Protein Engineering Reference Article

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Protein Engineering Methods and Applications
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2
Protein Engineering Methods and Applications

Burcu Turanli-Yildiz1,2, Ceren Alkim1,2 and Z. Petek Cakar1,2,
1Istanbul Technical University (ITU), Dept. of Molecular Biology and Genetics,
2ITU Dr. Orhan Ocalgiray Molecular Biology, Biotechnology and Genetics
Research Center (ITU-MOBGAM), Istanbul,
Turkey
1. Introduction
Protein engineering is the design of new enzymes or proteins with new or desirable
functions. It is based on the use of recombinant DNA technology to change amino acid
sequences. The first papers on protein engineering date back to early 1980ies: in a review by
Ulmer (1983), the prospects for protein engineering, such as X-ray crystallography, chemical
DNA synthesis, computer modelling of protein structure and folding were discussed and
the combination of crystal structure and protein chemistry information with artificial gene
synthesis was emphasized as a powerful approach to obtain proteins with desirable
properties (Ulmer, 1983). In a later review in 1992, protein engineering was mentioned as a
highly promising technique within the frame of biocatalyst engineering to improve enzyme
stability and efficiency in low water systems (Gupta, 1992). Today, owing to the
development in recombinant DNA technology and high-throughput screening techniques,
protein engineering methods and applications are becoming increasingly important and
widespread. In this Chapter, a chronological review of protein engineering methods and
applications is provided.
2. Protein engineering methods

Many different protein engineering methods are available today, owing to the rapid
development in biological sciences, more specifically, recombinant DNA technology. These
methods are chronologically reviewed in this section, and summarized in Table 1.
The most classical method in protein engineering is the so-called “rational design” approach
which involves “site-directed mutagenesis” of proteins (Arnold, 1993). Site-directed
mutagenesis allows introduction of specific amino acids into a target gene. There are two
common methods for site-directed mutagenesis. One is called the “overlap extension”
method. This method involves two primer pairs, where one primer of each primer pair
contains the mutant codon with a mismatched sequence. These four primers are used in the
first polymerase chain reaction (PCR), where two PCRs take place, and two double-stranded
DNA products are obtained. Upon denaturation and annealing of them, two heteroduplexes
are formed, and each strand of the heteroduplex involves the desired mutagenic codon.
DNA polymerase is then used to fill in the overlapping 3’ and 5’ ends of each heteroduplex
and the second PCR takes place using the nonmutated primer set to amplify the mutagenic
34 Protein Engineering
DNA. The other site-directed mutagenesis method is called “whole plasmid single round
PCR”. This method forms the basis of the commercial “QuikChange Site-Directed
Mutagenesis Kit” from Stratagene. It requires two oligonucleotide primers with the desired
mutation(s) which are complementary to the opposite strands of a double-stranded DNA
plasmid template. Using DNA polymerase PCR takes place, and both strands of the
template are replicated without displacing the primers and a mutated plasmid is obtained
with breaks that do not overlap. DpnI methylase is then used for selective digestion to
obtain a circular, nicked vector with the mutant gene. Upon transformation of the nicked
vector into competent cells, the nick in the DNA is repaired, and a circular, mutated plasmid
is obtained (Antikainen & Martin, 2005).
Rational design is an effective approach when the structure and mechanism of the protein of
interest are well-known. In many cases of protein engineering, however, there is limited
amount of information on the structure and mechanisms of the protein of interest. Thus, the
use of “evolutionary methods” that involve “random mutagenesis and selection” for the
desired protein properties was introduced as an alternative approach. Application of
random mutagenesis could be an effective method, particularly when there is limited
information on protein structure and mechanism. The only requirement here is the
availability of a suitable selection scheme that favours the desired protein properties
(Arnold, 1993). A simple and common technique for random mutagenesis is “saturation
mutagenesis”. It involves the replacement of a single amino acid within a protein with each
of the natural amino acids, and provides all possible variations at that site. “Localized or
region-specific random mutagenesis” is another technique which is a combination of
rational and random approaches of protein engineering. It includes the simultaneous
replacement of a few amino acid residues in a specific region, to obtain proteins with new
specificities. This technique also makes use of overlap extension, and the whole-plasmid,
single round PCR mutagenesis, as in the case of site-directed mutagenesis. However, the
major difference here is that the codons for the selected amino acids are randomized, such
that a mixture of 64 different forward and 64 different reverse primers are used, based on a
statistical mixture of four bases and three nucleotides in a randomized codon (Antikainen &
Martin, 2005).
In 1994, important fields for protein engineering were also discussed in a review article by
Anthonsen and co-workers (Anthonsen et al., 1994). The challenge in protein sequence
deduction from DNA sequence, resulting from post-transcriptional and post-translational
modifications and splicing, was emphasized. Homology modelling of protein structures,
NMR of large proteins, molecular dynamics simulations of protein structures, and
simulation of electrostatic effects (such as pH-dependent effects) were mentioned as
important scientific areas to provide additional key information to protein engineering
studies.
Another important method that finds applications in protein engineering is
“peptidomimetics”. It involves mimicking or blocking the activity of enzymes or natural
peptides upon design and synthesis of peptide analogs that are metabolically stable.
Peptidomimetics is an important approach for bioorganic and medical chemistry. It includes
a variety of synthesis methods such as the use of a common intermediate, solid phase
synthesis and combinatorial approaches (Venkatesan & Kim, 2002).
Protein Engineering Methods and Applications 35
“In vitro protein evolution systems” are also important methods in protein engineering.
They are based on the hierarchical evolution principle of genes. It was suggested that
modern genes developed from small genetic units upon hierarchical and combinatorial
processes. An example is MolCraft, an in silico evolved microgene which was then tandemly
polymerized, including insertion or deletion mutations at the junctions between microgene
units. The junctional perturbations allowed molecular diversity and the formation of
combinatorial peptide polymers, whereas the repetitiousness allowed the formation of
ordered structures (Shiba, 2004).
In a review article by Antikainen and Martin, (2005), the major protein engineering methods
were described in detail. These methods were classified as rational methods that involve
site-directed mutagenesis, random methods including random mutagenesis and
evolutionary methods which involve “DNA shuffling”. In DNA shuffling method, a group
of genes with a double-stranded DNA and similar sequences is obtained from various
organisms or produced by error-prone PCR. Digestion of these genes with DNaseI yields
randomly cleaved small fragments, which are purified and reassembled by PCR, using an
error-prone and thermostable DNA polymerase. The fragments themselves are used as PCR
primers, which align and cross-prime each other. Thus, a hybrid DNA with parts from
different parent genes is obtained. Variations of DNA shuffling method such as the use of a
mixture of restriction endonucleases instead of DNaseI, or the “staggered extension process”
that does not require parental gene fragmentation were also discussed (Antikainen &
Martin, 2005). Additionally, the development of efficient screening methods to screen large
libraries of proteins/enzymes such as “cell surface libraries coupled with fluorescence
activated cell sorting (FACS)”, or “phage display technology” were discussed (Antikainen &
Martin, 2005). The combination of cell surface libraries with FACS can be used to screen
very large libraries. The system is based on a scissile bond of the substrate, such as an Arg-
Val linkage, which can be cleaved by a surface-displayed enzyme or not. The scissile bond
on the designed substrate links a fluorophore and a quencher. If the scissile bond of the
substrate is not cleaved by the surface-displayed enzyme, the fluorophore emission is then
quenched by the quenching fluorophore. Thus, no fluorescence emission occurs. However,
if the enzyme cleaves the scissile bond of the substrate, the fluorophore and the quenching
fluorophore are then separated, and fluorescence occurs. Fluorescence of the clones with
cleavage of the scissile bond is then detected by FACS (Antikainen & Martin, 2005). Phage
display technology is another powerful technique for screening large libraries of proteins.
The method requires degenerate reverse primers to be used in a PCR for random
mutagenesis of the starting cDNA throughout a target region. The PCR products are then
subcloned into a bacteriophage vector coding for a phage coat protein. Each phage of the
mutant pool expresses a different protein displayed on the coat protein of the phage surface.
Elution experiments help screen and identify the variants that bind tightly to a substrate of
interest. Thus, the identified mutants are purified and sequenced (Antikainen & Martin,
2005).
“Flow cytometry”, a powerful method for single cell analysis, is also used in protein
engineering studies. A variety of examples are available where the sorting was done
according to ligand binding in antibody and peptide surface display studies, or enzyme
engineering of intra- and extracellular enzymes (Mattanovich & Borth, 2006).
The advantages and disadvantages of random mutagenesis methods used in protein

