Towards a "Golden Standard" for computing globin stability: Stability and structure sensitivity of myoglobin mutants
Fast and accurate computation of protein stability is increasingly important for e.g. protein engineering and protein misfolding diseases, but no consensus methods exist for important proteins such as globins, and performance may depend on the type of structural input given. This paper reports bench...
Published in: | Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics |
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ftdtupubl:oai:pure.atira.dk:publications/8e2522b2-e43c-43c3-8d39-d04f1e02261b 2024-06-23T07:56:59+00:00 Towards a "Golden Standard" for computing globin stability: Stability and structure sensitivity of myoglobin mutants Kepp, Kasper Planeta 2015 https://orbit.dtu.dk/en/publications/8e2522b2-e43c-43c3-8d39-d04f1e02261b https://doi.org/10.1016/j.bbapap.2015.06.002 eng eng https://orbit.dtu.dk/en/publications/8e2522b2-e43c-43c3-8d39-d04f1e02261b info:eu-repo/semantics/closedAccess Kepp , K P 2015 , ' Towards a "Golden Standard" for computing globin stability: Stability and structure sensitivity of myoglobin mutants ' , Biochimica et Biophysica Acta - Proteins and Proteomics , vol. 1854 , no. 10, Part A , pp. 1239-1248 . https://doi.org/10.1016/j.bbapap.2015.06.002 Myoglobin Mutant stability Protein calculation High-resolution crystal structure Structure sensitivity article 2015 ftdtupubl https://doi.org/10.1016/j.bbapap.2015.06.002 2024-06-04T15:10:52Z Fast and accurate computation of protein stability is increasingly important for e.g. protein engineering and protein misfolding diseases, but no consensus methods exist for important proteins such as globins, and performance may depend on the type of structural input given. This paper reports benchmarking of six protein stability calculators (POPMUSIC 2.1, I-Mutant 2.0, I-Mutant 3.0, CUPSAT, SDM, and mCSM) against 134 experimental stability changes for mutations of sperm-whale myoglobin. Six different high-resolution structures were used to test structure sensitivity that may impair protein calculations. The trend accuracy of the methods decreased as I-Mutant 2.0 (R=0.64-0.65), SDM (R=0.57-0.60), POPMUSIC2.1 (R=0.54-0.57), I-Mutant 3.0 (R=0.53-0.55), mCSM (R=0.35-0.47), and CUPSAT (R=0.25-0.48). The mean signed errors increased as SDM<CUPSAT<I-Mutant 2.0<I-Mutant 3.0<POPMUSIC 2.1<mCSM. Mean absolute errors increased as I-Mutant 2.0<I-Mutant 3.0<POPMUSIC 2.1<CUPSAT<SDM<mCSM. Structural sensitivity increased as I-Mutant 3.0 (0.05)<I-Mutant 2.0 (0.09)<POPMUSIC 2.1 (0.12)<SDM (0.18)<mCSM (0.27)<CUPSAT (0.58). Leaving out heterogeneous experimental data did not change conclusions. The distinct performances reveal room for improvement, but I-Mutant 2.0 is proficient for this purpose, as further validated against a data set of related cytochrome c like proteins. The results also emphasize the importance of high-quality crystal structures and reveal structure-dependent effects even in the near-atomic resolution limit. Article in Journal/Newspaper Sperm whale Technical University of Denmark: DTU Orbit Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1854 10 1239 1248 |
institution |
Open Polar |
collection |
Technical University of Denmark: DTU Orbit |
op_collection_id |
ftdtupubl |
language |
English |
topic |
Myoglobin Mutant stability Protein calculation High-resolution crystal structure Structure sensitivity |
spellingShingle |
Myoglobin Mutant stability Protein calculation High-resolution crystal structure Structure sensitivity Kepp, Kasper Planeta Towards a "Golden Standard" for computing globin stability: Stability and structure sensitivity of myoglobin mutants |
