Creating protein biocatalysts as tools for future industrial applications

Protein Engineering Methods and Applications

“…Rational design (Arnold, 1993) Site-directed mutagenesis (Arnold, 1993), (Antikainen & Martin, 2005) Evolutionary methods/directed evolution (Arnold, 1993) Random mutagenesis (Antikainen & Martin, 2005), (Wong et al, 2006), (Jackson et al, 2006), (Labrou, 2010) DNA shuffling (Antikainen & Martin, 2005), (Jackson et al, 2006) Molecular dynamics (Anthonsen et al, 1994) Homology modeling (Anthonsen et al, 1994) 'MolCraft'in vitro protein evolution systems (Shiba, 2004) Computational methods (computational protein design) (Jackson et al, 2006), (Van der Sloot et al, 2009), (Golynskiy & Seelig, 2010) Receptor-based QSAR methods (Lushington et al, 2007) NMR (Anthonsen et al, 1994) X-ray crystallography (Jackson et al, 2006) Peptidomimetics (Venkatesan & Kim, 2002) Phage display technology (Antikainen & Martin, 2005), (Sidhu & Koide, 2007), (Chaput et al, 2008) Cell surface display technology (Antikainen & Martin, 2005), (Gai & Wittrup, 2007), (Chaput et al, 2008) Flow cytometry / Cell sorting (Mattanovich & Borth, 2006 ) Cell-free translation systems (Shimizu et al, 2006) Designed divergent evolution (Yoshikuni & Keasling, 2007) Stimulus-responsive peptide systems (Chockalingam et al, 2007) Mechanical engineering of elastomeric proteins (Li, 2008) Engineering extracellular matrix variants (Carson & Barker, 2009) Traceless Staudinger ligation (Tam & Raines, 2009) De novo enzyme engineering (Golynskiy & Seelig, 2010) mRNA display …”

“…Yeast surface display has recently been suggested as an important methodology for protein characterization, and identifying protein-protein interactions (Gai & Wittrup, 2007). In a later review article, library creation methods and display technologies related with enzyme evolution and protein engineering were also discussed in detail (Chaput et al, 2008). …”

The unexpected structure of the designed protein Octarellin V.1 forms a challenge for protein structure prediction tools

“…This approach, which exploits a simple iterative Darwinian optimization process, has led to major improvements of properties such as catalytic activity (Reetz, 2007), stability (Eijsink et al, 2005) and solubility (Waldo, 2003). Not surprisingly, directed evolution has also emerged as the best way to optimize the properties of de novo designed enzymes (Khersonsky et al, 2010;Ward, 2008) or even generate new catalytic functions, when combined with computational methods (Chaput et al, 2008). This ''black box" approach remains the most effective way to break through the existing limitations of in silico design.…”

Proteins as biocatalysts and biomaterials

“…Biocatalyst is a substance that initiates or modifies the rate of chemical reaction in a living body, i.e., a biochemical catalyst. They provide an economical and energy efficient tool for future industrial applications [29]. The requirements for a useful biocatalyst are selectivity, volume efficiency, security of supply and technology integration [33].…”