engineering were also determined and compared to each other in detail. Based on the
nucleotide substitution method used, these random mutagenesis methods were divided into
four major groups: enzyme-based methods, synthetic chemistry-based methods, whole cell
methods and combined methods. Their comparison was made according to a variety of
parameters such as controllable mutation frequency, technical robustness, cost-effectiveness,
etc. (Wong et al., 2006).
“Cell-free translation systems” were also described as important tools for protein
engineering and production. They are an alternative to in vivo protein expression. When
template DNA or mRNA is added to a reaction mixture, proteins are produced upon
incubation in the absence of cells. PCR products can be used, and proteins are synthesized
from cDNA rapidly. Cell-free translation systems are based on the ribosomal protein system
of cells, which is provided as a cell extract from Escherichia coli etc. obtained as a supernatant
upon centrifugation at 30’000 g. This supernatant contains necessary compounds for protein
synthesis, such as ribosomes, t-RNAs, translation factors and aminoacyl-tRNA synthetases.
Potential applications involve production of biologically active proteins, synthesis of
membrane proteins for minimal cells, and artificial proteins. With further development, cell-
free translation systems could be a strong alternative to in vivo protein expression, due to
their high level of controllability and simplicity. The limitations of recombinant protein
expression in living cells, such as protein degradation and aggregation will also be avoided
(Shimizu et al., 2006).
Green fluorescent protein (GFP) is a very important protein that is widely used for
biological and medical research purposes. It is a 238-residue protein from the jellyfish
Aequorea victoria. GFP has unique spectroscopic characteristics, undergoes an autocatalytic
post-translational cyclization and oxidation of the polypeptide chain around Ser65, Tyr66,
and Gly67 residues, to form an extended and rigidly encapsulated conjugated Π system, the
chromophore, that emits green fluorescence. Additionally, no cofactors are required for the
formation or the function of the chromophore. GFP has high structural stability and high
fluorescence quantum yield, which are other important properties for its widespread use.
GFP has been modified extensively to be used as a marker for gene expression, protein
localization and protein-protein interactions, as well as a biosensor. The proper folding of
GFP is critical for its functional efficiency. Thus, protein engineering methods such as
random mutagenesis and screening, DNA shuffling, as well as computational methods and
X-ray crystallography improved the folding of GFP and emphasized the importance of the
use of different methods such as biophysical techniques in improving protein properties
(Jackson et al., 2006).
“Designed divergent evolution” is also an important protein engineering method that is
used in redesigning enzyme function. The method is based on the theories of divergent
molecular evolution. According to these theories, firstly, enzymes with more specialized and
active functions have evolved from those enzymes with promiscuous functions. Secondly,
this process is driven by a few amino acid substitutions; and finally, the effects of
double/multiple mutations are usually additive. Thus, the method allows the selection of
combinations of mutations that would confer the desired functions and their introduction
into the enzymes (Yoshikuni & Keasling, 2007).
“Stimulus-responsive peptide systems” are based on both naturally existing peptides and
rationally engineered systems. These systems exploit the fact that the peptides and proteins
are able to change their conformations as a response to external stimulants such as pH,
temperature or some specific molecules. There is a broad range of applications of these
systems in research fields such as biosensors, bioseparations, drug delivery, nanodevices
and tissue engineering. Directed evolution of stimulus-responsive peptides, however,
requires an appropriate selection or screening scheme. Thus, protein-based conformational
change sensors (CCSs) were developed using immunofluorescence and recombinant DNA
technology (Chockalingam et al., 2007).
Avidin and streptavidin are proteins that are structurally and functionally analogous.
Because of their ability to bind biotin very tightly, they are widely used in (strept)avidin-
biotin binding technology that is a common tool in life sciences and nanotechnology. To
further improve these protein tools and obtain genetically engineered (strept)avidins,
protein engineering methods were applied including simple amino acid substitutions to
change physico-chemical properties, or more complex changes, such as chimeric
(strept)avidins, topology rearrangements and non-natural amino acid stitching into the
active sites (Laitinen et al., 2007).
“Receptor-based QSAR methods” are also valuable for protein engineering studies. These
methods are based on a computational combination of structure-activity relationship
analysis and receptor structure-based design. They provide valuable pharmacological
information on therapeutic targets. The Comparative Binding Energy (COMBINE) analysis,
for example, probes bioactivity changes with respect to amino acid variations in a series of
homologous protein receptors and with respect to conformational changes within a protein
of interest (Lushington et al., 2007).
As mentioned previously, phage display technology is one of the most commonly known
molecular display technologies which relates phenotypes with their corresponding
genotypes. Phage display technique is used particularly in “synthetic binding protein
engineering”, where libraries of ‘synthetic’ binding proteins were developed with antigen-
binding sites constructed from man-made diversity. It was suggested that the combination
of phage display and synthetic combinatorial libraries will be preferred for synthetic
binding protein engineering (Sidhu & Koide, 2007). Similar to phage display technology,
“yeast surface display” is also a useful method for protein engineering and characterization.
Using this method, many different proteins can be displayed on yeast surface, and the yeast
secretory biosynthetic system promotes efficient N-linked glycosylation and oxidative
protein folding. Rapid and quantitative library screening by FACS analysis and easy
characterization of mutants without requiring their soluble expression and purification are
among the major advantages of this method. 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).
An interesting protein tool that was obtained by protein engineering methods is “anticalin”.
It offers a variety of applications in biochemical research as well as in medical therapy as
potential drugs. Anticalins are a combination of antibodies and lipocalins. Lipocalins are a
protein family with a binding site that has high structural plasticity. By applying protein
engineering methods such as site-directed random mutagenesis and selection by phage
display technology, artificial lipocalins with novel ligand specificities, i.e. “anticalins” were
obtained. Anticalins have many advantages such as being significantly smaller than
antibodies, not requiring post-translational modifications, having robust biophysical
properties and the ability to be produced in microbial expression systems (Skerra, 2008).
Method name Reference(s)
Rational design (Arnold, 1993)

