Protposer: The web server that readily proposes protein stabilizing mutations with high PPV
Protein stability is a requisite for most biotechnological and medical applications of proteins. As natural proteins tend to suffer from a low conformational stability ex vivo, great efforts have been devoted toward increasing their stability through rational design and engineering of appropriate mu...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | Computational and Structural Biotechnology Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037022001647 |
| _version_ | 1797978220111331328 |
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| author | Helena García-Cebollada Alfonso López Javier Sancho |
| author_facet | Helena García-Cebollada Alfonso López Javier Sancho |
| author_sort | Helena García-Cebollada |
| collection | DOAJ |
| description | Protein stability is a requisite for most biotechnological and medical applications of proteins. As natural proteins tend to suffer from a low conformational stability ex vivo, great efforts have been devoted toward increasing their stability through rational design and engineering of appropriate mutations. Unfortunately, even the best currently used predictors fail to compute the stability of protein variants with sufficient accuracy and their usefulness as tools to guide the rational stabilisation of proteins is limited. We present here Protposer, a protein stabilising tool based on a different approach. Instead of quantifying changes in stability, Protposer uses structure- and sequence-based screening modules to nominate candidate mutations for subsequent evaluation by a logistic regression model, carefully trained to avoid overfitting. Thus, Protposer analyses PDB files in search for stabilization opportunities and provides a ranked list of promising mutations with their estimated success rates (eSR), their probabilities of being stabilising by at least 0.5 kcal/mol. The agreement between eSRs and actual positive predictive values (PPV) on external datasets of mutations is excellent. When Protposer is used with its Optimal kappa selection threshold, its PPV is above 0.7. Even with less stringent thresholds, Protposer largely outperforms FoldX, Rosetta and PoPMusiC. Indicating the PDB file of the protein suffices to obtain a ranked list of mutations, their eSRs and hints on the likely source of the stabilization expected. Protposer is a distinct, straightforward and highly successful tool to design protein stabilising mutations, and it is freely available for academic use at http://webapps.bifi.es/the-protposer. |
| first_indexed | 2024-04-11T05:19:31Z |
| format | Article |
| id | doaj.art-65bfda52adc34491ace3af99c1d2b209 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-04-11T05:19:31Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-65bfda52adc34491ace3af99c1d2b2092022-12-24T04:52:21ZengElsevierComputational and Structural Biotechnology Journal2001-03702022-01-012024152433Protposer: The web server that readily proposes protein stabilizing mutations with high PPVHelena García-Cebollada0Alfonso López1Javier Sancho2Department of Biochemistry, Molecular and Cell Biology, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain; Biocomputation and Complex Systems Physics Institute (BIFI), Unit and GBs-CSIC, University of Zaragoza, 50018 Zaragoza, Spain; Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, SpainDepartment of Biochemistry, Molecular and Cell Biology, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain; Biocomputation and Complex Systems Physics Institute (BIFI), Unit and GBs-CSIC, University of Zaragoza, 50018 Zaragoza, Spain; Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, SpainDepartment of Biochemistry, Molecular and Cell Biology, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain; Biocomputation and Complex Systems Physics Institute (BIFI), Unit and GBs-CSIC, University of Zaragoza, 50018 Zaragoza, Spain; Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain; Corresponding author at: Department of Biochemistry, Molecular and Cell Biology, Faculty of Science, University of Zaragoza, 50009 Zaragoza, Spain.Protein stability is a requisite for most biotechnological and medical applications of proteins. As natural proteins tend to suffer from a low conformational stability ex vivo, great efforts have been devoted toward increasing their stability through rational design and engineering of appropriate mutations. Unfortunately, even the best currently used predictors fail to compute the stability of protein variants with sufficient accuracy and their usefulness as tools to guide the rational stabilisation of proteins is limited. We present here Protposer, a protein stabilising tool based on a different approach. Instead of quantifying changes in stability, Protposer uses structure- and sequence-based screening modules to nominate candidate mutations for subsequent evaluation by a logistic regression model, carefully trained to avoid overfitting. Thus, Protposer analyses PDB files in search for stabilization opportunities and provides a ranked list of promising mutations with their estimated success rates (eSR), their probabilities of being stabilising by at least 0.5 kcal/mol. The agreement between eSRs and actual positive predictive values (PPV) on external datasets of mutations is excellent. When Protposer is used with its Optimal kappa selection threshold, its PPV is above 0.7. Even with less stringent thresholds, Protposer largely outperforms FoldX, Rosetta and PoPMusiC. Indicating the PDB file of the protein suffices to obtain a ranked list of mutations, their eSRs and hints on the likely source of the stabilization expected. Protposer is a distinct, straightforward and highly successful tool to design protein stabilising mutations, and it is freely available for academic use at http://webapps.bifi.es/the-protposer.http://www.sciencedirect.com/science/article/pii/S2001037022001647Protein stabilizationProtein thermostabilizationStability predictorProtein engineeringProtein biotechnologyProtein expression |
| spellingShingle | Helena García-Cebollada Alfonso López Javier Sancho Protposer: The web server that readily proposes protein stabilizing mutations with high PPV Computational and Structural Biotechnology Journal Protein stabilization Protein thermostabilization Stability predictor Protein engineering Protein biotechnology Protein expression |
| title | Protposer: The web server that readily proposes protein stabilizing mutations with high PPV |
| title_full | Protposer: The web server that readily proposes protein stabilizing mutations with high PPV |
| title_fullStr | Protposer: The web server that readily proposes protein stabilizing mutations with high PPV |
| title_full_unstemmed | Protposer: The web server that readily proposes protein stabilizing mutations with high PPV |
| title_short | Protposer: The web server that readily proposes protein stabilizing mutations with high PPV |
| title_sort | protposer the web server that readily proposes protein stabilizing mutations with high ppv |
| topic | Protein stabilization Protein thermostabilization Stability predictor Protein engineering Protein biotechnology Protein expression |
| url | http://www.sciencedirect.com/science/article/pii/S2001037022001647 |
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