Computational protocol: Aedesin: Structure and Antimicrobial Activity against Multidrug Resistant Bacterial Strains

Similar protocols

Protocol publication

[…] Structure calculations were carried out by using the programs CYANA and CNS. From the NOESY at 283K, NOEs were classified from strong, medium and weak, corresponding to 2.8, 3.6 and 4.4 Å upper bound constraints, respectively. Structure calculations were performed with CYANA (v. 2.1) using the 372 distance restraints from 2D- NOESY experiments. The NH, Hα, 15N, 13Cα and 13Cβ chemical shifts were converted into 52 Φ/Ψ dihedral angle constraints using TALOS+ (v. 1.2).CYANA was used to calculate 100 structures, of which the 20 conformers with the lowest target function were refined by CNS (v. 1.2) using 1000 steps of torsion angle dynamics at 250 K and 1000 steps of slow cooling to 100K, followed by 200 steps of Powell minimization. The final 20 conformers were selected with the lowest NOE and dihedral angle violations, and are the structures discussed herein and deposited (PDBs). The final 20 structures contained no NOE violations greater than 0.3 Å and no dihedral angle constraint violations greater than 2°. Structures were validated using PROCHECK . The structure of Aedesin has been deposited at the Protein Data Bank (www.rcsb.org), under the entry assigned accession code: 2MMM. […]

Pipeline specifications

Software tools CYANA, CNS, TALOS+, PROCHECK
Applications NMR-based proteomics analysis, Protein structure analysis
Organisms Aedes aegypti, Homo sapiens
Diseases Infection
Chemicals Aminoglycosides, Cephalosporins, Folic Acid, Carbapenems, Fluoroquinolones