Cold unfolding of β-hairpins: A molecular-level rationalization
Angelo Riccio
Dipartimento di Scienze Applicate, Università di Napoli “Parthenope”, Centro Direzionale Isola C4, 80143 Napoli, Italy
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Giuseppe Graziano
Dipartimento di Scienze Biologiche ed Ambientali, Università del Sannio, Via Port'Arsa 11 - 82100 Benevento, Italy
Dipartimento di Scienze Biologiche ed Ambientali, Università del Sannio, Via Port'Arsa 11 – 82100 Benevento, Italy===Search for more papers by this authorAngelo Riccio
Dipartimento di Scienze Applicate, Università di Napoli “Parthenope”, Centro Direzionale Isola C4, 80143 Napoli, Italy
Search for more papers by this authorCorresponding Author
Giuseppe Graziano
Dipartimento di Scienze Biologiche ed Ambientali, Università del Sannio, Via Port'Arsa 11 - 82100 Benevento, Italy
Dipartimento di Scienze Biologiche ed Ambientali, Università del Sannio, Via Port'Arsa 11 – 82100 Benevento, Italy===Search for more papers by this authorAbstract
Isolated β-hairpins in water have a temperature dependence of their conformational stability qualitatively resembling that of globular proteins, showing both cold and hot unfolding transitions. It is shown that a molecular-level rationalization of this cold unfolding can be provided extending the approach devised for globular proteins (Graziano G. Phys Chem Chem Phys 2010; 12:14245-14252). The decrease in the solvent-excluded volume upon folding, measured by the decrease in the solvent accessible surface area, produces a gain in configurational/translational entropy of water molecules that is the main stabilizing contribution of the folded conformation. This always stabilizing Gibbs energy contribution has a parabolic-like temperature dependence in water and is exactly counterbalanced at two temperatures (i.e., the cold and hot unfolding temperatures) by the always destabilizing Gibbs energy contribution due to the loss in conformational degrees of freedom of the peptide chain. Proteins 2011; © 2011 Wiley-Liss, Inc.
REFERENCES
- 1 Privalov PL,Griko YV,Venyaminov SY,Kutyshenko VP. Cold denaturation of myoglobin. J Mol Biol 1986; 190: 487–498.
- 2 Privalov PL. Cold denaturation of proteins. Crit Rev Biochem Mol Biol 1990; 25: 281–305.
- 3 Franks F. Protein destabilization at low temperatures. Adv Protein Chem 1995; 46: 105–109.
- 4 Pastore A,Martin SR,Politou A,Kondapalli KC,Stemmler T,Temussi PA. Unbiased cold denaturation: low- and high-temperature unfolding of yeast frataxin under physiological conditions. J Am Chem Soc 2007; 129: 5374–5375.
- 5 Sanfelice D,Tancredi T,Politou A,Pastore A,Temussi PA. Cold denaturation and aggregation: a comparative NMR study of titin I28 in bulk and in a confined environment. J Am Chem Soc 2009; 131: 11662–11663.
- 6 Graziano G,Catanzano F,Riccio A,Barone G. A reassessment of the molecular origin of cold denaturation. J Biochem 1997; 122: 395–401.
- 7 Riccio A,Ascolese E,Graziano G. Cold denaturation in the Schellman-Brandts model of globular proteins. Chem Phys Lett 2010; 486: 65–69.
- 8 Chandler D. Interfaces and the driving force of hydrophobic assembly. Nature 2005; 437: 640–647.
- 9 Graziano G. Scaled particle theory study of the length scale dependence of cavity thermodynamics in different liquids. J Phys Chem B 2006; 110: 11421–11426.
- 10 Graziano G. On the molecular origin of cold denaturation of globular proteins. Phys Chem Chem Phys 2010; 12: 14245–14252.
- 11 Andersen NH,Cort JR,Liu Z,Sjoberg SJ,Tong H. Cold denaturation of monomeric peptide helices. J Am Chem Soc 1996; 118: 10309–10310.
