Parameter Estimation in Different Enzyme Reactions
Affiliation(s)
Department of ECE, School of Engineering, Penn State Erie, Erie, USA. Department of ECE, College of Engineering, Drexel University, Philadelphia, USA. Biology Department, Gannon University, Erie, USA.
Department of ECE, School of Engineering, Penn State Erie, Erie, USA. Department of ECE, College of Engineering, Drexel University, Philadelphia, USA. Biology Department, Gannon University, Erie, USA.
ABSTRACT
Enzyme kinetic parameters have been estimated using MATLAB software via the Wilkinson non-linear regression technique. The MATLAB script file written to implement this technique is short and very straightforward. Several software tools are commercially available for this purpose, with many graphical user interface (GUI) features. A routine use of these packages might offer immediate satisfaction of interactive hands-on experience; but in some cases the researcher might wish to write his/her own code and compare the results for further confirmation. Today MATLAB is in use in almost all the schools and laboratories as a standard software tool. So this paper is aimed at helping enzyme researchers to make use of this powerful software for estimation of parameters. It enables the incorporation of the analytical steps behind parameter estimation in an easy-to-follow manner and furnishes better visualization.
Enzyme kinetic parameters have been estimated using MATLAB software via the Wilkinson non-linear regression technique. The MATLAB script file written to implement this technique is short and very straightforward. Several software tools are commercially available for this purpose, with many graphical user interface (GUI) features. A routine use of these packages might offer immediate satisfaction of interactive hands-on experience; but in some cases the researcher might wish to write his/her own code and compare the results for further confirmation. Today MATLAB is in use in almost all the schools and laboratories as a standard software tool. So this paper is aimed at helping enzyme researchers to make use of this powerful software for estimation of parameters. It enables the incorporation of the analytical steps behind parameter estimation in an easy-to-follow manner and furnishes better visualization.
KEYWORDS
Michaelis-Menten Equation; Dixon Plot; Hill Equation; Wilkinson Nonlinear Regression; MATLAB
Michaelis-Menten Equation; Dixon Plot; Hill Equation; Wilkinson Nonlinear Regression; MATLAB
Cite this paper
Nelatury, S. , Nelatury, C. and Vagula, M. (2014) Parameter Estimation in Different Enzyme Reactions. Advances in Enzyme Research, 2, 14-26. doi: 10.4236/aer.2014.21002.
Nelatury, S. , Nelatury, C. and Vagula, M. (2014) Parameter Estimation in Different Enzyme Reactions. Advances in Enzyme Research, 2, 14-26. doi: 10.4236/aer.2014.21002.
References
[1] Cornish-Bowden, A. (2004) Fundamentals of Enzyme Kinetics. 3rd Edition, Portland Press Limited, London. [2] Engel, P. C. (1977) Enzyme Kinetics—The Steady State Approach. Chapman and Hill Limited, London. [3] Dixon, M. and Webb, E.C. (1964) Enzymes. 2nd Edition, Academic Press, New York. [4] Keener, J. and Snyed, J. (2004) Mathematical Physiology. Springer, New York. [5] Lineweaver, H. and Burk, D. (1934) The Determination of Enzyme Dissociation Constants. Journal of American Chemical Society, 56, 658. http://dx.doi.org/10.1021/ja01318a036 [6] Dixon, M. (1953) The Determination of Enzyme Inhibitor Constants. Biochemical Journal, 55, 170-171. [7] Fukushima, Y., Ushimaru, M. and Takahara, S. (2002) On the Error of the Dixon Plot for Estimating the Inhibition Constant between Enzyme and Inhibitor. Biochemistry and Molecular Biology Education, 30, 90-92. http://dx.doi.org/10.1002/bmb.2002.494030020022 [8] Wilkinson, G.N. (1961) Statistical Estimation of Enzyme Kinetics. Biochemical Journal, 80, 324-332. [9] Atkins, G.L. (1973) A Simple Digital Computer Program for Estimating the Parameters of the Hill Equation. European Journal of Biochemistry, 33, 175-180. http://dx.doi.org/10.1111/j.1432-1033.1973.tb02667.x [10] Williams, P.A. (1983) ENZPACK: A microcomputer program to aid in the teaching of enzyme kinetics. Biochemical Education, 11, 141-143. http://dx.doi.org/10.1016/0307-4412(83)90096-1 [11] Leatherbarrow, R.J. (1988) Enzfitter: A Non-Linear Regression Data Analysis Program for IBM PC. Journal of American Chemical Society, 110, 4100. [12] Hernandez, A. and Ruiz, M.T. (1998) An EXCEL Template for Calculation of Enzyme Kinetic Parameters by Non-Linear Regression. Bioinformatics (Applications Note), 14, 227-228.
