Protein engineering

Protein Engineering and Biomimetic Design

Biomimicry makes practical use of evolution to find efficient and sustainable ways to produce chemical compounds or engineer products. Exploring the natural machinery of enzymes for the production of desired compounds is a highly profitable investment, however, the design of efficient biomimetic systems is a considerable challenge. Further, the in vivo activity of designed systems and how they interact with other components in a biochemical network must be addressed (see (a) in Figure below).



1. Understanding the effects of directed evolution  

  • O6-alkylguanine-DNA alkyltransferase (hAGT) adopts a non-enzymatic suicide mechanism for the repair of methylated guanine bases by transferring the methyl adduct to itself, triggering unfolding and fast degradation.
  • SNAP-tag, a stable protein label, was evolved from hAGT through several rounds of directed evolution selecting for mutants with increased reactivity for O6-benzylguanine (BG) and BG derivatives (see (b) in Figure above).
  • We have been able to trace the key structural features that lead to the increased stability of SNAP-tag over hAGT using molecular dynamics simulations and thermal stability and proteolysis experiments
  • This project was a collaboration with Prof. Kai Johnsson and the LIP (EPFL)

2. Characterizing biomimetic peptidic scaffolds  

  • A novel strategy for the computational design of biomimetic compounds
  • Our approach consists of:
    • (i) characterization of the wild-type and biomimetic systems
    • (ii) identification of key descriptors for optimization
    • (iii) an efficient search through sequence and chemical space to tailor the catalytic capabilities of the biomimetic system
  • Applying a genetic algorithm together with an appropriate fitness function based on molecular mechanics (see (c) in Figure above)
  • We were able to re-engineer and optimize the catalytic properties of the peptide by introducing specific residues that mimic the native enzyme’s ability to localize CO2 in the metal binding site and lower the pKa of the zinc-bound water molecule
  • Reference Publications:
      • Mollwitz, B; Brunk, E; Schmitt, S; Pojer, F; Bannwarth, M; Schiltz, M; Rothlisberger U; Johnsson, K. Directed Evolution of the Suicide Protein O-6-Alkylguanine-DNA Alkyltransferase for Increased Reactivity Results in an Alkylated Protein with Exceptional Stability Biochemistry (2012) 51, 986.
      • Bozkurt, E; Ashari, N; Browning, N; Brunk, E; Campomanes, P; Perez, MAS; Rothlisberger, U. Lessons from Nature: Computational Design of Biomimetic Compounds and Processes (2014) CHIMIA 68 (9) 642.
      • Brunk, E; Perez, M; Athri, P; Rothlisberger, U. Genetic Algorithm Based Optimization of a Peptidic Scaffold for Sequestration and Hydration of CO2. chemphyschem (2016) just accepted
      • Browning, N*; Perez, M*; Brunk, E*; Athri, P; Rothlisberger, U. A Genetic Algorithm for the Design of Peptides and Proteins in preparation