Electrostatic contributions to residue-specific protonation equilibria and proton binding capacitance for a small protein

Biochemistry

Volumn 45, Issue 47, 2006, Pages 13993-14002

  Lindman, Stina ^a   Linse, Sara ^a   Mulder, Frans A A ^b   André, Ingemar ^a,c  

^a LUND UNIVERSITY   (Sweden)

^b UNIVERSITY OF GRONINGEN   (Netherlands)

^c UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CAPACITANCE; DATA REDUCTION; ELECTROSTATICS; NUCLEAR MAGNETIC RESONANCE; PH EFFECTS; PROTONS;

CHARGE CHARGE INTERACTIONS; ELECTROSTATIC CONTRIBUTIONS; PROTON BINDING CAPACITANCE; PROTONATION;

PROTEINS;

ARTICLE; BINDING AFFINITY; CARBON NUCLEAR MAGNETIC RESONANCE; ELECTRIC CAPACITANCE; ELECTRIC POTENTIAL; MATHEMATICAL ANALYSIS; PH; PKA; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTON TRANSPORT; TITRIMETRY;

ELECTROSTATICS; HYDROGEN-ION CONCENTRATION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEINS; PROTONS;

EID: 33751560650     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi061555v     Document Type: Article

References (30)

1. Warwicker, J., and Watson, H. C. (1982) Calculation of the electric potential in the active site cleft due to α-helix dipoles, J. Mol. Biol. 157, 671-9.
2. Gilson, M. K., Rashin, A., Fine, R., and Honig, B. (1985) On the calculation of electrostatic interactions in proteins, J. Mol. Biol. 184, 503-16.
3. Schutz, C. N., and Warshel, A. (2001) What are the dielectric "constants" of proteins and how to validate electrostatic models? Proteins 44, 400-17.
4. Simonson, T. (2001) Macromolecular electrostatics: Continuum models and their growing pains, Curr. Opin. Struct, Biol. 11, 243-52.
5. as in proteins, Biophys. J. 83, 1731-48.
6. a's of ionizable residues in proteins: Semi-microscopic and microscopic approaches, J. Phys. Chem. B 101, 4458-72.
7. Ivanov, I., Chen, B., Raugei, S., and Klein, M. L. (2006) Relative pKa values from first-principles molecular dynamics: The case of histidine deprotonation, J. Phys. Chem. B 110, 6365-71.
8. Oda, Y., Yamazaki, T., Nagayama, K., Kanaya, S., Kuroda, Y., and Nakamura, H. (1994) Individual ionization constants of all the carboxyl groups in ribonuclease HI from Escherichia coli determined by NMR, Biochemistry 33, 5275-84.
9. Tollinger, M., Crowhurst, K. A., Kay, L. E., and Forman-Kay, J. D. (2003) Site-specific contributions to the pH dependence of protein stability, Proc. Natl. Acad. Sci. U.S.A. 100, 4545-50.
10. Tollinger, M., Forman-Kay, J. D., and Kay, L. E. (2002) Measurement of side-chain carboxyl pKa values of glutamate and aspartate residues in an unfolded protein by multinuclear NMR spectroscopy, J. Am. Chem. Soc. 124, 5714-7.
11. Chen, H. A., Pfuhl, M., McAlister, M. S. B., and Driscoll, P. C. (2000) Determination of pKa values of carboxyl groups in the N-terminal domain of rat CD2: Anomalous pKa of a glutamate on the ligand-binding surface, Biochemistry 39, 6814-24.
12. Oliveberg, M., Arcus, V. L., and Fersht, A. R. (1995) 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 34, 9424-33.
13. Forman-Kay, J. D., Clore, G. M., and Gronenborn, A. M. (1992) Relationship between electrostatics and redox function in human thioredoxin: Characterization of pH titration shifts using two-dimensional homo- and heteronuclear NMR, Biochemistry 31, 3442-52.
14. Gronenborn, A. M., Filpula, D. R., Essig, N. Z., Achari, A., Whitlow, M., Wingfield, P. T., and Clore, G. M. (1991) A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G, Science 253, 657-61.
15. Gallagher, T., Alexander, P., Bryan, P., and Gilliland, G. L. (1994) Two crystal structures of the B1 immunoglobulin-binding domain of streptococcal protein G and comparison with NMR, Biochemistry 33, 4721-9.
16. Alexander, P., Fahnestock, S., Lee, T., Orban, J., and Bryan, P. (1992) Thermodynamic analysis of the folding of the streptococcal protein G IgG-binding domains B1 and B2: Why small proteins tend to have high denaturation temperatures, Biochemistry 31, 3597-603.
17. Lindman, S., Xue, W.-F., Szczepankiewicz, O., Bauer, M. C., Nilsson, H., and Linse, S. (2006) Salting the Charged Surface: pH and Salt Dependence of Protein G B1 Stability, Biophys. J. 90, 2911-21.
18. Yamazaki, T., Yoshida, M., and Nagayama, K. (1993) Complete assignments of magnetic resonances of ribonuclease H from Escherichia coli by double- and triple-resonance 2D and 3D NMR spectroscopies, Biochemistry 32, 5656-69.
19. Glasoe, P. K., and Long, F. A. (1960) Use of glass electrodes to measure acidities in deuterium oxide, J. Phys. Chem. 64, 188-90.
20. Markley, J. L. (1975) Observation of Histidine Residues in Proteins by Means of NMR Spectroscopy, Acc. Chem. Res. 8, 70-80.
21. Bevington, P. R., and Robinson, D. K. (2003) Data Reduction and Error Analysis, McGraw-Hill, New York.
22. Borkovec, M., Jönsson, B., and Koper, G. J. M. (2001) Ionization Processes and Proton Binding in Polyprotic Systems: Small Molecules, Proteins, Interfaces, and Polyelectrolytes, in Surface and Colloid Science (Matijevic, E., Ed.) pp 169-99, Kluwer Academic/Plenum Publishers, New York.
23. Markley, J. L. (1973) Nuclear Magnetic-Resonance Studies of Trypsin-Inhibitors. Histidines of Virgin and Modified Soybean Trypsin-Inhibitor (Kunitz), Biochemistry 12, 2245-50.
24. Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H., and Teller, E. (1953) Equation of State Calculations by Fast Computing Machines, J. Chem. Phys. 21, 1087-92.
25. Guex, N., and Peitsch, M. C. (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling, Electrophoresis 18, 2714-23.
26. Nozaki, Y., and Tanford, C. (1967) Examination of titration behavior, Methods Enzymol. 11, 715-34.
27. Onufriev, A., Case, D. A., and Ullmann, G. M. (2001) A novel view of pH titration in biomolecules, Biochemistry 40, 3413-9.
28. Lund, M., and Jönsson, B. (2005) On the charge regulation of proteins, Biochemistry 44, 5722-7.
29. Di Cera, E., Gill, S. J., and Wyman, J. (1988) Binding capacity: Cooperativity and buffering in biopolymers, Proc. Natl. Acad. Sci. U.S.A. 85, 449-52.
30. Koradi, R., Billeter, M., and Wüthrich, K. (1996) MOLMOL: A program for display and analysis of macromolecular structures, J. Mol. Graphics 14, 51-5.