SherbyNet - /page/wikibook/entry.mu

Micron Document

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In `F33f`_`[evolutionary biology`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Evolutionary_biology]`_`f, `!sequence space`! is a way of representing all possible sequences (for a `F33f`_`[protein`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Protein]`_`f, `F33f`_`[gene`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Gene]`_`f or `F33f`_`[genome`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Genome]`_`f).`:cite-ref-1[`F5bf`_`[1`#cite-note-1]`_`f]`:cite-ref-2[`F5bf`_`[2`#cite-note-2]`_`f] The sequence space has one dimension per `F33f`_`[amino acid`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Amino_acid]`_`f or `F33f`_`[nucleotide`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Nucleotide]`_`f in the sequence leading to `F33f`_`[highly dimensional spaces`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Dimension]`_`f.`:cite-ref-0-3-0[`F5bf`_`[3`#cite-note-0-3]`_`f]`:cite-ref-1-4-0[`F5bf`_`[4`#cite-note-1-4]`_`f]

Most sequences in sequence space have no function, leaving relatively small regions that are populated by naturally occurring genes.`:cite-ref-5[`F5bf`_`[5`#cite-note-5]`_`f] Each protein sequence is adjacent to all other sequences that can be reached through a single `F33f`_`[mutation`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Mutation]`_`f.`:cite-ref-6[`F5bf`_`[6`#cite-note-6]`_`f] It has been estimated that the whole functional protein sequence space has been explored by life on the Earth.`:cite-ref-7[`F5bf`_`[7`#cite-note-7]`_`f] Evolution by natural selection can be visualised as the process of sampling nearby sequences in sequence space and moving to any with improved `F33f`_`[fitness`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Fitness_(biology)]`_`f over the current one.

>>Contents

• `F0af`_`[Representation`#representation]`_`f

• `F0af`_`[Functional sequences in sequence space`#functional-sequences-in-sequence-space]`_`f

• `F0af`_`[Exploration through directed evolution and rational design`#exploration-through-directed-evolution-and-rational-design]`_`f

• `F0af`_`[See also`#see-also]`_`f

• `F0af`_`[References`#references]`_`f

-─

>>Representation

A sequence space is usually laid out as a grid. For `F33f`_`[protein`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Protein]`_`f sequence spaces, each `F33f`_`[residue`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Amino_acid]`_`f in the protein is represented by a `F33f`_`[dimension`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Dimension]`_`f with 20 possible positions along that axis corresponding to the possible amino acids.`:cite-ref-0-3-1[`F5bf`_`[3`#cite-note-0-3]`_`f]`:cite-ref-1-4-1[`F5bf`_`[4`#cite-note-1-4]`_`f] Hence there are 400 possible `F33f`_`[dipeptides`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Dipeptide]`_`f arranged in a 20x20 space but that expands to 10130 for even a small protein of 100 amino acids arranged in a space with 100 dimensions. Although such overwhelming multidimensionality cannot be visualised or represented diagrammatically, it provides a useful abstract model to think about the range of proteins and `F33f`_`[evolution`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Evolution]`_`f from one sequence to another.

These highly multidimensional spaces can be compressed to 2 or 3 dimensions using `F33f`_`[principal component analysis`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Principal_component_analysis]`_`f. A fitness landscape is simply a sequence space with an extra vertical axis of fitness added for each sequence.`:cite-ref-8[`F5bf`_`[8`#cite-note-8]`_`f]

>>Functional sequences in sequence space

Despite the diversity of protein superfamilies, sequence space is extremely sparsely populated by functional proteins. Most random protein sequences have no fold or function.`:cite-ref-9[`F5bf`_`[9`#cite-note-9]`_`f] `F33f`_`[Enzyme superfamilies`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Protein_superfamily]`_`f, therefore, exist as tiny clusters of active proteins in a vast empty space of non-functional sequence.`:cite-ref-10[`F5bf`_`[10`#cite-note-10]`_`f]`:cite-ref-11[`F5bf`_`[11`#cite-note-11]`_`f]

