2-Keto acids to branched-chain alcohols as biofuels: Application of reaction network analysis and high-level quantum chemical methods to understand thermodynamic landscapes

Computational and Theoretical Chemistry

Volumn 978, Issue 1-3, 2011, Pages 160-165

  Assary, Rajeev S ^a,b   Broadbelt, Linda J ^a  

^a Northwestern University   (United States)

^b ARGONNE NATIONAL LABORATORY   (United States)

Author keywords

ABE fermentation; Ehrlich's pathways; G3B3; Reaction network; Thermochemistry

Indexed keywords

EID: 84555190995     PISSN: 2210271X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.comptc.2011.10.009     Document Type: Article

References (35)

1. Becker S.A., Feist A.M., Mo M.L., Hannum G., Palsson B.O., Herrgard M.J. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA toolbox. Nat. Protoc. 2007, 2:727-738.
2. Duarte N.C., Becker S.A., Jamshidi N., Thiele I., Mo M.L., Vo T.D., Srivas R., Palsson B.O. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc. Natl. Acad. Sci. USA 2007, 104:1777-1782.
3. Fazelinia H., Cirino P.C., Maranas C.D. Extending iterative protein redesign and optimization (IPRO) in protein library design for ligand specificity. Biophys. J. 2007, 92:2120-2130.
4. Thomas R., Paredes C.J., Mehrotra S., Hatzimanikatis V., Papoutsakis E.T. A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression data. BMC Bioinform. 2007, 8:228-236.
5. Lee J., Yun H., Feist A.M., Palsson B.O., Lee S.Y. Genome-scale reconstruction and in silico analysis of the clostridium acetobutylicum ATCC 824 metabolic network. Appl. Microbiol. Biotechnol. 2008, 80:849-862.
6. Senger R.S., Papoutsakis E.T. Genome-scale model for clostridium acetobutylicum: Part I. Metabolic network resolution and analysis. Biotechnol. Bioeng. 2008, 101:1036-1052.
7. Senger R.S., Papoutsakis E.T. Genome-scale model for clostridium acetobutylicum: Part II. Development of specific proton flux states and numerically determined sub-systems. Biotechnol. Bioeng. 2008, 101:1053-1071.
8. Fazelinia H., Cirino P.C., Maranas C.D. Optgraft: a computational procedure for transferring a binding site onto an existing protein scaffold. Protein Sci. 2009, 18:180-195.
9. Feist A.M., Herrgard M.J., Thiele I., Reed J.L., Palsson B.O. Reconstruction of biochemical networks in microorganisms. Nat. Rev. Microbiol. 2009, 7:129-143.
10. Lee S.C., Chang Y.J., Shin D.M., Han J., Seo M.H., Fazelinia H., Maranas C.D., Kim H.S. Designing the substrate specificity of D-hydantoinase using a rational approach. Enzyme Microb. Technol. 2009, 44:170-175.
11. Broadbelt L.J., Stark S.M., Klein M.T. Computer-generated pyrolysis modeling - on-the-fly generation of species, reactions, and rates. Ind. Eng. Chem. Res. 1994, 33:790-799.
12. Broadbelt L.J., Stark S.M., Klein M.T. Computer generated reaction modelling: decomposition and encoding algorithms for determining species uniqueness. Comput. Chem. Eng. 1996, 20:113-129.
13. Li C.H., Henry C.S., Jankowski M.D., Ionita J.A., Hatzimanikatis V., Broadbelt L.J. Computational discovery of biochemical routes to specialty chemicals. Chem. Eng. Sci. 2004, 59:5051-5060.
14. Gonzalez-Lergier J., Broadbelt L.J., Hatzimanikatis V. Theoretical considerations and computational analysis of the complexity in polyketide synthesis pathways. J. Am. Chem. Soc. 2005, 127:9930-9938.
