Prediction of protein solubility in <i>Escherichia coli</i> using logistic regression

Diaz, Armando A.; Tomba, Emanuele; Lennarson, Reese; Richard, Rex; Bagajewicz, Miguel J.; Harrison, Roger G.

doi:10.1002/bit.22537

Cited by 77 publications

(64 citation statements)

References 32 publications

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“…(Table 3) Cysteine fraction, hydrophobicity-related parameters, approximate charge average and fractions of amino acids. The dataset for this study contained 212 protein sequences and the accuracy being reported was 93.9% [19]. Another method was proposed by Samak et al in which dataset contained almost 1600 protein sequences and the features reported were 39 in the count.…”

Section: Prediction Of Solubility and Performance Evaluationmentioning

confidence: 96%

Prediction of Protein Solubility using Primary Structure Compositional Features: A Machine Learning Perspective

Rasool¹,

Hussain²,

Mahmood³

2017

J Proteomics Bioinform

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Section: Prediction Of Solubility and Performance Evaluationmentioning

confidence: 96%

Prediction of Protein Solubility using Primary Structure Compositional Features: A Machine Learning Perspective

Rasool¹,

Hussain²,

Mahmood³

2017

J Proteomics Bioinform

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“…In previous study [30], it was found that overexpression caused conditions where even soluble proteins would form inclusion bodies because the cell became overly crowded. Accordingly, it was predicted that the inclusion body formation of fusion protein DsbA-trypsin may partly due to overexpression because under normal expression the protein could fold correctly and be soluble.…”

Section: Expression and Detection Of Dsba-trypsinmentioning

confidence: 98%

DsbA-DsbAmut fusion chaperon improved soluble expression of human trypsinogen-1 in Escherichia coli

Liu

Zhang

Yang

et al. 2015

Front. Chem. Sci. Eng.

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A co-expressing system of DsbA-DsbA mut was suggested for the first time to enhance the soluble expression of human trypsin-1. As a control, leaderless DsbA chaperone was also co-expressed with human trypsin-1. Vectors pET39b-trypsin and pET28a-DsbADsbA mut -trypsin with the above two DsbA fusion tag were constructed. The strain with vector pET39b-trypsin expressed fusion protein DsbA-trypsin in form of inclusion bodies. While in E. coli BL21 (DE3) strain with vector pET28a-DsbA-DsbA mut -trypsin, the soluble expression of trypsin fusion protein was achieved. Under the optimized expression conditions, the soluble fraction accounted for about 49.43% of total DsbA-DsbA mut -trypsin proteins in crude supernatant. The purification yield was 4.15% by nickel chelating chromatography and 3.3 mg activated trypsin with a purity of 88.68% was obtained from 1 L LB broth. To detect the possible functions of DsbA series chaperons in trypsin fusion protein, we analyzed the primary three-dimensional structure of fusion proteins, mainly focusing on the compatibleness between trypsin and fusion chaperons. The results suggested that (1) besides the primary function in periplasm, leaderless DsbA or DsbA mut may also act as a signal sequences-like leader targeted to periplasm that partly relieved the pressure from fusion protein overexpression and inclusion body formation, and (2) as there was significant soluble expression of DsbA-DsbA mut -trypsin compared with DsbA-trypsin, DsbA mut may function as charge or hydrophobic balance in recombinant protein DsbA-DsbA muttrypsin.

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“…molecular weight, pI theoretical isoelectric point, −R number of negative-charged residues (Arg+Lys), +R number of positive-charged residues (Asp+Glu), EC extinction coefficient at 280 nm, Inst. II instability index, AI aliphatic index, GRAVY grand average hydropathicity approach which uses parameters such as molecular weight, amino acid fractions, aliphatic index, alpha-helix propensity, beta-sheet propensity, average pI, approximate charge average, and hydrophilicity index for prediction of solubility of recombinant protein [63]. …”

Section: Evaluation Of the Primary Structure Of Designed Constructs Amentioning

confidence: 99%

Designing and Modeling of Complex DNA Vaccine Based on Tropomyosin Protein of Boophilus Genus Tick

Ranjbar

Gupta

Ghorban

et al. 2014

Appl Biochem Biotechnol

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Boophilus tick is a bloodsucking ectoparasite that transfers some pathogens, reducing production and thus leading to economical losses in the cattle industry. Tropomyosin (TPM) protein is a salivary protein, has actin regulator activity, and plays an important role in immune reactions against parasites. In the current study, besides developing a safe, effective, and broad spectrum protective measure against Boophilus genus tick based on TPM protein, we attempted to minimize possible problems occurring in the design of polytopic vaccines. Briefly, the steps that were followed in the present study were as follows: retrieving sequences and finding the mutational/conservative regions, selecting consensus and high immunogenic epitopes of B and CD4(+) T cells by different approaches, three-dimensional structure (3D structure) prediction and representation of epitopes and highly variable/conserve regions, designing vaccinal construct by fusion of B and T cell epitopes by special patterns and improving immunogenicity, evaluation of the constructs' primary structure and posttranslational modification, calculation of hydrophobic regions, reverse translation, codon optimization, open reading frame checking, insertion of start/end codon, Kozak sequence, and finally constructing the DNA vaccine. Variation plot showed some shared epitopes among the ticks' and mites' species that some might be effective only in some species. Finally, by following the steps mentioned above, two constructs for B and T cells were achieved. Checking constructs revealed their reliability and efficacy for in vitro production and utilization. Successful in silico modeling is an essential step of designing vigorous vaccines. We developed a novel protective and therapeutic vaccine against Boophilus genus (based on TPM protein). At the next step, constructed DNA vaccine would be produced in vitro and administrated to cattle, and its potency to induction of immune response and protection against Boophilus genus as well as other ticks and mites will be evaluated.

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Prediction of protein solubility in Escherichia coli using logistic regression

Cited by 77 publications

References 32 publications

Prediction of Protein Solubility using Primary Structure Compositional Features: A Machine Learning Perspective

Prediction of Protein Solubility using Primary Structure Compositional Features: A Machine Learning Perspective

DsbA-DsbAmut fusion chaperon improved soluble expression of human trypsinogen-1 in Escherichia coli

Designing and Modeling of Complex DNA Vaccine Based on Tropomyosin Protein of Boophilus Genus Tick

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