Highly Perturbed PKa Values in the Unfolded State of Hen Egg White Lysozyme

Overview

Journal Biophys J

Publisher Cell Press

Specialty Biophysics

Date 2012 Apr 17

PMID 22500764

Citations 4

Authors

John Bradley

Fergal OMeara

Damien Farrell

Jens Erik Nielsen

Affiliations

Soon will be listed here.

Abstract

The majority of pK(a) values in protein unfolded states are close to the amino acid model pK(a) values, thus reflecting the weak intramolecular interactions present in the unfolded ensemble of most proteins. We have carried out thermal denaturation measurements on the WT and eight mutants of HEWL from pH 1.5 to pH 11.0 to examine the unfolded state pK(a) values and the pH dependence of protein stability for this enzyme. The availability of accurate pK(a) values for the folded state of HEWL and separate measurements of mutant-induced effects on the folded state pK(a) values, allows us to estimate the pK(a) values of seven acidic residues in the unfolded state of HEWL. Asp-48 and Asp-66 display pK(a) values of 2.9 and 3.1 in our analysis, thus representing the most depressed unfolded state pK(a) values observed to date. We observe a strong correlation between the folded state pK(a) values and the unfolded state pK(a) values of HEWL, thus suggesting that the unfolded state of HEWL possesses a large degree of native state characteristics.

Citing Articles

Insight into polyproline II helical bundle stability in an antifreeze protein denatured state.

Trevino M, Lopez-Sanchez R, Moya M, Pantoja-Uceda D, Mompean M, Laurents D Biophys J. 2023; 121(23):4560-4568.

PMID: 36815707 PMC: 9748357. DOI: 10.1016/j.bpj.2022.10.034.

Atomistic basis of opening and conduction in mammalian inward rectifier potassium (Kir2.2) channels.

Zangerl-Plessl E, Lee S, Maksaev G, Bernsteiner H, Ren F, Yuan P J Gen Physiol. 2019; 152(1).

PMID: 31744859 PMC: 7034095. DOI: 10.1085/jgp.201912422.

Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation.

Zhou H, Pang X Chem Rev. 2018; 118(4):1691-1741.

PMID: 29319301 PMC: 5831536. DOI: 10.1021/acs.chemrev.7b00305.

Local and global anatomy of antibody-protein antigen recognition.

Wang M, Zhu D, Zhu J, Nussinov R, Ma B J Mol Recognit. 2017; 31(5):e2693.

PMID: 29218757 PMC: 5903993. DOI: 10.1002/jmr.2693.

References

Cho T, Byrne N, Moore D, Pethica B, Angell C, Debenedetti P . Structure-energy relations in hen egg white lysozyme observed during refolding from a quenched unfolded state. Chem Commun (Camb). 2009; (29):4441-3. DOI: 10.1039/b907656e. View

Lindman S, Bauer M, Lund M, Diehl C, Mulder F, Akke M . pK(a) values for the unfolded state under native conditions explain the pH-dependent stability of PGB1. Biophys J. 2010; 99(10):3365-73. PMC: 2980744. DOI: 10.1016/j.bpj.2010.08.078. View

Oliveberg M, Arcus V, Fersht A . pKA values of carboxyl groups in the native and denatured states of barnase: the pKA values of the denatured state are on average 0.4 units lower than those of model compounds. Biochemistry. 1995; 34(29):9424-33. DOI: 10.1021/bi00029a018. View

Meng W, Raleigh D . Analysis of electrostatic interactions in the denatured state ensemble of the N-terminal domain of L9 under native conditions. Proteins. 2011; 79(12):3500-10. DOI: 10.1002/prot.23145. View

Guerois R, Nielsen J, Serrano L . Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol. 2002; 320(2):369-87. DOI: 10.1016/S0022-2836(02)00442-4. View

Elcock A . Realistic modeling of the denatured states of proteins allows accurate calculations of the pH dependence of protein stability. J Mol Biol. 1999; 294(4):1051-62. DOI: 10.1006/jmbi.1999.3305. View

Lambeir A, Backmann J, Filimonov V, Nielsen J, Kursula I, Norledge B . The ionization of a buried glutamic acid is thermodynamically linked to the stability of Leishmania mexicana triose phosphate isomerase. Eur J Biochem. 2000; 267(9):2516-24. DOI: 10.1046/j.1432-1327.2000.01254.x. View

Tollinger M, Forman-Kay J, Kay L . Measurement of side-chain carboxyl pK(a) values of glutamate and aspartate residues in an unfolded protein by multinuclear NMR spectroscopy. J Am Chem Soc. 2002; 124(20):5714-7. DOI: 10.1021/ja020066p. View

Farrell D, OMeara F, Johnston M, Bradley J, Sondergaard C, Georgi N . Capturing, sharing and analysing biophysical data from protein engineering and protein characterization studies. Nucleic Acids Res. 2010; 38(20):e186. PMC: 2978379. DOI: 10.1093/nar/gkq726. View

10.

Bessler C, Schmitt J, Maurer K, Schmid R . Directed evolution of a bacterial alpha-amylase: toward enhanced pH-performance and higher specific activity. Protein Sci. 2003; 12(10):2141-9. PMC: 2366932. DOI: 10.1110/ps.0384403. View

11.

Hooft R, Sander C, Vriend G . Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures. Proteins. 1996; 26(4):363-76. DOI: 10.1002/(SICI)1097-0134(199612)26:4<363::AID-PROT1>3.0.CO;2-D. View

12.

Meng W, Shan B, Tang Y, Raleigh D . Native like structure in the unfolded state of the villin headpiece helical subdomain, an ultrafast folding protein. Protein Sci. 2009; 18(8):1692-701. PMC: 2776957. DOI: 10.1002/pro.152. View

13.

Cherry J, Lamsa M, Schneider P, Vind J, Svendsen A, Jones A . Directed evolution of a fungal peroxidase. Nat Biotechnol. 1999; 17(4):379-84. DOI: 10.1038/7939. View

14.

Johnston M, Sondergaard C, Nielsen J . Integrated prediction of the effect of mutations on multiple protein characteristics. Proteins. 2010; 79(1):165-78. DOI: 10.1002/prot.22870. View

15.

Grimsley G, Scholtz J, Pace C . A summary of the measured pK values of the ionizable groups in folded proteins. Protein Sci. 2009; 18(1):247-51. PMC: 2708032. DOI: 10.1002/pro.19. View

16.

Yang A, Honig B . On the pH dependence of protein stability. J Mol Biol. 1993; 231(2):459-74. DOI: 10.1006/jmbi.1993.1294. View

17.

Yang A, Honig B . Structural origins of pH and ionic strength effects on protein stability. Acid denaturation of sperm whale apomyoglobin. J Mol Biol. 1994; 237(5):602-14. DOI: 10.1006/jmbi.1994.1258. View

18.

Aune K, Salahuddin A, Zarlengo M, Tanford C . Evidence for residual structure in acid- and heat-denatured proteins. J Biol Chem. 1967; 242(19):4486-9. View

19.

SOPHIANOPOULOS A, WEISS B . THERMODYNAMICS OF CONFORMATIONAL CHANGES OF PROTEINS. I. PH-DEPENDENT DENATURATION OF MURAMIDASE. Biochemistry. 1964; 3:1920-8. DOI: 10.1021/bi00900a023. View

20.

Tollinger M, Kay L, Forman-Kay J . Measuring pK(a) values in protein folding transition state ensembles by NMR spectroscopy. J Am Chem Soc. 2005; 127(25):8904-5. DOI: 10.1021/ja051942c. View