References
Aghamollaei, H., Mousavi Gargari, S. L., Ghanei, M., Rasaee, M. J.,
Amani, J., Bakherad, H., & Farnoosh, G. (2017). Structure prediction,
expression, and antigenicity of c‐terminal of GRP78. Biotechnology
and applied biochemistry, 64 (1), 117-125.
Agostini, F., Vendruscolo, M., & Tartaglia, G. G. (2012).
Sequence-based prediction of protein solubility. Journal of
molecular biology, 421 (2-3), 237-241.
Ai, D., Cheng, S., Chang, H., Yang, T., Wang, G., & Yu, C. (2018). Gene
Cloning, Prokaryotic Expression, and Biochemical Characterization of a
Soluble Trehalase in Helicoverpa armigera Hübner (Lepidoptera:
Noctuidae). Journal of Insect Science, 18 (3), 22.
Al-Hejin, A. M., Bora, R. S., & Ahmed, M. M. M. (2019). Plasmids for
Optimizing Expression of Recombinant Proteins in E. coli Plasmid :
IntechOpen.
Asadi-Ghalehni, M., Rasaee, M. J., Javanmardi, M., Khalili, S.,
Mohamadi, M., & Fatemi, F. (2015). In silico and in vitro evaluation of
a recombinant fusion peptide as a novel candidate vaccine for
EGFR-positive tumors. Biosciences Biotechnology Research Asia,
12 (3), 2405-2410.
Baeshen, M. N., Al-Hejin, A. M., Bora, R. S., Ahmed, M., Ramadan, H.,
Saini, K. S., . . . Redwan, E. M. (2015). Production of
biopharmaceuticals in E. coli: current scenario and future perspectives.J Microbiol Biotechnol, 25 (7), 953-962.
Baldani, C. D., Hilario, E., Nakaghi, A. C. H., Bertolini, M. C., &
Machado, R. Z. (2011). Production of recombinant EMA-1 protein and its
application for the diagnosis of Theileria equi using an enzyme immuno
assay in horses from São Paulo State, Brazil. Revista Brasileira
de Parasitologia Veterinária, 20 (1), 54-60.
Bauerová-Hlinková, V., Hostinová, E., Gašperík, J., Beck, K., Borko, Ľ.,
Lai, F. A., . . . Ševčík, J. (2010). Bioinformatic mapping and
production of recombinant N-terminal domains of human cardiac ryanodine
receptor 2. Protein expression and purification, 71 (1), 33-41.
Berkmen, M. (2012). Production of disulfide-bonded proteins in
Escherichia coli. Protein expression and purification, 82 (1),
240-251.
Bertone, P., Kluger, Y., Lan, N., Zheng, D., Christendat, D., Yee, A., .
. . Gerstein, M. (2001). SPINE: an integrated tracking database and data
mining approach for identifying feasible targets in high-throughput
structural proteomics. Nucleic acids research, 29 (13), 2884-2898.
Bhandari, B. K., Gardner, P. P., & Lim, C. S. (2020).
Solubility-Weighted Index: fast and accurate prediction of protein
solubility. BioRxiv .
Chang, C. C. H., Li, C., Webb, G. I., Tey, B., Song, J., & Ramanan, R.
N. (2016). Periscope: quantitative prediction of soluble protein
expression in the periplasm of Escherichia coli. Scientific
reports, 6 , 21844.
Chang, C. C. H., Song, J., Tey, B. T., & Ramanan, R. N. (2014).
Bioinformatics approaches for improved recombinant protein production in
Escherichia coli: protein solubility prediction. Briefings in
bioinformatics, 15 (6), 953-962.
Chauhan, S., Samanta, S., Thakur, J. K., & Sourirajan, A. (2015).
Cloning, expression and purification of functionally active
Saccharomyces cerevisiae Polo-like Kinase, Cdc5 in E. coli. J.
Appl. Biol. Biotechnol, 3 , 20-24.
Cobb, R. E., Chao, R., & Zhao, H. (2013). Directed evolution: past,
present, and future. AIChE Journal, 59 (5), 1432-1440.
