Optimizing pKA computation in proteins with pH adapted conformations

Proteins: Structure, Function and Genetics

Volumn 71, Issue 3, 2008, Pages 1335-1348

  Kieseritzky, Gernot ^a   Knapp, Ernst Walter ^a  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

Author keywords

Conformational flexibility; Continuum electrostatics; pH dependence; PKA; Salt bridges

Indexed keywords

ACIDITY; ARTICLE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DIELECTRIC CONSTANT; ELECTRICITY; HYDROGEN BOND; MOLECULAR INTERACTION; PH MEASUREMENT; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTON TRANSPORT; STRUCTURE ANALYSIS; BIOLOGY; CHEMISTRY; METHODOLOGY; PH; PHYSIOLOGY; THERMODYNAMICS;

PROTEIN;

COMPUTATIONAL BIOLOGY; ELECTROSTATICS; HYDROGEN-ION CONCENTRATION; PROTEIN CONFORMATION; PROTEINS; THERMODYNAMICS;

EID: 42449113368     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21820     Document Type: Article

References (54)

1. Bashford D, Karplus M. pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model. Biochemistry 1990;29:10219-10225.
2. You TJ, Bashford D. Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility. Biophys J 1995;69:1721-1733.
3. Beroza P, Case DA. Including side chain flexibility in continuum electrostatic calculations of protein titration. J Phys Chem 1996; 100:20156-20163.
4. Antosiewicz J, McCammon JA. The determinants of pKas in proteins. Biochemistry 1996;35:7819-7833.
5. Demchuk E, Wade RC. Improving the continuum dielectric approach to calculating pKas of ionizable groups in proteins. J Phys Chem 1996;100:17373-17387.
6. Nielsen JE, Vriend G. Optimizing the hydrogen-bond network in poisson-boltzmann equation-based pKa calculations. Proteins: Struct Funct Genetics 2001;43:403-412.
7. Georgescu RE, Alexov EG, Gunner MR. Combining conformational flexibility and continuum electrostatics for calculation pKas in proteins. Biophys J 2002;83:1731-1748.
8. Luo R, Head MS, Moult J, Gilson MK. pKa shifts in small molecules and HIV protease: electrostatics and conformation. J Am Chem Soc 1998;120:6138-6146.
9. Kuhn B, Kollman PA, Stahl M. Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations. J Comput Chem 2004;25:1865-1872.
10. Warwicker J. Improved pKa calculations through flexibility based sampling of a water-dominated interaction scheme. Protein Sci 2004;13:2793-2805.
11. Mehler EL, Guarnieri F. A self-consistent, microenvironment modulated screened coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins. Biophys J 1999;75: 3-22.
12. Warshel A, Sussman F, King G. Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process. Biochemistry 1986;25:8368-8372.
13. a calculations with explicit and implicit solvent models. J Am Chem Soc 2004;126:4167-4180.
14. Lee FS, Chu ZT, Warshel A. Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs. J Comput Chem 1992;14:161-185.
15. Sham YY, Chu ZT, Warshel A. Consistent calculations of pKa's of ionizable residues in proteins: semi-microscopic and microscopic approaches. J Phys Chem B 1997;101:4458-4472.
16. Baptista AM, Teixeira VH, Soares CM. Constant-pH molecular dynamics using stochastic titration. J Chem Phys 2002;117:4184-4200.
17. Li H, Robertson AD, Jensen JH. Very fast empirical prediction and rationalization of protein pKa values. Proteins: Struct Funct Bioinformat 2005;61:704-721.
18. Warshel A, Aqvist J, Creighton S. Enzymes work by solvation substitution rather than by desolvation. Proc Natl Acad Sci USA 1989; 86:5820-5824.
19. Warshel A, Sharma PK, Kato M, Parson WW. Modeling electrostatic effects in proteins. Biochimica et Biophysica Acta 2006;1764:1647-1676.
20. Schutz CN, Warshel A. What are the dielectric "constants" of proteins and how to validate electrostatic models? Proteins: Struct Funct Genetics 2001;44:400-417.
21. Langen R, Brayer GD, Berghuis AM, McLendon G, Sherman F, Warshel A. Effect of the Asn52->Ile mutation on the redox potential of yeast cytochrome c. J Mol Biol 1992;224:589-600.
22. Lee MS, Freddie R Salsbury J, Charles L Brooks I. Constant-pH molecular dynamics using continuous titration coordinates. Proteins: Struct Funct Bioinformat 2004;56:738-752.
23. Im W, Lee MS, C L Brooks I. Generalized born model with a simple smoothing function. J Comput Chem 2003;24:1691-1702.
24. Ullmann GM, Knapp EW. Electrostatic models for computing protonation and redox equilibria in proteins. Eur Biophys J 1999;28: 533-551.
25. Rabenstein B, Knapp EW. Calculated pH-dependent population and protonation of carbon-monoxy-myoglobin conformers. Biophys J 2001;80:1141-1150.
26. Rabenstein B, Ullmann GM, Knapp EW. Calculation of protonation patterns in proteins with structural relaxation and molecular ensembles - application to the photosynthetic reaction center. Eur Biophys J 1998;27:626-637.
