scholarly journals Periscope: quantitative prediction of soluble protein expression in the periplasm of Escherichia coli

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Catherine Ching Han Chang ◽  
Chen Li ◽  
Geoffrey I. Webb ◽  
BengTi Tey ◽  
Jiangning Song ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Protein Expression ◽  
Soluble Protein ◽  
Quantitative Prediction

scholarly journals SoluProt: Prediction of Soluble Protein Expression in Escherichia coli

2020 ◽  
Author(s):  
Jiri Hon ◽  
Martin Marusiak ◽  
Tomas Martinek ◽  
Antonin Kunka ◽  
Jaroslav Zendulka ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Protein Expression ◽  
Soluble Protein ◽  
Experimental Studies ◽  
Computational Prediction ◽  
Supplementary Information ◽  
Gradient Boosting ◽  
Sequence Information ◽  
Success Rates ◽  
Solubility Prediction

<p><b>Motivation:</b> Poor protein solubility hinders the production of many therapeutic and industrially useful proteins. Experimental efforts to increase solubility are plagued by low success rates and often reduce biological activity. Computational prediction of protein expressibility and solubility in <i>Escherichia coli</i> using only sequence information could reduce the cost of experimental studies by enabling prioritisation of highly soluble proteins.</p> <p><b>Results:</b> A new tool for sequence-based prediction of soluble protein expression in <i>Escherichia coli, </i>SoluProt, was created using the gradient boosting machine technique with the TargetTrack database as a training set. When evaluated against a balanced independent test set derived from the NESG database, SoluProt’s accuracy of 58.4% and AUC of 0.60 exceeded those of a suite of alternative solubility prediction tools. There is also evidence that it could significantly increase the success rate of experimental protein studies. SoluProt is freely available as a standalone program and a user-friendly webserver at <a href="https://loschmidt.chemi.muni.cz/soluprot/">https://loschmidt.chemi.muni.cz/soluprot/</a>.</p> <p> </p> <p>Availability and Implementation: <a href="https://loschmidt.chemi.muni.cz/soluprot/">https://loschmidt.chemi.muni.cz/soluprot/</a></p> <p>Contact: [email protected]</p> Supplementary Information: Supplementary data are available at Bioinformatics online

scholarly journals SoluProt: Prediction of Soluble Protein Expression in Escherichia coli

2020 ◽  
Author(s):  
Jiri Hon ◽  
Martin Marusiak ◽  
Tomas Martinek ◽  
Antonin Kunka ◽  
Jaroslav Zendulka ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Protein Expression ◽  
Soluble Protein ◽  
Experimental Studies ◽  
Computational Prediction ◽  
Supplementary Information ◽  
Gradient Boosting ◽  
Sequence Information ◽  
Success Rates ◽  
Solubility Prediction

<p><b>Motivation:</b> Poor protein solubility hinders the production of many therapeutic and industrially useful proteins. Experimental efforts to increase solubility are plagued by low success rates and often reduce biological activity. Computational prediction of protein expressibility and solubility in <i>Escherichia coli</i> using only sequence information could reduce the cost of experimental studies by enabling prioritisation of highly soluble proteins.</p> <p><b>Results:</b> A new tool for sequence-based prediction of soluble protein expression in <i>Escherichia coli, </i>SoluProt, was created using the gradient boosting machine technique with the TargetTrack database as a training set. When evaluated against a balanced independent test set derived from the NESG database, SoluProt’s accuracy of 58.4% and AUC of 0.60 exceeded those of a suite of alternative solubility prediction tools. There is also evidence that it could significantly increase the success rate of experimental protein studies. SoluProt is freely available as a standalone program and a user-friendly webserver at <a href="https://loschmidt.chemi.muni.cz/soluprot/">https://loschmidt.chemi.muni.cz/soluprot/</a>.</p> <p> </p> <p>Availability and Implementation: <a href="https://loschmidt.chemi.muni.cz/soluprot/">https://loschmidt.chemi.muni.cz/soluprot/</a></p> <p>Contact: [email protected]</p> Supplementary Information: Supplementary data are available at Bioinformatics online

scholarly journals Structural and biochemical studies of an NB-ARC domain from a plant NLR immune receptor

2019 ◽  
Author(s):  
John FC Steele ◽  
Richard K Hughes ◽  
Mark J Banfield
Keyword(s):  
Escherichia Coli ◽  
Cell Death ◽  
Protein Expression ◽  
Soluble Protein ◽  
Insect Cells ◽  
Molecular Switch ◽  
Structural Studies ◽  
Immune Receptor ◽  
Biochemical Studies ◽  
Insight Into

AbstractPlant NLRs are modular immune receptors that trigger rapid cell death in response to attempted infection by pathogens. A highly conserved nucleotide-binding domain shared with APAF-1, various R-proteins and CED-4 (NB-ARC domain) is proposed to act as a molecular switch, cycling between ADP (repressed) and ATP (active) bound forms. Studies of plant NLR NB-ARC domains have revealed functional similarities to mammalian homologues, and provided insight into potential mechanisms of regulation. However, further advances have been limited by difficulties in obtaining sufficient yields of protein suitable for structural and biochemical techniques. From protein expression screens in Escherichia coli and Sf9 insect cells, we defined suitable conditions to produce the NB-ARC domain from the tomato NLR NRC1. Biophysical analyses of this domain showed it is a folded, soluble protein. Structural studies revealed the NRC1 NB-ARC domain had co-purified with ADP, and confirmed predicted structural similarities between plant NLR NB-ARC domains and their mammalian homologues.

Screening of genetic parameters for soluble protein expression in Escherichia coli

2011 ◽  
Vol 77 (1) ◽  
pp. 104-111 ◽  
Author(s):  
Erik Vernet ◽  
Alexander Kotzsch ◽  
Bjørn Voldborg ◽  
Michael Sundström
Keyword(s):  
Escherichia Coli ◽  
Protein Expression ◽  
Soluble Protein ◽  
Genetic Parameters ◽  
Expression In Escherichia Coli

Colony filtration blot: a new screening method for soluble protein expression in Escherichia coli

2005 ◽  
Vol 2 (7) ◽  
pp. 507-509 ◽  
Author(s):  
Tobias Cornvik ◽  
Sue-Li Dahlroth ◽  
Audur Magnusdottir ◽  
Maria Dolores Herman ◽  
Rosemarie Knaust ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Protein Expression ◽  
Soluble Protein ◽  
Screening Method ◽  
Expression In Escherichia Coli
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