COMPUTER SIMULATION OF ENZYMATIC REACTIONS

Summary

Principal Investigator: A Warshel
Affiliation: University of Southern California
Country: USA
Abstract: Gaining a quantitative description of enzyme action is one of the most important challenges of molecular biology. Thus, we propose a continuation of our research projects aimed at the development, refinement, and implementation of computational models for simulations of enzymatic reactions. During previous grant periods we have demonstrated the general applicability of our empirical valence bond (EVB) approach. In recent years we started to develop more rigorous ab initio approaches that exploit the increasing availability of computer power. Our new strategies include: (a) quantum mechanical (ab initio)/Langevin dipole (QM(ai)/LD) model which provide crucial information about potential surfaces of reactions in solution. This allows us to calibrate EVB surfaces for studies of enzymes; (b) an ab initio free energy perturbation (QM(ai)/FEP) which uses EVB surfaces as reference potentials and thus allows us to start evaluating ab initio free energies of enzymatic reactions; and (c) a constrain density functional theory (CDFT) approach, which allows us to represent large parts of the protein at the ab initio level. Although these approaches still require further validation, we are ready to use them in studies of enzymatic catalysis. In addition to the method development projects, we have made significant progress in studying different classes of enzymatic reactions and in exploring the feasibility of different catalytic mechanisms. In order to exploit our advanced we propose to advance in the following three directions: (a) we will conduct method development studies that will include: (i) improving our ab initio approaches for constructing reference solution reactions. In particular, we will focus on transition state search and evaluation of entropic corrections for solution reactions; (ii) using solution surfaces in automated refined of EVB surfaces; (iii) using the EVB surfaces as reference potentials in automated refinement of EVB surfaces; (iii) using the EVB surfaces as reference potentials for QM(ai)/FEP studies of enzymes; (iv) CDFT studies of metalloenzyme. (b) We will conduct systematic studies of several important classes of enzymatic reactions including: (i) serine and cysteine proteases; (ii) DNA polymerase; and (iii) ribonuclease. (c) We will conduct studies of the relative importance of different catalytic proposals, including (i) entropic effects; (ii) low barrier hydrogen bond; (iii) near attack conformers; and (iv) pre-organization of enzyme active sites.
Funding Period: 1978-01-01 - 2006-03-31
more information: NIH RePORT

Top Publications

  1. pmc Validating computer simulations of enantioselective catalysis; reproducing the large steric and entropic contributions in Candida Antarctica lipase B
    Patrick Schopf
    Department of Chemistry, University of Southern California, Los Angeles, California, 90089
    Proteins 82:1387-99. 2014
  2. doi Why nature really chose phosphate
    Shina C L Kamerlin
    Department of Cell and Molecular Biology ICM, Uppsala Biomedical Centre, Uppsala University, Box 596, S 751 24 Uppsala, Sweden
    Q Rev Biophys 46:1-132. 2013
  3. pmc Addressing open questions about phosphate hydrolysis pathways by careful free energy mapping
    B Ram Prasad
    Department of Chemistry, University of Southern California, SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, United States
    J Phys Chem B 117:153-63. 2013
  4. pmc Electrostatic origin of the catalytic effect of a supramolecular host catalyst
    Maria P Frushicheva
    Department of Chemistry, 418 SGM Building, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
    J Phys Chem B 116:13353-60. 2012
  5. pmc Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions
    Nidhi Singh
    Department of Chemistry, University of Southern California, Los Angeles, California 90089 1062, USA
    Proteins 78:1705-23. 2010
  6. pmc On catalytic preorganization in oxyanion holes: highlighting the problems with the gas-phase modeling of oxyanion holes and illustrating the need for complete enzyme models
    Shina C L Kamerlin
    Department of Chemistry SGM418, University of Southern California, 3620 McClintock Avenue, Los Angeles California 90089, USA
    J Org Chem 75:6391-401. 2010
  7. pmc Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase
    Maria P Frushicheva
    Department of Chemistry, 418 SGM Building, University of Southern California, 3620 McClintock Avenue, Los Angeles, CA 90089 1062, USA
    Proc Natl Acad Sci U S A 107:16869-74. 2010
  8. pmc Examining the case for the effect of barrier compression on tunneling, vibrationally enhanced catalysis, catalytic entropy and related issues
    Shina Caroline Lynn Kamerlin
    Department of Chemistry SGM418, University of Southern California, Los Angeles, CA 90089, USA
    FEBS Lett 584:2759-66. 2010
  9. pmc A comprehensive examination of the contributions to the binding entropy of protein-ligand complexes
    Nidhi Singh
    Department of Chemistry, University of Southern California, Los Angeles, California 90089 1062, USA
    Proteins 78:1724-35. 2010
  10. pmc Toward accurate microscopic calculation of solvation entropies: extending the restraint release approach to studies of solvation effects
    Nidhi Singh
    Department of Chemistry, 418 SGM Building, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
    J Phys Chem B 113:7372-82. 2009

