Characterization of active/binding site residues of peptidyl-tRNA hydrolase using biophysical and computational studies
| Autor: | Krishna Kishore Inampudi, Rajkumar Kulandaisamy, Santosh Kumar Upadhyay, Saroj Kumar, Tushar Kushwaha, Manoj Kumar, Soumya De, Vikas Kumar |
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| Rok vydání: | 2020 |
| Předmět: |
Molecular Conformation
Peptide 02 engineering and technology Molecular Dynamics Simulation RNA Transfer Amino Acyl Biochemistry Structure-Activity Relationship 03 medical and health sciences chemistry.chemical_compound Structural Biology Catalytic Domain Spectroscopy Fourier Transform Infrared Hydrolase Amino Acid Sequence Binding site Molecular Biology Protein secondary structure 030304 developmental biology chemistry.chemical_classification 0303 health sciences Binding Sites Molecular Structure biology Active site General Medicine 021001 nanoscience & nanotechnology Recombinant Proteins Molecular Docking Simulation Enzyme chemistry Docking (molecular) Puromycin biology.protein 0210 nano-technology Carboxylic Ester Hydrolases hormones hormone substitutes and hormone antagonists |
| Zdroj: | International Journal of Biological Macromolecules. 159:877-885 |
| ISSN: | 0141-8130 |
| DOI: | 10.1016/j.ijbiomac.2020.05.133 |
| Popis: | All mRNAs cannot be translated into full-length proteins due to ribosome-stalling that leads to release of peptidyl-tRNA which can be lethal for bacterial survival. The enzyme peptidyl-tRNA hydrolase (PtH) hydrolyses the ester bond between nascent peptide and tRNA of peptidyl-tRNA and rescues the cells from toxicity. PtH is an essential enzyme in bacteria and inhibiting this crucial enzyme can serve to combat bacterial diseases. But due to lack of understanding about the catalytic mechanism of PtH, its inhibitors have not been developed. In this work, we have carried out the binding studies of M. tuberculosis and E. coli PtH with the peptidyl-tRNA analogue (puromycin) using ITC, FTIR, CD experiments followed by docking and MD simulations to identify the potential active site residues that would help to design PtH inhibitors. Binding studies of puromycin with both PtH by ITC experiments demonstrate similar thermodynamic parameters and three fold difference in their KD. CD and FTIR studies detected changes in secondary structure composition of PtH in the presence of puromycin with different degree of perturbation. Though interactions with puromycin are conserved in both proteins, modelling studies revealed that water mediated interactions in M. tb-PtH resulting in higher affinity to puromycin. |
| Databáze: | OpenAIRE |
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