Local Order in the Unfolded State: Conformational Biases and Nearest Neighbor Interactions
The discovery of Intrinsically Disordered Proteins, which contain significant levels of disorder yet perform complex biologically functions, as well as unwanted aggregation, has motivated numerous experimental and theoretical studies aimed at describing residue-level conformational ensembles. Multip...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2014-07-01
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| Series: | Biomolecules |
| Subjects: | |
| Online Access: | http://www.mdpi.com/2218-273X/4/3/725 |
| _version_ | 1811208788695318528 |
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| author | Siobhan Toal Reinhard Schweitzer-Stenner |
| author_facet | Siobhan Toal Reinhard Schweitzer-Stenner |
| author_sort | Siobhan Toal |
| collection | DOAJ |
| description | The discovery of Intrinsically Disordered Proteins, which contain significant levels of disorder yet perform complex biologically functions, as well as unwanted aggregation, has motivated numerous experimental and theoretical studies aimed at describing residue-level conformational ensembles. Multiple lines of evidence gathered over the last 15 years strongly suggest that amino acids residues display unique and restricted conformational preferences in the unfolded state of peptides and proteins, contrary to one of the basic assumptions of the canonical random coil model. To fully understand residue level order/disorder, however, one has to gain a quantitative, experimentally based picture of conformational distributions and to determine the physical basis underlying residue-level conformational biases. Here, we review the experimental, computational and bioinformatic evidence for conformational preferences of amino acid residues in (mostly short) peptides that can be utilized as suitable model systems for unfolded states of peptides and proteins. In this context particular attention is paid to the alleged high polyproline II preference of alanine. We discuss how these conformational propensities may be modulated by peptide solvent interactions and so called nearest-neighbor interactions. The relevance of conformational propensities for the protein folding problem and the understanding of IDPs is briefly discussed. |
| first_indexed | 2024-04-12T04:27:32Z |
| format | Article |
| id | doaj.art-2b77dee905254615b1bdcc7b0cd59d68 |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-04-12T04:27:32Z |
| publishDate | 2014-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-2b77dee905254615b1bdcc7b0cd59d682022-12-22T03:48:02ZengMDPI AGBiomolecules2218-273X2014-07-014372577310.3390/biom4030725biom4030725Local Order in the Unfolded State: Conformational Biases and Nearest Neighbor InteractionsSiobhan Toal0Reinhard Schweitzer-Stenner1Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19026, USADepartment of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19026, USAThe discovery of Intrinsically Disordered Proteins, which contain significant levels of disorder yet perform complex biologically functions, as well as unwanted aggregation, has motivated numerous experimental and theoretical studies aimed at describing residue-level conformational ensembles. Multiple lines of evidence gathered over the last 15 years strongly suggest that amino acids residues display unique and restricted conformational preferences in the unfolded state of peptides and proteins, contrary to one of the basic assumptions of the canonical random coil model. To fully understand residue level order/disorder, however, one has to gain a quantitative, experimentally based picture of conformational distributions and to determine the physical basis underlying residue-level conformational biases. Here, we review the experimental, computational and bioinformatic evidence for conformational preferences of amino acid residues in (mostly short) peptides that can be utilized as suitable model systems for unfolded states of peptides and proteins. In this context particular attention is paid to the alleged high polyproline II preference of alanine. We discuss how these conformational propensities may be modulated by peptide solvent interactions and so called nearest-neighbor interactions. The relevance of conformational propensities for the protein folding problem and the understanding of IDPs is briefly discussed.http://www.mdpi.com/2218-273X/4/3/725unfoldedpeptide conformationpPIInearest-neighboralanine |
| spellingShingle | Siobhan Toal Reinhard Schweitzer-Stenner Local Order in the Unfolded State: Conformational Biases and Nearest Neighbor Interactions Biomolecules unfolded peptide conformation pPII nearest-neighbor alanine |
| title | Local Order in the Unfolded State: Conformational Biases and Nearest Neighbor Interactions |
| title_full | Local Order in the Unfolded State: Conformational Biases and Nearest Neighbor Interactions |
| title_fullStr | Local Order in the Unfolded State: Conformational Biases and Nearest Neighbor Interactions |
| title_full_unstemmed | Local Order in the Unfolded State: Conformational Biases and Nearest Neighbor Interactions |
| title_short | Local Order in the Unfolded State: Conformational Biases and Nearest Neighbor Interactions |
| title_sort | local order in the unfolded state conformational biases and nearest neighbor interactions |
| topic | unfolded peptide conformation pPII nearest-neighbor alanine |
| url | http://www.mdpi.com/2218-273X/4/3/725 |
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