Editing Alanine (section)

==Alanine world hypothesis==
Alanine is one of the twenty [[Proteinogenic amino acid|canonical α-amino acids]] used as building blocks (monomers) for the ribosome-mediated biosynthesis of proteins. Alanine is believed to be one of the earliest amino acids to be included in the genetic code standard repertoire.<ref>{{cite journal | vauthors = Trifonov EN | title = Consensus temporal order of amino acids and evolution of the triplet code | journal = Gene | volume = 261 | issue = 1 | pages = 139–51 | date = December 2000 | pmid = 11164045 | doi = 10.1016/S0378-1119(00)00476-5 }}</ref><ref>{{cite journal | vauthors = Higgs PG, Pudritz RE | title = A thermodynamic basis for prebiotic amino acid synthesis and the nature of the first genetic code | journal = Astrobiology | volume = 9 | issue = 5 | pages = 483–90 | date = June 2009 | pmid = 19566427 | doi = 10.1089/ast.2008.0280 | arxiv = 0904.0402 | s2cid = 9039622 | bibcode = 2009AsBio...9..483H }}</ref><ref>{{cite journal | vauthors = Kubyshkin V, Budisa N | title = The Alanine World Model for the Development of the Amino Acid Repertoire in Protein Biosynthesis | journal = International Journal of Molecular Sciences | volume = 20 | issue = 21 | pages = 5507 | date = November 2019 | pmid = 31694194 | pmc = 6862034 | doi = 10.3390/ijms20215507 | doi-access = free }}</ref><ref name=":2">{{cite journal | vauthors = Ntountoumi C, Vlastaridis P, Mossialos D, Stathopoulos C, Iliopoulos I, Promponas V, Oliver SG, Amoutzias GD | display-authors = 6 | title = Low complexity regions in the proteins of prokaryotes perform important functional roles and are highly conserved | journal = Nucleic Acids Research | volume = 47 | issue = 19 | pages = 9998–10009 | date = November 2019 | pmid = 31504783 | pmc = 6821194 | doi = 10.1093/nar/gkz730 }}</ref> 
On the basis of this fact the "alanine world" hypothesis was proposed.<ref>{{cite journal | vauthors = Kubyshkin V, Budisa N | title = Anticipating alien cells with alternative genetic codes: away from the alanine world! | journal = Current Opinion in Biotechnology | volume = 60 | pages = 242–249 | date = December 2019 | pmid = 31279217 | doi = 10.1016/j.copbio.2019.05.006 | doi-access = free }}</ref> This hypothesis explains the evolutionary choice of amino acids in the repertoire of the genetic code from a chemical point of view. In this model the selection of monomers (i.e. amino acids) for [[Protein translation|ribosomal protein synthesis]] is rather limited to those alanine derivatives that are suitable for building [[Alpha helix|α-helix]] or [[Beta sheet|β-sheet]] [[secondary structure|secondary structural]] elements. Dominant secondary structures in life as we know it are α-helices and β-sheets and most canonical amino acids can be regarded as chemical derivatives of alanine. Therefore, most canonical amino acids in proteins can be exchanged with alanine by point mutations while the secondary structure remains intact. The fact that alanine mimics the secondary structure preferences of the majority of the encoded amino acids is practically exploited in [[alanine scanning]] mutagenesis. In addition, classical [[X-ray crystallography]] often employs the polyalanine-backbone model<ref>{{cite journal | vauthors = Karmali AM, Blundell TL, Furnham N | title = Model-building strategies for low-resolution X-ray crystallographic data | journal = Acta Crystallographica. Section D, Biological Crystallography | volume = 65 | issue = Pt 2 | pages = 121–7 | date = February 2009 | pmid = 19171966 | pmc = 2631632 | doi = 10.1107/S0907444908040006 | doi-access = free | bibcode = 2009AcCrD..65..121K }}</ref> to determine three-dimensional structures of proteins using [[molecular replacement]]—a model-based [[phase problem|phasing]] method.