A generic HTS assay for kinase screening: Validation for the isolation of an engineered malate kinase

PLoS One. 2018 Feb 20;13(2):e0193036. doi: 10.1371/journal.pone.0193036. eCollection 2018.

Abstract

An end-point ADP/NAD+ acid/alkali assay procedure, directly applicable to library screening of any type of ATP-utilising/ADP producing enzyme activity, was implemented. Typically, ADP production is coupled to NAD+ co-enzyme formation by the conventional addition of pyruvate kinase and lactate dehydrogenase. Transformation of enzymatically generated NAD+ into a photometrically active alkali derivative product is then achieved through the successive application of acidic/alkali treatment steps. The assay was successfully miniaturized to search for malate kinase activity in a structurally-guided library of LysC aspartate kinase variants comprising 6,700 clones. The screening procedure enabled the isolation of nine positive variants showing novel kinase activity on (L)-malate, the best mutant, LysC V115A:E119S:E434V exhibited strong substrate selectivity for (L)-malate compared to (L)-aspartate with a (kcat/Km)malate/(kcat/Km)aspartate ratio of 86. Double mutants V115A:E119S, V115A:E119C and E119S:E434V were constructed to further probe the origins of stabilising substrate binding energy gains for (L)-malate due to mutation. The introduction of less sterically hindering side-chains in engineered enzymes carrying E119S and V115A mutations increases the effective volume available for substrate binding in the catalytic pocket. Improved binding of the (L)-malate substrate may be assisted by less hindered movement of the Phe184 aromatic side-chain. Additional favourable long-range electostatic effects on binding arising from the E434V surface mutation are conditionally dependent upon the presence of the V115A mutation close to Phe184 in the active-site.

Publication types

  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Amino Acid Substitution
  • Aspartate Kinase / genetics
  • Aspartate Kinase / metabolism
  • Catalytic Domain / genetics
  • Directed Molecular Evolution
  • Gene Library
  • Genetic Variation
  • High-Throughput Screening Assays / methods*
  • Kinetics
  • Malates / metabolism*
  • Models, Molecular
  • Mutagenesis, Site-Directed
  • Phosphotransferases / genetics*
  • Phosphotransferases / isolation & purification
  • Phosphotransferases / metabolism*
  • Protein Engineering / methods
  • Recombinant Proteins / genetics
  • Recombinant Proteins / isolation & purification
  • Recombinant Proteins / metabolism
  • Static Electricity
  • Substrate Specificity

Substances

  • Malates
  • Recombinant Proteins
  • malic acid
  • Phosphotransferases
  • lysC aspartokinase
  • Aspartate Kinase

Grants and funding

This work was supported by the French National Research Agency (ANR programme d’Investissement d’Avenir, Project SYNTHACS, ANR-10-BTBR-05-01) and by the Adisseo Company. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.