SCOPE (protein engineering)
Encyclopedia
Structure-Based Combinatorial
Protein Engineering
(SCOPE) is a synthetic biology
technique for creating gene libraries
(lineages
) of defined composition designed from structural and probabilistic constraints of the encoded proteins. The development of this technique was driven by fundamental questions about protein structure
, function, and evolution, although the technique is generally applicable for the creation of engineered proteins with commercially desirable properties. Combinatorial Travel Through Sequence Space-Time
is the goal of SCOPE.
At its inception, SCOPE was developed as a homology
-independent recombination technique to enable the creation of multiple crossover libraries from distantly related genes. In this application, an “exon plate tectonics
” design strategy was devised to assemble “equivalent” elements of structure (continental plates) with variability in the junctions linking them (fault lines) to explore global protein space. To create the corresponding library of genes, the breeding scheme of Gregor Mendel
was adapted into a PCR
strategy to selectively cross hybrid genes, a process of iterative
inbreeding to create all possible combinations of coding segments with variable linkages. Genetic complementation
in temperature-sensitive E. coli
was used as the selection system to successfully identify functional hybrid DNA polymerases of minimal architecture with enhanced phenotype
s.
SCOPE was then used to construct a synthetic enzyme
lineage, which was biochemically characterized to recapitulate the evolutionary divergence of two modern day enzymes. The rapid evolvability of chemical diversity in terpene
synthase
s were demonstrated through processes akin to both Darwinian gradualism
and saltation
: some mutational pathways show steady, additive changes, whereas others show drastic jumps between contrasting product specificities with single mutational steps. Further, a metric was devised to describe the chemical distance of mutational steps to derive a chemical-based phylogeny
relating sequence variation to chemical output. These examples establish SCOPE as a standardized method for the construction of synthetic gene libraries from close or distantly related parental sequences to identify functional novelty among the encoded proteins.
Combinatorics
Combinatorics is a branch of mathematics concerning the study of finite or countable discrete structures. Aspects of combinatorics include counting the structures of a given kind and size , deciding when certain criteria can be met, and constructing and analyzing objects meeting the criteria ,...
Protein Engineering
Protein engineering
Protein engineering is the process of developing useful or valuable proteins. It is a young discipline, with much research taking place into the understanding of protein folding and recognition for protein design principles....
(SCOPE) is a synthetic biology
Synthetic biology
Synthetic biology is a new area of biological research that combines science and engineering. It encompasses a variety of different approaches, methodologies, and disciplines with a variety of definitions...
technique for creating gene libraries
Gene library
A genomic library is a population of host bacteria, each of which carries a DNA molecule that was inserted into a cloning vector, such that the collection of cloned DNA molecules represents the entire genome of the source organism...
(lineages
Lineage (evolution)
An evolutionary lineage is a sequence of species, that form a line of descent, each new species the direct result of speciation from an immediate ancestral species. Lineages are subsets of the evolutionary tree of life. Lineages are often determined by the techniques of molecular systematics.-...
) of defined composition designed from structural and probabilistic constraints of the encoded proteins. The development of this technique was driven by fundamental questions about protein structure
Protein structure
Proteins are an important class of biological macromolecules present in all organisms. Proteins are polymers of amino acids. Classified by their physical size, proteins are nanoparticles . Each protein polymer – also known as a polypeptide – consists of a sequence formed from 20 possible L-α-amino...
, function, and evolution, although the technique is generally applicable for the creation of engineered proteins with commercially desirable properties. Combinatorial Travel Through Sequence Space-Time
Spacetime
In physics, spacetime is any mathematical model that combines space and time into a single continuum. Spacetime is usually interpreted with space as being three-dimensional and time playing the role of a fourth dimension that is of a different sort from the spatial dimensions...
is the goal of SCOPE.
At its inception, SCOPE was developed as a homology
Homology (biology)
Homology forms the basis of organization for comparative biology. In 1843, Richard Owen defined homology as "the same organ in different animals under every variety of form and function". Organs as different as a bat's wing, a seal's flipper, a cat's paw and a human hand have a common underlying...
-independent recombination technique to enable the creation of multiple crossover libraries from distantly related genes. In this application, an “exon plate tectonics
Plate tectonics
Plate tectonics is a scientific theory that describes the large scale motions of Earth's lithosphere...
