A molecular dynamics simulation study of peptide deformylase from Leptospira interrogans complex:Exploring the closing mechanism of the substrate pocket

To explore the closing mechanism of the substrate pocket,we perform a 16,000 ps molecular dynamics simulation separately on the ligand-free and actinonin-bound peptide deformylase from Leptospira interrogans.Our results show that the CD-loop, hydrophilic inhibitor and hydrophobic cluster are necessary for the formation of semi-open conformation,and Tyr71 plays an important role in mediating the movements of CD-loop.The average MD structure of the actinonin-bound LiPDF complex approaches to the crystal structure.These are consistent with experiment very well.

High tolerance to mutations in a Chlamydia trachomatis peptide deformylase loop

AIM:To determine if and how a loop region in the peptide deformylase(PDF)of Chlamydia trachomatis regulates enzyme function. METHODS:Molecular dynamics simulation was used to study a structural model of the chlamydial PDF(cPDF) and predict the temperature factor per residue for the protein backbone atoms.Site-directed mutagenesis was performed to construct cPDF variants.Catalytic properties of the resulting variants were determined by an enzyme assay using formyl-Met-Ala-Ser as a substrate. RESULTS:In silico analysis predicted a significant increase in atomic motion in the DGELV sequence(residues 68-72)of a loop region in a cPDF mutant,which isresistant to PDF inhibitors due to two amino acid substitutions near the active site,as compared to wild-type cPDF.The D68R and D68R/E70R cPDF variants demonstrated significantly increased catalytic efficiency.The E70R mutant showed only slightly decreased efficiency. Although deletion of residues 68-72 resulted in a nearly threefold loss in substrate binding,this deficiency was compensated for by increased catalytic efficiency. CONCLUSION:Movement of the DGELV loop region is involved in a rate-limiting conformational change of the enzyme during catalysis.However,there is no stringent sequence requirement for this region for cPDF enzyme activity.

Molecular Interaction Study to Explore the Nigella sativa Bioactive Components as an Inhibitor of Peptide Deformylase to Inhibit the Xanthomonas oryzae pv.oryzae via Applying Computational Approach

Bacterial leaf blight(BLB)caused by Xanthomonas oryzae pv.oryzae(Xoo)is one of the most damaging diseases to rice across the world.Various chemicals have been employed so far for the management of bacterial leaf blight.On the other hand,these compounds are damaging to the ecosystem and have an impact on non-target species such as humans and animals.As a result,there is a need to create a new natural inhibitor for BLB management.Deformylase(PDF)enzyme is present in all eubacteria and its necessity in bacterial protein synthesis reveals it as an attractive target for drug development.In this study,the active components of Nigella sativa have been selected based on their previously reported antimicrobial activity and screened on the active site of bacterial PDF by the in silico art of techniques.Among these compounds,dithymoquinone and p-cymene strongly bind with the PDF enzyme with binding energy values of 7.77 kcal/mol and 7.26 kcal/mol,respectively,which is comparatively higher than the control compound(−6.73 kcal/mol).Hence,the“dithymoquinone-PDF”and“p-cymene-PDF”complexes were selected for further study,and their stability was assessed by molecular dynamic(MD)simulation.In MD simulation,both selected compounds exhibited steady-state interaction with PDF for 20 ns.It has been hypothesized that p-cymene and dithymoquinone inhibit peptide deformylase and could be used as antibacterials or pesticides against Xoo against the BLB disease.

Identification of a New Peptide Deformylase Gene From Enterococcus faecium and Establishment of a New Screening Model Targeted on PDF for Novel Antibiotics

Objective To identify a new peptide deformylase (PDF) gene (Genebank Accession AY238515) from Enterococcus faecium and to establish a new screening model targeted on PDF. Methods A new PDF gene was identified by BLAST analysis and PCR and was subsequently over-expressed in the prokaryotic expression host E.coli Bl21(DE3). Over-expressed protein was purified for enzymatic assay by metal affinity chromatography and a new screening model was established for novel antibiotics. Result A new PDF gene of Enterococcus faecium was identified successfully. Ten positive samples were picked up from 8000 compound library and the microbial fermentation broth samples. Conclusion A new PDF of gene Enterococcus faecium was first identified and the model had a high efficacy. Positive samples screened may be antibacterial agents of broad spectrum.