- 12 Maynard AJ,Sharman GJ,Searle MS. Origin of β-hairpin stability in solution: structural and thermodynamic analysis of the folding of a model peptide supports hydrophobic stabilization in water. J Am Chem Soc 1998; 120: 1996–2007.
- 13 Andersen NH,Dyer RB,Fesinmeyer RM,Gai F,Liu Z,Neidigh JW,Tong H. Effect of hexafluoroisopropanol on the thermodynamics of peptide secondary structure formation. J Am Chem Soc 1999; 121: 9879–9880.
- 14 Searle MS. Insights into stabilizing weak interactions in designed peptide β-hairpins. Biopolym Pept Sci 2004; 76: 185–195.
- 15 Dyer RB,Maness SJ,Franzen S,Fesinmeyer RM,Olsen KA,Andersen NH. Hairpin folding dynamics: the cold-denatured state is predisposed for rapid refolding. Biochemistry 2005; 44: 10406–10415.
- 16
Ben-Naim A.
Solvation thermodynamics.
New York:
Plenum Press;
1987.
10.1007/978-1-4757-6550-2 Google Scholar
- 17 Lee B. Solvent reorganization contribution to the transfer thermodynamics of small nonpolar molecules. Biopolymers 1991; 31: 993–1008.
- 18 Graziano G. Benzene solubility in water: a reassessment. Chem Phys Lett 2006; 429: 114–118.
- 19 Ben-Naim A. Hydrophobic interaction and structural changes in the solvent. Biopolymers 1975; 14: 1337–1355.
- 20 Lee B. Enthalpy-entropy compensation in the thermodynamics of hydrophobicity. Biophys Chem 1994; 51: 271–278.
- 21 Lee B,Graziano G. A two-state model of hydrophobic hydration that produces compensating enthalpy and entropy changes. J Am Chem Soc 1996; 118: 5163–5168.
- 22 Graziano G. Dimerization thermodynamics of large hydrophobic plates: a scaled particle theory study. J Phys Chem B 2009; 113: 11232–11239.
- 23 Lee B,Richards FM. The interpretation of protein structures: estimation of static accessibility. J Mol Biol 1971; 55: 379–400.
- 24
Reiss H.
Scaled particle methods in the statistical thermodynamics of fluids.
Adv Chem Phys
1966;
9:
1–84.
10.1002/9780470143551.ch1 Google Scholar
- 25 Wallqvist A,Berne BJ. Molecular dynamics study of the dependence of water salvation free energy on solute curvature and surface area. J Phys Chem 1995; 99: 2885–2892.
- 26 Patel AJ,Varilly P,Chandler D. Fluctuations of water near extended hydrophobic and hydrophilic surfaces. J Phys Chem B 2010; 114: 1632–1637.
- 27 Gong H,Rose GD. Assessing the solvent-dependent surface area of unfolded proteins using an ensemble model. Proc Natl Acad Sci USA 2008; 105: 3321–3326.
- 28 Creamer TP,Rose GD. Side-chain entropy opposes alpha-helix formation but rationalizes experimentally determined helix-forming propensities. Proc Natl Acad Sci USA 1992; 89: 5937–5941.
- 29 Doig AJ,Sternberg MJE. Side-chain conformational entropy in protein folding. Protein Sci 1995; 4: 2247–2251.
- 30 Honig B,Yang AS. Free energy balance in protein folding. Adv Protein Chem 1995; 46: 27–58.
- 31 Privalov PL. Thermodynamic problems in structural molecular biology. Pure Appl Chem 2007; 79: 1445–1462.
- 32 Pierotti RA. On the scaled-particle theory of dilute aqueous solutions. J Phys Chem 1967; 71: 2366–2367.
- 33 Kell GS. Density, thermal expansivity, and compressibility of liquid water from 0 to 150°C: correlations and tables for atmospheric pressure and saturation reviewed and expressed on 1968 temperature scale. J Chem Eng Data 1975; 20: 97–105.
- 34 Cibulka I,Takagi T,Ruzicka K. P-ρ-T data of liquids: summarization and evaluation. VII. Selected halogenated hydrocarbons J Chem Eng Data 2001; 46: 2–28.