Correa, A., & Oppezzo, P. (2015). Overcoming the solubility problem in
E. coli: available approaches for recombinant protein productionInsoluble proteins (pp. 27-44): Springer.
Dai, X., Guo, W., Long, Q., Yang, Y., Harvey, L., McNeil, B., & Bai, Z.
(2014). Prediction of soluble heterologous protein expression levels
inEscherichia colifrom sequence-based features and its potential in
biopharmaceutical process development. Pharmaceutical
Bioprocessing, 2 (3), 253-266.
Diaz, A. A., Tomba, E., Lennarson, R., Richard, R., Bagajewicz, M. J.,
& Harrison, R. G. (2010). Prediction of protein solubility in
Escherichia coli using logistic regression. Biotechnology and
bioengineering, 105 (2), 374-383.
Ebrahimi, F., Rasaee, M. J., Mousavi, S. L., & Babaeipour, V. (2010).
Production and characterization of a recombinant chimeric antigen
consisting botulinum neurotoxin serotypes A, B and E binding subdomains.The Journal of toxicological sciences, 35 (1), 9-19.
Esmaili, I., Sadeghi, H. M. M., & Akbari, V. (2018). Effect of buffer
additives on solubilization and refolding of reteplase inclusion bodies.Research in pharmaceutical sciences, 13 (5), 413.
Fakruddin, M., Mohammad Mazumdar, R., Bin Mannan, K. S., Chowdhury, A.,
& Hossain, M. N. (2012). Critical factors affecting the success of
cloning, expression, and mass production of enzymes by recombinant E.
coli. ISRN biotechnology, 2013 .
Fang, Y., & Fang, J. (2013). Discrimination of soluble and
aggregation-prone proteins based on sequence information.Molecular BioSystems, 9 (4), 806-811.
Gheybi, E., Amani, J., Salmanian, A. H., Mashayekhi, F., & Khodi, S.
(2014). Designing a recombinant chimeric construct contain MUC1 and HER2
extracellular domain for prediagnostic breast cancer. Tumor
Biology, 35 (11), 11489-11497.
Golovanov, A. P., Hautbergue, G. M., Wilson, S. A., & Lian, L.-Y.
(2004). A simple method for improving protein solubility and long-term
stability. Journal of the American Chemical Society, 126 (29),
8933-8939.
Gopal, G. J., & Kumar, A. (2013). Strategies for the production of
recombinant protein in Escherichia coli. The protein journal,
32 (6), 419-425.
Grishin, D., Zhdanov, D., Gladilina, J. A., Pokrovsky, V., Podobed, O.,
Pokrovskaya, M., . . . Sokolov, N. (2018). Construction and
characterization of a recombinant mutant homolog of the CheW protein
from Thermotoga petrophila RKU-1. Biochemistry (Moscow),
Supplement Series B: Biomedical Chemistry, 12 (2), 143-150.
Gupta, S. K., & Shukla, P. (2016). Advanced technologies for improved
expression of recombinant proteins in bacteria: perspectives and
applications. Critical reviews in biotechnology, 36 (6),
1089-1098.
Gutiérrez-González, M., Farías, C., Tello, S., Pérez-Etcheverry, D.,
Romero, A., Zúñiga, R., . . . Molina, M. C. (2019). Optimization of
culture conditions for the expression of three different insoluble
proteins in Escherichia coli. Scientific reports, 9 (1), 1-11.
Habibi, N., Hashim, S. Z. M., Norouzi, A., & Samian, M. R. (2014). A
review of machine learning methods to predict the solubility of
overexpressed recombinant proteins in Escherichia coli. BMC
bioinformatics, 15 (1), 134.
Hamada, H., Arakawa, T., & Shiraki, K. (2009). Effect of additives on
protein aggregation. Current pharmaceutical biotechnology, 10 (4),
400-407.