topic_facet |
Myoglobin Mutant stability Protein calculation High-resolution crystal structure Structure sensitivity |
description |
Fast and accurate computation of protein stability is increasingly important for e.g. protein engineering and protein misfolding diseases, but no consensus methods exist for important proteins such as globins, and performance may depend on the type of structural input given. This paper reports benchmarking of six protein stability calculators (POPMUSIC 2.1, I-Mutant 2.0, I-Mutant 3.0, CUPSAT, SDM, and mCSM) against 134 experimental stability changes for mutations of sperm-whale myoglobin. Six different high-resolution structures were used to test structure sensitivity that may impair protein calculations. The trend accuracy of the methods decreased as I-Mutant 2.0 (R=0.64-0.65), SDM (R=0.57-0.60), POPMUSIC2.1 (R=0.54-0.57), I-Mutant 3.0 (R=0.53-0.55), mCSM (R=0.35-0.47), and CUPSAT (R=0.25-0.48). The mean signed errors increased as SDM<CUPSAT<I-Mutant 2.0<I-Mutant 3.0<POPMUSIC 2.1<mCSM. Mean absolute errors increased as I-Mutant 2.0<I-Mutant 3.0<POPMUSIC 2.1<CUPSAT<SDM<mCSM. Structural sensitivity increased as I-Mutant 3.0 (0.05)<I-Mutant 2.0 (0.09)<POPMUSIC 2.1 (0.12)<SDM (0.18)<mCSM (0.27)<CUPSAT (0.58). Leaving out heterogeneous experimental data did not change conclusions. The distinct performances reveal room for improvement, but I-Mutant 2.0 is proficient for this purpose, as further validated against a data set of related cytochrome c like proteins. The results also emphasize the importance of high-quality crystal structures and reveal structure-dependent effects even in the near-atomic resolution limit. |
format |
Article in Journal/Newspaper |
author |
Kepp, Kasper Planeta |
author_facet |
Kepp, Kasper Planeta |
author_sort |
Kepp, Kasper Planeta |
title |
Towards a "Golden Standard" for computing globin stability: Stability and structure sensitivity of myoglobin mutants |
title_short |
Towards a "Golden Standard" for computing globin stability: Stability and structure sensitivity of myoglobin mutants |
title_full |
Towards a "Golden Standard" for computing globin stability: Stability and structure sensitivity of myoglobin mutants |
title_fullStr |
Towards a "Golden Standard" for computing globin stability: Stability and structure sensitivity of myoglobin mutants |
title_full_unstemmed |
Towards a "Golden Standard" for computing globin stability: Stability and structure sensitivity of myoglobin mutants |
title_sort |
towards a "golden standard" for computing globin stability: stability and structure sensitivity of myoglobin mutants |
publishDate |
2015 |
url |
https://orbit.dtu.dk/en/publications/8e2522b2-e43c-43c3-8d39-d04f1e02261b https://doi.org/10.1016/j.bbapap.2015.06.002 |
genre |
Sperm whale |
genre_facet |
Sperm whale |
op_source |
Kepp , K P 2015 , ' Towards a "Golden Standard" for computing globin stability: Stability and structure sensitivity of myoglobin mutants ' , Biochimica et Biophysica Acta - Proteins and Proteomics , vol. 1854 , no. 10, Part A , pp. 1239-1248 . https://doi.org/10.1016/j.bbapap.2015.06.002 |
op_relation |
https://orbit.dtu.dk/en/publications/8e2522b2-e43c-43c3-8d39-d04f1e02261b |
op_rights |
info:eu-repo/semantics/closedAccess |
op_doi |
https://doi.org/10.1016/j.bbapap.2015.06.002 |
container_title |
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics |
container_volume |
1854 |
container_issue |
10 |
container_start_page |
1239 |
op_container_end_page |
1248 |
_version_ |
1802650398148788224 |