A pK determination method for proteins from titration curves using principle component analysis

AIChE Journal

Volumn 54, Issue 9, 2008, Pages 2238-2249

  Shim, Jaesool ^a   Dutta, Prashanta ^a   Ivory, Cornelius F ^a  

^a Washington State University   (United States)

Author keywords

IEF; pK extraction; Principal component analysis; Proteins; Titration curves

Indexed keywords

AMPHOLYTES; AMPHOTERIC MOLECULES; DOMAIN METHODS; EARLY STAGES; EFFECTIVE CHARGES; FOCUSING TIME; GLUTAMIC ACID; HEN EGG-WHITE LYSOZYME; IEF; ISOELECTRIC FOCUSING; MICRO CHANNELS; NEW ALGORITHM; PARTIAL-DOMAIN METHOD; PCA METHOD; PK EXTRACTION; PK VALUES; PRINCIPAL COMPONENT ANALYSIS (PCA); PRINCIPLE COMPONENT ANALYSIS; REGRESSION MODELLING; SAMPLING ERRORS; TITRATION CURVES;

ACIDS; AMINES; AMINO ACIDS; ELECTROLYTES; ELECTROPHORESIS; ENZYMES; ERRORS; FINANCIAL DATA PROCESSING; FOOD PROCESSING; ORGANIC ACIDS; PRINCIPAL COMPONENT ANALYSIS; PROTEINS; REGRESSION ANALYSIS; TITRATION; TWO DIMENSIONAL; VOLUMETRIC ANALYSIS;

ERROR ANALYSIS;

EID: 52649130372     PISSN: 00011541     EISSN: 15475905     Source Type: Journal    
DOI: 10.1002/aic.11528     Document Type: Article

References (28)

1. Kaufman JJ, Semo NM, Koski WS. Micmelecirometric titration measurement of the p/Ca's and partition and drug distribution coefticients of narcotics and narcotic antagonists and their pH and temperature dependence. J Med Chem. 1975;18:647-655.
2. Kuramitsu S, Hamaguchi K Analysis of the acid-base titration curve of hen lysozyme. J Biochem. 1980;87:1215-1219.
3. Peacocke A. Historical article: Titration studies and the structure of DNA. TRENDS Biochem Sci. 2005:30:160-162.
4. Lucas LH, Ersoy BA, Kueltzo LA, Joshi SB, Brandau DT, Thyagarajapuram N, Peek LJ, Middaugh CR. Probing protein structure and dynamics by second-derivative ultraviolet absorption analysis of cation-pi interactions. Prot Sci. 2006;15:2228-2243.
5. van Vlijmen HW, Schaefer M. Karplus M. Improving the accuracy of protein pK(a) calculations: Conformational averaging versus the average structure, Prot: Struct Funct Genet. 1998;32:145-158.
6. Szakacs Z, Hagele G. Accurate determination of low pK values by H-1 NMR titration. Talanta. 2004;62:819-825.
7. Tynan-Connolly BM, Nielsen JL. pKD: re-designing protein pK(a) values. Nucleic Acids Res. 2006;34:48-51.
8. Shim J, Dutta P, Ivory CF. Modeling and simulation of IEF in 2-D microgeometries. Electrophoresis. 2007;28:572-586.
9. Neto AA, Filho ED, Fossey MA, Neto JR. pK determination. A mean field, Poisson-Boltzmann approach. Phys Chem B. 1999;103:6809-6814.
10. Kahyaoglu A, Jordan, F. Direct proton magnetic resonance determination of the pKa of the active center histidine in thiolsubtilisin. Prat Sci. 2002; 1:965-973.
11. Li H, Robertson AD, Jensen JH, Very fast empirical prediction and rationalization of protein pK(a) values. Prots: Struct Funct Bioinform. 2005;61:704-721.
12. Ivanov I, Chen B, Raugei S, Klein ML. Relative pK(a) values from first-principles molecular dynamics: The case of histidine deprotonation. J Phys Chem B. 2006; 110:6365-6371.
13. Doltsinis NL, Sprik M. Theoretical pK(a) estimates for solvated P(OH)(5) from coordination constrained Car-Parrinello molecular dynamics. Phys Chem Chem Phys. 2003;5:2612-2618.
14. Salwa KP, Sneha P, Karen D, Heather W. Colin FP. Determination of acid dissociation constants by capillary electrophoresis. J Chromatogr A. 2004;1037:445-454.
15. Valentini L, Gianazza E, Righetti PG. pK determinatinations via pH-mobility curves obtained by isoelectric focusing electrophoresis. J Biochem Biophys. 1980;6:323-338.
16. Meloun M, Syrovy T, Bordovska S, Vrana A. Reliability and uncertainty in the estimation of pK (a) by least squares nonlinear regression analysis of multiwavelength spectrophotometric pH titration data. Anal Bioanal Chem. 2007;387:941-955.
17. Mosher RA, Dewey D, Thormann W, Saville DA, Bier M. Computer simulation and experimental validation of the electrophoretic behavior of proteins. Anal Chem. 1989;61:362-366.
18. Mosher RA, Gebauer P, Caslavska J, Thormann, W. Computer simulation and experimental validation of the electrophoretic behavior of proteins. Anal Chem. 1992;64:2991-2997.
19. Thormann W. Huang TM, Pawliszyn J, Mosher RA. High-resolution computer simulation of the dynamics of isoelectric focusing of proteins, Electrophoresis 2004:25:324-337.
20. Shim J, Dutta P, Ivory CF. Effects of ampholyte dissociation constants on protein separation in on-chip isoelectric focusing. J Nanosci Nanotechnol. 2008:8:3719-3728.
21. Powell RE, Seering W. Multichannel structural inverse filtering. ASME J Vihr Acoust Stress Reliab Des. 1984;106:22-28.
22. Ahn B, Shim J. Force prediction by indirect force measurement and pseudo inverse Technique. Kor Soc Prec Eng. 2002;19:43-50.
23. Pearson K. On lines and planes of closest fit to systems of points in space. Philosoph Mag. 1901;6(2):559-572.
24. Cui H, Horiuchi K, Dutta P, Ivory CF. Isoelectric focusing in a poly (dimethylsiloxane) microfluidic chip. Anal Chem. 2005;77:1303-1309.
25. Cui H, Horiuchi K, Dutta P, Ivory CF. Multistage isoelectric focusing in a polymeric microfluidic chip. Anal Chem. 2005;77:7878-7886.
26. Mosher RA, Saville DA, Thormann W. The Dynamics of Electrophoresis. VCH: Weinheim; 1992.
27. Mosher RA, Gebauer P, Thormann W. Computer-simulation and experimental validation of the electrophoretic behavior of proteins. J Chromatogr. 1993;638:155-164.
28. Shim J, Dutta P, Ivory CF. Finite volume methods for isotachophoretic separation in microchannels: part A. Num Heat Trans. 2007;52:441-461.