Charges in the hydrophobic interior of proteins

Proceedings of the National Academy of Sciences of the United States of America

Volumn 107, Issue 37, 2010, Pages 16096-16100

  Isom, Daniel G ^a,b   Castañeda, Carlos A ^a,c   Cannon, Brian R ^a,d   Velu, Priya D ^a,e   García Moreno E, Bertrand ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^c Bldg 142   (United States)

^d UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Bioenergetics; Dielectric effect; Electrostatics; Hydration; pKa

Indexed keywords

BACTERIAL ENZYME; GLOBULAR PROTEIN; GLUTAMIC ACID; NUCLEASE; MICROCOCCAL NUCLEASE;

ARTICLE; CIRCULAR DICHROISM; DIELECTRIC CONSTANT; ENZYME ACTIVE SITE; FLUORESCENCE; HYDROPHOBICITY; IONIZATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STABILITY; STAPHYLOCOCCUS; STATIC ELECTRICITY; THERMODYNAMICS; TITRIMETRY; ULTRAVIOLET RADIATION; CHEMICAL PHENOMENA; CHEMICAL STRUCTURE; CHEMISTRY; ENZYME STABILITY; ENZYMOLOGY; PROTEIN TERTIARY STRUCTURE;

CIRCULAR DICHROISM; ENZYME STABILITY; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MICROCOCCAL NUCLEASE; MODELS, MOLECULAR; PROTEIN STRUCTURE, TERTIARY; STAPHYLOCOCCUS; THERMODYNAMICS;

EID: 77958001543     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1004213107     Document Type: Article

References (34)

1. Perutz MF, Kendrew JC, Watson HC (1965) Structure and function of haemoglobin: II. Some relations betwen polypeptide chain configuration and amio acid sequence. J Mol Biol 13:669-678.
2. Warshel A (1978) Energetics of enzyme catalysis. Proc Nat'l Acad Sci USA 75:5250-5254.
3. Abrahams JP, Leslie AGW, Lutter R, Walker JE (1994) Structure at 2.8 A resolution of F1-ATPase from bovine heart mitochondria. Nature 370:621-628. (Pubitemid 24987531)
4. Iwata S, Ostermeier C, Ludwig B, Michel H (2002) Structure at 2.9 A resolution of cytochrome c oxidase from Paracoccus denitrificans. Nature 376:660-669.
5. + channel. Nature 423:33-41.
6. + conduction and selectivity. Science 280:69-77.
7. Luecke H, Richter HT, Lanyi JK (1998) Proton transfer pathways in bacteriorhodopsin at 2.3 A resolution. Science 280:1934-1937. (Pubitemid 28299400)
8. Pebay-Peyroula E, Rummel G, Rosenbusch JP, Landau EM (1997) X-ray structure of bacteriorhodoopsin at 2.5 A from microcrystals grown in lipidic cubic phases. Science 277:1676-1681.
9. Karp DA, et al. (2007) High apparent dielectric constant inside a protein reflects structural reorganization coupled to the ionization of an internal Asp. Biophys J 92:2041-2053.
10. Dwyer J, et al. (2000) High apparent dielectric constants in the interior of a protein reflect water penetration. Biophys J 79:1610-1620.
11. García-Moreno EB, et al. (1997) Experimental measurement of the effective dielectric in the hydrophobic core of a protein. Biophys Chem 64:211-224.
12. Stites WE, Gittis AG, Lattman EE, Shortle D (1991) In a staphylococcal nuclease mutant the side chain of a lysine replacing valine 66 is fully buried in the hydrophobic core. J Mol Biol 221:7-14.
13. Nguyen DM, Reynald RL, Gittis AG, Lattman EE (2004) X-ray and thermodynamic studies of staphylococcal nuclease variants I92E and I92K: insights into polarity of the protein interior. J Mol Biol 341:565-574.
14. a values of acidic and basic residues buried at the same internal location in a protein are governed by different factors. J Mol Biol 389:34-47.
15. a values. Protein Sci 17:833-845.
16. Isom DG, et al. (2008) High tolerance for ionizable residues in the hydrophobic interior of proteins. Proc Natl Acad Sci USA 105:17784-17788.
17. a values of buried residues: analysis with continuum methods and role of water penetration. Biophys J 82:3289-3304.
18. Castañeda CA, et al. (2009) Molecular determinants of the pKa values of Asp and Glu residues in staphylococcal nuclease. Proteins 77:570-588.
19. Lee KK, Fitch CA, Lecomte JTJ, García-Moreno EB (2002) Electrostatic effects in highly charged proteins: salt sensitivity of pKa values of histidines in staphylococcal nuclease. Biochemistry 41:5656-5667.
20. Matthew JB, et al. (1985) pH-dependent properties in proteins. CRC Crit Rev Biochem 18:91-197.
21. Simonson T, Brooks CL, III (1996) Charge screening and the dielectric constant of proteins: insights from molecular dynamics. J Am Chem Soc 118:8452-8458.
22. Simonson T, Perahia D (1995) Internal and interfacial dielectric properties of cytochrome c from molecular dynamics in aqueous solution. Proc Nat'l Acad Sci USA 92:1082-1086.
23. Smith PE, Brunne RM, Mark AE, van Gunsteren WF (1993) Dielectric properties of trypsin inhibitor and lysozyme calculated from molecular dynamics simulations. J Phys Chem-US 97:2009-2014.
24. Gong H, Hocky G, Freed KF (2008) Influence of nonlinear electrostatics on transfer energies between liquid phases: charge burial is far less expensive than Born Model. Proc Natl Acad Sci USA 105:11146-11151.
25. Schlessman JL, et al. (2008) Crystallographic study of hydration of an internal cavity in engineered proteins with buried polar or ionizable groups. Biophys J 94:3208-3216.
26. Karp DA, Stahley MR, García-Moreno EB (2010) Conformational consequences of ionization of Lys, Asp, and Glu buried at position 66 in staphylococcal nuclease. Biochemistry 49:4138-4146.
27. Dao-pin S, et al. (1991) Structural and thermodynamic consequences of burying a charged residue within the hydrophobic core of T4 lysozyme. Biochemistry 30:11521-11529.
28. Zheng Z, Sosnick TR (2010) Protein vivisection reveals elusive intermediates in folding. J Mol Biol 397:777-788.
29. Iuchi SHC, Paesani F, Voth GA (2009) The hydrated excess proton at water-hydrophobic interface. J Phys Chem B 113:4017-4030.
30. Gunner M, Alexov E (2000) A pragmatic approach to structure based calculation of coupled proton and electron transfer in proteins. Biochimica et Biophysica Acta 1458:63-87.
31. Bloom JD, Labthavikul ST, Otey CR, Arnold FH (2006) Protein stability promotes evolvability. Proc Natl Acad Sci USA 103:5869-5874.
32. Tokuriki N, Stricher F, Serrano L, Tawfik D (2008) How protein stability and new functions trade off. PLoS Computational Biol 4:1-7.
33. Shortle D (1986) Guanidine hydrochloride denaturation studies of mutant forms of staphylococcal nuclease. J Cell Biochem 30:281-289.
34. Whitten ST, García-Moreno EB (2000) pH dependence of stability of staphylococcal nuclease: evidence of substantial electrostatic interactions in the denatured state. Biochemistry 39:14292-14304.