Computational protocol: Structural Analysis of Prolyl Oligopeptidases Using Molecular Docking and Dynamics: Insights into Conformational Changes and Ligand Binding

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Protocol publication

[…] Protein sequence of A. thaliana POP was retrieved from TIGR (The Institute of Genomic Research) database . The sequence obtained was subjected to BLAST (Basic Local Alignment Tool) against PDB (Protein Data Bank) to extract information about suitable structural template and to PSIPRED (Protein Structure Prediction Server) for predicting secondary structural elements, respectively –. Sequence alignment was done using CLUSTALW and Joy4.0 program was used to annotate the alignment using three dimensional structural information of template . DSSP (Database of secondary structure assignment) was employed for the assignment of secondary structure . Crystal structure of porcine POP (PDB ID: 1E5T) was used as a template for the construction of model. Alignment of query and template was considered to build the model using MODELLER (version 9.1, ). A set of 100 models were generated, from which lower energy structure according to DOPE (Discrete optimized protein energy) score was used for further processes. Geometric inaccuracies of the structural model were evaluated by subjecting the model to PDB-ADIT validation server, which validates using PROCHECK –. The structure was further energy minimized with the SYBYL software package (version 7.1) using Tripos forcefield . For first 500 steps minimization was carried out with steepest descent which was followed by 200 iterations of conjugate gradient with distant dependent dielectric constant equal to 1, non-bonded interaction cutoff value of 8 and was terminated at the convergence of 0.05 kcal mol Å−1. The final structure was validated again using the PROCHECK and PROSA that checks for high energy regions of the modeled structure . Structural model was structurally aligned with the experimental structure and rendered using PyMOL. [...] The set of ligand molecules studied in this work include known inhibitor Z pro prolinal (ZPR) and related molecules like Z-prolyl pyrrolidine, Z-prolyl prolinol, Z-prolyl azetidine, Z-phenyl alanine azetidine, pyrazinone , . Besides this, naturally occurring plant flavonoid inhibitors baicalein and berberine were also used which are known porcine POP inhibitors. These ligands were either downloaded from PubChem or were constructed using CHEMDRAW software. Few other ligands like Y-29794 –, UAMC , ono-1603 –, S-17092 –, SUAM-1221 –, and JTP4819 – were also considered for this study. Coordinates were saved and subjected to CORINA for two dimensional to three dimensional conversions. The three dimensional structure of porcine POP (1QFS), which is ligand bound form with Z pro prolinal was downloaded from PDB. This structure was determined using X ray crystallography with resolution of 2 Å. The energy of ligand molecules were minimized for 200 runs using steepest descent followed by 100 runs of conjugate gradient using SYBYL software. Each of the minimization methods were carried out with Tripos forcefield. […]

Pipeline specifications

Software tools PSIPRED, Clustal W, JOY, MODELLER, PROCHECK, PyMOL, ChemDraw
Applications Drug design, Small-angle scattering, Protein structure analysis
Organisms Homo sapiens
Diseases Neurodegenerative Diseases, Genetic Diseases, Inborn