http://dx.doi.org/10.1093/bioinformatics/14.2.227 [13] Heinrich, R., Melendez-Hevia, E. and Cabezas, H. (2002) Optimization of Kinetic Parameters of Enzymes. Biochemistry and Molecular Biology Education, 30, 184-188.
http://dx.doi.org/10.1002/bmb.2002.494030030065 [14] Miller, J.R. (2003) GraphPad Prism version 4.0 Step-by-step Examples. GraphPad Software Inc., San Diego, 111-119. [15] Gonzalez-Cruz, J., Rodreguez-Sotres, R. and Rodriguez-Penagos, M. (2003) On the Convenience of Using a Computer Simulation to Teach Enzyme Kinetics to Undergraduate Students with Biological Chemistry-Related Curricula. Biochemistry and Molecular Biology Education, 31, 93-101.
http://dx.doi.org/10.1002/bmb.2003.494031020193 [16] Clark, A.G. (2004) Lucenz Simulator—A Tool for the Teaching of Enzyme Kinetics. Biochemistry and Molecular Biology Education, 32, 201-206. http://dx.doi.org/10.1002/bmb.2004.494032030350 [17] Leone, F.A., Baranauskas, J.A., and Furriel, R.P.M. (2005) SigrafW: An Easy to Use Program for Fitting Enzyme Kinetic Data. Biochemistry and Molecular Biology Education, 33, 399-403.
http://dx.doi.org/10.1002/bmb.2005.49403306399 [18] Palm III, W.J. (2008) A Concise Introduction to MATLAB. 1st Edition. McGraw Hill, New York. [19] Daku, B. (2005) MATLAB Tutorial CD: Learning MATLAB Superfast. Wiley, New York. [20] Pratap, R. (2005) Getting Started with MATLAB 7—A Quick Introduction for Scientists and Engineers. Oxford University Press, Oxford. [21] Davis, T.A. and Sigmon K. (2004) MATLAB Primer. CRC Press. http://dx.doi.org/10.1201/9781420034950 [22] Cobelli, C. and Carson, E. (2008) Introduction to Modeling in Physiology and Medicine. Academic Press, Waltham, 212-220. [23] Moore, E.H. (1920) On the Reciprocal of the General Algebraic Matrix. (Abstract) Bulletin of American Mathematical Society, 26, 394-395. [24] Penrose, R.A. (1955) A Generalized Inverse for Matrices. Proceedings of Cambridge Philosophical Society, 51, 406- 413. http://dx.doi.org/10.1017/S0305004100030401
[1] Cornish-Bowden, A. (2004) Fundamentals of Enzyme Kinetics. 3rd Edition, Portland Press Limited, London. [2] Engel, P. C. (1977) Enzyme Kinetics—The Steady State Approach. Chapman and Hill Limited, London. [3] Dixon, M. and Webb, E.C. (1964) Enzymes. 2nd Edition, Academic Press, New York. [4] Keener, J. and Snyed, J. (2004) Mathematical Physiology. Springer, New York. [5] Lineweaver, H. and Burk, D. (1934) The Determination of Enzyme Dissociation Constants. Journal of American Chemical Society, 56, 658. http://dx.doi.org/10.1021/ja01318a036 [6] Dixon, M. (1953) The Determination of Enzyme Inhibitor Constants. Biochemical Journal, 55, 170-171. [7] Fukushima, Y., Ushimaru, M. and Takahara, S. (2002) On the Error of the Dixon Plot for Estimating the Inhibition Constant between Enzyme and Inhibitor. Biochemistry and Molecular Biology Education, 30, 