RCD+: Fast loop modeling server

Modeling loops is a critical and challenging step in protein modeling and prediction. We have developed a quick online service (http://rcd.chaconlab.org) for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. Our original Random Coordinate Descent (RCD) loop closure algorithm has been greatly improved to enrich the sampling distribution towards nearnative conformations. These improvements include a new workflow optimization, MPI-parallelization and fast backbone angle sampling based on neighbordependent Ramachandran probability distributions. The server starts by efficiently searching the vast conformational space from only the loop sequence information and the environment atomic coordinates. The generated closed loop models are subsequently ranked using a fast distance-orientation dependent energy filter. Top ranked loops are refined with the Rosetta energy function to obtain accurate all-atom predictions that can be interactively inspected in an user-friendly web interface. Using standard benchmarks, the average root mean squared deviation (RMSD) is 0.8 and 1.4 Å for 8 and 12 residues loops, respectively, in the challenging modeling scenario in where the side chains of the loop environment are fully remodeled. These results are not only very competitive compared to those obtained with public state of the art methods, but also they are obtained ∼10- fold faster.Peer Reviewe

Nucleotide and Osmolyte Induced Folding of FtsZ from Staphylococcus aureus

Joint 12th EBSA congress / 10th ICBP – IUPAP congress: Biophysics for life and technology, Madrid, Spain, July 20-24, 2019. -- http://www.ebsa2019.org/Peer reviewe

Running title: FtsZ folding is induced by nucleotide binding

48 p.-6 fig.-1 tab.-9 fig-supl.-3 tab.supl.The essential bacterial division protein FtsZ uses GTP binding and hydrolysis to assemble into dynamic filaments that treadmill around the Z-ring, guiding septal wall synthesis and cell division. FtsZ is a structural homolog of tubulin and a target for discovering new antibiotics. Here, using FtsZ from the pathogen S aureus (SaFtsZ), we reveal that, prior to assembly, FtsZ monomers require nucleotide binding for folding; this is possibly relevant to other mesophilic FtsZs. Apo-SaFtsZ is essentially unfolded, as assessed by nuclear magnetic resonance and circular dichroism. Binding of GTP (≥ 1mM) dramatically shifts the equilibrium towards the active folded protein. Supportingly, SaFtsZ refolded with GDP crystallizes in a native structure. Apo-SaFtsZ also folds with 3.4 M glycerol, enabling high-affinity GTP binding (KD 20 nM determined by isothermal titration calorimetry) similar to thermophilic stable FtsZ. Other stabilizing agents that enhance nucleotide binding include ethylene glycol, trimethylamine N-oxide (TMAO), and several bacterial osmolytes. High salt stabilizes SaFtsZ without bound nucleotide in an inactive twisted conformation. We identified a cavity behind the SaFtsZ-GDP nucleotide-binding pocket that harbors different small compounds, which is available for extended nucleotide-replacing inhibitors. Furthermore, we devised a competition assay to detect any inhibitors that overlap the nucleotide site of SaFtsZ, or Escherichia coli FtsZ, employing osmolyte-stabilized apo-FtsZs and the specific fluorescence anisotropy change of mant-GTP upon dissociation from the protein. This robust assay provides a basis to screening for high affinity GTP-replacing ligands, which combined with structural studies and phenotypic profiling should facilitate development of a next generation of FtsZ-targeting antibacterial inhibitors.This work was supported by grants BFU 2014-51823-R (JMA), BFU 2017-87387-P (CFT), SAF-2016-76678-C2-2-R (DVL) and a FPI fellowship (AJCV).Peer reviewe

Cohort Profile : The Cardiovascular Research Data Catalogue

Volume 53, Issue 1, February 202