The density of functional proteins in sequence space, and the proximity of different functions to one another is a key determinant in understanding `F33f`_`[evolvability`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Evolvability]`_`f.`:cite-ref-12[`F5bf`_`[12`#cite-note-12]`_`f] The degree of interpenetration of two `F33f`_`[neutral networks`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Neutral_network_(evolution)]`_`f of different `F33f`_`[activities`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Enzyme_activity]`_`f in sequence space will determine how easy it is to evolve from one activity to another. The more overlap between different activities in sequence space, the more `F33f`_`[cryptic variation`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Cryptic_variation]`_`f for `F33f`_`[promiscuous activity`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Promiscuous_activity]`_`f will be.`:cite-ref-13[`F5bf`_`[13`#cite-note-13]`_`f]

Protein sequence space has been compared to the `*`F33f`_`[Library of Babel`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Library_of_Babel]`_`f`*, a theoretical library containing all possible books that are 410 pages long.`:cite-ref-14[`F5bf`_`[14`#cite-note-14]`_`f]`:cite-ref-15[`F5bf`_`[15`#cite-note-15]`_`f] In the `*Library of Babel`*, finding any book that made sense was impossible due to the sheer number and lack of order. The same would be true of protein sequences if it were not for natural selection, which has selected out only protein sequences that make sense. Additionally, each protein sequences is surrounded by a set of neighbours (point mutants) that are likely to have at least some function.

On the other hand, the effective "alphabet" of the sequence space may in fact be quite small, reducing the useful number of amino acids from 20 to a much lower number. For example, in an extremely simplified view, all amino acids can be sorted into two classes (hydrophobic/polar) by `F33f`_`[hydrophobicity`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Hydrophobicity]`_`f and still allow many common structures to show up. Early life on Earth may have only four or five types of amino acids to work with,`:cite-ref-16[`F5bf`_`[16`#cite-note-16]`_`f] and researches have shown that functional proteins can be created from wild-type ones by a similar alphabet-reduction process.`:cite-ref-17[`F5bf`_`[17`#cite-note-17]`_`f]`:cite-ref-18[`F5bf`_`[18`#cite-note-18]`_`f] Reduced alphabets are also useful in `F33f`_`[bioinformatics`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Bioinformatics]`_`f, as they provide an easy way of analyzing protein similarity.`:cite-ref-19[`F5bf`_`[19`#cite-note-19]`_`f]`:cite-ref-20[`F5bf`_`[20`#cite-note-20]`_`f]

>>Exploration through directed evolution and rational design

A major focus in the field of `F33f`_`[protein engineering`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Protein_engineering]`_`f is on creating `F33f`_`[DNA libraries`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Library_(biology)]`_`f that `F33f`_`[sample`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Sampling_(statistics)]`_`f regions of sequence space, often with the goal of finding mutants of proteins with enhanced functions compared to the `F33f`_`[wild type`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Wild_type]`_`f. These libraries are created either by using a wild type sequence as a template and applying one or more `F33f`_`[mutagenesis`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Mutagenesis_(molecular_biology_technique)]`_`f techniques to make different variants of it, or by creating proteins from scratch using `F33f`_`[artificial gene synthesis`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Artificial_gene_synthesis]`_`f. These libraries are then `F33f`_`[screened or selected`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Protein_engineering]`_`f, and ones with improved `F33f`_`[phenotypes`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Phenotype]`_`f are used for the next round of mutagenesis.

>>See also

• `F33f`_`[Protein`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Protein]`_`f

• `F33f`_`[Sequence space`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Sequence_space]`_`f

• `F33f`_`[Directed evolution`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Directed_evolution]`_`f

• `F33f`_`[Protein engineering`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Protein_engineering]`_`f

• `F33f`_`[High-dimensional space`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=High-dimensional_space]`_`f

>>References

`:cite-note-1`!1.`! `F0af`_`[↑`#cite-ref-1]`_`f `:citerefdepristoweinreich-daniel-m-hartl-daniel-l-2005`aDePristo, Mark A.; Weinreich, Daniel M.; Hartl, Daniel L. (2 August 2005). "Missense meanderings in sequence space: a biophysical view of protein evolution". `*Nature Reviews Genetics`*. `!6`! (9): 678–687. `F33f`_`[doi`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Doi_(identifier)]`_`f:10.1038/nrg1672. `F33f`_`[PMID`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMID_(identifier)]`_`f 16074985. `F33f`_`[S2CID`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=S2CID_(identifier)]`_`f 13236893.