15. Hatzimanikatis V., Li C.H., Ionita J.A., Henry C.S., Jankowski M.D., Broadbelt L.J. Exploring the diversity of complex metabolic networks. Bioinformatics 2005, 21:1603-1609.
16. Finley S.D., Broadbelt L.J., Hatzimanikatis V. Thermodynamic analysis of biodegradation pathways. Biotechnol. Bioeng. 2009, 103:532-541.
17. Henry C.S., Jankowski M.D., Broadbelt L.J., Hatzimanikatis V. Genome-scale thermodynamic analysis of escherichia coli metabolism. Biophys. J. 2006, 90:1453-1461.
18. Henry C.S., Broadbelt L.J., Hatzimanikatis V. Thermodynamics-based metabolic flux analysis. Biophys. J. 2007, 92:1792-1805.
19. Jankowski M.D., Henry C.S., Broadbelt L.J., Hatzimanikatis V. Group contribution method for thermodynamic analysis of complex metabolic networks. Biophys. J. 2008, 95:1487-1499.
20. Wu D., Wang Q., Assary R.S., Broadbelt L.J., Krilov G. A computational approach to design and evaluate enzymatic reaction pathways: application to 1-butanol production from pyruvate. J. Chem. Inf. Model. 2011, 51:1634-1647.
21. Ezeji T.C., Qureshi N., Blaschek H.P. Acetone butanol ethanol (ABE) production from concentrated substrate: reduction in substrate inhibition by fed-batch technique and product inhibition by gas stripping. Appl. Microbiol. Biotechnol. 2004, 63:653-658.
22. Sentheshanmuganathan S., Elsden S.R. The mechanism of the formation of tyrosol by Saccharomyces cerevisiae. Biochem. J. 1958, 69:210-218.
23. Curtiss L.A., Redfern P.C., Raghavachari K., Rassolov V., Pople J.A. Gaussian-3 theory using reduced Moller-Plesset order. J. Chem. Phys. 1999, 110:4703-4709.
24. Cossi M., Rega N., Scalmani G., Barone V. Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model. J. Comput. Chem. 2003, 24:669-681.
25. Barone V., Cossi M. Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model. J. Phys. Chem. A 1998, 102:1995-2001.
26. Assary R.S., Broadbelt L.J. Computational screening of novel thiamine-catalyzed decarboxylation reactions of 2-keto acids. Bioprocess Biosys. Eng. 2010, 34:375-388.
27. Assary R.S., Broadbelt L.J., Curtiss L.A. Bronsted-Evans-Polanyi relationships for C-C bond forming and C-C bond breaking reactions in thiamine-catalyzed decarboxylation of 2-keto acids using density functional theory. J. Mol. Model. 2011, 1-6. doi:10.1007/s00894-011-1062-z.
28. M.J. Frisch et al., Gaussian 03, Revision C.02, 2003.
29. Zheng Y.N., Li L.Z., Xian M., Ma Y.J., Yang J.M., Xu X., He D.Z. Problems with the microbial production of butanol. J. Ind. Microbiol. Biotechnol. 2009, 36:1127-1138.
30. Assary R.S., Redfern P.C., Hammond J.R., Greeley J., Curtiss L.A. Predicted thermochemistry for chemical conversions of 5-hydroxymethylfurfural. Chem. Phys. Lett. 2010, 497:123-128.
31. Hazelwood L.A., Daran J.M., van Maris A.J.A., Pronk J.T., Dickinson J.R. The Ehrlich pathway for fusel alcohol production: a century of research on Saccharomyces Cerevisiae Metabolism. Appl. Environ. Microbiol. 2008, 74:2259-2266.
32. Shen C.R., Liao J.C. Metabolic engineering of escherichia coli for 1-butanol and 1-propanol production via the keto-acid pathways. Metab. Eng. 2008, 10:312-320.
33. Liao J.C., Higashide W. Metabolic engineering of next-generation biofuels. Chem. Eng. Prog. 2008, 104:S19-S23.
34. Atsumi S., Hanai T., Liao J.C. Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 2008, 451:86-93.
35. Bach R.D., Canepa C. Electronic factors influencing the decarboxylation of beta-keto acids: a model enzyme study. J. Org. Chem. 1996, 61:6346-6353.