Scientific Experts

  • A Warshel
  • Mats H M Olsson
  • Jan Florian
  • Shina C L Kamerlin
  • Maciej Haranczyk
  • Maite Roca
  • Maria P Frushicheva
  • Nidhi Singh
  • Hanbin Liu
  • B Ram Prasad
  • Edina Rosta
  • Jie Cao
  • Zhen T Chu
  • Nikolay V Plotnikov
  • Pankaz K Sharma
  • Spyridon Vicatos
  • Alexandra Vardi Kilshtain
  • Alexandra Vardi-Kilshtain
  • Benjamin Messer
  • Yun Xiang
  • Patrick Schopf
  • Andrew J Adamczyk
  • Anatoly Dryga
  • Benjamin M Messer
  • Andrei V Pisliakov
  • Janez Mavri
  • Gongyi Hong
  • Shayantani Mukherjee
  • Donald Hilvert
  • Marco Klahn
  • Mitsunori Kato

Detail Information

Publications51

  1. pmc Validating computer simulations of enantioselective catalysis; reproducing the large steric and entropic contributions in Candida Antarctica lipase B
    Patrick Schopf
    Department of Chemistry, University of Southern California, Los Angeles, California, 90089
    Proteins 82:1387-99. 2014
    ..This is particularly true in cases with large changes in steric effects where alternative approaches may have difficulties in capturing the interplay between steric clashes with the reacting substrate and protein flexibility...
  2. doi Why nature really chose phosphate
    Shina C L Kamerlin
    Department of Cell and Molecular Biology ICM, Uppsala Biomedical Centre, Uppsala University, Box 596, S 751 24 Uppsala, Sweden
    Q Rev Biophys 46:1-132. 2013
    ..This makes phosphate esters the ideal compounds to facilitate life as we know it...
  3. pmc Addressing open questions about phosphate hydrolysis pathways by careful free energy mapping
    B Ram Prasad
    Department of Chemistry, University of Southern California, SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, United States
    J Phys Chem B 117:153-63. 2013
    ....
  4. pmc Electrostatic origin of the catalytic effect of a supramolecular host catalyst
    Maria P Frushicheva
    Department of Chemistry, 418 SGM Building, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
    J Phys Chem B 116:13353-60. 2012
    ..Finally, our finding of the large stabilization of the bound H(3)O(+) points out the very low "local pH" inside the host system even when the solvent is kept at a high pH...
  5. pmc Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions
    Nidhi Singh
    Department of Chemistry, University of Southern California, Los Angeles, California 90089 1062, USA
    Proteins 78:1705-23. 2010
    ..Overall, the PDLD/S-LRA/beta appears to offer an appealing option for the final stages of massive screening approaches...
  6. pmc On catalytic preorganization in oxyanion holes: highlighting the problems with the gas-phase modeling of oxyanion holes and illustrating the need for complete enzyme models
    Shina C L Kamerlin
    Department of Chemistry SGM418, University of Southern California, 3620 McClintock Avenue, Los Angeles California 90089, USA
    J Org Chem 75:6391-401. 2010
    ..Simply calculating interaction energies with relatively fixed species cannot capture this crucial point, and considering it may help in advancing rational enzyme design...
  7. pmc Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase
    Maria P Frushicheva
    Department of Chemistry, 418 SGM Building, University of Southern California, 3620 McClintock Avenue, Los Angeles, CA 90089 1062, USA
    Proc Natl Acad Sci U S A 107:16869-74. 2010
    ....
  8. pmc Examining the case for the effect of barrier compression on tunneling, vibrationally enhanced catalysis, catalytic entropy and related issues
    Shina Caroline Lynn Kamerlin
    Department of Chemistry SGM418, University of Southern California, Los Angeles, CA 90089, USA
    FEBS Lett 584:2759-66. 2010
    ..Finally, the temperature dependence of the entropy change in hydride transfer reactions is shown to reflect simple electrostatic effects...
  9. pmc A comprehensive examination of the contributions to the binding entropy of protein-ligand complexes
    Nidhi Singh
    Department of Chemistry, University of Southern California, Los Angeles, California 90089 1062, USA
    Proteins 78:1724-35. 2010
    ..This study also helps in analyzing some problems with the widely used molecular mechanics/Poisson-Boltzmann surface area approach...
  10. pmc Toward accurate microscopic calculation of solvation entropies: extending the restraint release approach to studies of solvation effects
    Nidhi Singh
    Department of Chemistry, 418 SGM Building, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
    J Phys Chem B 113:7372-82. 2009
    ..This holds promise for extending the information theory modeling to proteins and protein-ligand complexes in aqueous solutions and consequently, facilitating computer-aided drug design...
  11. pmc At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?
