PHYSIOCHEMICAL ANALYSIS OF SNAKIN 1 PEPTIDE IN FAMILY SOLANACEAE
PLANT CELL BIOTECHNOLOGY AND MOLECULAR BIOLOGY,
Page 74-84
Abstract
Snakin protein is a class of cysteine rich peptides. Snakin 1 is the cell wall associated proteins and act as anti-fungal as well as anti-bacterial peptides and caused a quick aggregation of gram negative as well as positive bacteria. In this article, physiochemical analysis of Snakin 1 peptide in seven members of Solanaceae family was carried out using bioinformatics tools. It included their isoelectric point, molecular weight, extinction coefficient, aliphatic index, negative and positive R group, instability index and the grand average hydropathy. Moreover, their primary structures analysis showed that all proteins are hydrophobic in nature. Secondary structures were evaluated using SOPMA. Helical wheel structure was also identified using Pep Wheel software. Sequence alignment and phylogenetic analysis was also done. Swiss model of the protein was also analysed with its rampage analysis. The given information may be helpful to provide an efficient basis in the functional analysis for experimentally isolated or derived Snakin peptides.
Keywords:
- Snakin 1
- physiochemical properties
- anti-microbial
- pI
- EC
- AI
- helical wheel
- hydrophobicity
- swiss model.
How to Cite
SALEEM, M. Z., ABBAS, J., SAIF, S., AHMAD, S., AHMAD, N., HADI, F., AHMED, W., TAHIR, M., & ALI, Q. (2021). PHYSIOCHEMICAL ANALYSIS OF SNAKIN 1 PEPTIDE IN FAMILY SOLANACEAE. PLANT CELL BIOTECHNOLOGY AND MOLECULAR BIOLOGY, 22(15-16), 74-84. Retrieved from https://ikppress.org/index.php/PCBMB/article/view/6031
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Berrocal-Lobo M, Segura A, Moreno M, López G, Garcıa-Olmedo F, et al. Snakin-2, an antimicrobial peptide from potato whose gene is locally induced by wounding and responds to pathogen infection. Plant Physiology. 2002;128(3):951-961.
Padovan L, Scocchi M, Tossi A. Structural aspects of plant antimicrobial peptides. Current Protein and Peptide Science. 2010;11(3):210-219.
Ali M, Rafique F, Ali Q, Malik A. Genetic modification for salt and drought tolerance in plants through SODERF3. Biological and Clinical Sciences Research Journal. 2020;2020(e022).
Ben‐Nissan G, Lee JY, Borohov A, Weiss D. GIP, a Petunia hybrida GA‐induced cysteine‐rich protein: a possible role in shoot elongation and transition to flowering. The Plant Journal. 2004;37(2): 229-238.
Rubinovich L, Weiss D. The Arabidopsis cysteine‐rich protein GASA4 promotes GA responses and exhibits redox activity in bacteria and in planta. The Plant Journal. 2010;64(6):1018-1027.
Porto WF, Franco OL. Theoretical structural insights into the snakin/GASA family. Peptides. 2013;44163-167.
Segura A, Moreno M, Madueño F, Molina A, García-Olmedo F. Snakin-1, a peptide from potato that is active against plant pathogens. Molecular Plant-Microbe Interactions. 1999;12(1):16-23.
Zimmermann R, Sakai H, Hochholdinger F. The gibberellic acid stimulated-like gene family in maize and its role in lateral root development. Plant Physiology. 2010; 152(1):356-365.
López-Solanilla E, García-Olmedo F, Rodríguez-Palenzuela P. Inactivation of the sapA to sapF locus of Erwinia chrysanthemi reveals common features in plant and animal bacterial pathogenesis. The Plant Cell. 1998; 10(6):917-924.
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Algradi AM, Liu Y, Yang B-Y, Kuang H-X. Review on the genus Brugmansia: traditional usage, phytochemistry, pharmacology, and toxicity. Journal of Ethnopharmacology. 2021;113910.
Bilal M, Nasir I, Tabassum B, Akrem A, Ahmad A, et al. Cytotoxicity and in-vitro antiviral activity of lectin from Crocus vernus l. against potato virus Y. Applied Ecology and Environmental Research. 2020;18(1):1301-1315.
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Ashfaq F, Ali Q, Haider MA, Hafeez MM, Malik A. Therapeutic activities of garlic constituent phytochemicals. Biological and Clinical Sciences Research Journal. 2021;2021(1):e007.
Almasia NI, Bazzini AA, Hopp HE, Vazquez‐rovere C. Overexpression of snakin‐1 gene enhances resistance to Rhizoctonia solani and Erwinia carotovora in transgenic potato plants. Molecular Plant Pathology. 2008;9(3):329- 338.
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Khalil R, Ali QHM, Malik A. Phenolic acid profiling by RP-HPLC: evaluation of antibacterial and anticancer activities of Conocarpus erectus plant extracts. Biol Clin Sci Res J. 2020;2020e010.
Khalil R, Ali QHM, Malik A. Phytochemical activities of Conocarpus erectus: An overview. Biol Clin Sci Res J. 2020;2020e008.