`:cite-note-2`!2.`! `F0af`_`[↑`#cite-ref-2]`_`f `:citerefmaynard-smith1970`aMaynard Smith, John (7 February 1970). "Natural Selection and the Concept of a Protein Space". `*Nature`*. `!225`! (5232): 563–564. `F33f`_`[Bibcode`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Bibcode_(identifier)]`_`f:1970Natur.225..563M. `F33f`_`[doi`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Doi_(identifier)]`_`f:10.1038/225563a0. `F33f`_`[PMID`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMID_(identifier)]`_`f 5411867. `F33f`_`[S2CID`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=S2CID_(identifier)]`_`f 204994726.

`:cite-note-0-3`!3.`! `F0af`_`[↑`#cite-ref-0-3-0]`_`f `:citerefbornberg-bauerchan-h-s-1999`aBornberg-Bauer, E.; Chan, H. S. (14 September 1999). "Modeling evolutionary landscapes: Mutational stability, topology, and superfunnels in sequence space". `*Proceedings of the National Academy of Sciences`*. `!96`! (19): 10689–10694. `F33f`_`[Bibcode`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Bibcode_(identifier)]`_`f:1999PNAS...9610689B. `F33f`_`[doi`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Doi_(identifier)]`_`f:10.1073/pnas.96.19.10689. `F33f`_`[PMC`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMC_(identifier)]`_`f 17944. `F33f`_`[PMID`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMID_(identifier)]`_`f 10485887.

`:cite-note-1-4`!4.`! `F0af`_`[↑`#cite-ref-1-4-0]`_`f `:citerefcordesdavidson-arsauer-rt1996`aCordes, MH; Davidson, AR; Sauer, RT (Feb 1996). "Sequence space, folding and protein design". `*Current Opinion in Structural Biology`*. `!6`! (1): 3–10. `F33f`_`[doi`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Doi_(identifier)]`_`f:10.1016/S0959-440X(96)80088-1. `F33f`_`[PMID`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMID_(identifier)]`_`f 8696970.

`:cite-note-5`!5.`! `F0af`_`[↑`#cite-ref-5]`_`f `:citerefhermesblacklow-scknowles-jr1990`aHermes, JD; Blacklow, SC; Knowles, JR (Jan 1990). "Searching sequence space by definably random mutagenesis: improving the catalytic potency of an enzyme". `*Proceedings of the National Academy of Sciences of the United States of America`*. `!87`! (2): 696–700. `F33f`_`[Bibcode`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Bibcode_(identifier)]`_`f:1990PNAS...87..696H. `F33f`_`[doi`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Doi_(identifier)]`_`f:10.1073/pnas.87.2.696. `F33f`_`[PMC`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMC_(identifier)]`_`f 53332. `F33f`_`[PMID`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMID_(identifier)]`_`f 1967829.

`:cite-note-6`!6.`! `F0af`_`[↑`#cite-ref-6]`_`f `:citerefromeroarnold2009`aRomero, Philip A.; Arnold, Frances H. (December 2009). "Exploring protein fitness landscapes by directed evolution". `*Nature Reviews Molecular Cell Biology`*. `!10`! (12): 866–876. `F33f`_`[doi`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Doi_(identifier)]`_`f:10.1038/nrm2805. `F33f`_`[ISSN`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=ISSN_(identifier)]`_`f 1471-0080. `F33f`_`[PMC`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMC_(identifier)]`_`f 2997618. `F33f`_`[PMID`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMID_(identifier)]`_`f 19935669.

