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Structural Insights into Protein–Aptamer Recognitions Emerged from Experimental and Computational Studies

Aptamers are synthetic nucleic acids that are developed to target with high affinity and specificity chemical entities ranging from single ions to macromolecules and present a wide range of chemical and physical properties. Their ability to selectively bind proteins has made these compounds very att...

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Autores principales: Troisi, Romualdo, Balasco, Nicole, Autiero, Ida, Vitagliano, Luigi, Sica, Filomena
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10671752/
https://www.ncbi.nlm.nih.gov/pubmed/38003510
http://dx.doi.org/10.3390/ijms242216318
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author Troisi, Romualdo
Balasco, Nicole
Autiero, Ida
Vitagliano, Luigi
Sica, Filomena
author_facet Troisi, Romualdo
Balasco, Nicole
Autiero, Ida
Vitagliano, Luigi
Sica, Filomena
author_sort Troisi, Romualdo
collection PubMed
description Aptamers are synthetic nucleic acids that are developed to target with high affinity and specificity chemical entities ranging from single ions to macromolecules and present a wide range of chemical and physical properties. Their ability to selectively bind proteins has made these compounds very attractive and versatile tools, in both basic and applied sciences, to such an extent that they are considered an appealing alternative to antibodies. Here, by exhaustively surveying the content of the Protein Data Bank (PDB), we review the structural aspects of the protein–aptamer recognition process. As a result of three decades of structural studies, we identified 144 PDB entries containing atomic-level information on protein–aptamer complexes. Interestingly, we found a remarkable increase in the number of determined structures in the last two years as a consequence of the effective application of the cryo-electron microscopy technique to these systems. In the present paper, particular attention is devoted to the articulated architectures that protein–aptamer complexes may exhibit. Moreover, the molecular mechanism of the binding process was analyzed by collecting all available information on the structural transitions that aptamers undergo, from their protein-unbound to the protein-bound state. The contribution of computational approaches in this area is also highlighted.
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spelling pubmed-106717522023-11-14 Structural Insights into Protein–Aptamer Recognitions Emerged from Experimental and Computational Studies Troisi, Romualdo Balasco, Nicole Autiero, Ida Vitagliano, Luigi Sica, Filomena Int J Mol Sci Review Aptamers are synthetic nucleic acids that are developed to target with high affinity and specificity chemical entities ranging from single ions to macromolecules and present a wide range of chemical and physical properties. Their ability to selectively bind proteins has made these compounds very attractive and versatile tools, in both basic and applied sciences, to such an extent that they are considered an appealing alternative to antibodies. Here, by exhaustively surveying the content of the Protein Data Bank (PDB), we review the structural aspects of the protein–aptamer recognition process. As a result of three decades of structural studies, we identified 144 PDB entries containing atomic-level information on protein–aptamer complexes. Interestingly, we found a remarkable increase in the number of determined structures in the last two years as a consequence of the effective application of the cryo-electron microscopy technique to these systems. In the present paper, particular attention is devoted to the articulated architectures that protein–aptamer complexes may exhibit. Moreover, the molecular mechanism of the binding process was analyzed by collecting all available information on the structural transitions that aptamers undergo, from their protein-unbound to the protein-bound state. The contribution of computational approaches in this area is also highlighted. MDPI 2023-11-14 /pmc/articles/PMC10671752/ /pubmed/38003510 http://dx.doi.org/10.3390/ijms242216318 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Review
Troisi, Romualdo
Balasco, Nicole
Autiero, Ida
Vitagliano, Luigi
Sica, Filomena
Structural Insights into Protein–Aptamer Recognitions Emerged from Experimental and Computational Studies
title Structural Insights into Protein–Aptamer Recognitions Emerged from Experimental and Computational Studies
title_full Structural Insights into Protein–Aptamer Recognitions Emerged from Experimental and Computational Studies
title_fullStr Structural Insights into Protein–Aptamer Recognitions Emerged from Experimental and Computational Studies
title_full_unstemmed Structural Insights into Protein–Aptamer Recognitions Emerged from Experimental and Computational Studies
title_short Structural Insights into Protein–Aptamer Recognitions Emerged from Experimental and Computational Studies
title_sort structural insights into protein–aptamer recognitions emerged from experimental and computational studies
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10671752/
https://www.ncbi.nlm.nih.gov/pubmed/38003510
http://dx.doi.org/10.3390/ijms242216318
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