Distribution of Charged Residues Affects the Average Size and Shape of Intrinsically Disordered Proteins
Abstract
:1. Introduction
2. Materials and Methods
2.1. Gene Design and Cloning
2.2. Production and Purification of κ Variants
2.3. Bioinformatics Analysis
2.4. Far-UV Circular Dichroism (CD) Spectroscopy
2.5. Analytical SEC
2.6. Native MS Analyses
2.7. Application of Ellipsoid Model
3. Results
3.1. Design of Model IDPs by Permutation of Charged Residues
3.2. Impact of Charge Clustering on the Rh of the Model IDPs
3.3. Impact of Charge Clustering on the Conformational Ensemble of the Model IDPs
3.4. Average Shape of the Model IDPs
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Protein | Number of Residues | Number of Prolines | Mean Hydropathy | FCR | NCPR | Rt (nm) | κ | Variant |
---|---|---|---|---|---|---|---|---|
NTAIL | 134 | 7 | 3.35 | 0.299 | −0.045 | 2.64 | 0.078 | Low κ |
0.153 | wt | |||||||
0.431 | High κ | |||||||
NFM | 136 | 1 | 3.40 | 0.390 | −0.051 | 2.54 | 0.037 | Low κ |
0.134 | wt | |||||||
0.516 | High κ | |||||||
PNT4 | 114 | 13 | 3.26 | 0.298 | 0.018 | 2.54 | 0.044 | Low κ |
0.213 | wt | |||||||
0.421 | High κ |
Protein Variant | Rh (nm) | SASA (nm2) | Volume (nm3) | fb * | fc * | |
---|---|---|---|---|---|---|
NTAIL | Low κ | 2.78 ± 0.03 | 113.2 ± 2.1 | 49.5 ± 2.2 | 0.26 ± 0.02 | 0.41 ± 0.16 |
wt | 2.73 ± 0.03 | 105.6 ± 1.4 | 46.3 ± 1.8 | 0.25 ± 0.01 | 0.39 ± 0.16 | |
High κ | 2.58 ± 0.05 | 89.3 ± 1.0 | 37.5 ± 2.3 | 0.24 ± 0.02 | 0.38 ± 0.16 | |
NFM | Low κ | 3.37 ± 0.05 | 136.2 ± 2.0 | 99.1 ± 5.0 | 0.14 ± 0.02 | 0.23 ± 0.12 |
wt | 3.31 ± 0.04 | 124.5 ± 2.4 | 93.2 ± 4.8 | 0.12 ± 0.02 | 0.19 ± 0.10 | |
High κ | 3.05 ± 0.10 | 81.5 ± 0.4 | 69.7 ± 8.0 | -0.03 ± 0.08 | 0.02 ± 0.09 | |
PNT4 | Low κ | 2.39 ± 0.04 | 106.8 ± 3.0 | 28.1 ± 2.1 | 0.42 ± 0.03 | 0.53 ± 0.13 |
wt | 2.36 ± 0.05 | 106.8 ± 2.5 | 26.8 ± 2.1 | 0.44 ± 0.03 | 0.54 ± 0.12 | |
High κ | 2.43 ± 0.05 | 69.0 ± 1.0 | 29.9 ± 2.4 | 0.19 ± 0.03 | 0.31 ± 0.15 |
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Bianchi, G.; Mangiagalli, M.; Barbiroli, A.; Longhi, S.; Grandori, R.; Santambrogio, C.; Brocca, S. Distribution of Charged Residues Affects the Average Size and Shape of Intrinsically Disordered Proteins. Biomolecules 2022, 12, 561. https://doi.org/10.3390/biom12040561
Bianchi G, Mangiagalli M, Barbiroli A, Longhi S, Grandori R, Santambrogio C, Brocca S. Distribution of Charged Residues Affects the Average Size and Shape of Intrinsically Disordered Proteins. Biomolecules. 2022; 12(4):561. https://doi.org/10.3390/biom12040561
Chicago/Turabian StyleBianchi, Greta, Marco Mangiagalli, Alberto Barbiroli, Sonia Longhi, Rita Grandori, Carlo Santambrogio, and Stefania Brocca. 2022. "Distribution of Charged Residues Affects the Average Size and Shape of Intrinsically Disordered Proteins" Biomolecules 12, no. 4: 561. https://doi.org/10.3390/biom12040561
APA StyleBianchi, G., Mangiagalli, M., Barbiroli, A., Longhi, S., Grandori, R., Santambrogio, C., & Brocca, S. (2022). Distribution of Charged Residues Affects the Average Size and Shape of Intrinsically Disordered Proteins. Biomolecules, 12(4), 561. https://doi.org/10.3390/biom12040561