    Shina C L Kamerlin
    Department of Chemistry, University of Southern California, Los Angeles, 90089, USA
    Proteins 78:1339-75. 2010
    ..Finally, it is pointed out that electrostatic preorganization actually accounts for the observed catalytic effects of enzymes, through the corresponding changes in the activation free energies...
  12. pmc Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models
    Benjamin M Messer
    Department of Chemistry, University of Southern California, Los Angeles, California 90089 1062, USA
    Proteins 78:1212-27. 2010
    ..Furthermore, the general potential of our approach in overcoming major challenges in studies of structure function correlation in proteins is discussed...
  13. pmc Renormalizing SMD: the renormalization approach and its use in long time simulations and accelerated PMF calculations of macromolecules
    Anatoly Dryga
    Department of Chemistry, University of Southern California, Los Angeles, California 90089 1062, USA
    J Phys Chem B 114:12720-8. 2010
    ..The renormalization approach, which is illustrated here in realistic calculations, is expected to provide a major help in studies of complex landscapes and in exploring long time dynamics of biomolecules...
  14. doi Coarse-grained (multiscale) simulations in studies of biophysical and chemical systems
    Shina C L Kamerlin
    Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
    Annu Rev Phys Chem 62:41-64. 2011
    ....
  15. pmc Challenges and advances in validating enzyme design proposals: the case of kemp eliminase catalysis
    Maria P Frushicheva
    Department of Chemistry, 418 SGM Building, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
    Biochemistry 50:3849-58. 2011
    ..We also point out the trade-off between the reliability and speed of the calculations and try to determine what it takes to realize reliable computer-aided screening...
  16. pmc Towards quantitative computer-aided studies of enzymatic enantioselectivity: the case of Candida antarctica lipase A
    Maria P Frushicheva
    Department of Chemistry, University of Southern California, Los Angeles, CA 90089 1062, USA
    Chembiochem 13:215-23. 2012
    ..We also explore faster strategies for identifying mutations that will help in augmenting directed-evolution experiments, but these approaches require further refinement...
  17. pmc Multiscale modeling of biological functions
    Shina Caroline Lynn Kamerlin
    Department of Organic Chemistry, Stockholm University, S 10691, Stockholm, Sweden
    Phys Chem Chem Phys 13:10401-11. 2011
    ..Finally, some potential future directions will be discussed...
  18. pmc Paradynamics: an effective and reliable model for ab initio QM/MM free-energy calculations and related tasks
    Nikolay V Plotnikov
    Department of Chemistry SGM418, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089, United States
    J Phys Chem B 115:7950-62. 2011
    ....
  19. pmc Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions
    Andrew J Adamczyk
    Department of Chemistry Seeley G Mudd 418, University of Southern California, 3620 McClintock Avenue, Los Angeles, CA 90089, USA
    Proc Natl Acad Sci U S A 108:14115-20. 2011
    ..However, this motion is never the reason for catalysis, but rather simply a reflection of the shape of the reaction potential surface...
  20. pmc Validating the vitality strategy for fighting drug resistance
    Nidhi Singh
    Department of Chemistry, University of Southern California, Los Angeles, California 90089 1062, USA
    Proteins 80:1110-22. 2012
    ..This ability should be very useful in guiding the design of drug molecules that will lead to the slowest resistance...
  21. pmc Prechemistry versus preorganization in DNA replication fidelity
    B Ram Prasad
    Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
    Proteins 79:2900-19. 2011
    ....
  22. doi Simulating electrostatic energies in proteins: perspectives and some recent studies of pKas, redox, and other crucial functional properties
    Arieh Warshel
    Department of Chemistry, University of Southern California, Los Angeles, California 90089 1062, USA
    Proteins 79:3469-84. 2011
    ..We also emphasize recent advances in coarse grained models with a physically based electrostatic treatment and provide some examples including further directions in treating voltage activated ion channels...
  23. ncbi Using the constrained DFT approach in generating diabatic surfaces and off diagonal empirical valence bond terms for modeling reactions in condensed phases
    Gongyi Hong
    Department of Chemistry, University of Southern California, 3620 S McClintock Ave, Los Angeles, 90089 1062, USA
    J Phys Chem B 110:19570-4. 2006