Site-directed mutagenesis (Arnold, 1993), (Antikainen & Martin, 2005)
Evolutionary methods/directed (Arnold, 1993)
evolution
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 (Shiba, 2004)
systems
Computational methods (Jackson et al., 2006), (Van der Sloot et al., 2009),
(computational protein design) (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 (Li, 2008)
elastomeric proteins
Engineering extracellular matrix (Carson & Barker, 2009)
variants
Traceless Staudinger ligation (Tam & Raines, 2009)
De novo enzyme engineering (Golynskiy & Seelig, 2010)
mRNA display (Golynskiy & Seelig, 2010)
Table 1. A summary of different methods used in protein engineering
In a recent review by Goodey and Benkovic (2008), the allosteric regulation of proteins was
discussed in detail. Ligand binding or an amino acid mutation at an allosteric site can
significantly change enzymatic activity or binding affinity at another site such as the active
site. Thus, this site-to-site communication of allosteric regulation is an important concept to
be considered for protein engineering studies. Particularly, if the allosteric mechanisms are
well understood, new proteins with switch-like properties could be designed for drug
delivery, etc. (Goodey & Benkovic, 2008).
Recently, engineering of elastomeric proteins has been discussed as a new approach to
improve the mechanical properties for the construction of biomaterials. Elastomeric proteins
are important in regulating the mechanical properties in biological machineries. Using a
combination of protein engineering methods and single molecule atomic force microscopy,
the molecular basis of the mechanical stability of elastomeric proteins could be understood,
and the mechanical properties of elastomeric proteins could be further improved by their
‘mechanical engineering’ (Li, 2008).
Protein and catalytic promiscuity are also important concepts for protein engineering.
Catalytic promiscuity is defined as the ability of a single active site to catalyse more than one
chemical reaction (Kazlauskas, 2005). Understanding protein and catalytic promiscuity is
important for optimizing protein engineering applications (Nobeli et al., 2009).
In a recent review, the advances in mammalian cell and protein evolution were discussed,
which would have important applications in commercial mammalian cell biotechnology. As
mutagenesis and selection of mammalian cells is quite elaborate, the improvement of
mammalian protein evolution systems would be crucial for obtaining new diagnostic tools
and designer polypeptides (Majors et al., 2009).
Another recent concept in protein engineering research is the “engineering of extracellular
matrix variants” to direct cell behaviour, particularly differentiation, as a response to
biomaterials, in regenerative medicine applications. Extracellular matrix-derived peptides,
such as Arg-Gly-Asp, are useful in supporting cell adhesion and specific integrin-signalling
scaffolds and growth factor-receptor signalling are required for directing cell phenotype.
Thus, by making use of this information, engineering of extracellular matrix variants could
be a promising protein engineering approach (Carson & Barker, 2009).
Manipulation of proteins in a controlled way is a key requirement for many protein
engineering studies. To facilitate that, “the traceless Staudinger ligation” method was
recently introduced. It is based on the Staudinger reaction, where a phosphine is used to
reduce an azide to an amide. The reaction occurs by means of a stable intermediate, an
iminophosphorane, that has a nucleophilic nitrogen which can be acylated in inter- and
intramolecular ligations. In peptide synthesis, the Staudinger reaction is applied by using a
phosphinothiol for uniting an azide and a thioester. This method allows convergent
chemical synthesis of proteins, and can ligate peptides at noncysteine residues. Thus, it
overcomes a limitation of other strategies, and can be used as a powerful method for protein
engineering (Tam & Raines, 2009).
In addition to the traditional methods of protein engineering, such as ‘classical’ rational
design and directed-evolution methods, computational protein design tools are becoming
increasingly important. In a recent review by Van der Sloot et al. (2009), “computational
protein design principles and applications” were discussed. Computational protein design
principles are based on the combination of a force field and a search algorithm to identify
the amino acid sequence that is most compatible with a given protein three-dimensional
backbone structure. At selected positions, the computational protein design algorithm
‘mutates’ or changes the original amino acid to all other natural amino acids and results in
new conformations. The energy of the structure is determined after simultaneous
optimization of the side-chain and/or backbone conformations of the substituted amino
acid and the interacting amino acids. Thus, low energy substitutions which are favorable are
retained (Van der Sloot et al., 2009). Another recent review article on random mutagenesis
methods used in protein engineering/enzyme evolution also discussed different methods
such as “error-prone” PCR mutagenesis, chemical mutagenesis, rolling circle error-prone
PCR, saturation mutagenesis and novel methodologies (Labrou, 2010). The potential of “de
novo enzyme engineering” method was also emphasized recently (Golynskiy & Seelig, 2010).
De novo means that the enzymes are not based on a related parent protein regarding
substrate or reaction mechanism. Obtaining de novo enzymes from scratch has been possible
by i) in silico rational design; ii) utilizing the understanding of a reaction mechanism and the
diversity of the immune system by means of catalytic antibodies; and iii) empirical search of
large protein libraries by using mRNA display. mRNA display is a powerful new technique
that can select de novo proteins from libraries that are several orders of magnitude larger
than most other selection methods such as phage display and cell surface display. The
proteins obtained by mRNA display method are covalently attached to the mRNA encoding
them. Thus, each protein becomes directly amplifiable. The key feature of this method is the
presence of the antibiotic puromycin that mimics a charged tRNA. Thus, puromycin is
added into the growing polypeptide chain by the ribosome. The transcription of a synthetic
DNA library into mRNA and its modification with puromycin is usually followed by in vitro
translation, where a covalent link is made between each protein and the mRNA encoding
that protein. This step is followed by reverse transcription of the library of mRNA-displayed
proteins with a substrate-modified primer, and attachment of the substrate to the
cDNA/RNA/protein complex. Proteins catalyzing the substrate reaction change their
encoding cDNA with the product, and selected cDNA sequences are amplified by PCR and
used for the next selection step (Golynskiy & Seelig, 2010). The future of protein engineering
will definitely involve many new technologies and combinational use of existing methods.
3. Protein engineering applications