Hamidi, S. R., Safdari, Y., & Arabi, M. S. (2019). Test bacterial
inclusion body for activity prior to start denaturing and refolding
processes to obtain active eukaryotic proteins. Protein expression
and purification, 154 , 147-151.
Hao, J.-H., Huang, L.-P., Chen, X.-t., Sun, J.-J., Liu, J.-Z., & Sun,
M. (2017). Identification, cloning and expression analysis of an
alpha-CGTase produced by stain Y112. Protein expression and
purification, 140 , 8-15.
Harrison, R. (2000). Expression of soluble heterologous proteins via
fusion with NusA protein. Innovations, 11 , 4-7.
He, C., & Ohnishi, K. (2017). Efficient renaturation of inclusion body
proteins denatured by SDS. Biochemical and biophysical research
communications, 490 (4), 1250-1253.
Hebditch, M., Carballo-Amador, M. A., Charonis, S., Curtis, R., &
Warwicker, J. (2017). Protein–Sol: a web tool for predicting protein
solubility from sequence. Bioinformatics, 33 (19), 3098-3100.
Hebditch, M., & Warwicker, J. (2019). Charge and hydrophobicity are key
features in sequence-trained machine learning models for predicting the
biophysical properties of clinical-stage antibodies. PeerJ, 7 ,
e8199.
Hesaraki, M., Saadati, M., Honari, H., Olad, G., Heiat, M., Malaei, F.,
& Ranjbar, R. (2013). Molecular cloning and biologically active
production of IpaD N-terminal region. Biologicals, 41 (4),
269-274.
Heydari-Zarnagh, H., Hassanpour, K., & Rasaee, M. (2015). Constructing
Chimeric Antigen for Precise Screening of HTLV-I Infection.Iranian Journal of Allergy, Asthma and Immunology, 14 (4),
427-436.
HEYDARI, Z. H., Ravanshad, M., POURFATHOLLAH, A. A., & Rasaee, M. J.
(2015). Expression and purification of a novel computationally designed
antigen for simultaneously detection of htlv-1 and hbv antibodies.
Huang, H.-L., Charoenkwan, P., Kao, T.-F., Lee, H.-C., Chang, F.-L.,
Huang, W.-L., . . . Ho, S.-Y. (2012). Prediction and analysis of
protein solubility using a novel scoring card method with dipeptide
composition. Paper presented at the BMC bioinformatics.
Idicula‐Thomas, S., & Balaji, P. V. (2005). Understanding the
relationship between the primary structure of proteins and its
propensity to be soluble on overexpression in Escherichia coli.Protein Science, 14 (3), 582-592.
Kazemi-Lomedasht, F., Behdani, M., Bagheri, K. P., Anbouhi, M. H.,
Abolhassani, M., Khanahmad, H., . . . Mirzahoseini, H. (2014).
Expression and purification of functional human vascular endothelial
growth factor-a121; the most important angiogenesis factor.Advanced pharmaceutical bulletin, 4 (4), 323.
Khalili, S., Rasaee, M. J., Bamdad, T., Mard-Soltani, M., Ghalehni, M.
A., Jahangiri, A., . . . Malaei, F. (2018). A novel molecular design for
a hybrid phage-DNA construct against DKK1. Molecular
biotechnology, 60 (11), 833-842.
Khalili, S., Rasaee, M. J., Mousavi, S. L., Amani, J., Jahangiri, A., &
Borna, H. (2017). In silico prediction and in vitro verification of a
novel multi-epitope antigen for HBV detection. Molecular Genetics,
Microbiology and Virology, 32 (4), 230-240.
Lebendiker, M., & Danieli, T. (2014). Production of prone-to-aggregate
proteins. FEBS letters, 588 (2), 236-246.
Leibly, D. J., Nguyen, T. N., Kao, L. T., Hewitt, S. N., Barrett, L. K.,
& Van Voorhis, W. C. (2012). Stabilizing Additives Added during Cell
Lysis Aid in the Solubilization of Recombinant Proteins. PloS one,
7 (12), e52482. doi: 10.1371/journal.pone.0052482
Leong, C., Chua, G., Samah, R., & Chew, F. (2019). The Effect of
Refolding Conditions on the Protein Solubility Recovered from Inclusion
Bodies. Journal of Engineering and Technology (JET), 10 (1).
