Optimization of the electrostatic interactions between ionized groups and peptide dipoles in proteins

Protein Science

Volumn 6, Issue 6, 1997, Pages 1190-1196

  Spassov, Velin Z ^a,b   Ladenstein, Rudolf ^a   Karshikoff, Andrej D ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

^b BULGARIAN ACADEMY OF SCIENCES   (Bulgaria)

Author keywords

Electrostatic interactions; Monte Carlo simulations; Peptide dipoles; Protein stability

Indexed keywords

AMINO ACID; PEPTIDE; PROTEIN;

ARTICLE; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STABILITY; SYSTEM ANALYSIS;

EID: 0030926503     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560060607     Document Type: Article

References (28)

1. Åqvist J, Luecke H, Quiocho FA, Warshel A. 1991. Dipoles localized at helix termini of proteins stabilize charges. Proc Natl Acad Sci USA 88:2026-2030.
2. a's of ionizable groups in proteins: Atomic detail from a continuum electrostatic model. Biochemistry 29:10219-10225.
3. Bernstein FC, Koetzle TF, Williams GJB, Meyer EF Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. 1977. The Protein Data Bank: A computer-based archival file for macromolecular structures. J Mol Biol 112:535-542.
4. Boberg J, Salakoski T, Vihinen M. 1995. Representative selection of proteins based on nuclear families. Protein Eng 8:501-503.
5. Brooks BB, Bruccoleri RE, Olafson BD, States DG, Swaminathan S, Karplus M. 1983. CHARMM: A program for macromolecular energy minimization and dynamics calculations. J Comp Chem 4:187-217.
6. Evans AG, Hamann SD. 1951. Energy and entropy change of organic reactions. Trans Faraday Soc 47:25-49.
7. Friend SH, Gurd FRN. 1979. Electrostatic stabilization in myoglobin. pH dependence of summed electrostatic contribution. Biochemistry 18:4612-4619.
8. Gandini D, Gogioso L, Bolognesi M, Bordo D. 1996. Patterns in ionizable side chain interactions in proteins. Proteins Struct Fund Genet 24:439-449.
9. Gilson MK, Honig B. 1989. Destabilization of an α-helix-bundle protein by helix dipoles. Proc Natl Acad Sci USA 86:1524-1528.
10. Hol WGJ. 1985. The variable effective dielectric constant and the importance of the direction of the peptide dipole moment: An investigation of dipole-dipole interactions in αα and αβα proteins. J Mol Struct (Theochem) 123:27-43.
11. Hol WGJ, Halie LM, Sander C. 1981. Dipoles of the α-helix and β-sheet: Their role in protein folding. Nature 294:532-536.
12. Hol WGJ, van Duijnen PT, Berendsen HJC. 1978. The α-helix dipole and the properties of proteins. Nature 273:443-446.
13. Hwang JK, Warshel A. 1988. Why ion pair reversal by protein engineering is unlikely to succeed. Nature 334:270-272.
14. Karshikoff A. 1995. A simple algorithm for calculation of multiple site titration curves. Protein Eng 8:243-248.
15. Karshikov A, Reinemer P, Huber R, Ladenstein R. 1993. Electrostatic evidence for the activation of the glutathione thiol by Tyrosine 7 in p class GSH transferases. Eur J Biochem 215:663-670.
16. Miller S, Janin J, Lesk AM, Chothia C. 1987. Interior and surface of monomeric proteins. J Mol Biol 196:641-656.
17. ras. Structure 4:475-489.
18. Oberoi H, Trikha J, Yuan X, Allewell NM. 1996. Identification and analysis of long-range electrostatic effects in proteins by computer modeling: Aspartate transcarbamylase. Proteins Struct Funct Genet 25:300-314.
19. Olson AJ, Spassov V. 1987. Electrostatic environments of charged residues in folded proteins. In: Scientific Report 1986-87, Research Institute of Scripps Clinic 13:200.
20. Plesniak LA, Connelli GP, Wakarchuk WW, McIntosh LP. 1996. Characterization of a buried neutral histidine residue in Bacillus circulans xylanase: NMR assignment, pH titration, and hydrogen exchange. Protein Sci 5:2319-2328.
21. Rogers NK, Steinberg MJE. 1984. Electrostatic interactions in globular proteins. Different dielectric models applied to the packing of α-helix. J Mol Biol 175:527-542.
22. Spassov VZ, Atanasov BP. 1994. Spatial optimization of electrostatic interactions between the ionized groups in globular proteins. Proteins Struct Funct Genet 19:222-229.
23. Spassov VZ, Karshikoff AD, Ladenstein R. 1994. The optimisation of the electrostatic interactions in proteins of different functional and folding type. Protein Sci 3:1556-1569.
24. Spassov VZ, Karshikoff AD, Ladenstein R. 1995. The optimization of protein solvent interactions. Thermostability and the role of hydrophobic and electrostatic interactions. Protein Sci 4:1516-1527.
25. a values. Biopolymers 3(2):897-909.
26. Wada A. 1976. The α-helix as an electric macro-dipole. Adv Biophys 9:1-63.
27. Warshel A, Russell ST, Churg AK. 1984. Macroscopic models for studies of electrostatic interactions in proteins: Limitations and applicability. Proc Natl Acad Sci USA 81:4785-4789.
28. Warwicker J, Watson NC. 1982. Calculation of the electric field potential in the active site cleft due to α-helix dipoles. J Mol Biol 157:671-679.