In Silico Design and 3D Structural Data for a Multi-Epitope Vaccine Construct targeting Tilapia Parvovirus (TiPV)
Description
Research Hypothesis The central hypothesis of this study is that a rationally engineered, 58-amino acid Multi-Epitope Vaccine Construct (MEVC) integrating highly conserved B-cell and T-cell epitopes from the Tilapia Parvovirus (TiPV) VP1 capsid protein with an N-terminal Tuftsin adjuvant will form a thermodynamically stable, high-affinity complex with the teleost Toll-Like Receptor 3 (TLR3) to trigger a robust innate and adaptive immune cascade. What the Data Shows and Notable Findings The provided dataset contains the raw viral sequences, multiple sequence alignments, 3D structural coordinate files (.pdb), and the final docked receptor-ligand complex. Structural validation data confirms the de novo modeled vaccine construct possesses optimal stereochemical geometry, with 100% of residues situated in Ramachandran favored or allowed regions. Molecular docking and thermodynamic profiling data show a highly spontaneous binding affinity (ΔG = -21.5 kcal/mol) and a sub-femtomolar dissociation constant (1.6 x 10^-16M). Interface analysis of the docked .pdb complex reveals a massive 2074.4 Ų contact area stabilized by 9 intermolecular hydrogen bonds. Furthermore, kinetic data from Normal Mode Analysis (NMA) yields an eigenvalue of 4.498936 x 10^-7, indicating exceptional dynamic stability of the receptor-vaccine complex under simulated physiological motion. Finally, the dataset includes a 174 bp DNA sequence demonstrating perfect in silico codon optimization (CAI = 1.0, GC = 50.57%) for Escherichia coli K12 expression. How the Data Can Be Interpreted and Used This computational dataset serves as a mathematically validated structural blueprint. Researchers can directly download the provided .pdb coordinate files to conduct independent, long-duration Molecular Dynamics (MD) simulations or execute comparative molecular docking against other teleost pattern recognition receptors (PRRs). Additionally, the provided consensus sequences and codon-optimized E. coli DNA files can be directly utilized by wet-lab researchers and molecular biologists to physically synthesize the gene, transitioning this design into in vitro recombinant mass production and subsequent in vivo biological challenge trials in Oreochromis species.
Files
Steps to reproduce
1. Sequence Retrieval and Consensus Generation: Retrieve TiPV VP1 sequences from the NCBI GenBank database. Perform Multiple Sequence Alignment (MSA) using Clustal Omega to generate a consensus sequence, ensuring broad-spectrum conservation across geographical isolates. 2. Epitope Mapping: Predict linear B-cell epitopes using BepiPred, and T-cell epitopes (CTL and HTL) using NetMHCpan and NetMHCIIpan servers. Map discontinuous epitopes onto the AlphaFold-predicted 3D VP1 monomer using ElliPro. 3. Vaccine Construction: Concatenate overlapping, highly antigenic epitopes using EAAAK and GPGPG linkers. Conjugate the Tuftsin (TKPR) adjuvant to the N-terminus to yield the final 58-amino acid construct. 4. Physicochemical Validation: Evaluate the construct's antigenicity (VaxiJen v2.0), allergenicity (AllerTOP v.2), toxicity (ToxinPred), and physical stability parameters (ExPASy ProtParam). 3D Structural Modeling: Generate the 3D model of the 58-mer construct using ColabFold (AlphaFold2 architecture) and refine the stereochemical geometry using the GalaxyRefine server. Validate the finalized structure using a PROCHECK Ramachandran plot. Molecular Docking: Perform rigid-body molecular docking between the refined vaccine construct and the teleost TLR3 receptor using the PatchDock algorithm. Thermodynamic & Interface Analysis: Quantify the binding affinity (ΔG) and dissociation constant (Kd) using the PRODIGY server. Analyze the interface area, hydrogen bonds, and salt bridges using the PDBePISA server. Molecular Dynamics: Submit the top-ranked docked complex to the iMODS server for Normal Mode Analysis (NMA) to evaluate kinetic stability, eigenvalue, and covariance. In Silico Cloning: Reverse-translate and codon-optimize the 58-amino acid sequence for Escherichia coli (strain K12) expression utilizing the Java Codon Adaptation Tool (JCat) to verify manufacturability.