Fast NMR method to probe solvent accessibility and disordered regions in proteins

André F. Faustino, Glauce M. Barbosa, Micael Silva, Miguel A. R. B. Castanho, Andrea T. Da Poian, Eurico J. Cabrita, Nuno C. Santos, Fabio C. L. Almeida, Ivo C. Martins

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Abstract

Understanding protein structure and dynamics, which govern key cellular processes, is crucial for basic and applied research. Intrinsically disordered protein (IDP) regions display multifunctionality via alternative transient conformations, being key players in disease mechanisms. IDP regions are abundant, namely in small viruses, allowing a large number of functions out of a small proteome. The relation between protein function and structure is thus now seen from a different perspective: as IDP regions enable transient structural arrangements, each conformer can play different roles within the cell. However, as IDP regions are hard and time-consuming to study via classical techniques (optimized for globular proteins with unique conformations), new methods are required. Here, employing the dengue virus (DENV) capsid (C) protein and the immunoglobulin-binding domain of streptococcal protein G, we describe a straightforward NMR method to differentiate the solvent accessibility of single amino acid N-H groups in structured and IDP regions. We also gain insights into DENV C flexible fold region biological activity. The method, based on minimal pH changes, uses the well-established 1 H- 15 N HSQC pulse sequence and is easily implementable in current protein NMR routines. The data generated are simple to interpret, with this rapid approach being an useful first-choice IDPs characterization method.

Original languageEnglish
Article number1647
JournalScientific Reports
Volume9
Issue number1
DOIs
Publication statusPublished - 1 Dec 2019

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Intrinsically Disordered Proteins
Dengue Virus
Proteins
Inosine Diphosphate
Capsid Proteins
Proteome
Protein Binding
Viruses
Amino Acids
Research

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Faustino, A. F., Barbosa, G. M., Silva, M., Castanho, M. A. R. B., Da Poian, A. T., Cabrita, E. J., ... Martins, I. C. (2019). Fast NMR method to probe solvent accessibility and disordered regions in proteins. Scientific Reports, 9(1), [1647]. https://doi.org/10.1038/s41598-018-37599-z
Faustino, André F. ; Barbosa, Glauce M. ; Silva, Micael ; Castanho, Miguel A. R. B. ; Da Poian, Andrea T. ; Cabrita, Eurico J. ; Santos, Nuno C. ; Almeida, Fabio C. L. ; Martins, Ivo C. / Fast NMR method to probe solvent accessibility and disordered regions in proteins. In: Scientific Reports. 2019 ; Vol. 9, No. 1.
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abstract = "Understanding protein structure and dynamics, which govern key cellular processes, is crucial for basic and applied research. Intrinsically disordered protein (IDP) regions display multifunctionality via alternative transient conformations, being key players in disease mechanisms. IDP regions are abundant, namely in small viruses, allowing a large number of functions out of a small proteome. The relation between protein function and structure is thus now seen from a different perspective: as IDP regions enable transient structural arrangements, each conformer can play different roles within the cell. However, as IDP regions are hard and time-consuming to study via classical techniques (optimized for globular proteins with unique conformations), new methods are required. Here, employing the dengue virus (DENV) capsid (C) protein and the immunoglobulin-binding domain of streptococcal protein G, we describe a straightforward NMR method to differentiate the solvent accessibility of single amino acid N-H groups in structured and IDP regions. We also gain insights into DENV C flexible fold region biological activity. The method, based on minimal pH changes, uses the well-established 1 H- 15 N HSQC pulse sequence and is easily implementable in current protein NMR routines. The data generated are simple to interpret, with this rapid approach being an useful first-choice IDPs characterization method.",
author = "Faustino, {Andr{\'e} F.} and Barbosa, {Glauce M.} and Micael Silva and Castanho, {Miguel A. R. B.} and {Da Poian}, {Andrea T.} and Cabrita, {Eurico J.} and Santos, {Nuno C.} and Almeida, {Fabio C. L.} and Martins, {Ivo C.}",
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Faustino, AF, Barbosa, GM, Silva, M, Castanho, MARB, Da Poian, AT, Cabrita, EJ, Santos, NC, Almeida, FCL & Martins, IC 2019, 'Fast NMR method to probe solvent accessibility and disordered regions in proteins' Scientific Reports, vol. 9, no. 1, 1647. https://doi.org/10.1038/s41598-018-37599-z

Fast NMR method to probe solvent accessibility and disordered regions in proteins. / Faustino, André F.; Barbosa, Glauce M.; Silva, Micael; Castanho, Miguel A. R. B.; Da Poian, Andrea T.; Cabrita, Eurico J.; Santos, Nuno C.; Almeida, Fabio C. L.; Martins, Ivo C.

In: Scientific Reports, Vol. 9, No. 1, 1647, 01.12.2019.

Research output: Contribution to journalArticle

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T1 - Fast NMR method to probe solvent accessibility and disordered regions in proteins

AU - Faustino, André F.

AU - Barbosa, Glauce M.

AU - Silva, Micael

AU - Castanho, Miguel A. R. B.

AU - Da Poian, Andrea T.

AU - Cabrita, Eurico J.

AU - Santos, Nuno C.

AU - Almeida, Fabio C. L.

AU - Martins, Ivo C.

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N2 - Understanding protein structure and dynamics, which govern key cellular processes, is crucial for basic and applied research. Intrinsically disordered protein (IDP) regions display multifunctionality via alternative transient conformations, being key players in disease mechanisms. IDP regions are abundant, namely in small viruses, allowing a large number of functions out of a small proteome. The relation between protein function and structure is thus now seen from a different perspective: as IDP regions enable transient structural arrangements, each conformer can play different roles within the cell. However, as IDP regions are hard and time-consuming to study via classical techniques (optimized for globular proteins with unique conformations), new methods are required. Here, employing the dengue virus (DENV) capsid (C) protein and the immunoglobulin-binding domain of streptococcal protein G, we describe a straightforward NMR method to differentiate the solvent accessibility of single amino acid N-H groups in structured and IDP regions. We also gain insights into DENV C flexible fold region biological activity. The method, based on minimal pH changes, uses the well-established 1 H- 15 N HSQC pulse sequence and is easily implementable in current protein NMR routines. The data generated are simple to interpret, with this rapid approach being an useful first-choice IDPs characterization method.

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