Literature DB >> 21370922

Catalytic versus inhibitory promiscuity in cytochrome P450s: implications for evolution of new function.

Robert S Foti1, Mathew Honaker, Abhinav Nath, Josh T Pearson, Brian Buttrick, Nina Isoherranen, William M Atkins.   

Abstract

Catalytically promiscuous enzymes are intermediates in the evolution of new function from an existing pool of protein scaffolds. However, promiscuity will only confer an evolutionary advantage if other useful properties are not compromised or if there is no "negative trade-off" induced by the mutations that yield promiscuity. Therefore, identification and characterization of negative trade-offs incurred during the emergence of promiscuity are required to further develop the evolutionary models and to optimize in vitro evolution. One potential negative trade-off of catalytic promiscuity is increased susceptibility to inhibition, or inhibitory promiscuity. Here we exploit cytochrome P450s (CYPs) as a model protein scaffold that spans a vast range of catalytic promiscuity and apply a quantitative index to determine the relationship between promiscuity of catalysis and promiscuity of inhibition for a series of homologues. The aim of these studies is to begin to identify properties that, in general, correlate with catalytic promiscuity, hypothetically such as inhibitory promiscuity. Interestingly, the data indicate that the potential negative trade-off of inhibitory promiscuity is nearly insignificant because even highly substrate specific CYPs have high inhibitory promiscuity, with little incremental increase in susceptibility to inhibitory interactions as the substrate promiscuity increases across the series of enzymes. In the context of evolution, inhibitory promiscuity is not an obligate negative trade-off for catalytic promiscuity.

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Year:  2011        PMID: 21370922      PMCID: PMC3068220          DOI: 10.1021/bi1020716

Source DB:  PubMed          Journal:  Biochemistry        ISSN: 0006-2960            Impact factor:   3.162


  27 in total

1.  Quantifying and predicting the promiscuity and isoform specificity of small-molecule cytochrome P450 inhibitors.

Authors:  Abhinav Nath; Michael A Zientek; Benjamin J Burke; Ying Jiang; William M Atkins
Journal:  Drug Metab Dispos       Date:  2010-09-14       Impact factor: 3.922

Review 2.  The quest for molecular quasi-species in ligand-activity space and its application to directed enzyme evolution.

Authors:  Bengt Mannervik; Arna Runarsdottir
Journal:  FEBS Lett       Date:  2010-04-18       Impact factor: 4.124

Review 3.  Enzyme promiscuity: a mechanistic and evolutionary perspective.

Authors:  Olga Khersonsky; Dan S Tawfik
Journal:  Annu Rev Biochem       Date:  2010       Impact factor: 23.643

4.  Transition towards antigen-binding promiscuity of a monospecific antibody.

Authors:  Jordan D Dimitrov; Sébastien Lacroix-Desmazes; Srinivas V Kaveri; Tchavdar L Vassilev
Journal:  Mol Immunol       Date:  2006-11-09       Impact factor: 4.407

5.  Multi-substrate-activity space and quasi-species in enzyme evolution: Ohno's dilemma, promiscuity and functional orthogonality.

Authors:  Bengt Mannervik; Arna Runarsdottir; Sanela Kurtovic
Journal:  Biochem Soc Trans       Date:  2009-08       Impact factor: 5.407

6.  Evolution of enzymatic activities in the enolase superfamily: D-tartrate dehydratase from Bradyrhizobium japonicum.

Authors:  Wen Shan Yew; Alexander A Fedorov; Elena V Fedorov; Bryant McKay Wood; Steven C Almo; John A Gerlt
Journal:  Biochemistry       Date:  2006-12-12       Impact factor: 3.162

Review 7.  Cholesterol-metabolizing cytochromes P450: implications for cholesterol lowering.

Authors:  Irina A Pikuleva
Journal:  Expert Opin Drug Metab Toxicol       Date:  2008-11       Impact factor: 4.481

Review 8.  The chemical versatility of the beta-alpha-beta fold: catalytic promiscuity and divergent evolution in the tautomerase superfamily.

Authors:  G J Poelarends; V Puthan Veetil; C P Whitman
Journal:  Cell Mol Life Sci       Date:  2008-11       Impact factor: 9.261

9.  A quantitative index of substrate promiscuity.

Authors:  Abhinav Nath; William M Atkins
Journal:  Biochemistry       Date:  2007-12-15       Impact factor: 3.162

Review 10.  Cytochrome p450 and chemical toxicology.

Authors:  F Peter Guengerich
Journal:  Chem Res Toxicol       Date:  2007-12-06       Impact factor: 3.739

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  8 in total

1.  Ensemble perspective for catalytic promiscuity: calorimetric analysis of the active site conformational landscape of a detoxification enzyme.

Authors:  Matthew T Honaker; Mauro Acchione; John P Sumida; William M Atkins
Journal:  J Biol Chem       Date:  2011-10-14       Impact factor: 5.157

Review 2.  Substrate tunnels in enzymes: structure-function relationships and computational methodology.

Authors:  Laura J Kingsley; Markus A Lill
Journal:  Proteins       Date:  2015-02-28

3.  Numerical Methods for Modeling Enzyme Kinetics.

Authors:  Jaydeep Yadav; Ken Korzekwa; Swati Nagar
Journal:  Methods Mol Biol       Date:  2021

Review 4.  Biological messiness vs. biological genius: Mechanistic aspects and roles of protein promiscuity.

Authors:  William M Atkins
Journal:  J Steroid Biochem Mol Biol       Date:  2014-09-12       Impact factor: 4.292

5.  Comparison of the ligand binding site of CYP2C8 with CYP26A1 and CYP26B1: a structural basis for the identification of new inhibitors of the retinoic acid hydroxylases.

Authors:  Robert S Foti; Philippe Diaz; Dominique Douguet
Journal:  J Enzyme Inhib Med Chem       Date:  2016-07-17       Impact factor: 5.051

6.  Molecular Lego of Human Cytochrome P450: The Key Role of Heme Domain Flexibility for the Activity of the Chimeric Proteins.

Authors:  Gianluca Catucci; Alberto Ciaramella; Giovanna Di Nardo; Chao Zhang; Silvia Castrignanò; Gianfranco Gilardi
Journal:  Int J Mol Sci       Date:  2022-03-25       Impact factor: 5.923

Review 7.  Mechanisms of promiscuity among drug metabolizing enzymes and drug transporters.

Authors:  William M Atkins
Journal:  FEBS J       Date:  2019-11-12       Impact factor: 5.542

Review 8.  A Review of Oxidative Stress Products and Related Genes in Early Alzheimer's Disease.

Authors:  Federica Cioffi; Rayan Hassan Ibrahim Adam; Ruchi Bansal; Kerensa Broersen
Journal:  J Alzheimers Dis       Date:  2021       Impact factor: 4.472

  8 in total

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