Magnan, C. N., Randall, A., & Baldi, P. (2009). SOLpro: accurate
sequence-based prediction of protein solubility. Bioinformatics,
25 (17), 2200-2207.
Majidi, B., Najafi, M. F., & Saeedian, S. (2019). Cloning, expression
and purification of Brucella lumazine synthase protein in E. coli BL21.Journal of Advanced Pharmacy Education & Research|
Apr-Jun, 9 (S2).
Malaei, F., Hesaraki, M., Saadati, M., Ahdi, A. M., Sadraeian, M.,
Honari, H., & Nazarian, S. (2013). Immunogenicity of a new recombinant
IpaC from Shigella dysenteriae type I in guinea pig as a vaccine
candidate. Iranian Journal of Immunology, 10 (2), 110-117.
Malaei, F., Rasaee, M. J., Latifi, A. M., & Rahbarizadeh, F. (2019). In
Silico Structural Prediction and Production of a Chimeric Recombinant
Dickkopf-1 (DKK-1) Antigen. Iranian Journal of Allergy, Asthma and
Immunology .
Malaei, F., Rasaee, M. J., Paknejad, M., Latifi, A. M., & Rahbarizadeh,
F. (2018). Production and Characterization of Monoclonal and Polyclonal
Antibodies Against Truncated Recombinant Dickkopf-1 as a Candidate
Biomarker. Monoclonal Antibodies in Immunodiagnosis and
Immunotherapy, 37 (6), 257-264.
Malekian, R., Sima, S., Jahanian-Najafabadi, A., Moazen, F., & Akbari,
V. (2019). Improvement of soluble expression of GM-CSF in the cytoplasm
of Escherichia coli using chemical and molecular chaperones.Protein expression and purification, 160 , 66-72.
Mansour, A. A., Mousavi, S. L., Rasooli, I., Nazarian, S., Amani, J., &
Farhadi, N. (2010). Cloning, high level expression and immunogenicity of
1163-1256 residues of C-terminal heavy chain of C. botulinum neurotoxin
type E. Biologicals, 38 (2), 260-264.
Mard-Soltani, M., Rasaee, M. J., Khalili, S., Sheikhi, A.-K., Hedayati,
M., Ghaderi-Zefrehi, H., & Alasvand, M. (2018). The effect of
differentially designed fusion proteins to elicit efficient anti-human
thyroid stimulating hormone immune responses. Iranian Journal of
Allergy, Asthma and Immunology, 17 (2), 158-170.
Mard-Soltani, M., Rasaee, M. J., Sheikhi, A., & Hedayati, M. (2017).
Eliciting an antibody response against a recombinant TSH containing
fusion protein. Journal of Immunoassay and Immunochemistry,
38 (3), 257-270.
Meagher, R. B. (2011). Plant Production and Delivery System for
Recombinant Proteins as Protein-Flour or Protein-Oil Compositions:
Google Patents.
Mousavi, M. L., NAZARIAN, S., AMANI, J., MONTASER, K. S., & RASOULI, I.
(2004). Cloning, expression and purification of Clostridium botulinum
neurotoxin type E binding domain.
Ni, W., Liu, H., Wang, P., Wang, L., Sun, X., Wang, H., . . . Zheng, Z.
(2019). Evaluation of multiple fused partners on enhancing soluble level
of prenyltransferase NovQ in Escherichia coli. Bioprocess and
biosystems engineering, 42 (3), 465-474.
Niwa, T., Ying, B.-W., Saito, K., Jin, W., Takada, S., Ueda, T., &
Taguchi, H. (2009). Bimodal protein solubility distribution revealed by
an aggregation analysis of the entire ensemble of Escherichia coli
proteins. Proceedings of the National Academy of Sciences,
106 (11), 4201-4206.
