Overlapping and cutting of peptides: For the determination of an epitope in the allergen, the individual peptides are docked against the whole antibody. For this, the entire sequences of the allergen which were retrieved from UniProt are cut into short overlapping peptide fragments using Sigma-Aldrich tools [Peptide Library design and calculator tool]. Sigma Aldrich’s “Overlapping Peptide Fragment Library” tool is used to chop the peptides with a convenient amino acid gap into the appropriate lengths and can also help calculate hydropathy. This tool of Sigma Aldrich is used to cut the amino acid sequence of allergens as short peptides of length 10 and with five overlapping amino acids.
Protein-Peptide Docking: Docking is performed to predict how short peptide (or allergen peptide) sequences interact with a protein (or antibody). The tool used for docking is HPEPDOCK (A server for protein-peptide docking). HPEPDOCK performs a docking check for the binding site attributable to the respective protein receptor structure and a peptide sequence, allowing the peptide to be completely flexible and predicting the protein-peptide complex structure, beginning from random peptide conformations and locations. Computational methods for the docking process will be used to scan for rotational space among the protein receptor and its peptide-binding partner in all possible binding modes. The entire antibody is docked against each overlapping peptide fragment of the pollen sequence. All potential models for each peptide fragment with their attained docking scores are estimated by the HPEPDOCK docking. For further analysis, the peptide model with the highest docking score will be identified and picked for every overlapping peptide fragment that’s docked with the antibody, among all potential models that have been predicted by the server.
Author(s) Details:
Praveen Kumar Vemuri
Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Green Fields, Vaddeswaram, Andhra Pradesh, India.
Varshitha Katta
Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Green Fields, Vaddeswaram, Andhra Pradesh, India.
Anupama Ammulu Manne
Department of Civil Engineering, PVP Siddhartha Institute of Technology, Kanuru, Vijayawada, Andhra Pradesh, India.
Kanaka Durga Devi Nelluri
KVSR Siddhartha College of Pharmaceutical Sciences, Vijayawada, Andhra Pradesh, India.
Suryanarayana Veeravilli
Department of Humanities and Basic Sciences, Aditya University, Surampalem, Andhra Pradesh, India.
KRS Sambasiva Rao
Department of Pharmacy, Mangalayatan University, Jabalpur, Madhya Pradesh, India.
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References
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- Cooper, M. D., & Miller, J. F. (2019). Discovery of 2 distinctive lineages of lymphocytes, T cells and B cells, as the basis of the adaptive immune system and immunologic function: 2019 Albert Lasker Basic Medical Research Award. JAMA, 322(13), 1247-1248.
- LeBien, T. W., & Tedder, T. F. (2008). B lymphocytes: how they develop and function. Blood, The Journal of the American Society of Hematology, 112(5), 1570-1580.
- Bhattacharya, Malavika. Understanding B lymphocyte development: a long way to go. IntechOpen: Rijeka, 2019.