    ..It is found that, at least for the test case of S(N)()2 reactions, the off diagonal element does not change significantly upon moving from the gas phase to solutions and thus the EVB assumption is valid and extremely useful...
  24. pmc On the relationship between folding and chemical landscapes in enzyme catalysis
    Maite Roca
    Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA, 90089 1062, USA
    Proc Natl Acad Sci U S A 105:13877-82. 2008
    ..This work provides insight into the relationship between folding landscapes and catalysis. The computational approach used here may also provide a powerful strategy for modeling single-molecule experiments and designing enzymes...
  25. ncbi Effective approach for calculations of absolute stability of proteins using focused dielectric constants
    Spyridon Vicatos
    Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
    Proteins 77:670-84. 2009
    ..8 kcal/mole compared to the observed values, making our method very promising for estimating protein stability. It also provides valuable insight into the complex electrostatic phenomena taking place in folded proteins...
  26. pmc Enzyme millisecond conformational dynamics do not catalyze the chemical step
    Andrei V Pisliakov
    Department of Chemistry SGM 418, University of Southern California, 3620 McClintock Avenue, Los Angeles, CA 90089, USA
    Proc Natl Acad Sci U S A 106:17359-64. 2009
    ..Nevertheless, the precise nature of this coupling is a question of great importance...
  27. ncbi The catalytic effect of dihydrofolate reductase and its mutants is determined by reorganization energies
    Hanbin Liu
    Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
    Biochemistry 46:6011-25. 2007
    ..Thus, as far as catalysis is concerned, the change in the activation barrier is due to the change in the electrostatic preorganization energy...
  28. ncbi Electrostatic contributions to protein stability and folding energy
    Maite Roca
    Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089 1062, USA
    FEBS Lett 581:2065-71. 2007
    ..Although this description should be examined by further microscopic studies, the practical use of the current approach seems to offer a powerful tool for protein design and for studies of the energetics of protein folding...
  29. pmc Exploring pathways and barriers for coupled ET/PT in cytochrome c oxidase: a general framework for examining energetics and mechanistic alternatives
    Mats H M Olsson
    University of Southern California, 3620 McClintock Avenue, Department of Chemistry, SGM 418, Los Angeles, CA 90089 1062, USA
    Biochim Biophys Acta 1767:244-60. 2007
    ....
  30. ncbi Electrostatic contributions to binding of transition state analogues can be very different from the corresponding contributions to catalysis: phenolates binding to the oxyanion hole of ketosteroid isomerase
    Arieh Warshel
    Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
    Biochemistry 46:1466-76. 2007
    ..It seems to us that this work provides an excellent example of the need for computational studies in analyzing key experimental findings about enzyme catalysis...
  31. ncbi Modeling electrostatic effects in proteins
    Arieh Warshel
    University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089 1062, USA
    Biochim Biophys Acta 1764:1647-76. 2006
    ....
  32. ncbi Electrostatic basis for enzyme catalysis
    Arieh Warshel
    Department of Chemistry, University of Southern California, SGM Building 418, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
    Chem Rev 106:3210-35. 2006
  33. pmc Transition state theory can be used in studies of enzyme catalysis: lessons from simulations of tunnelling and dynamical effects in lipoxygenase and other systems
    Mats H M Olsson
    Department of Chemistry, University of Southern California, 3620 South McClintock Avenue, Los Angeles, CA 90089 1062, USA
    Philos Trans R Soc Lond B Biol Sci 361:1417-32. 2006
    ....
  34. ncbi Dynamical contributions to enzyme catalysis: critical tests of a popular hypothesis
    Mats H M Olsson
    Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
    Chem Rev 106:1737-56. 2006
  35. ncbi Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions
    Edina Rosta
    Department of Chemistry, University of Southern California, 3620 South McClintock Avenue, Los Angeles, California 90089 1062, USA
    J Phys Chem B 110:2934-41. 2006
    ..Our advance allows one to explore consistently various mechanistic and catalytic proposals while using ab initio (ai) QM/MM approaches...
  36. ncbi What are the roles of substrate-assisted catalysis and proximity effects in peptide bond formation by the ribosome?
    Pankaz K Sharma
    University of Southern California, SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
    Biochemistry 44:11307-14. 2005