A variety of protein engineering applications have been reported in the literature. These
applications range from biocatalysis for food and industry to environmental, medical and
nanobiotechnology applications (as summarized in Table 2), and will be discussed in this
section.
3.1 Food and detergent industry applications

Early reports on the importance of protein engineering methods to design new enzymes for
enzyme biotechnological industries date back to 1993 (Wiseman, 1993). Particularly, the
enzymes used in food industry were emphasized as an important group of enzymes, the
industrially important properties of which could be further improved by protein

engineering. Those properties include thermostability, specificity and catalytic efficiency.
Additionally, the design and production of new enzymes for food industry by using protein
engineering was discussed to produce new food ingredients (James & Simpson, 1996). In a
later review, new application areas of enzymes were discussed, resulting from significant
developments in biotechnology, such as protein engineering and directed evolution.
Successful combinations of rational protein engineering with directed evolution (Voigt et al.,
2000; Altamirano et al., 2000) have also been mentioned and it was emphasized that the
combined use of rational design, directed evolution and the diversity of the nature would be
much more powerful than the use of a single technique (Kirk et al., 2002).
Application name Example reference(s)

Food industry applications (James & Simpson, 1996), (Kirk et al., 2002), (Akoh et al.,
2008)
Detergent industry (Gupta et al., 2002)
applications (proteases)
Environmental applications (Wiseman, 1993), (Cirino & Arnold, 2002), (Le Borgne &
Quintero, 2003), (Ayala et al., 2008), (Cao et al., 2009)
Medical applications (Buckel, 1996), (Filpula & McGuire, 1999), (Paques &
Duchateau, 2007), (Nuttall & Walsh, 2008), (Liu et al., 2009),
(Lam et al., 2003), (Zafir-Lavie et al., 2007), (Vazquez et al.,
2009), (Olafsen & Wu, 2010)
Biopolymer production (Chow et al., 2008), (Rehm, 2010), (Banta et al., 2010)
applications
Nanobiotechnology (Hamada et al., 2004), (Banta et al., 2007) (Sarikaya et al.,
applications 2003) (Tamerler et al., 2010)
Applications with redox (Saab-Rincon & Valderrama, 2009), (Kumar, 2010)
proteins and enzymes
Applications with various (Martinkova & Kren, 2010), (Clapes et al., 2010), (Jordan &
industrially important Wagschal, 2010), (Rao et al., 2009), (Marcaida et al., 2010).
enzymes
Other new applications (Lofblom et al., 2010), (Elleuche & Poggeler, 2010), (Klug,
2010),
(Guven et al., 2010),(Nagahara et al., 2009), (Henriques &
Craik, 2010)
Table 2. A general summary of selected protein engineering applications
An important application area of protein engineering regarding food industry is the wheat
gluten proteins. Their heterologous expression and protein engineering has been studied
using a variety of expression systems, such as E.coli, yeasts or cultured insect cells. Wild-
type and mutant wheat gluten proteins were produced to compare them to each other for
protein structure-function studies. Generally, E.coli expression systems were suggested as
suitable systems for many applications, because of their availability, rapid and easy use, as
well as high expression levels (Tamas & Shewry, 2006). Food industry makes use of a
variety of food-processing enzymes, such as amylases and lipases, the properties of which
are improved using recombinant DNA technology and protein engineering. The deletion of
native genes encoding extracellular proteases, for example, increased enzyme production
yields of microbial hosts. In fungi, for example, the production of toxic secondary
metabolites has been reduced to improve their productivity as enzyme-producing hosts
(Olempska-Beer et al., 2006).
Some large groups of enzymes like proteases, amylases and lipases are important for both
food and detergent industries, as they have a broad range of industrial applications.
Proteases, for example, are used in several applications of food industry regarding low
allergenic infant formulas, milk clotting and flavors. They are also important for detergent
industry for removing protein stains (Kirk et al., 2002). The improvement of proteases for
industry to have, for example, high activity at alkaline pH and low temperatures, or
improved stability at high temperatures is a challenge for protein engineering. Microbial
protease production is industrially suitable because of low costs, high production yields,
and easy genetic manipulation. Microbial protease genes have also been investigated for
protein engineering of the enzymatic properties, clarifying the role of proteases in
pathogenicity, as well as for overproduction purposes (Rao et al., 1998). There are some
protein engineering applications to improve proteases: cold adaptation of a mesophilic
subtilisin-like protease was performed using laboratory evolution (Wintrode et al., 2000);
and DNA shuffling was applied to isolate new proteases with improved properties from an
initial material of 26 subtilisin proteases (Ness et al., 1999).
Among different proteases, bacterial alkaline proteases are a commercially important group.
They are particularly important for detergent industry and commercial products include
subtilisin Carlsberg, subtilisin BPN and Savinase. The use of protein engineering techniques
resulted in improvement of their catalytic efficiency, stability against high temperatures,
oxidation and changes in washing conditions. Site directed mutagenesis and/or random
mutagenesis resulted in new alkaline proteases, such as Durazym, Maxapem and Purafect,
whereas new subtilisin products with improved stability and specificity were also obtained
by directed evolution. The recent “metagenomic” approaches to discover natural and
molecular diversities were also suggested as new technologies to isolate new microbial
sources with better alkaline protease activities (Gupta et al., 2002). Among many bacteria,
Bacillus species play an important role in microbial commercial enzyme production. The fact
that some Bacillus species are classified as GRAS (generally regarded as safe) organisms, and
have the ability to produce and secrete high amounts of extracellular enzymes, makes them
valuable hosts for industrial enzyme production. Classical mutation and selection
techniques, as well as protein engineering methods resulted in high-efficiency production of
new enzymes with improved properties (Schallmey et al., 2004).
Amylases are also important for both food and detergent industries. In food industry, they
are used for liquefaction and saccharification of starch, as well as in adjustment of flour and
bread softness and volume in baking. The detergent industry makes use of amylases in
removal of starch stains (Kirk et al., 2002). Recently, the production of “functional foods” is
becoming increasingly important for food industry. Particularly, the production of
industrial products and functional foods from cheap and renewable raw agricultural
materials is desirable. Conversion of starch to bioethanol or to functional ingredients like
fructose, wine, glucose and trehalose, for example, has been studied. Such a conversion
requires microbial fermentation in the presence of biocatalysts such as amylases to liquefy

