A Structure-Based Mechanism for the Denaturing Action of Urea, Guanidinium Ion and Thiocyanate Ion
An exhaustive analysis of all the protein structures deposited in the Protein Data Bank, here performed, has allowed the identification of hundredths of protein-bound urea molecules and the structural characterization of such binding sites. It emerged that, even though urea molecules are largely inv...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-12-01
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| Series: | Biology |
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| Online Access: | https://www.mdpi.com/2079-7737/11/12/1764 |
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| author | Antonella Paladino Nicole Balasco Luigi Vitagliano Giuseppe Graziano |
| author_facet | Antonella Paladino Nicole Balasco Luigi Vitagliano Giuseppe Graziano |
| author_sort | Antonella Paladino |
| collection | DOAJ |
| description | An exhaustive analysis of all the protein structures deposited in the Protein Data Bank, here performed, has allowed the identification of hundredths of protein-bound urea molecules and the structural characterization of such binding sites. It emerged that, even though urea molecules are largely involved in hydrogen bonds with both backbone and side chains, they are also able to make van der Waals contacts with nonpolar moieties. As similar findings have also been previously reported for guanidinium and thiocyanate, this observation suggests that promiscuity is a general property of protein denaturants. Present data provide strong support for a mechanism based on the protein-denaturant direct interactions with a denaturant binding model to equal and independent sites. In this general framework, our investigations also highlight some interesting insights into the different denaturing power of urea compared to guanidinium/thiocyanate. |
| first_indexed | 2024-03-09T17:19:11Z |
| format | Article |
| id | doaj.art-6667b041afd4471485023d081d853eda |
| institution | Directory Open Access Journal |
| issn | 2079-7737 |
| language | English |
| last_indexed | 2024-03-09T17:19:11Z |
| publishDate | 2022-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biology |
| spelling | doaj.art-6667b041afd4471485023d081d853eda2023-11-24T13:23:05ZengMDPI AGBiology2079-77372022-12-011112176410.3390/biology11121764A Structure-Based Mechanism for the Denaturing Action of Urea, Guanidinium Ion and Thiocyanate IonAntonella Paladino0Nicole Balasco1Luigi Vitagliano2Giuseppe Graziano3Institute of Biostructures and Bioimaging, CNR, Via Pietro Castellino 111, 80131 Naples, ItalyInstitute of Molecular Biology and Pathology, CNR c/o Department Chemistry, Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, ItalyInstitute of Biostructures and Bioimaging, CNR, Via Pietro Castellino 111, 80131 Naples, ItalyDepartment of Science and Technology, University of Sannio, Via Francesco de Sanctis snc, 82100 Benevento, ItalyAn exhaustive analysis of all the protein structures deposited in the Protein Data Bank, here performed, has allowed the identification of hundredths of protein-bound urea molecules and the structural characterization of such binding sites. It emerged that, even though urea molecules are largely involved in hydrogen bonds with both backbone and side chains, they are also able to make van der Waals contacts with nonpolar moieties. As similar findings have also been previously reported for guanidinium and thiocyanate, this observation suggests that promiscuity is a general property of protein denaturants. Present data provide strong support for a mechanism based on the protein-denaturant direct interactions with a denaturant binding model to equal and independent sites. In this general framework, our investigations also highlight some interesting insights into the different denaturing power of urea compared to guanidinium/thiocyanate.https://www.mdpi.com/2079-7737/11/12/1764ureaprotein stabilityurea-protein interactionschemical denaturants |
| spellingShingle | Antonella Paladino Nicole Balasco Luigi Vitagliano Giuseppe Graziano A Structure-Based Mechanism for the Denaturing Action of Urea, Guanidinium Ion and Thiocyanate Ion Biology urea protein stability urea-protein interactions chemical denaturants |
| title | A Structure-Based Mechanism for the Denaturing Action of Urea, Guanidinium Ion and Thiocyanate Ion |
| title_full | A Structure-Based Mechanism for the Denaturing Action of Urea, Guanidinium Ion and Thiocyanate Ion |
| title_fullStr | A Structure-Based Mechanism for the Denaturing Action of Urea, Guanidinium Ion and Thiocyanate Ion |
| title_full_unstemmed | A Structure-Based Mechanism for the Denaturing Action of Urea, Guanidinium Ion and Thiocyanate Ion |
| title_short | A Structure-Based Mechanism for the Denaturing Action of Urea, Guanidinium Ion and Thiocyanate Ion |
| title_sort | structure based mechanism for the denaturing action of urea guanidinium ion and thiocyanate ion |
| topic | urea protein stability urea-protein interactions chemical denaturants |
| url | https://www.mdpi.com/2079-7737/11/12/1764 |
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