    ..The nature of these effects and their relationship to catalytic factors in modern enzymes is analyzed and discussed...
  37. pmc A new paradigm for electrostatic catalysis of radical reactions in vitamin B12 enzymes
    Pankaz K Sharma
    Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089 1062, USA
    Proc Natl Acad Sci U S A 104:9661-6. 2007
    ..The trick used by B(12) enzymes may, in fact, be a very powerful new strategy in enzyme design...
  38. ncbi Origin of the temperature dependence of isotope effects in enzymatic reactions: the case of dihydrofolate reductase
    Hanbin Liu
    Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
    J Phys Chem B 111:7852-61. 2007
    ....
  39. pmc On unjustifiably misrepresenting the EVB approach while simultaneously adopting it
    Shina C L Kamerlin
    Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089, USA
    J Phys Chem B 113:10905-15. 2009
    ..which where presented as verification of the unreliability of the EVB model were in fact obtained by the use of incorrect parameters, without comparing to the correct surface obtained by our program...
  40. pmc On the origin of the catalytic power of carboxypeptidase A and other metalloenzymes
    Alexandra Vardi Kilshtain
    Department of Chemistry, University of Southern California, Los Angeles, California 90089 1062, USA
    Proteins 77:536-50. 2009
    ..This and earlier studies show that the catalytic effect of the metal is not some constant electrostatic effect, that can be assessed from gas phase studies, but a reflection of the dielectric effect of the specific environment...
  41. pmc The empirical valence bond as an effective strategy for computer-aided enzyme design
    Alexandra Vardi-Kilshtain
    Department of Chemistry, University of Southern California, Los Angeles, USA
    Biotechnol J 4:495-500. 2009
    ..The ability of the model to predict quantitatively the catalytic power of enzymes should augment the capacity of current approaches for enzyme design...
  42. pmc Toward accurate screening in computer-aided enzyme design
    Maite Roca
    Department of Chemistry, University of Southern California, Los Angeles, California 90089 1062, USA
    Biochemistry 48:3046-56. 2009
    ....
  43. pmc Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies
    Shina C L Kamerlin
    Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
    J Phys Chem B 113:1253-72. 2009
    ....
  44. pmc Solvation free energies of molecules. The most stable anionic tautomers of uracil
    Maciej Haranczyk
    Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089 1062, USA
    Phys Chem Chem Phys 10:4442-8. 2008
    ..We found that in water solution three of the recently identified anionic tautomers are 6.5-3.6 kcal mol(-1) more stable than the anion of the canonical tautomer...
  45. pmc Accelerating QM/MM free energy calculations: representing the surroundings by an updated mean charge distribution
    Edina Rosta
    Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
    J Phys Chem B 112:5680-92. 2008
    ..This approach should provide a very powerful tool for QM(ai)/MM evaluation of solvation free energies in aqueous solutions and proteins...
  46. doi Quantifying free energy profiles of proton transfer reactions in solution and proteins by using a diabatic FDFT mapping
    Yun Xiang
    Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
    J Phys Chem B 112:1007-15. 2008
    ..Our results point out that the present implementation of the FDFT approach provides a very promising approach for evaluating QM(ai)/MM free energy surfaces...
  47. ncbi Simulation of tunneling in enzyme catalysis by combining a biased propagation approach and the quantum classical path method: application to lipoxygenase
    Janez Mavri
    National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
    J Phys Chem B 112:5950-4. 2008
    ..In particular, this approach can be used to evaluate the quantum mechanical transmission factor or other dynamical effects, while still obtaining reliable quantized activation free energies due to the QCP correction...
  48. pmc On the relationship between thermal stability and catalytic power of enzymes
    Maite Roca
    Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, California 90089 1062, USA
    Biochemistry 46:15076-88. 2007
    ..Thus, the optimized catalysts are less stable. This trend is clearly observed in the DHFR case...
  49. pmc Computer simulations of protein functions: searching for the molecular origin of the replication fidelity of DNA polymerases
    Jan Florian
    Department of Chemistry, Loyola University, Chicago, IL 60626, USA
    Proc Natl Acad Sci U S A 102:6819-24. 2005
    ..The calculations demonstrate the potential for further integration of theoretical and experimental studies to analyze high- and low-fidelity DNA polymerases...