and saccharify starch. To improve the industrially important properties of amylases, such as
high activity, high thermo- and pH-stability, high productivity, etc.; recombinant enzyme
technology, protein engineering and enzyme immobilization have been used. In a recent
review article, rice was given as a typical example for biocatalytical production of useful
industrial products and functional foods from cheap agricultural raw materials and
transgenic plants (Akoh et al., 2008).
Another major group of enzymes utilized by food and detergent industries is constituted by
lipases. They are used in many applications of food industry such as for the stability and
conditioning of dough (as an in situ emulsifier), and in cheese flavor applications. Lipases
are also crucial for the detergent industry, as they are used in removal of lipid stains (Kirk et
al., 2002). As lipases are commonly used in food industrial applications, having
toxicologically safe lipases is an important requirement of food industry. The commercial
lipase isoform mixtures prepared from Candida rugosa meet this requirement. Obtaining
pure and different C. rugosa lipase isoforms is possible by means of computer modelling of
lipase isoforms, and protein engineering methods such as lid swapping and DNA shuffling
(Akoh et al., 2004). A recent review on microbial lipases focused on non-aqueous microbial
lipase catalysis and major factors affecting esterification/transesterification processes in
organic media. Additionally, protein engineering, directed evolution, metagenomics and
application of these strategies on lipase catalysis were discussed (Verma et al., 2008).
Similarly, lipases from other organisms such as mammals and fishes were also reviewed
(Kurtovic et al., 2009).
3.2 Environmental applications

Environmental applications of enzyme and protein engineering are also another important
field. Early reports on enzyme and cell applications in industry and in environmental
monitoring, such as environmental biosensors, date back to 1993 (Wiseman, 1993). One year
later, recent genetic methods and strategies for designing microorganisms to eliminate
environmental pollutants were discussed in detail. Those methods and strategies included
gene expression regulation to provide high catalytic activity under environmental stress
conditions, such as the presence of a toxic compound, rational changes introduced in
regulatory proteins that control catabolic activities, creation of new metabolic routes and
combinations thereof etc. (Timmis et al., 1994).
In a later review in 2000, the importance of microbial strains and their enzymes in
bioremediation and biotransformation applications was discussed, pointing out the
utilization of modern strategies such as protein engineering or pathway engineering to
improve microbial processes. Molybdenum hydroxylases, enzymes that catalyze the initial
bacterial hydroxylation of a N-heteroaromatic compound, and ring-opening 2,4-
dioxygenases that play a role in the bacterial quinaldine degradation, were investigated in
detail, to study and improve the enzymes involved in aerobic bacterial degradation of N-
heteroaromatic compounds (Fetzner, 2000). Protein engineering of oxygenases, an important
group of enzymes with high selectivity and specificity, which enable the microbial
utilization and biodegradation of organic, toxic compounds, was also discussed. The
potential application of oxygenases in chemical synthesis and bioremediation was also
emphasized (Cirino & Arnold, 2002). Apart from oxygenases, other oxidative enzymes such
as peroxidases and laccases are also important for the treatment of organic pollutants. These
enzymes have broad substrate specificities and can catalyze the oxidation of a wide range of
toxic organic compounds. Many organic pollutants such as phenols, azo dyes,
organophosphorus pesticides and polycyclic aromatic hydrocarbons can be detoxified using
enzymatic oxidation. However, there are some limitations of enzymatic treatment which
should be overcome. These include enzyme denaturation by the use of organic solvents
used in enzymatic reactions, inhibition/stabilization of enzyme-substrate complexes, low
reaction rates of laccases, toxicity of mediators, high costs and limited availability of the
enzymes, etc. Chemical modification or protein engineering of oxidative enzymes to have
robust enzymes with high activity was suggested (Torres et al., 2003). Another review article
published in 2004 focused on the environmental applications with enzymes, such as the use
of enzymes in waste management and pollution control. Protein engineering, rational
enzyme design and recombinant DNA technology were mentioned as important research
areas that would influence environmental enzyme applications. Utilization of new
technologies such as gene shuffling, high throughput screening, and nanotechnology was
suggested as future prospects of environmental enzyme applications (Ahuja et al., 2004).
Petroleum biorefining is also an important environmental application area, where new
biocatalysts are required. Protein engineering, isolation and study of new extremophilic
microorganisms, genetic engineering developments are all promising advances to develop
new biocatalysts for petroleum refining. Petroleum biorefining applications such as fuel
biodesulfurization, denitrogenation of fuels, heavy metal removal, depolymerisation of
asphaltenes, etc. were discussed (Le Borgne & Quintero, 2003).
Microbial bioplastics, or polyhydroxyalkanoates (PHAs), are also an important research area
in environmental biotechnology. They are storage polymers produced by many bacteria and
archea, and their properties are similar to those of petroleum-derived plastics. PHAs are,
however, biodegradable and thus, environment-friendly. Thus, microbial large-scale and
low-cost production of PHAs is a challenge for biotechnologists. PHAs are deposited in cells
as water-soluble, cytoplasmic granules of nano-size. Protein engineering of polyester
synthases and phasins, the two proteins involved in PHA polyester formation, and
structural issues, respectively, was used to understand the genetics and biochemistry of
PHA granule self-assembly. This information would also be used for medical applications
involving biocompatible and biodegradable biomaterials (Rehm, 2006). The biogenesis of
microbial polyhydroxyalkanoate granules, and protein engineering of polyester synthases
and phasins to functionalize the polyester particle surface allowed microbial and
biocatalytic production of particles with controlled size, polyester care composition and
surface functionality. This would allow a platform technology for the production of tailor-
made bioparticles, particularly for medical applications (Rehm, 2007).
In a recent review, microbial surface display applications for environmental bioremediation
and biofuels production were discussed. Yeast and bacterial cell systems where proteins or
peptides are expected on the cell exterior were reported to be used as biocatalysts,
biosorbents and biostimulants (Wu et al., 2008).
Another important environmental application of protein engineering involves fungal
enzymes. Particularly peroxidases isolated from fungi can transform xenobiotics and many
pollutants. For the development of applications, the enzyme stability and availability need
to be improved. Thus, many protein engineering strategies were identified such as
improvement of hydrogen peroxide stability, increasing the redox potential to broaden the
substrate range, heterologous expression and industrial production development (Ayala et
al., 2008).
In recent reviews on environmental applications of protein engineering, recent ‘omics’
technologies have also been discussed. Metagenomic libraries, which identify and analyze
genetic resources of complex microbial communities were suggested to help identify
microbial enzymatic diversity, with implications in medicine, environmental issues,
agriculture etc. Thus, contributions in renewable energy sources, decrease in pollutant
burdens and process energies were expected with metagenomics applications in the future
(Ferrer et al., 2009). Similarly, in a review on biodegradation of aromatic compounds such as
benzene, toluene, ethylbenzene and xylene, the importance of metabolic engineering,
protein engineering, and “omics” technologies were emphasized (Cao et al., 2009).
3.3 Medical applications