`:cite-note-7`!7.`! `F0af`_`[↑`#cite-ref-7]`_`f `:citerefdrydenthomsonwhite2008`aDryden, David T.F; Thomson, Andrew R.; White, John H. (2008). "How much of protein sequence space has been explored by life on Earth?". `*Journal of the Royal Society Interface`*. `!5`! (25): 953–956. `F33f`_`[doi`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Doi_(identifier)]`_`f:10.1098/rsif.2008.0085. `F33f`_`[PMC`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMC_(identifier)]`_`f 2459213. `F33f`_`[PMID`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMID_(identifier)]`_`f 18426772.

`:cite-note-8`!8.`! `F0af`_`[↑`#cite-ref-8]`_`f `:citerefromeroarnold-fh2009`aRomero, PA; Arnold, FH (Dec 2009). "Exploring protein fitness landscapes by directed evolution". `*Nature Reviews Molecular Cell Biology`*. `!10`! (12): 866–76. `F33f`_`[doi`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Doi_(identifier)]`_`f:10.1038/nrm2805. `F33f`_`[PMC`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMC_(identifier)]`_`f 2997618. `F33f`_`[PMID`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMID_(identifier)]`_`f 19935669.

`:cite-note-9`!9.`! `F0af`_`[↑`#cite-ref-9]`_`f `:citerefkeefeszostak-jw2001`aKeefe, AD; Szostak, JW (Apr 5, 2001). "Functional proteins from a random-sequence library". `*Nature`*. `!410`! (6829): 715–8. `F33f`_`[Bibcode`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Bibcode_(identifier)]`_`f:2001Natur.410..715K. `F33f`_`[doi`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Doi_(identifier)]`_`f:10.1038/35070613. `F33f`_`[PMC`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMC_(identifier)]`_`f 4476321. `F33f`_`[PMID`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMID_(identifier)]`_`f 11287961.

`:cite-note-10`!10.`! `F0af`_`[↑`#cite-ref-10]`_`f `:citerefstemmer1995`aStemmer, Willem P. C. (June 1995). "Searching Sequence Space". `*Bio/Technology`*. `!13`! (6): 549–553. `F33f`_`[doi`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Doi_(identifier)]`_`f:10.1038/nbt0695-549. `F33f`_`[S2CID`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=S2CID_(identifier)]`_`f 20117819.

`:cite-note-11`!11.`! `F0af`_`[↑`#cite-ref-11]`_`f `:citerefbornberg-bauer1997`aBornberg-Bauer, E (Nov 1997). "How are model protein structures distributed in sequence space?". `*Biophysical Journal`*. `!73`! (5): 2393–403. `F33f`_`[Bibcode`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Bibcode_(identifier)]`_`f:1997BpJ....73.2393B. `F33f`_`[doi`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Doi_(identifier)]`_`f:10.1016/S0006-3495(97)78268-7. `F33f`_`[PMC`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMC_(identifier)]`_`f 1181141. `F33f`_`[PMID`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMID_(identifier)]`_`f 9370433.

`:cite-note-12`!12.`! `F0af`_`[↑`#cite-ref-12]`_`f `:citerefbornberg-bauerhuylmans-aksikosek-t2010`aBornberg-Bauer, E; Huylmans, AK; Sikosek, T (Jun 2010). "How do new proteins arise?". `*Current Opinion in Structural Biology`*. `!20`! (3): 390–6. `F33f`_`[doi`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Doi_(identifier)]`_`f:10.1016/j.sbi.2010.02.005. `F33f`_`[PMID`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMID_(identifier)]`_`f 20347587.

`:cite-note-13`!13.`! `F0af`_`[↑`#cite-ref-13]`_`f `:citerefwagner2011`aWagner, Andreas (2011-07-14). `*The origins of evolutionary innovations : a theory of transformative change in living systems`*. Oxford [etc.]: Oxford University Press. `F33f`_`[ISBN`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=ISBN_(identifier)]`_`f 978-0199692590.