” design strategy was devised to assemble “equivalent” elements of structure (continental plates) with variability in the junctions linking them (fault lines) to explore global protein space. To create the corresponding library of genes, the breeding scheme of Gregor Mendel
Gregor Mendel
Gregor Johann Mendel was an Austrian scientist and Augustinian friar who gained posthumous fame as the founder of the new science of genetics. Mendel demonstrated that the inheritance of certain traits in pea plants follows particular patterns, now referred to as the laws of Mendelian inheritance...
was adapted into a PCR
Polymerase chain reaction
The polymerase chain reaction is a scientific technique in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence....
strategy to selectively cross hybrid genes, a process of iterative
Iteration
Iteration means the act of repeating a process usually with the aim of approaching a desired goal or target or result. Each repetition of the process is also called an "iteration," and the results of one iteration are used as the starting point for the next iteration.-Mathematics:Iteration in...
inbreeding to create all possible combinations of coding segments with variable linkages. Genetic complementation
Complementation (genetics)
In genetics, complementation refers to a relationship between two different strains of an organism which both have homozygous recessive mutations that produce the same phenotype . These strains are true breeding for their mutation...
in temperature-sensitive E. coli
Escherichia coli
Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms . Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls...
was used as the selection system to successfully identify functional hybrid DNA polymerases of minimal architecture with enhanced phenotype
Phenotype
A phenotype is an organism's observable characteristics or traits: such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior...
s.
SCOPE was then used to construct a synthetic enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
lineage, which was biochemically characterized to recapitulate the evolutionary divergence of two modern day enzymes. The rapid evolvability of chemical diversity in terpene
Terpene
Terpenes are a large and diverse class of organic compounds, produced by a variety of plants, particularly conifers, though also by some insects such as termites or swallowtail butterflies, which emit terpenes from their osmeterium. They are often strong smelling and thus may have had a protective...
synthase
Synthase
In biochemistry, a synthase is an enzyme that catalyses a synthesis process.Following the EC number classification, they belong to the group of ligases, with lyases catalysing the reverse reaction....
s were demonstrated through processes akin to both Darwinian gradualism
Gradualism
Gradualism is the belief in or the policy of advancing toward a goal by gradual, often slow stages.-Politics and society:In politics, the concept of gradualism is used to describe the belief that change ought to be brought about in small, discrete increments rather than in abrupt strokes such as...
and saltation
Saltation (biology)
In biology, ""saltation"" is a sudden change from one generation to the next, that is large, or very large, in comparison with the usual variation of an organism...
: some mutational pathways show steady, additive changes, whereas others show drastic jumps between contrasting product specificities with single mutational steps. Further, a metric was devised to describe the chemical distance of mutational steps to derive a chemical-based phylogeny
Phylogenetics
In biology, phylogenetics is the study of evolutionary relatedness among groups of organisms , which is discovered through molecular sequencing data and morphological data matrices...
relating sequence variation to chemical output. These examples establish SCOPE as a standardized method for the construction of synthetic gene libraries from close or distantly related parental sequences to identify functional novelty among the encoded proteins.
See also
- Directed evolutionDirected evolutionthumb|250px|right|An example of a possible round to evolve a protein based fluorescent sensor for a specific analyte using two consecutive FACS sortings...
- Enzymology
- Expanded genetic codeExpanded genetic codeAn expanded genetic code refers to an artificially modified genetic code in which one or more specific codons have been allocated to encode an amino acid which is not among the twenty/twenty-two found in nature.-Background:...
- Gene synthesisGene synthesisArtificial gene synthesis is the process of synthesizing a gene in vitro without the need for initial template DNA samples. The main method is currently by oligonucleotide synthesis from digital genetic sequences and subsequent annealing of the resultant fragments...
- GenomeGenomeIn modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
- Nucleic acid analoguesNucleic acid analoguesNucleic acid analogues are compounds structurally similar to naturally occurring RNA and DNA, used in medicine and in molecular biology research....
- Protein designProtein designProtein design is the design of new protein molecules, either from scratch or by making calculated variations on a known structure. The use of rational design techniques for proteins is a major aspect of protein engineering....
- Protein engineeringProtein engineeringProtein engineering is the process of developing useful or valuable proteins. It is a young discipline, with much research taking place into the understanding of protein folding and recognition for protein design principles....
- Protein foldingProtein foldingProtein folding is the process by which a protein structure assumes its functional shape or conformation. It is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from random coil....
- ProteomicsProteomicsProteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells. The term "proteomics" was first coined in 1997 to make an analogy with...
- ProteomeProteomeThe proteome is the entire set of proteins expressed by a genome, cell, tissue or organism. More specifically, it is the set of expressed proteins in a given type of cells or an organism at a given time under defined conditions. The term is a portmanteau of proteins and genome.The term has been...
- Structural biologyStructural biologyStructural biology is a branch of molecular biology, biochemistry, and biophysics concerned with the molecular structure of biological macromolecules, especially proteins and nucleic acids, how they acquire the structures they have, and how alterations in their structures affect their function...
- Synthetic biologySynthetic biologySynthetic biology is a new area of biological research that combines science and engineering. It encompasses a variety of different approaches, methodologies, and disciplines with a variety of definitions...