- 35 Lee B. The physical origin of the low solubility of nonpolar solutes in water. Biopolymers 1985; 24: 813–823.
- 36 Graziano G. Comment on reevaluation in interpretation of hydrophobicity by scaled particle theory. J Phys Chem B 2002; 106: 7713–7716.
- 37 Rees DC,Robertson AD. Some thermodynamic implications for the thermostability of proteins. Protein Sci 2001; 10: 1187–1194.
- 38 Garde S,Hummer G,Garcia AE,Paulaitis ME,Pratt LR. Origin of entropy convergence in hydrophobic hydration and protein folding. Phys Rev Lett 1996; 77: 4966–4968.
- 39 Graziano G,Lee B. Entropy convergence in hydrophobic hydration: a scaled particle theory analysis. Biophys Chem 2003; 105: 241–250.
- 40 Ashbaugh HS,Pratt LR. Contrasting nonaqueous against aqueous salvation on the basis of scaled-particle theory. J Phys Chem B 2007; 111: 9330–9336.
- 41 Lee B. A procedure for calculating thermodynamic functions of cavity formation from the pure solvent simulation data. J Chem Phys 1985; 83: 2421–2425.
- 42 Graziano G,Lee B. Hydration of aromatic hydrocarbons. J Phys Chem B 2001; 105: 10367–10372.
- 43 Graziano G. Entropy convergence in the hydration thermodynamics of n-alcohols. J Phys Chem B 2005; 109: 12160–12166.
- 44 Frank HS,Evans MW. Free volume and entropy in condensed systems. III. Entropy in binary liquid mixtures; partial molar entropy in dilute solutions; structure and thermodynamics of aqueous electrolytes. J Chem Phys 1945; 13: 507–532.
- 45 Kauzmann W. Some factors in the interpretation of protein denaturation. Adv Protein Chem 1959; 14: 1–63.
- 46 Graziano G,Lee B. On the intactness of hydrogen bonds around nonpolar solutes dissolved in water. J Phys Chem B 2005; 109: 8103–8107.
- 47 Finney JL,Bowron DT,Daniel RM,Timmins PA,Roberts MA. Molecular and mesoscale structures in hydrophobically driven aqueous solutions. Biophys Chem 2003; 105: 391–409.
- 48 Buchanan P,Aldiwan N,Soper AK,Creek JL,Koh CA. Decreased structure on dissolving methane in water. Chem Phys Lett 2005; 415: 89–93.
- 49 Filipponi A,Bowron DT,Lobban C,Finney JL. Structural determination of the hydrophobic hydration shell of Kr. Phys Rev Lett 1997; 79: 1293–1296.
- 50 Dec SF,Bowler KE,Stadterman LL,Koh CA,Sloan ED. Direct measure of the hydration number of methane. J Am Chem Soc 2006; 128: 414–415.
- 51 Qvist J,Halle B. Thermal signature of hydrophobic hydration dynamics. J Am Chem Soc 2008; 130: 10345–10353.
- 52 Graziano G. Case study of enthalpy-entropy non-compensation. J Chem Phys 2004; 120: 4467–4471.
- 53 Lum K,Chandler D,Weeks JD. Hydrophobicity at small and large length scales. J Phys Chem B 1999; 103: 4570–4577.
- 54 Rajamani S,Truskett TM,Garde S. Hydrophobic hydration from small to large lengthscale: understanding and manipulating the crossover. Proc Natl Acad Sci USA 2005; 102: 9475–9480.
- 55 Ashbaugh HS,Pratt LR. Scaled particle theory and length scales of hydrophobicity. Rev Mod Phys 2006; 78: 159–178.
- 56 Graziano G. Salting out of methane by sodium chloride: a scaled particle theory study. J Chem Phys 2008; 129: 084506.
- 57 Graziano G. Hydration entropy of polar, nonpolar and charged species. Chem Phys Lett 2009; 479: 56–59.
- 58 Graziano G. Role of salts on the strength of pairwise hydrophobic interaction. Chem Phys Lett 2009; 483: 67–71.