Papaneophytou, C. P., & Kontopidis, G. (2014). Statistical approaches
to maximize recombinant protein expression in Escherichia coli: a
general review. Protein expression and purification, 94 , 22-32.
Paraskevopoulou, V., & Falcone, F. H. (2018). Polyionic tags as
enhancers of protein solubility in recombinant protein expression.Microorganisms, 6 (2), 47.
Plückthun, A. (2012). Ribosome display: a perspective Ribosome
display and related technologies (pp. 3-28): Springer.
Prilusky, J., Felder, C. E., Zeev-Ben-Mordehai, T., Rydberg, E. H., Man,
O., Beckmann, J. S., . . . Sussman, J. L. (2005). FoldIndex©: a simple
tool to predict whether a given protein sequence is intrinsically
unfolded. Bioinformatics, 21 (16), 3435-3438.
Ragionieri, L., Vitorino, R., Frommlet, J., Oliveira, J. L., Gaspar, P.,
Ribas de Pouplana, L., . . . Moura, G. R. (2015). Improving the accuracy
of recombinant protein production through integration of bioinformatics,
statistical and mass spectrometry methodologies. The FEBS journal,
282 (4), 769-787.
Ranka, R., Capligina, V., Brangulis, K., Sondore, V., & Baumanis, V.
(2009). Cloning and expression of a recombinant immunogenic truncated
BBK32 protein of Borrelia afzelii. LATVIJAS UNIVERSITĀTES RAKSTI ,
33.
Rawi, R., Mall, R., Kunji, K., Shen, C.-H., Kwong, P. D., & Chuang,
G.-Y. (2018). PaRSnIP: sequence-based protein solubility prediction
using gradient boosting machine. Bioinformatics, 34 (7),
1092-1098.
Rosano, G. L., & Ceccarelli, E. A. (2014). Recombinant protein
expression in Escherichia coli: advances and challenges. Frontiers
in microbiology, 5 , 172.
Rosano, G. L., Morales, E. S., & Ceccarelli, E. A. (2019). New tools
for recombinant protein production in Escherichia coli: A 5‐year update.Protein Science, 28 (8), 1412-1422.
Roy, A., Nair, S., Sen, N., Soni, N., & Madhusudhan, M. (2017). In
silico methods for design of biological therapeutics. Methods,
131 , 33-65.
Roy, A. K., Acharjee, S., Upadhyay, A. D., & Ghosh, R. (2017). Insilico
analysis of myostatin protein of Labeo calbasu. Journal of Applied
Biotechnology & Bioengineering, 3 (3).
Saadati, M., Heiat, M., Nazarian, S., Barati, B., HONARI, H., Doroudian,
M., . . . Rahbar, M. (2010). Cloning and Expression of N-terminal Region
of IpaD from Shigella dysenteriae in E. coli.
Sandini, S., La Valle, R., Deaglio, S., Malavasi, F., Cassone, A., & De
Bernardis, F. (2011). A highly immunogenic recombinant and truncated
protein of the secreted aspartic proteases family (rSap2t) of Candida
albicans as a mucosal anticandidal vaccine. FEMS Immunology &
Medical Microbiology, 62 (2), 215-224.
Sengupta, I., & Udgaonkar, J. B. (2017). Expression and purification of
single cysteine-containing mutant variants of the mouse prion protein by
oxidative refolding. Protein expression and purification, 140 ,
1-7.
Shao, H., Hu, X., Sun, L., & Zhou, W. (2019). Gene cloning, expression
in E. coli, and in vitro refolding of a lipase from Proteus sp. NH 2-2
and its application for biodiesel production. Biotechnology
letters, 41 (1), 159-169.
Singhvi, P., Saneja, A., Srichandan, S., & Panda, A. K. (2020).
Bacterial Inclusion Bodies: A Treasure Trove of Bioactive Proteins.Trends in Biotechnology .
Smialowski, P., Doose, G., Torkler, P., Kaufmann, S., & Frishman, D.
(2012). PROSO II–a new method for protein solubility prediction.The FEBS journal, 279 (12), 2192-2200.
