Probing electric fields in proteins in solution by NMR spectroscopy

Proteins: Structure, Function and Genetics

Volumn 72, Issue 1, 2008, Pages 333-343

  Hass, Mathias A S ^a   Jensen, Malene Ringkjøbing ^a   Led, Jens J ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

1H and 15N chemical shift; Electric field; NMR; Nuclear shielding polarizability; Plastocyanin

Indexed keywords

METAL ION; PLASTOCYANIN;

ARTICLE; DIELECTRIC CONSTANT; ELECTRIC FIELD; ELECTRICITY; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; POLARIZATION; PRIORITY JOURNAL; PROTON NUCLEAR MAGNETIC RESONANCE; PROTON TRANSPORT; SUBSTITUTION REACTION;

AMIDES; AMINO ACID SEQUENCE; ANABAENA; ELECTRICITY; ELECTROSTATICS; HISTIDINE; HYDROGEN-ION CONCENTRATION; MAGNETIC RESONANCE SPECTROSCOPY; PEPTIDES; PLASTOCYANIN; PROTONS; SOLUTIONS;

EID: 44949260034     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21929     Document Type: Article

References (36)

1. Sternberg MJE, Hayes FRF, Russel AJ, Thomas PG, Fersht AR. Prediction of electric effects of engineering of protein charges. Nature 1987;330:86-88.
2. Gilson MK, Honig BH. Calculation of electrostatic potentials in an enzyme active site. Nature 1987;330:84-86.
3. Kesvatera T, Jönsson B, Thulin E, Linse S. Focusing of the electrostatic potential at EF-hands of calbindin D(9k): titration of acidic residues. Proteins 2001;45:129-135.
4. Lindman S, Linse S, Mulder FA, André I. Electrostatic contributions to residues-specific protonation equiliberia and proteon binding capacitance for a small protein. Biochemistry 2006;45:3993-4002.
5. Anderson JS, LeMaster DM, Hernández G. Electrostatic potential energy within a protein monitored by metal charge-dependent hydrogen exchange. Biophys J 2006;91:93-95.
6. LeMaster DM, Anderson JS, Hernández G. Spatial distribution of dielectric shielding in the interior of Pyrococcus furiosus rubredoxin as sampled in the subnanosecond timeframe by hydrogen exchange. Biophys Chem 2007;129:43-48.
7. Warshel A, Papazyan A. Electrostatic effects in macromolecules: fundamental concepts and practical modeling. Curr Opin Struct Biol 1998;8:211-217.
8. Schutz CN, Warshel A. What are the dielectric "constants" of proteins and how to validate electrostatic models. Proteins 2001;44:400-417.
9. Suydam IT, Snow CD, Pande VS, Boxer SG. Electric fields at the active site of an enzyme: direct comparison of experiment with theory. Science 2006;313:200-204.
10. Wishhart DS, Case DA. Use of chemical shift in molecular structure determination. Methods Enzymol 2001;338:3-34.
11. Hunter CA, Packer MJ, Zonta C. From structure to chemical shift and vice-versa. Prog Nucl Magn Reson Spect 2005;47:27-39.
12. Schneider WG, Bernstein HJ, Pople JA. Proton magnetic resonance chemical shift of free (gaseous) and associated (liquid) hydride molecules. J Chem Phys 1958;28:601-607.
13. Buckingham AD. Chemical shifts in the nuclear magnetic resonance spectra of molecules containing polar groups. Can J Chem 1960;38:300-307.
14. 15N NMR relaxation and chemical shift: conformational exchange in plastocyanin induced by histidine protonations. J Am Chem Soc 2004;126:753-765.
15. Jensen MR, Petersen G, Lauritzen C, Pedersen J, Led JJ. Metal binding sites in proteins: identification and characterization by paramagnetic NMR relaxation. Biochemistry 2005;44:11014-11023.
