Statistical Evidence for a Helical Nascent Chain
We investigate the hypothesis that protein folding is a kinetic, non-equilibrium process, in which the structure of the nascent chain is crucial. We compare actual amino acid frequencies in loops, <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inlin...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-02-01
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| Series: | Biomolecules |
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| Online Access: | https://www.mdpi.com/2218-273X/11/3/357 |
| _version_ | 1797395066035109888 |
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| author | Leonor Cruzeiro Andrew C. Gill J. Chris Eilbeck |
| author_facet | Leonor Cruzeiro Andrew C. Gill J. Chris Eilbeck |
| author_sort | Leonor Cruzeiro |
| collection | DOAJ |
| description | We investigate the hypothesis that protein folding is a kinetic, non-equilibrium process, in which the structure of the nascent chain is crucial. We compare actual amino acid frequencies in loops, <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>α</mi></semantics></math></inline-formula>-helices and <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>β</mi></semantics></math></inline-formula>-sheets with the frequencies that would arise in the absence of any amino acid bias for those secondary structures. The novel analysis suggests that while specific amino acids exist to drive the formation of loops and sheets, none stand out as drivers for <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>α</mi></semantics></math></inline-formula>-helices. This favours the idea that the <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>α</mi></semantics></math></inline-formula>-helix is the initial structure of most proteins before the folding process begins. |
| first_indexed | 2024-03-09T00:29:00Z |
| format | Article |
| id | doaj.art-03b2985c07c845a9b9cdf00b7678fd6a |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-09T00:29:00Z |
| publishDate | 2021-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-03b2985c07c845a9b9cdf00b7678fd6a2023-12-11T18:35:51ZengMDPI AGBiomolecules2218-273X2021-02-0111335710.3390/biom11030357Statistical Evidence for a Helical Nascent ChainLeonor Cruzeiro0Andrew C. Gill1J. Chris Eilbeck2CCMAR/CIMAR—Centro de Ciências do Mar, FCT, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, PortugalSchool of Chemistry, Joseph Banks Laboratories, University of Lincoln, Green Lane, Lincoln LN67DL, UKDepartment of Mathematics and Maxwell Institute, Heriot-Watt University, Edinburgh EH14 4AS, UKWe investigate the hypothesis that protein folding is a kinetic, non-equilibrium process, in which the structure of the nascent chain is crucial. We compare actual amino acid frequencies in loops, <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>α</mi></semantics></math></inline-formula>-helices and <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>β</mi></semantics></math></inline-formula>-sheets with the frequencies that would arise in the absence of any amino acid bias for those secondary structures. The novel analysis suggests that while specific amino acids exist to drive the formation of loops and sheets, none stand out as drivers for <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>α</mi></semantics></math></inline-formula>-helices. This favours the idea that the <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>α</mi></semantics></math></inline-formula>-helix is the initial structure of most proteins before the folding process begins.https://www.mdpi.com/2218-273X/11/3/357protein foldingsingle amino acid distributionssecondary structure predictionfolding pathway |
| spellingShingle | Leonor Cruzeiro Andrew C. Gill J. Chris Eilbeck Statistical Evidence for a Helical Nascent Chain Biomolecules protein folding single amino acid distributions secondary structure prediction folding pathway |
| title | Statistical Evidence for a Helical Nascent Chain |
| title_full | Statistical Evidence for a Helical Nascent Chain |
| title_fullStr | Statistical Evidence for a Helical Nascent Chain |
| title_full_unstemmed | Statistical Evidence for a Helical Nascent Chain |
| title_short | Statistical Evidence for a Helical Nascent Chain |
| title_sort | statistical evidence for a helical nascent chain |
| topic | protein folding single amino acid distributions secondary structure prediction folding pathway |
| url | https://www.mdpi.com/2218-273X/11/3/357 |
| work_keys_str_mv | AT leonorcruzeiro statisticalevidenceforahelicalnascentchain AT andrewcgill statisticalevidenceforahelicalnascentchain AT jchriseilbeck statisticalevidenceforahelicalnascentchain |