Analysis of Enzyme Reaction Kinetics, 2 Volume Set

F. Xavier Malcata, PhD, is Full Professor at the Department of Chemical Engineering at the University of Porto in Portugal, and Researcher at LEPABE – Laboratory for Process Engineering, Environment, Biotechnology and Energy. He is the author of more than 400 highly cited journal papers, eleven books, four edited books, and fifty chapters in edited books. He has been awarded the Elmer Marth Educator Award by the International Association of Food Protection (USA) and the William V. Cruess Award for excellence in teaching by the Institute of Food Technologists (USA).

• About the AuthorSeries PrefacePrefaceVolume One7. Mathematical Approach to Rate Expressions 2 7.1. Introduction 37.1.1. Basic concepts 37.1.2. Chemical mechanism and rate expression 47.1.3. Historical perspective 77.1.4. Further refinements 107.1.5. Multisubstrate approaches 127.1.6. Objective 157.1.7. Strategy 167.2. Rate expression 177.2.1. Kinetic features 177.2.2. Order of reaction 317.3. Michaelis & Menten’s rate expression with single enzyme 367.3.1. Michaelis & Menten’s rationale 377.3.2. Graphical interpretation 417.3.3. Semilogarithmic plot 477.3.4. Eisenthal, Cornish & Bowden’s plot 507.3.5. Dixon’s plot 547.3.6. Concentration of enzyme forms 577.3.7. Best reparameterization 607.3.8. van Slyke & Cullen’s rationale 627.3.9. Briggs & Haldane’s rationale 647.3.10. Absolute sensitivity to lumped parameters 707.3.11. Relative error of alternative derivations 747.3.12. Relative sensitivity to intrinsic parameters 777.3.13. Biochemical rationale 827.3.14. Derivatives of rate expression 927.4. Michaelis & Menten’s rate expression with multiple enzymes 947.4.1. Several isozymes 957.4.2. Two isozymes 1007.4.3. Infinite isozymes 1177.5. Michaelis & Menten’s rate expression with autocatalysis 947.6. Michaelis & Menten’s rate expression with multiphasic systems 1377.7. Improved rate expression with single enzyme 1517.7.1. Morrison’s rationale 1527.7.2. Graphical interpretation 1557.7.3. Low enzyme concentration 1687.7.4. Best reparameterization 1727.7.5. Kim’s rationale 1757.7.6. Graphical interpretation 1807.7.7. Specific kinetic features 2007.7.8. Absolute sensitivity to intrinsic parameters 2247.7.9. Improved simulation of initial transients 2287.7.9.1. Batch stirred system 2307.7.9.2. Flow stirred system 2507.7.10. Improved simulation of final transients 2857.8. Alternative forms of Michaelis & Menten’s rate expression 3147.8.1. Integrated form 3157.8.1.1. Lambert’s function 3197.8.1.2. Taylor’s expansion 3247.8.2. Linearized form 3377.8.2.1. Differential expression 3397.8.2.2. Integrated expression 3507.9. Rate expressions for multisubstrate reactions 3617.9.1. Shortcut approaches to pseudo steady state 3627.9.1.1. King & Altman’s method 3627.9.1.2. Cleland’s nomenclature 3857.9.1.3. Supplementary simplifications 3967.9.2. Uni Uni mechanism 4107.9.2.1. Pseudo steady state 4117.9.2.1.1. Classical approach 4117.9.2.1.2. King & Altman’s approach 4197.9.2.2. Rapid equilibrium 4277.9.2.2.1. Classical approach 4277.9.2.2.2. King & Altman’s approach with Cha’s aproximation 4317.9.3. Ordered Bi Uni mechanism 4397.9.3.1. Pseudo steady state 4417.9.3.2. Rapid equilibrium 4527.9.4. Other Uni/Bi and Bi/Bi mechanisms 4627.9.5. Simplification of multisubstrate rate expressions 4767.9.5.1. Uni Uni mechanism 4837.9.5.2. Ordered Bi Uni mechanism 4907.10. Further reading 4978. Statistical Approach to Rate Expressions 18.1. Introduction 28.1.1. Basic concepts 28.1.2. Objective 278.1.3. Strategy 288.2. Assessment of data and models 298.2.1. Independence checks 308.2.2. Normality checks 338.2.3. Homoskedasticity checks 378.2.4. Linearity checks 418.2.5. Relationship checks 458.2.6. Adequacy checks 488.2.7. Sufficiency checks 548.3. Fitting of models to data 578.3.1. Linear regression analysis 608.3.1.1. Unipredictor/uniresponse 628.3.1.2. Multipredictor/uniresponse 968.3.1.3. Multipredictor/multiresponse 1148.3.2. Improved regression analysis 1308.3.2.1. Data transformation 1318.3.2.2. Statistical tools 1468.3.2.2.1. Weighed least squares 1478.3.2.2.2. Nonparametric techniques 1548.3.3. Nonlinear regression analysis 1558.3.3.1. General form 1558.3.3.2. Enzymatic reaction 1578.3.3.2.1. Estimation 1578.3.3.2.2. Stationarity 1688.3.3.2.3. Inference 