Medical applications of protein engineering are also diverse. The use of protein engineering
for cancer treatment studies is a major area of interest. Pretargeted radioimmunotherapy has
been discussed as a potential cancer treatment. By pretargeting, radiation toxicity is
minimized by separating the rapidly cleared radionuclide and the long-circulating antibody.
Advances in protein engineering and recombinant DNA technology were expected to
increase the use of pretargeted radioimmunotherapy (Lam et al., 2003). The use of novel
antibodies as anticancer agents is also an important field of application, where the ability of
antibodies to select antigens specifically and with high affinity is exploited, and protein
engineering methods are used to modify antibodies to target cancer cells for clinical
applications (Zafir-Lavie et al., 2007). Recently, the term “modular protein engineering” has
been introduced for emerging cancer therapies. Treatment strategies based on targeted
nanoconjugates to be specifically directed against target cells are becoming increasingly
important. Additionally, multifunctional and smart drug vehicles can be produced at the
nanoscale, by protein engineering. These strategies could be combined to identify and select
targets for protein-based drug delivery (Vazquez et al., 2009).
Protein engineering applications for therapeutic protein production is an important area,
particularly for medicine. In 1996, recombinant protein production for therapeutic purposes
was reviewed. It was stated that protein engineering resulted in a second generation of
therapeutic protein products with application-specific properties obtained by mutation,
deletion of fusion. The third generation of such products were mentioned as “gene therapy”
protein products to be produced by the patients, upon gene transfer (Buckel, 1996). Other
studies on therapeutic protein production include single-chain Fv designs for protein, cell
and gene therapy (Filpula & McGuire, 1999). DNA shuffling and recursive genetic
recombination studies to improve therapeutic proteins (Kurtzman et al., 2001); development
of secreted proteins such as insulin, interferon, erythropoietin as biotherapeutics agents
(Bonin-Debs et al., 2004), combinatorial protein biochemistry for therapeutics and
proteomics (Lowe & Jermutus, 2004), meganucleases and DNA double-strand break-
induced recombination for gene therapy (Paques & Duchateau, 2007), the use of protein
cationization techniques for future drug discovery and development (Futami et al., 2007),
protein display scaffolds for protein engineering of new therapeutics (Nuttall & Walsh,
2008), and polymer-based therapeutics for drug delivery and tissue regeneration (Liu et al.,
2009).
Protein engineering applications with antibodies are also diverse. Owing to advances in
recombinant DNA technology, “antibody engineering” is possible. Improvements such as
minimal recognition units and antigenized antibodies were described. Combinational
approaches such as bacteriophage display libraries have been introduced as a strong
alternative to hybridoma technology for antibody production with desired antigen binding
characteristics (Sandhu, 1992). Studies on genetic manipulation of mouse monoclonals for
producing humanized antibodies and bacteriophage display libraries for Ig repertoires have
been reported (Zaccolo & Malavasi, 1993). Phage display has become a powerful technique
in protein engineering, immunology, oncology, etc. Phage display of antibody fragments,
particularly the production of artificial epitopes by phage antibodies is an important
application (Pini & Bracci, 2000). “Antibody modeling” studies to engineer antibody-like
molecules and increase their stability and specificity are also common, particularly for
humanization of antibodies of animal origin (Morea et al., 2000). Recently, the use of
antibodies as vectors for molecular imaging has become popular. Pharmacokinetic
properties of antibodies have been improved by protein engineering and antibody variants
of different size and antigen binding sites have been produced for the ultimate use as
imaging probes specific to target tissues. A variety of examples include antibody fragments
which have been conjugated to bioluminescence, fluorescence, quantum dots for optical
imaging, as well as iron oxide nanoparticles for magnetic resonance imaging. It is obvious
that molecular imaging tools based on antibodies will find more applications in the future
regarding diagnosis and treatment of cancer and other complex diseases (Olafsen & Wu,
2010).
3.4 Applications for biopolymer production

Protein engineering applications for biopolymer production are also promising. Particularly,
peptides are becoming increasingly important as biomaterials because of their specific
physical, chemical and biological properties. Protein engineering and macromolecular self-
assembly are utilized to produce peptide-based biomaterials, such as elastin-like
polypeptides, silk-like polymers, etc. (Chow et al., 2008). Similarly, biosynthesis,
modification and applications of bacterial polymers have also been discussed recently
(Rehm, 2010).
The ability of protein engineering to create and improve protein domains can be utilized for
producing new biomaterials for medical and engineering applications. One such example is
the use of protein engineering to make new protein and peptide domains which enable
advanced functional hydrogel formation. These domains include leucine zipper coiled-coil
domains, the EF-band domains and elastin-like polypeptides (Banta et al., 2010).
3.5 Nanobiotechnology applications

