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INTERNATIONAL JOURNAL OF SCIENTIFIC DEVELOPMENT AND RESEARCH International Peer Reviewed & Refereed Journals, Open Access Journal ISSN Approved Journal No: 2455-2631 | Impact factor: 8.15 | ESTD Year: 2016 open access , Peer-reviewed, and Refereed Journals, Impact factor 8.15 |
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| Paper Title: | Trpcage Folding Simulation based on Co-Translational Protein Folding |
| Authors Name: | Ankita Mehta , Dr. Navneet Batra , Dr. Rupinderjeet kaur |
| Unique Id: | IJSDR2311055 |
| Published In: | Volume 8 Issue 11, November-2023 |
| Abstract: | A novel algorithm has been formulated to enable an enhanced and more accurate simulation of Trpcage folding. This computational method primarily draws upon the principles of cotranslational protein folding. In biological systems, polypeptides undergo sequential synthesis with translation rates varying based on codon speed. Studies have demonstrated that helices and sheets typically fold in a timeframe measured within lower milliseconds. As such, certain proteins exhibit faster-folding than elongation capabilities which suggests a high probability for these resulting chains to assume secondary or tertiary structures during cotranslational processes. The examination of the ribosomal exit tunnel likewise demonstrates that peptides can navigate through it in an α-helical structure. Consequently, this study suggests a molecular dynamics simulation algorithm predicated on including one amino acid residue successively during simulations. In biological systems, proteins synthesis occurs at ribosomes by incorporating single amino acids consecutively into sequences. The launch set-up for such simulations need not comprise fully polypeptide chains but could initiate with minimal segments. Commencing the folding simulation with a minimal segment of amino acids, followed by sequential supplementation of individual amino acids during each ensuing simulation cycle strengthen our need to consider interatomic connections between newly incorporated amino acids and their existing counterparts in the protein chain. Essentially, each atom within a protein impacts every other atom. Therefore, during subsequent procedures, we continuously incorporate an amino acid; this allows the newly introduced amino acid to comprehensively examine its interactions with the remaining amino acids in the protein. Such method could be employed for both ab initio prediction of protein structures and for designing new proteins. In our study, we analyzed Trpcage simulations and determined that all-atoms root-mean-square deviation is 4.621 Å while backbone root-mean-square deviation is 3.444 Å when compared to original NMR solved structure submitted in Protein Data Bank. |
| Keywords: | Algorithm, Trp-Cage, Protein folding, Molecular Dynamics Simulation, RMSD |
| Cite Article: | "Trpcage Folding Simulation based on Co-Translational Protein Folding", International Journal of Science & Engineering Development Research (www.ijsdr.org), ISSN:2455-2631, Vol.8, Issue 11, page no.376 - 381, November-2023, Available :http://www.ijsdr.org/papers/IJSDR2311055.pdf |
| Downloads: | 000338719 |
| Publication Details: | Published Paper ID: IJSDR2311055 Registration ID:209302 Published In: Volume 8 Issue 11, November-2023 DOI (Digital Object Identifier): https://doi.org/10.5281/zenodo.11208496 Page No: 376 - 381 Publisher: IJSDR | www.ijsdr.org ISSN Number: 2455-2631 |
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