1868.4. Generation of data 2018.4.1. Empirical designs 2028.4.2. Mechanistic designs 2148.4.2.1. Starting designs 2148.4.2.2. Sequential designs 2208.4.2.3. Subset designs 2228.4.2.4. Conditional linearity 2268.4.2.5. Enzymatic reaction 2298.4.2.6. Enzymatic reaction with enzyme decay 2348.5. Further reading 246Volume 29. Physical Modulation of Reaction Rate 1 9.1. Introduction 29.1.1. Basic concepts 29.1.2. Thermodynamic approach 59.1.3. Kinetic approach 299.1.4. Physical deactivation of enzymes 389.1.5. Objective 339.1.6. Strategy 449.2. Unimodal deactivation 459.2.1. Simple reversible deactivation 469.2.2. Simple irreversible deactivation 539.2.3. General deactivation 599.2.3.1. Series reversible deactivation 659.2.3.2. Series irreversible deactivation 779.2.3.2.1. Stirred batch reactor 799.2.3.2.2. Stirred flow reactor 1099.2.3.2.3. Model discrimination 1209.2.3.2.4. Infinite isozymes 1429.2.3.3. Series reversible and parallel irreversible deactivation 1519.2.3.4. Series irreversible and parallel reversible deactivation 1729.3. Bimodal deactivation 2089.3.1. Simple reversible deactivation 2099.3.2. Simple irreversible deactivation 2229.4. Effects upon nonelementary reactions 2429.5. Temperature-driven modulation 2459.5.1. Thermodynamic formulation of temperature-dependence of elementary steps 2489.5.1.1. Reversible reaction 2489.5.1.2. Reversible deactivation 2529.5.2. Kinetic formulation of temperature-dependence of elementary steps 2589.5.2.1. Collision theory 2589.5.2.2. Transition state theory 2939.5.3. Improvement of parameter fitting 3009.6. Mechanical force-driven modulation 3079.6.1. Normal elastic forces 3109.6.1.1. Effect of pressure 3119.6.1.2. Combined effect of pressure and temperature 3169.6.2. Tangential elastic forces 3369.6.2.1. Gibbs’ adsorption isotherm 3389.6.2.2. Langmuir’s adsorption isotherm 3469.6.3. Tangential plastic forces 3639.6.3.1. Effect of shear 3649.7. Response of enzyme deactivation 3839.8. Response of enzyme reaction 3899.9. Further reading 39310. Chemical Modulation of Reaction Rate 1 10.1. Introduction 210.1.1. Basic concepts 210.1.2. Thermodynamic approach 410.1.3. Kinetic approach 2910.1.4. Chemical deactivation 4410.1.4.1. Denaturation 4510.1.4.2. Condensation 5210.1.4.3. Stabilization 5610.1.4.4. Inhibition 6810.1.4.4.1. Reversible inhibitors 7110.1.4.4.2. Irreversible inhibitors 7810.1.5. Chemical modulation 8210.1.5.1. Effects of pH 8310.1.5.2. Self-control 9410.1.6. Objective 9610.1.7. Strategy 9710.2. pH-driven modulation 9910.2.1. Protolysis of enzyme only 10010.2.2. Protolysis of enzyme and substrate 12710.3. Ionic strength-driven modulation 14710.4. pH-driven deactivation 17510.4.1. Reversible decay 17610.4.2. Irreversible decay 18410.5. Self-deactivation 19710.6. Microbial deactivation 20610.7. Heterologous bimodal deactivation 21710.7.1. Reversible deactivation 21810.7.1.1. Mixed inhibition 21810.7.1.1.1. Michaelis & Menten’s plot 22210.7.1.1.2. Lineweaver & Burk’s plot 23010.7.1.1.3. Hanes & Woolf’s plot 23710.7.1.1.4. Woolf, Augustinsson & Hofstee’s plot 24510.7.1.1.5. Eadie & Scatchard’s plot 25410.7.1.1.6. Dixon’s plot 26310.7.1.1.7. Cornish-Bowden’s plot 26910.7.1.1.8. Hunter & Downs’ plot 27510.7.1.2. General mixed inhibition 28010.7.1.3. Competitive inhibition 31110.7.1.4. Uncompetitive inhibition 32610.7.2. Irreversible deactivation 35010.8. Heterologous unimodal deactivation 36310.8.1. Reversible deactivation 36410.8.1.1. Noncompetitive inhibition 36410.8.2. Irreversible deactivation 38210.9. Mechanism discrimination 38910.9.1. Sequential random Bi Bi 39210.9.2. Sequential ordered Bi Bi 40010.9.3. Ping pong Bi Bi 40510.9.4. Graphical comparison 41410.10. Homologous modulation 42310.10.1. Independent sites 43410.10.1.1. Two-sited enzyme 43410.10.1.2. N-sited enzyme 43710.10.2. Sequential transition 44110.10.2.1. Equivalent sites 44210.10.2.1.1. Three-sited enzyme 44210.10.2.1.2. N-sited enzyme 45410.10.2.2. Nonequivalent sites 47110.10.2.2.1. Three-sited enzyme 47110.10.2.2.2. N-sited enzyme 48310.10.3. Concerted transition 51610.10.3.1. Equivalent sites 51710.10.3.1.1. Two-sited enzyme 51710.10.3.1.2. N-sited enzyme 54110.10.3.2. Hybrid behaviors 56310.10.4. Asymptotic patterns 57110.11. Further reading 597INDEX

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