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
spacetime is the goal of SCOPE.
Description
At its inception, SCOPE was developed as a
homology
Homology may refer to:
Sciences
Biology
*Homology (biology), any characteristic of biological organisms that is derived from a common ancestor
* Sequence homology, biological homology between DNA, RNA, or protein sequences
*Homologous chrom ...
-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
Plate tectonics (from the la, label=Late Latin, tectonicus, from the grc, τεκτονικός, lit=pertaining to building) is the generally accepted scientific theory that considers the Earth's lithosphere to comprise a number of large ...
) 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 PCR or pcr may refer to:
Science
* Phosphocreatine, a phosphorylated creatine molecule
* Principal component regression, a statistical technique
Medicine
* Polymerase chain reaction
** COVID-19 testing, often performed using the polymerase chain r ...
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 genetics, complementation occurs when two strains of an organism with different homozygous recessive mutations that produce the same mutant phenotype (for example, a change in wing structure in flies) have offspring that express the wild-typ ...
in temperature-sensitive
E. coli
''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus ''Escher ...
was used as the selection system to successfully identify functional
hybrid DNA polymerases of minimal architecture with enhanced
phenotypes.
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 In biochemistry, a synthase is an enzyme that catalyses a synthesis process.
Note that, originally, biochemical nomenclature distinguished synthetases and synthases. Under the original definition, synthases do not use energy from nucleoside tripho ...
s were demonstrated through processes akin to both Darwinian
gradualism
Gradualism, from the Latin ''gradus'' ("step"), is a hypothesis, a theory or a tenet assuming that change comes about gradually or that variation is gradual in nature and happens over time as opposed to in large steps. Uniformitarianism, incrementa ...
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.
See also
*
Directed evolution
*
Enzymology
Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. A ...
*
Expanded genetic code
*
Gene synthesis
Artificial gene synthesis, or simply gene synthesis, refers to a group of methods that are used in synthetic biology to construct and assemble genes from nucleotides '' de novo''. Unlike DNA synthesis in living cells, artificial gene synthesis do ...
*
Genome
*
Nucleic acid analogues
*
Protein design
*
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. It has been used to imp ...
*
Protein folding
*
Proteomics
Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In ...
*
Proteome
*
Structural biology
*
Synthetic biology
Further reading
*
*
* {{cite journal , vauthors = O'Maille PE, Malone A, Dellas N, Andes Hess B, Smentek L, Sheehan I, Greenhagen BT, Chappell J, Manning G, Noel JP , title = Quantitative exploration of the catalytic landscape separating divergent plant sesquiterpene synthases , journal = Nature Chemical Biology , volume = 4 , issue = 10 , pages = 617–23 , date = Oct 2008 , pmid = 18776889 , pmc = 2664519 , doi = 10.1038/nchembio.113
External links
SCOPE Patent
Combinatorial chemistry
Evolutionary biology
Protein engineering