10.1021/bi00421a014
Schellman JA (1987) The thermodynamic stability of proteins. Biophys Biophys Chem 16:115–137. https://doi.org/10.1146/annurev.bb.16.060187.000555
Schön A, Clarkson BR, Jaime M, Freire E (2017) Temperature stability of proteins: analysis of irreversible denaturation using isothermal calorimetry. Proteins 79:211–227. https://doi.org/10.1177/0003122413519445.Are
Serdyuk IN, Zaccai NR, Zaccai J (2007) Methods in molecular biophysics structure, dynamics, function. Cambridge University Press, Cambridge, pp 194–220
Shamsi M, Akram Shirdel S, Jafarian V et al (2016) Optimization of conformational stability and catalytic efficiency in chondroitinase ABC I by protein engineering methods. Eng Life Sci 16:690–696. https://doi.org/10.1002/elsc.201600034
Swint L, Robertson AD (1993) Thermodynamics of unfolding for turkey ovomucoid third domain: thermal and chemical denaturation. Protein Sci 2:2037–2049
Tanford C (1968a) Protein denaturation. Part A. Characterization of the denatured state. Adv Protein Chem 23:121–217. https://doi.org/10.1016/S0065-3233(08)60401-5
Tanford C (1968b) Protein denaturation. Part B. The transition from native to denatured state. Adv Protein Chem 23:218–275
Tanford C (1970) Protein denaturation: part C. Theoretical models for the mechanism of denaturation. Adv Protein Chem 24:1–95. https://doi.org/10.1016/S0065-3233(08)60241-7
Walters J, Milam SL, Clark AC (2009) Practical approaches to protein folding and assembly. Methods Enzymol 455:1–39. https://doi.org/10.1016/S0076-6879(08)04201-8.Practical
Watson ES, O’neill MJ, Justin J, Brenner N (1964) A differential scanning calorimeter for quantitative differential thermal analysis. Anal Chem 36:1233–1238
Wintrode PL, Makhatadze GI, Privalov PL (1994) Thermodynamics of ubiquitin unfolding. Proteins Struct Funct Bioinform 18:246–253. https://doi.org/10.1002/prot.340180305
Acknowledgements
The authors confirm that there are no known conflicts of interest associated with this publication. There has been no significant financial support for this work.
Author information
Authors and Affiliations
Corresponding author
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Shirdel, S.A., Khalifeh, K. Thermodynamics of protein folding: methodology, data analysis and interpretation of data. Eur Biophys J 48, 305–316 (2019). https://doi.org/10.1007/s00249-019-01362-7
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00249-019-01362-7