27. Bernard R. Brooks REB, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983;4: 187-217.
28. MacKerell A,Jr, Bashford D, Bellott M, Dunbrack R, Jr, Evanseck J, Field M, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau F, Mattos C, Michnick S, Ngo T, Nguyen D, Prodhom B, Reiher W, III, Roux B, Schlenkrich M, Smith J, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins (Charmm22 force field). J Phys Chem B 1998;102:3586-3616.
29. Baker NA, Sept D, Joseph S, Hoist MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA 2001;98:10037-10041.
30. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000;28:235-242.
31. Curtis DE, Dolinsky T, Baker N. The PROPKA web interface. 2006.
32. Forsyth WR, Gilson MK, Antosiewicz J, Jaren OR, Robertson AD. Theoretical and experimental analysis of ionization equilibria in ovomucoid third domain. Biochemistry 1998;37:8643-8652.
33. Mauguen Y, Hartley RW, Dodson EJ, Dodsen GG, Bricogne G, Chothia C, Jack A. Molecular structure of a new family of ribonucleases. Nature 1982;297:162-164.
34. Dunback RL, Jr, Cohen FE. Baysian statistical analysis of protein side-chain rotamer preferences. Protein Sci 1997;6:1661-1681.
35. Bartik K, Redfield C, Dobson CM. Measurement of the individual pKa values of acidic residues of hen and turkey lysozymes by two-dimensional 1H NMR. Biophys J 1994;66:1180-1184.
36. Kuramitsu S, Hamaguchi K. Analysis of the acid-base titration curve of hen lysozyme. J Biochem 1980;87:1215-1219.
37. White A, Rose DR. Mechanism of catalysis by retaining β-glycosyl hydrolases. Curr Opin Struct Biol 1997;7:645-651.
38. Joshi MD, Hedberg A, McIntosh LP. Complete measurement of the pKa values of the carboxyl and imidazole groups in Bacillus circulans xylanase. Protein Sci 1997;6:2667-2670.
39. 13C-NMR study of Bacillus circulans xylanase. Biochemistry 1996; 35:9958-9966.
40. Berisio R, Lamzin VS, Sica F, Wilson KS, Zagari A, Mazzarella L. Protein titration in the crystal state. J Mol Biol 1999;292:845-854.
41. Berisio R, Sica F, Lamzin VS, Wilson KS, Zagari A, Mazzarella L. Atomic resolution structures of ribonuclease A at six pH values. Acta Crystallogr 2002;D58:441-450.
42. Howlin B, Moss DS, Harris GW. Segmented anisotropic refinement of bovine ribonuclease A by the application of the rigid-body TLS model. Acta Crystallogr 1989;A45:851-861.
43. Wlodawer A, Svensson LA, Sjolin L, Gilliland GL. Structure of phosphate-free ribonuclease A refined at 1.26 A. Biochemistry 1988; 27:2705-2717.
44. Mel VSJd, Doscher MS, Martin PD, Edwards BFP. The occupancy of two distinct conformations by active-site histidine-119 in crystals of ribonuclease is modulated by pH. FEBS 1994;349:155-160.
45. Yang W, Hendrickson WA, Crouch RJ, Satow Y. Structure of ribonuclease H phased at 2 A resolution by MAD analysis of the selenomethionyl protein. Science 1990;249:1398-1405.
46. Katayanagi K, Miyagawa M, Matsushima M, Ishikawa M, Kanaya S, Nakamura H, Ikehara M, Matsuzaki T, Morikawa K. Structural details of ribonuclease H from Escherichia coli as refined to an atomic resolution. J Mol Biol 1992;223:1029-1052.
47. Katayanagi K, Okumura M, Morikawa K. Crystal structure of Escherichia coli RNase HI in complex with Mg2+ at 2.8 A resolution: proof for a single Mg(2+)-binding site. Proteins: Struct Funct Genetics 1993;17:337-346.
48. Oda Y, Yamazaki T, Nagayama K, Kanaya S, Kuroda Y, Nakamura H. Individual ionization constants of all the carboxyl groups in ribonuclease HI from Escherichia coli determined by NMR. Biochemistry 1994;33:5275-5284.
49. Oliveberg M, Arcus VL, Fersht AR. 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;34:9424-9433.
50. Meadows DH, Roberts GCK, Jardetzky O. Nuclear magnetic resonance studies of the structure and binding sites of enzymes. VIII. Inhibitor binding to ribonuclease. J Mol Biol 1969;45:491-511.
51. Markley JL. Correlation proton magnetic resonance studies at 250 MHz of bovine pancreatic ribonuclease. I. reinvestigation of the histidine peak assignments. Biochemistry 1975;14:3546-3553.
52. Walters DE, Allerhand A. Tautomeric states of the histidine residues of bovine pancreatic ribonuclease A. Application of carbon 13 nuclear magnetic resonance spectroscopy. J Biol Chem 1980;255:6200-6204.
53. Markley JL. Correlation proton magnetic resonance studies at 250 MHz of bovine pancreatic ribonuclease. II. pH and inhibitor-induced conformational transitions affecting histidine-48 and one tyrosine residue of ribonuclease A. Biochemistry 1975;14:3554-3561.
54. Humphrey W, Dalke A, Schulten K. VMD - visual molecular dynamics. J Mol Graph Model 1996;14:33-38.