Smialowski, P., Martin-Galiano, A. J., Mikolajka, A., Girschick, T.,
Holak, T. A., & Frishman, D. (2007). Protein solubility: sequence based
prediction and experimental verification. Bioinformatics, 23 (19),
2536-2542.
Sørensen, H. P., & Mortensen, K. K. (2005). Soluble expression of
recombinant proteins in the cytoplasm of Escherichia coli.Microbial cell factories, 4 (1), 1.
Soukhtehzari, S., Rasaee, M. J., & Javanmardi, M. (2019). Production
and Characterization of High-Affinity Antibodies Reactive Towards HEp-2
Cells Nuclei by Injection of an In Silico Designed Recombinant Truncated
Nuclear Mitotic Apparatus Protein. International Journal of
Peptide Research and Therapeutics, 25 (2), 727-738.
Soulari, R. N., Basafa, M., Rajabibazl, M., & Hashemi, A. (2020).
Effective Strategies to Overcome the Insolubility of Recombinant ScFv
Antibody against EpCAM Extracellular Domain in E. coli.International Journal of Peptide Research and Therapeutics , 1-10.
Suykens, J. A., & Vandewalle, J. (1999). Least squares support vector
machine classifiers. Neural processing letters, 9 (3), 293-300.
Terol, G. L., Gallego-Jara, J., Martínez, R. A. S., Díaz, M. C., & de
Diego Puente, T. (2019). Engineering protein production by rationally
choosing a carbon and nitrogen source using E. coli BL21 acetate
metabolism knockout strains. Microbial cell factories, 18 (1),
1-19.
Tolentino, G. J., Meng, S.-Y., Bennett, G. N., & San, K.-Y. (1992). A
pH-regulated promoter for the expression of recombinant proteins
inEscherichia coli. Biotechnology letters, 14 (3), 157-162. doi:
10.1007/BF01023351
Trainor, K., Broom, A., & Meiering, E. M. (2017). Exploring the
relationships between protein sequence, structure and solubility.Current opinion in structural biology, 42 , 136-146.
Valiyari, S., Mahdian, R., Salami, M., Oloomi, M., Golshani, M.,
Shokrgozar, M. A., & Bouzari, S. (2017). Expression, Purification and
Functional Assessment of Smallest Isoform of Human Interleukin-24 in
Escherichia coli. Brazilian Archives of Biology and Technology,
60 .
Voulgaridou, G.-P., Mantso, T., Chlichlia, K., Panayiotidis, M. I., &
Pappa, A. (2013). Efficient E. coli expression strategies for production
of soluble human crystallin ALDH3A1. PloS one, 8 (2).
Wang, H., Zhong, X., Li, J., Zhu, M., Wang, L., Ji, X., . . . Wang, L.
(2018). Cloning and Expression of H. influenzae 49247 IgA Protease in E.
coli. Molecular biotechnology, 60 (2), 134-140.
Wilkinson, D. L., & Harrison, R. G. (1991). Predicting the solubility
of recombinant proteins in Escherichia coli. Bio/technology,
9 (5), 443-448.
Yangbo, F., Yong, H., Huang, C., Bai, Y., Qiu, L., Cao, C., & Gao, T.
(2015). Expression and purification of nucleocapsid protein of MERS
coronavirus in E. coli. Military Medical Sciences, 39 (12),
919-922.
Yari, K., Afzali, S., Mozafari, H., Mansouri, K., & Mostafaie, A.
(2013). Molecular cloning, expression and purification of recombinant
soluble mouse endostatin as an anti-angiogenic protein in Escherichia
coli. Molecular biology reports, 40 (2), 1027-1033.
Zarschler, K., Witecy, S., Kapplusch, F., Foerster, C., & Stephan, H.
(2013). High-yield production of functional soluble single-domain
antibodies in the cytoplasm of Escherichia coli. Microbial cell
factories, 12 (1), 97.
Table 1. Sequence-based predictor tools used for the prediction of
protein solubility.