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`:cite-note-15`!15.`! `F0af`_`[↑`#cite-ref-15]`_`f `:citerefostermeier2007`aOstermeier, M (March 2007). "Beyond cataloging the Library of Babel". `*Chemistry & Biology`*. `!14`! (3): 237–8. `F33f`_`[doi`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Doi_(identifier)]`_`f:10.1016/j.chembiol.2007.03.002. `F33f`_`[PMID`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMID_(identifier)]`_`f 17379136.

`:cite-note-16`!16.`! `F0af`_`[↑`#cite-ref-16]`_`f `:citerefdrydenthomsonwhite2008`aDryden, DT; Thomson, AR; White, JH (6 August 2008). "How much of protein sequence space has been explored by life on Earth?". `*Journal of the Royal Society, Interface`*. `!5`! (25): 953–6. `F33f`_`[doi`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Doi_(identifier)]`_`f:10.1098/rsif.2008.0085. `F33f`_`[PMC`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMC_(identifier)]`_`f 2459213. `F33f`_`[PMID`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMID_(identifier)]`_`f 18426772.

`:cite-note-17`!17.`! `F0af`_`[↑`#cite-ref-17]`_`f `:citerefakanumakigawayokoyama2002`aAkanuma, S.; Kigawa, T.; Yokoyama, S. (2 October 2002). "Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set". `*Proceedings of the National Academy of Sciences`*. `!99`! (21): 13549–13553. `F33f`_`[Bibcode`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Bibcode_(identifier)]`_`f:2002PNAS...9913549A. `F33f`_`[doi`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Doi_(identifier)]`_`f:10.1073/pnas.222243999. `F33f`_`[PMC`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMC_(identifier)]`_`f 129711. `F33f`_`[PMID`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMID_(identifier)]`_`f 12361984.

`:cite-note-18`!18.`! `F0af`_`[↑`#cite-ref-18]`_`f `:citereffujishimawangpalmerabe2018`a`F33f`_`[Fujishima, Kosuke`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Lynn_J._Rothschild]`_`f; Wang, Kendrick M.; Palmer, Jesse A.; Abe, Nozomi; Nakahigashi, Kenji; Endy, Drew; Rothschild, Lynn J. (29 January 2018). "Reconstruction of cysteine biosynthesis using engineered cysteine-free enzymes". `*Scientific Reports`*. `!8`! (1): 1776. `F33f`_`[Bibcode`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Bibcode_(identifier)]`_`f:2018NatSR...8.1776F. `F33f`_`[doi`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Doi_(identifier)]`_`f:10.1038/s41598-018-19920-y. `F33f`_`[PMC`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMC_(identifier)]`_`f 5788988. `F33f`_`[PMID`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMID_(identifier)]`_`f 29379050.

`:cite-note-19`!19.`! `F0af`_`[↑`#cite-ref-19]`_`f `:citerefbacarditstouthirstvalencia2009`aBacardit, Jaume; Stout, Michael; Hirst, Jonathan D; Valencia, Alfonso; Smith, Robert E; Krasnogor, Natalio (6 January 2009). "Automated Alphabet Reduction for Protein Datasets". `*BMC Bioinformatics`*. `!10`! (1): 6. `F33f`_`[doi`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Doi_(identifier)]`_`f:10.1186/1471-2105-10-6. `F33f`_`[PMC`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMC_(identifier)]`_`f 2646702. `F33f`_`[PMID`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMID_(identifier)]`_`f 19126227.

`:cite-note-20`!20.`! `F0af`_`[↑`#cite-ref-20]`_`f `:citerefsolis2019`aSolis, Armando D. (30 July 2019). "Reduced alphabet of prebiotic amino acids optimally encodes the conformational space of diverse extant protein folds". `*BMC Evolutionary Biology`*. `!19`! (1) 158. `F33f`_`[Bibcode`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Bibcode_(identifier)]`_`f:2019BMCEE..19..158S. `F33f`_`[doi`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Doi_(identifier)]`_`f:10.1186/s12862-019-1464-6. `F33f`_`[PMC`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMC_(identifier)]`_`f 6668081. `F33f`_`[PMID`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMID_(identifier)]`_`f 31362700.

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