Srinivasulu B, Syvitski R, Seo J-K, Mattatall N, Knickle L, et al. Expression, purification and structural characterization of recombinant hepcidin, an antimicrobial peptide identified in Japanese flounder, Paralichthys olivaceus. Protein Expression and Purification. 2008;61(1):36-44.
Li Y. Recombinant production of antimicrobial peptides in Escherichia coli: a review. Protein Expression and Purification. 2011;80(2):260-267.
Yaqoob SFN, Khan S, Ali Q, Hafeez MM, Malik A. Begomoviruses and betasatellites associated with CLCuD. Biol Clin Sci Res J. 2020;2020e002.
Tsai CW, Duggan PF, Shimp Jr RL, Miller LH, Narum DL. Overproduction of Pichia pastoris or Plasmodium falciparum protein disulfide isomerase affects expression, folding and O-linked glycosylation of a malaria vaccine candidate expressed in P. pastoris. Journal of Biotechnology. 2006; 121(4):458-470.
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Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, et al. UniProt: the universal protein knowledgebase. Nucleic Acids Research. 2004;32(suppl_1):D115-D119.
Gasteiger E, Hoogland C, Gattiker A, Wilkins MR, Appel RD, et al. Protein identification and analysis tools on the ExPASy server. The proteomics protocols handbook: Springer. 2005;571-607.
Gill SC, Von Hippel PH. Calculation of protein extinction coefficients from amino acid sequence data. Analytical Biochemistry. 1989;182(2):319-326.
Guruprasad K, Reddy BB, Pandit MW. Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Engineering, Design and Selection. 1990;4(2):155-161.
Ikai A. Thermostability and aliphatic index of globular proteins. The Journal of Biochemistry. 1980;88(6):1895- 1898.
Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology. 1982;157(1):105-132.
Geourjon C, Deleage G. SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Bioinformatics. 1995;11(6): 681-684.
Qin C, Yu, C, Shen Y, Fang X, Chen L, Min J, Yang Y. Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proceedings of the National Academy of Sciences. 2014;111(14):5135-5140.
Lesk A, Chothia C. The response of protein structures to amino-acid sequence changes. Philosophical Transactions of the Royal Society of London Series A, Mathematical and Physical Sciences. 1986;317(1540): 345-356.
Afroz M, Akter S, Ahmed A, Rouf R, Shilpi JA, et al. Ethnobotany and antimicrobial peptides from plants of the solanaceae family: An Update and Future Prospects. Frontiers in Pharmacology. 2020;11565.
Aubert D, Chevillard M, Dorne A-M, Arlaud G, Herzog M. Expression patterns of GASA genes in Arabidopsis thaliana: the GASA4 gene is up-regulated by gibberellins in meristematic regions. Plant Molecular Biology. 1998;36(6):871-883.
Berrocal-Lobo M, Segura A, Moreno M, López G, Garcıa-Olmedo F, et al. Snakin-2, an antimicrobial peptide from potato whose gene is locally induced by wounding and responds to pathogen infection. Plant Physiology. 2002;128(3):951-961.
Padovan L, Scocchi M, Tossi A. Structural aspects of plant antimicrobial peptides. Current Protein and Peptide Science. 2010;11(3):210-219.
Ali M, Rafique F, Ali Q, Malik A. Genetic modification for salt and drought tolerance in plants through SODERF3. Biological and Clinical Sciences Research Journal. 2020;2020(e022).
Ben‐Nissan G, Lee JY, Borohov A, Weiss D. GIP, a Petunia hybrida GA‐induced cysteine‐rich protein: a possible role in shoot elongation and transition to flowering. The Plant Journal. 2004;37(2): 229-238.
Rubinovich L, Weiss D. The Arabidopsis cysteine‐rich protein GASA4 promotes GA responses and exhibits redox activity in bacteria and in planta. The Plant Journal. 2010;64(6):1018-1027.
Porto WF, Franco OL. Theoretical structural insights into the snakin/GASA family. Peptides. 2013;44163-167.
Segura A, Moreno M, Madueño F, Molina A, García-Olmedo F. Snakin-1, a peptide from potato that is active against plant pathogens. Molecular Plant-Microbe Interactions. 1999;12(1):16-23.
Zimmermann R, Sakai H, Hochholdinger F. The gibberellic acid stimulated-like gene family in maize and its role in lateral root development. Plant Physiology. 2010; 152(1):356-365.
López-Solanilla E, García-Olmedo F, Rodríguez-Palenzuela P. Inactivation of the sapA to sapF locus of Erwinia chrysanthemi reveals common features in plant and animal bacterial pathogenesis. The Plant Cell. 1998; 10(6):917-924.
Kuddus MR, Rumi F, Tsutsumi M, Takahashi R, Yamano M, et al. Expression, purification and characterization of the recombinant cysteine-rich antimicrobial peptide snakin-1 in Pichia pastoris. Protein Expression and Purification. 2016;12215-22.
Algradi AM, Liu Y, Yang B-Y, Kuang H-X. Review on the genus Brugmansia: traditional usage, phytochemistry, pharmacology, and toxicity. Journal of Ethnopharmacology. 2021;113910.
