Community-Wide Experimental Evaluation of the PROSS Stability-Design Method - Archive ouverte HAL Access content directly
Journal Articles Journal of Molecular Biology Year : 2021

Community-Wide Experimental Evaluation of the PROSS Stability-Design Method

Yoav Peleg
  • Function : Author
  • PersonId : 1118538
Brett M Collins
  • Function : Author
Kai-En Chen
  • Function : Author
Emma K Livingstone
  • Function : Author
Saroja Weeratunga
  • Function : Author
Natalya Leneva
  • Function : Author
Qian Guo
  • Function : Author
Kathryn Perez
  • Function : Author
Gro E.K Bjerga
  • Function : Author
Øivind Larsen
  • Function : Author
Ondřej Vaněk
  • Function : Author
Ondřej Skořepa
  • Function : Author
Svend Kjaer
  • Function : Author
Evangelos Christodoulou
  • Function : Author
Shira Albeck
  • Function : Author
Orly Dym
  • Function : Author
Elena Ainbinder
  • Function : Author
Tamar Unger
  • Function : Author
Anja Schuetz
  • Function : Author
Susann Matthes
  • Function : Author
Michael Bader
Ario de Marco
  • Function : Author
Paola Storici
  • Function : Author
Marta S Semrau
  • Function : Author
Peggy Stolt-Bergner
  • Function : Author
Christian Aigner
  • Function : Author
Sabine Suppmann
  • Function : Author
Adi Goldenzweig
  • Function : Author
Sarel J Fleishman
  • Function : Author
  • PersonId : 1118539

Abstract

Recent years have seen a dramatic improvement in protein-design methodology. Nevertheless, most methods demand expert intervention, limiting their widespread adoption. By contrast, the PROSS algorithm for improving protein stability and heterologous expression levels has been successfully applied to a range of challenging enzymes and binding proteins. Here, we benchmark the application of PROSS as a stand-alone tool for protein scientists with no or limited experience in modeling. Twelve laboratories from the Protein Production and Purification Partnership in Europe (P4EU) challenged the PROSS algorithm with 14 unrelated protein targets without support from the PROSS developers. For each target, up to six designs were evaluated for expression levels and in some cases, for thermal stability and activity. In nine targets, designs exhibited increased heterologous expression levels either in prokaryotic and/or eukaryotic expression systems under experimental conditions that were tailored for each target protein. Furthermore, we observed increased thermal stability in nine of ten tested targets. In two prime examples, the human Stem Cell Factor (hSCF) and human Cadherin-Like Domain (CLD12) from the RET receptor, the wild type proteins were not expressible as soluble proteins in E. coli, yet the PROSS designs exhibited high expression levels in E. coli and HEK293 cells, respectively, and improved thermal stability. We conclude that PROSS may improve stability and expressibility in diverse cases, and that improvement typically requires target-specific expression conditions. This study demonstrates the strengths of community-wide efforts to probe the generality of new methods and recommends areas for future research to advance practically useful algorithms for protein science.
Fichier principal
Vignette du fichier
PROSS_main_text 5_10_2020_JMB_corr.pdf (698.8 Ko) Télécharger le fichier
Origin : Files produced by the author(s)

Dates and versions

hal-03454151 , version 1 (17-12-2021)

Identifiers

Cite

Yoav Peleg, Renaud Vincentelli, Brett M Collins, Kai-En Chen, Emma K Livingstone, et al.. Community-Wide Experimental Evaluation of the PROSS Stability-Design Method. Journal of Molecular Biology, 2021, 433 (13), pp.166964. ⟨10.1016/j.jmb.2021.166964⟩. ⟨hal-03454151⟩
61 View
147 Download

Altmetric

Share

Gmail Facebook X LinkedIn More