In-Silico structure prediction of p27SJ, a novel protein in St John’s Wort that suppresses expression of HIV-1 genome. Online Journal of Bioinformatics.

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Online Journal of Bioinformatics©
Established 1995

ISSN 1443-2250

Volume 19(3):281-288, 2018.

In-Silico structure prediction of p27^SJ, a novel protein in St John’s Wort that suppresses expression of HIV-1 genome.

Ashish Gupta¹*, Varsha Gupta², Santosh Kumar Pal², Jitendra Narayan²,

M. Sharada Potukuchi¹, V. Verma¹

¹College of Engineering, School of Biotechnology, Shri Mata Vaishno Devi University, Katra (J&K), India. ²BCS-InSilico Biology, Lucknow, India

ABSTRACT

Ashish Gupta¹*, Varsha Gupta², Santosh Kumar Pal², Jitendra Narayan², M. Sharada Potukuchi¹, V. Verma¹In-Silico structure prediction of p27SJ, a novel protein in St John’s Wort that suppresses expression of HIV-1 genome, Onl J Bioinform., 19(3):281-288, 2018. Hypericum perforatum, also known as St John’s Wort, has received special attention due to its pharmacological properties. Extracts from this plant are also utilized in the treatment of mild to moderately severe depression. A novel protein, p27^SJ present in a laboratory callus culture of Hypericum perforatum suppresses transcription of the HIV-1 genome in several human cell types including primary culture of microglia and astrocytes. p27^SJ associates with C/EBPβ, a transcription factor that regulates expression of the HIV-1 genome in macrophages and monocytic cells, and the viral transactivator, Tat. It has been found that it can suppress transcription of the HIV-1 genome. Despite its importance, the three dimensional (3D) structure of p27^SJhas not yet been reported. A homology modeling method was used for the prediction of the structure of p27^SJ protein. For the modeling, template protein was obtained by Geno3D server, template protein pdb|2Q9T|chain A having identity 88%, E value 3e-129 and alignment Score 1140. By comparing the template protein a rough model was constructed for the target protein using MODELLER, a program for comparative modelling. The structure of p27^SJ protein of Hypericum perforatum was found to resemble the structure of peroxiredoxin high resolution structure of Ding Protein of Pseudomonas fluorescence. From Ramachandran plot analysis it was found that the portion of residues falling into the most favoured regions was 95.4%. The predicted 3-D model may be further characterized and analyzed using other techniques.

Keywords:- Hypericum perforatum, homology modeling, Schrodinger, HyperChem, 3-D model, MODELLER, geno3D, mGenTHERADER, X-ray crystallography, Swiss-PdbViewer, PROCHECK.

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