Web tools support predicting protein-nucleic acid complexes stability with affinity changes

doi:10.1002/wrna.1781

Review

. 2023 Sep-Oct;14(5):e1781.

doi: 10.1002/wrna.1781. Epub 2023 Jan 24.

Web tools support predicting protein-nucleic acid complexes stability with affinity changes

Xiao Zhang¹, Long-Can Mei², Yang-Yang Gao¹, Ge-Fei Hao^{1

2}, Bao-An Song¹

Affiliations

¹ National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China.
² National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan, China.

PMID: 36693636
DOI: 10.1002/wrna.1781

Review

Web tools support predicting protein-nucleic acid complexes stability with affinity changes

Xiao Zhang et al. Wiley Interdiscip Rev RNA. 2023 Sep-Oct.

. 2023 Sep-Oct;14(5):e1781.

doi: 10.1002/wrna.1781. Epub 2023 Jan 24.

Authors

Xiao Zhang¹, Long-Can Mei², Yang-Yang Gao¹, Ge-Fei Hao^{1

2}, Bao-An Song¹

Affiliations

¹ National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China.
² National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan, China.

PMID: 36693636
DOI: 10.1002/wrna.1781

Abstract

Numerous biological processes, such as transcription, replication, and translation, rely on protein-nucleic acid interactions (PNIs). Demonstrating the binding stability of protein-nucleic acid complexes is vital to deciphering the code for PNIs. Numerous web-based tools have been developed to attach importance to protein-nucleic acid stability, facilitating the prediction of PNIs characteristics rapidly. However, the data and tools are dispersed and lack comprehensive integration to understand the stability of PNIs better. In this review, we first summarize existing databases for evaluating the stability of protein-nucleic acid binding. Then, we compare and evaluate the pros and cons of web tools for forecasting the interaction energies of protein-nucleic acid complexes. Finally, we discuss the application of combining models and capabilities of PNIs. We may hope these web-based tools will facilitate the discovery of recognition mechanisms for protein-nucleic acid binding stability. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.

Keywords: affinities and stabilities; mutations; protein-nucleic acid interactions; structural bioinformatics.

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Cited by

Predicting the Effect of Single Mutations on Protein Stability and Binding with Respect to Types of Mutations.
Pandey P, Panday SK, Rimal P, Ancona N, Alexov E. Pandey P, et al. Int J Mol Sci. 2023 Jul 28;24(15):12073. doi: 10.3390/ijms241512073. Int J Mol Sci. 2023. PMID: 37569449 Free PMC article.

References

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1. Agnarelli, A., El Omari, K., Duman, R., Wagner, A., & Mancini, E. J. (2021). Phosphorus and sulfur SAD phasing of the nucleic acid-bound DNA-binding domain of interferon regulatory factor 4. Acta Crystallographica Section F-Structural Biology Communications, 77, 202-207. https://doi.org/10.1107/S2053230x21006506
1. Alley, E. C., Khimulya, G., Biswas, S., AlQuraishi, M., & Church, G. M. (2019). Unified rational protein engineering with sequence-based deep representation learning. Nature Methods, 16(12), 1315-1322. https://doi.org/10.1038/s41592-019-0598-1
1. AlQuraishi, M., Tang, S., & Xia, X. (2015). An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system. BMC Bioinformatics, 16(1), 390. https://doi.org/10.1186/s12859-015-0819-2
1. Bennett, C. F., Krainer, A. R., & Cleveland, D. W. (2019). Antisense oligonucleotide therapies for neurodegenerative diseases. Annual Review of Neuroscience, 42, 385-406. https://doi.org/10.1146/annurev-neuro-070918-050501

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[1] Afek, A., Shi, H., Rangadurai, A., Sahay, H., Senitzki, A., Xhani, S., & Gordân, R. (2020). DNA mismatches reveal conformational penalties in protein-DNA recognition. Nature, 587(7833), 291-296. https://doi.org/10.1038/s41586-020-2843-2

[2] Afek, A., Shi, H., Rangadurai, A., Sahay, H., Senitzki, A., Xhani, S., & Gordân, R. (2020). DNA mismatches reveal conformational penalties in protein-DNA recognition. Nature, 587(7833), 291-296. https://doi.org/10.1038/s41586-020-2843-2

[3] Agnarelli, A., El Omari, K., Duman, R., Wagner, A., & Mancini, E. J. (2021). Phosphorus and sulfur SAD phasing of the nucleic acid-bound DNA-binding domain of interferon regulatory factor 4. Acta Crystallographica Section F-Structural Biology Communications, 77, 202-207. https://doi.org/10.1107/S2053230x21006506

[4] Agnarelli, A., El Omari, K., Duman, R., Wagner, A., & Mancini, E. J. (2021). Phosphorus and sulfur SAD phasing of the nucleic acid-bound DNA-binding domain of interferon regulatory factor 4. Acta Crystallographica Section F-Structural Biology Communications, 77, 202-207. https://doi.org/10.1107/S2053230x21006506

[5] Alley, E. C., Khimulya, G., Biswas, S., AlQuraishi, M., & Church, G. M. (2019). Unified rational protein engineering with sequence-based deep representation learning. Nature Methods, 16(12), 1315-1322. https://doi.org/10.1038/s41592-019-0598-1

[6] Alley, E. C., Khimulya, G., Biswas, S., AlQuraishi, M., & Church, G. M. (2019). Unified rational protein engineering with sequence-based deep representation learning. Nature Methods, 16(12), 1315-1322. https://doi.org/10.1038/s41592-019-0598-1

[7] AlQuraishi, M., Tang, S., & Xia, X. (2015). An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system. BMC Bioinformatics, 16(1), 390. https://doi.org/10.1186/s12859-015-0819-2

[8] AlQuraishi, M., Tang, S., & Xia, X. (2015). An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system. BMC Bioinformatics, 16(1), 390. https://doi.org/10.1186/s12859-015-0819-2

[9] Bennett, C. F., Krainer, A. R., & Cleveland, D. W. (2019). Antisense oligonucleotide therapies for neurodegenerative diseases. Annual Review of Neuroscience, 42, 385-406. https://doi.org/10.1146/annurev-neuro-070918-050501

[10] Bennett, C. F., Krainer, A. R., & Cleveland, D. W. (2019). Antisense oligonucleotide therapies for neurodegenerative diseases. Annual Review of Neuroscience, 42, 385-406. https://doi.org/10.1146/annurev-neuro-070918-050501

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Web tools support predicting protein-nucleic acid complexes stability with affinity changes

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Web tools support predicting protein-nucleic acid complexes stability with affinity changes

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