Nanobiotechnology applications of protein engineering are becoming increasingly
important. The synthesis and assembly of nanotechnological systems into functional
structures and devices has been difficult and limiting their potential applications for a long
time. However, when biomaterials are investigated, it can be realized that they are highly
organized from molecular to the nano- and macroscales, hierarchically. Biological
macromolecules, such as proteins, carbohydrates and lipids are used in the synthesis of
biological tissues in aqueous environments and mild physiological conditions, where this
biosynthetic process is under genetic regulation. Particularly proteins are crucial elements of
biological systems, based on their roles in transport, regulation of tissue formation, physical
performance and biological functions. Thus, they are suitable components for controlled
synthesis and assembly of nanotechnological systems. Combinatorial biology methods
commonly applied in protein engineering studies, such as phage display and bacterial cell
surface display technologies, are also used to select polypeptide sequences which selectively
bind to inorganic compound surfaces, for ultimate applications of nanobiotechnology.
Biopanning procedures that involve washing cycles of the phages or the cells to remove
nonbinders from the surface reveal individual clones that strongly bind to a given inorganic
surface. Those clones are then sequenced to identify the amino acid sequences of the
polypeptides which bind strongly to the inorganic target compound surface, such as (noble)
metals, semiconducting oxides and other important compounds for nanotechnology. The so-
called “genetically engineered proteins for inorganics” (GEPIs) were suggested as important
tools for the self-assembly of molecular systems in nanobiotechnology (Sarikaya et al., 2003).
Since then, many genetically engineered peptides have been selected that specifically bind a
variety of inorganic materials such as platinum, gold, and quartz; and their binding
characteristics were investigated (Seker et al., 2009; Oren et al., 2010). Combining
experimental approaches with computational tools allows engineering of the peptide
binding and assembly characteristics. Thus, higher generation function-specific peptides can
be obtained for applications in tissue engineering, therapeutics, and nanotechnology where
inorganic, organic and biological materials are used (Tamerler et al., 2010). Engineering
protein and peptide building blocks to be used as molecular motors, transducers,
biosensors, and structural elements of nanodevices, and the importance of proteins and
peptides for the development of biocompatible nanomaterials, as well as the impact of
computational techniques in this field have been well recognized (Banta et al., 2007).
Another interesting nanotechnology application is the use of amyloid fibrils as structural
templates for nanowire construction. This application is based on the fact that some proteins
form well-ordered fibrillar aggregates that are called amyloid fibrils. As the self-
organization and assembly of small molecules are crucial for nanotechnology, the self-
association of well-ordered growth fibrils through noncovalent bonds under controlled
conditions was suggested to have a high potential to be used for nanobiotechnology. The
use of amyloid fibrils as structural templates for nanowire construction was explained as a
typical example of potential applications (Hamada et al., 2004).
3.6 Applications with redox proteins and enzymes

Improvement of redox proteins and enzymes by protein engineering is also an important
application field. Such proteins and enzymes can be modified to be used in nanodevices for
biosensing, as well as for nanobiotechnology applications (Gilardi & Fantuzzi, 2001). The
electrochemistry of redox proteins particularly draws attention for applications in biofuel
cells, chemical synthesis and biosensors. Thus, protein engineering applications using
rational design, directed evolution and combination thereof are found for bioelectrocatalysis
(Wong & Schwaneberg, 2003). A recent review on protein engineering of redox-active

enzymes pointed out two emerging areas of protein engineering of redox-active enzymes:
novel nucleic acid-based catalyst construction, and intra-molecular electron transfer
network remodelling (Saab-Rincon & Valderrama, 2009). A variety of studies focused on
cytochrome P450 superfamily of enzymes, such as heme monooxygenases which are
involved in biosynthesis and biodegradation of metabolic compounds and in the oxidation
of xenobiotics. Thus, protein engineering of P450 enzymes for degradation of xenobiotics is
a biotechnological challenge (Wong et al., 1997). Additionally, the fact that heterologous
expression of P450s in bacteria resulted in blue pigment formation required detailed studies
of intermediary metabolism, toxicology, further protein engineering studies and suggested
potential applications in dye industry (Gillam & Guengerich, 2001). More recently, review
articles were published on cytochrome P450 monooxygenases (Urlacher & Eiben, 2006) and
protein engineering of cytochrome P450 biocatalysts for medical, biotechnological and
bioremediation applications (Kumar, 2010).
3.7 Applications with various industrially important enzymes

Protein engineering applications with a variety of industrially important enzymes can be
found in the literature. These include nitrilases (Martinkova & Kren, 2010), aldolases (Clapes
et al., 2010), microbial beta-D-xylosidases (Jordan & Wagschal, 2010) etc. Nitrilases are
important enzymes for biotransformation, but the enzymatic reactions require improvement
for higher industrial process efficiencies. For this purpose, new enzymes were screened
from new isolates, medium and protein engineering methods were applied (Martinkova &
Kren, 2010). Aldolases are also important enzymes for stereoselective synthesis reactions
regarding carbon-carbon bond formation in synthetic organic chemistry. Protein
engineering or screening methods improved aldolases for such synthesis reactions. De novo
computational design of aldolases, aldolase ribozymes etc. are promising applications
(Clapes et al., 2010). Microbial beta-D-xylosidases are also an industrially important group of
enzymes, particularly for baking industry, animal feeding, D-xylose production for xylitol
manufacturing and deinking of recycled paper. As they catalyse hydrolysis of non-reducing
end xylose residues from xylooligosaccharides, they could be used for the hydrolysis of
lignocellulosic biomass in biofuel fermentations to produce ethanol and butanol. Thus,
improving the catalytic efficiency of beta-D-xylosidases is crucial for many industrial
applications (Jordan & Wagschal, 2010). As the use of organic solvents is industrially
suitable for enzymatic reactions, but has adverse effects on enzyme activity and/or stability,
protein engineering of organic solvent tolerant enzymes (Gupta, 1992; Doukyu & Ogino,
2010) has become an important research area. Screening organic solvent-tolerant bacteria or
extremophiles has been preferred to isolate and improve naturally solvent-stable enzymes
(Gupta & Khare, 2009; Doukyu & Ogino, 2010). Other protein engineering examples with
industrially and/or pharmacologically important enzymes include studies on cholesterol
oxidase (Pollegioni et al., 2009), cyclodextrin glucanotransferases (Leemhuis et al., 2010),
human butyrylcholinesterase (Masson et al., 2009), microbial glucoamylases (Kumar &
Satyanarayana, 2009), lipases of different origins (Akoh et al., 2004; Verma et al., 2008;
Kurtovic et al., 2009), phospholipases (Song et al., 2005; De Maria et al., 2007; Simockova &
Griac, 2009) and phytases (Rao et al., 2009). Studies on extremozymes, enzymes isolated
from extremophilic species, revealed their different structural and functional characteristics
which could be exploited for biotechnological applications and improved further by protein
engineering (Bjarnason et al., 1993; Hough & Danson, 1999; Georlette et al., 2004). Homing
endonucleases are another important group of enzymes with application potential in gene
therapy of monogenic diseases. They are double-stranded DNases with extremely rare
recognition sites, and are used as templates for engineering genetic tools to cleave DNA
sequences different from the wild-type targets (Marcaida et al., 2010).
3.8 Other new applications