Bilal M, Nasir I, Tabassum B, Akrem A, Ahmad A, et al. Cytotoxicity and in-vitro antiviral activity of lectin from Crocus vernus l. against potato virus Y. Applied Ecology and Environmental Research. 2020;18(1):1301-1315.
Danish P, Ali QH, MM, Malik A. Antifungal and antibacterial activity of aloe vera plant extract. Biol Clin Sci Res J. 2020;2020e003.
Shelton-Inloes BB, Titani K, Sadler JE. cDNA sequences for human von Willebrand factor reveal five types of repeated domains and five possible protein sequence polymorphisms. Biochemistry. 1986;25(11):3164-3171.
Aguieiras MC, Resende LM, Souza TA, Nagano CS, Chaves RP, et al. Potent anti-candida fraction isolated from capsicum chinense fruits contains an antimicrobial peptide that is similar to plant defensin and is able to inhibit the activity of different α-amylase enzymes. Probiotics and Antimicrobial Proteins. 2021;1-11.
Ashfaq F, Ali Q, Haider MA, Hafeez MM, Malik A. Therapeutic activities of garlic constituent phytochemicals. Biological and Clinical Sciences Research Journal. 2021;2021(1):e007.
Almasia NI, Bazzini AA, Hopp HE, Vazquez‐rovere C. Overexpression of snakin‐1 gene enhances resistance to Rhizoctonia solani and Erwinia carotovora in transgenic potato plants. Molecular Plant Pathology. 2008;9(3):329- 338.
Hameed B, Ali Q, Hafeez M, A M. Antibacterial and antifungal activity of fruit, seed and root extracts of Citrullus colocynthis plant. Biol Clin Sci Res J. 2020;2020(e033).
Ali Q, Khalil R, Nadeem M, Hafeez, MM, Malik, A. Antibacterial, antioxidant activities and association among plant growth related traits of Lepidium draba. Biol Clin Sci Res J. 2020; 2020e011.
Ejaz RM, S Ahmad, M Ali, H Choudhry, S Anti-biofilm potential of menthol purified from Mentha piperita L. (Mint). Biol Clin Sci Res J. 2020;202(e037).
Khalil R, Ali QHM, Malik A. Phenolic acid profiling by RP-HPLC: evaluation of antibacterial and anticancer activities of Conocarpus erectus plant extracts. Biol Clin Sci Res J. 2020;2020e010.
Khalil R, Ali QHM, Malik A. Phytochemical activities of Conocarpus erectus: An overview. Biol Clin Sci Res J. 2020;2020e008.
Srinivasulu B, Syvitski R, Seo J-K, Mattatall N, Knickle L, et al. Expression, purification and structural characterization of recombinant hepcidin, an antimicrobial peptide identified in Japanese flounder, Paralichthys olivaceus. Protein Expression and Purification. 2008;61(1):36-44.
Li Y. Recombinant production of antimicrobial peptides in Escherichia coli: a review. Protein Expression and Purification. 2011;80(2):260-267.
Yaqoob SFN, Khan S, Ali Q, Hafeez MM, Malik A. Begomoviruses and betasatellites associated with CLCuD. Biol Clin Sci Res J. 2020;2020e002.
Tsai CW, Duggan PF, Shimp Jr RL, Miller LH, Narum DL. Overproduction of Pichia pastoris or Plasmodium falciparum protein disulfide isomerase affects expression, folding and O-linked glycosylation of a malaria vaccine candidate expressed in P. pastoris. Journal of Biotechnology. 2006; 121(4):458-470.
Coordinators NR. Database resources of the national center for biotechnology information. Nucleic Acids Research. 2017;45(Database issue):D12.
Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, et al. UniProt: the universal protein knowledgebase. Nucleic Acids Research. 2004;32(suppl_1):D115-D119.
Gasteiger E, Hoogland C, Gattiker A, Wilkins MR, Appel RD, et al. Protein identification and analysis tools on the ExPASy server. The proteomics protocols handbook: Springer. 2005;571-607.
Gill SC, Von Hippel PH. Calculation of protein extinction coefficients from amino acid sequence data. Analytical Biochemistry. 1989;182(2):319-326.
Guruprasad K, Reddy BB, Pandit MW. Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Engineering, Design and Selection. 1990;4(2):155-161.
Ikai A. Thermostability and aliphatic index of globular proteins. The Journal of Biochemistry. 1980;88(6):1895- 1898.
Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology. 1982;157(1):105-132.
Geourjon C, Deleage G. SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Bioinformatics. 1995;11(6): 681-684.
Qin C, Yu, C, Shen Y, Fang X, Chen L, Min J, Yang Y. Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proceedings of the National Academy of Sciences. 2014;111(14):5135-5140.
Lesk A, Chothia C. The response of protein structures to amino-acid sequence changes. Philosophical Transactions of the Royal Society of London Series A, Mathematical and Physical Sciences. 1986;317(1540): 345-356.
Afroz M, Akter S, Ahmed A, Rouf R, Shilpi JA, et al. Ethnobotany and antimicrobial peptides from plants of the solanaceae family: An Update and Future Prospects. Frontiers in Pharmacology. 2020;11565.
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