16. Palmer AG. NMR characterization of the dynamics of biomacromolecules. Chem Rev 2002;104:3623-3640.
17. Korzhnev DM, Neudecker P, Mittermaier A, Orekhov VY, Kay LE. Multiple-site exchange in proteins studied with a suite of six NMR relaxation dispersion experiments: an application to the folding of a Fyn SH3 domain mutant. J Am Chem Soc 2005;127:15602-15611.
18. Raynes WT. Electric field effects on shielding constants. In: Grant DM, Harris RK, editors. Encyclopedia of nuclear magnetic resonance, Vol. 3. Chichester: Wiley; 1996. p 1846-1856.
19. Augspurger J, Pearson JG, Oldfield E, Dykstra CE, Park KD, Schwartz D. Chemical-shift ranges in proteins. J Magn Reson 1992; 100:342-357.
20. 17O nuclear shieldings of amides. Chem Phys Lett 1994;224:275-282.
21. αβγ): the influence of uniform electric field effects on the shielding of backbone nuclei in proteins. J Am Chem Soc 2003;125:9556-9557.
22. Jensen MR, Hansen DF, Ayna U, Dagil R, Hass MAS, Christensen HEM, Led JJ. On the use of pseudocontact shifts in the structure determination of metalloproteins. Magn Reson Chem 2006;44:294-301.
23. Schmidt L, Christensen HEM, Harris P. 1.6 Å structure of plastocyanin from Anabaena variabilis. Acta Cryst D 2006;62:1022-1029.
24. Rocchia W, Alexov E, Honig B. Extending the applicability of the nonlinear Poisson-Boltzmann equation: multiple dielectric constants and multivalent ions. J Phys Chem B 2001;105:6507-6514.
25. Rocchia W, Sridharan S, Nicholls A, Alexov E, Chiabrera A, Honig B. Rapid grid-based construction of the molecular surface for both molecules and geometric objects: applications to the finite difference Poisson-Boltzmann method. J Comput Chem 2002;23:128-137.
26. I) poplar plastocyanin at six pH values. J Mol Biol 1986;192:361-387.
27. Badsberg U, Jørgensen AMM, Sørensen GO, Ulstrup J, Led JJ. Solution structure of reduced plastocyanin from the blue-green alga Anabaena variabilis. Biochemistry 1996;35:7021-7031.
28. 1 relaxation of heteronuclei and protons in Cu(II) plastocyanin from Anabaena variabilis. J Am Chem Soc 2000;122:9473-9485.
29. Augspurger J, Dykstra CE. Electromagnetic properties of molecules from a uniform procedure for differentation of molecular wave-functions to high-order. J Phys Chem 1991;95:9230-9238.
30. Church WB, Guss JM, Potter JJ, Freeman HC. The crystal-structure of mercury-substituted poplar plastocyanin at 1.9 Å resolution. J Biol Chem 1986;261:234-237.
31. Gilson MK, Honig BH. The dielectric constant of a folded protein. Biopolymers 1986;25:2097-2119.
32. 15N chemical shifts. J Biomol NMR 2003;26:215-240.
33. Xu XP, Case DA. Automated prediction of N-15, C13(alpha), C-13(beta) and C-13′ chemical shifts in proteins using a density functional database. J Biomol NMR 2001;21:321-333.
34. Dominguez C, Boelens R, Bovin AMJJ. HADDOCK: a protein-protein docking approach based on biochemical and/or biophysical information. J Am Chem Soc 2003;125:1731-1737.
35. LeMaster DM, Minnich M, Parson PJ, Anderson JS, Hernández G. Tetrathiolate coordination of germanium(IV) in a protein active site. J Inorg Biochem 2006;100:1410-1412.
36. Maher M, Cross M, Wilce MCJ, Guss JM, Wedd AG. Metal-substituted derivatives of the rubredoxin from Clostridium pasteurianum. Acta Cryst D 2004;60:298-303.