90-92. http://dx.doi.org/10.1002/bmb.2002.494030020022 [8] Wilkinson, G.N. (1961) Statistical Estimation of Enzyme Kinetics. Biochemical Journal, 80, 324-332. [9] Atkins, G.L. (1973) A Simple Digital Computer Program for Estimating the Parameters of the Hill Equation. European Journal of Biochemistry, 33, 175-180. http://dx.doi.org/10.1111/j.1432-1033.1973.tb02667.x [10] Williams, P.A. (1983) ENZPACK: A microcomputer program to aid in the teaching of enzyme kinetics. Biochemical Education, 11, 141-143. http://dx.doi.org/10.1016/0307-4412(83)90096-1 [11] Leatherbarrow, R.J. (1988) Enzfitter: A Non-Linear Regression Data Analysis Program for IBM PC. Journal of American Chemical Society, 110, 4100. [12] Hernandez, A. and Ruiz, M.T. (1998) An EXCEL Template for Calculation of Enzyme Kinetic Parameters by Non-Linear Regression. Bioinformatics (Applications Note), 14, 227-228.
http://dx.doi.org/10.1093/bioinformatics/14.2.227 [13] Heinrich, R., Melendez-Hevia, E. and Cabezas, H. (2002) Optimization of Kinetic Parameters of Enzymes. Biochemistry and Molecular Biology Education, 30, 184-188.
http://dx.doi.org/10.1002/bmb.2002.494030030065 [14] Miller, J.R. (2003) GraphPad Prism version 4.0 Step-by-step Examples. GraphPad Software Inc., San Diego, 111-119. [15] Gonzalez-Cruz, J., Rodreguez-Sotres, R. and Rodriguez-Penagos, M. (2003) On the Convenience of Using a Computer Simulation to Teach Enzyme Kinetics to Undergraduate Students with Biological Chemistry-Related Curricula. Biochemistry and Molecular Biology Education, 31, 93-101.
http://dx.doi.org/10.1002/bmb.2003.494031020193 [16] Clark, A.G. (2004) Lucenz Simulator—A Tool for the Teaching of Enzyme Kinetics. Biochemistry and Molecular Biology Education, 32, 201-206. http://dx.doi.org/10.1002/bmb.2004.494032030350 [17] Leone, F.A., Baranauskas, J.A., and Furriel, R.P.M. (2005) SigrafW: An Easy to Use Program for Fitting Enzyme Kinetic Data. Biochemistry and Molecular Biology Education, 33, 399-403.
http://dx.doi.org/10.1002/bmb.2005.49403306399 [18] Palm III, W.J. (2008) A Concise Introduction to MATLAB. 1st Edition. McGraw Hill, New York. [19] Daku, B. (2005) MATLAB Tutorial CD: Learning MATLAB Superfast. Wiley, New York. [20] Pratap, R. (2005) Getting Started with MATLAB 7—A Quick Introduction for Scientists and Engineers. Oxford University Press, Oxford. [21] Davis, T.A. and Sigmon K. (2004) MATLAB Primer. CRC Press. http://dx.doi.org/10.1201/9781420034950 [22] Cobelli, C. and Carson, E. (2008) Introduction to Modeling in Physiology and Medicine. Academic Press, Waltham, 212-220. [23] Moore, E.H. (1920) On the Reciprocal of the General Algebraic Matrix. (Abstract) Bulletin of American Mathematical Society, 26, 394-395. [24] Penrose, R.A. (1955) A Generalized Inverse for Matrices. Proceedings of Cambridge Philosophical Society, 51, 406- 413. http://dx.doi.org/10.1017/S0305004100030401