Recently, novel types of proteins have been developed, using combinatorial protein
engineering techniques. These binding proteins of non-Ig origin are called “affibody binding
proteins”. With their high affinity, these proteins have been used in many different
applications such as diagnostics, bioseparation, functional inhibition, viral targeting, and in
vivo tumor imaging or therapy (Nygren, 2008). More recently, comprehensive reviews on
engineered affinity proteins (Gronwall & Stahl, 2009), and affibody molecules (Lofblom et
al., 2010) were published, where their therapeutic, diagnostic and biotechnological
applications were discussed in detail.
Inteins are protein splicing elements that are involved in a variety of applications such as
protein purification, protein semisynthesis, in vivo and in vitro protein modifications. The
use of intein tags for protein purification in plants with high protein production could
potentially enable industrial production of pharmaceutically important proteins (Evans et
al., 2005). The proteolytic cleavage and ligation activities of inteins have been understood,
which resulted in novel intein applications in protein engineering, enzymology, microarray
production, target detection and transgene activation in plants. The conversion of inteins
into molecular switches was introduced by intein-mediated protein attachment to solid
supports for microarray and western blot studies and by linking nucleic acids to proteins
and controlled splicing (Perler, 2005). Recent intein-mediated protein engineering
applications like protein purification, ligation, cyclization and selenoprotein production
have been discussed in detail lately (Elleuche & Poggeler, 2010).
“Insertional protein engineering” applications are also becoming important, particularly for
biosensor studies. The applications of insertional protein engineering for analytical
molecular sensing have been reviewed by Ferraz and coworkers (Ferraz et al., 2006).
“Zinc finger protein engineering” is another approach that has been used in gene regulation
applications. The zinc finger design and principle is used to design DNA binding proteins to
control gene expression. Examples include a three-finger protein to block the expression of
an oncogene that was transformed into a mouse cell line. Fusion of zinc finger peptides to
repression or activation domains allows selective gene switching off and on (Klug, 2010).
Applications of protein engineering in enzymatic biofuel cell design is also becoming
increasingly important. Particularly, obtaining biofuels from lignocellulosic resources is a
challenge, as the enzyme hydrolysis efficiency of lignocellulose is low which increases the
costs of biofuels. Thus, protein engineering methods have been used to improve the
performance of lignocellulose-degrading enzymes, and biofuels-synthesizing enzymes (Wen
et al., 2009). Protein engineering is also applied to obtain an efficient electrical
communication between biocatalyst(s) and the electrode by rational design and directed
evolution, within the frame of biocatalyst engineering (Guven et al., 2010).
“Virus engineering” is another emerging field, where the virus particles are modified by
protein engineering. Viruses have many promising applications in medicine, biotechnology
and nanotechnology. They could be used as new vaccines, gene therapy and targeted drug
delivery vectors, molecular imaging agents and as building blocks for electronic
nanodevices or nanomaterials construction. Thus, the improvement of the physical stability
of viral particles is crucial for efficient applications with them. Protein engineering methods
are employed to improve physical stability of viral particles (Mateu, 2011).
“Protein cysteine modifications” are also important protein engineering applications. As
cysteine modifications in proteins cause diversities in protein functions, cysteine thiol
chemistry has been applied for in vitro glycoprotein synthesis. This method could be
potentially used for development of new protein-based drugs, improving their half-life,
reducing their toxicity and preventing multidrug resistance development (Nagahara et al.,
2009).
Cyclotides are important proteins that have recently been popular for protein engineering
applications. They are plant proteins made up from small disulfide-rich peptides and are
exceptionally stable to thermal, chemical or enzymatic degradation. This property of
cyclotides makes them valuable molecular templates for many protein engineering and drug
design applications (Craik et al., 2007; Daly et al., 2009; Henriques & Craik, 2010).
4. Conclusion
The modification of natural enzymes and proteins by protein engineering is an increasingly
important scientific field. The well-known methods of rational design and directed
evolution, as well as new techniques will enable efficient and easy modification of proteins.
New technologies such as computational design, catalytic antibodies and mRNA display
would be crucial for de novo engineering of enzymes and also for new areas of protein
engineering.
Protein engineering applications cover a broad range, including biocatalysis for food and
industry, as well as medical, environmental and nanobiotechnological applications. With
advances in recombinant DNA technology tools, “omics” technologies and high-throughput
screening facilities, improved methods for protein engineering will be available, which
would enable easy modification or improvement of more proteins/enzymes for further
specific applications.
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Protein Engineering Methods and Applications

Chapter · February 2012

Burcu Turanli Ceren Alkim

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Evolutionary engineering View project

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Protein Engineering Methods and Applications

2. Protein engineering methods

The advantages and disadvantages of random mutagenesis methods used in protein

Method name Reference(s)

Rational design (Arnold, 1993)

3. Protein engineering applications

3.1 Food and detergent industry applications

industrially important properties of which could be further improved by protein

Application name Example reference(s)

requires microbial fermentation in the presence of biocatalysts such as amylases to liquefy

3.2 Environmental applications

3.3 Medical applications

3.4 Applications for biopolymer production

3.5 Nanobiotechnology applications

3.6 Applications with redox proteins and enzymes

(Wong & Schwaneberg, 2003). A recent review on protein engineering of redox-active

3.7 Applications with various industrially important enzymes

3.8 Other new applications

Kumar, P. & Satyanarayana, T. (2009). Microbial glucoamylases: characteristics and

Skerra, A. (2008). Alternative binding proteins: Anticalins-harnessing the structural

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