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Project description:The efficiency of the ligand-building module of ARP/wARP version 6.1 has been assessed through extensive tests on a large variety of protein-ligand complexes from the PDB, as available from the Uppsala Electron Density Server. Ligand building in ARP/wARP involves two main steps: automatic identification of the location of the ligand and the actual construction of its atomic model. The first step is most successful for large ligands. The second step, ligand construction, is more powerful with X-ray data at high resolution and ligands of small to medium size. Both steps are successful for ligands with low to moderate atomic displacement parameters. The results highlight the strengths and weaknesses of both the method of ligand building and the large-scale validation procedure and help to identify means of further improvement.
| S-EPMC2483501 | biostudies-literature
Project description:Automatic iterative model (re-)building, as implemented in ARP/wARP and its new control system flex-wARP, is particularly well suited to follow structure solution by molecular replacement. More than 100 molecular-replacement solutions automatically solved by the BALBES software were submitted to three standard protocols in flex-wARP and the results were compared with final models from the PDB. Standard metrics were gathered in a systematic way and enabled the drawing of statistical conclusions on the advantages of each protocol. Based on this analysis, an empirical estimator was proposed that predicts how good the final model produced by flex-wARP is likely to be based on the experimental data and the quality of the molecular-replacement solution. To introduce the differences between the three flex-wARP protocols (keeping the complete search model, converting it to atomic coordinates but ignoring atom identities or using the electron-density map calculated from the molecular-replacement solution), two examples are also discussed in detail, focusing on the evolution of the models during iterative rebuilding. This highlights the diversity of paths that the flex-wARP control system can employ to reach a nearly complete and accurate model while actually starting from the same initial information.
| S-EPMC2394809 | biostudies-literature
Project description:The automated building of a protein model into an electron density map remains a challenging problem. In the ARP/wARP approach, model building is facilitated by initially interpreting a density map with free atoms of unknown chemical identity; all structural information for such chemically unassigned atoms is discarded. Here, this is remedied by applying restraints between free atoms, and between free atoms and a partial protein model. These are based on geometric considerations of protein structure and tentative (conditional) assignments for the free atoms. Restraints are applied in the REFMAC5 refinement program and are generated on an ad hoc basis, allowing them to fluctuate from step to step. A large set of experimentally phased and molecular replacement structures showcases individual structures where automated building is improved drastically by the conditional restraints. The concept and implementation we present can also find application in restraining geometries, such as hydrogen bonds, in low-resolution refinement.
| S-EPMC2670983 | biostudies-literature
Project description:The presence and functions of nuclear actin have been controversial due to the lack of molecular mechanisms. Nuclear actin and actin-related proteins (Arps) are subunits of several chromatin remodelers, including the evolutionarily conserved INO80 chromatin-remodeling complex. Here, we present an improved cryo-EM structure of the yeast INO80 complex and the first 3D reconstruction of the INO80 actin/Arp module. The modular and subunit architecture is defined using a combination of subunit deletion analysis and published crosslinking-mass spectrometry. The functional interactions of the INO80 actin/Arp module with a nucleosome is 3D EM reconstructed in two different binding states. Nucleosomes initially bind to the Arp8 subunit and the substantial conformational changes maximize nucleosome contacts of the actin/Arp module, which could promote the bound nucleosome to be engaged onto the INO80 ATPase domain. Our findings suggest that the conserved nuclear actin/Arp module acts a conformational switch of the INO80 for nucleosome binding.
| S-EPMC6548343 | biostudies-literature
Project description:Aims:Extragalactic observations of water emission can provide valuable insights into the excitation of the interstellar medium. In particular they allow us to investigate the excitation mechanisms in obscured nuclei, i.e. whether an active galactic nucleus or a starburst dominate. Methods:We use sub-arcsecond resolution observations to tackle the nature of the water emission in Arp 220. ALMA Band 5 science verification observations of the 183 GHz H2O 313-220 line, in conjunction with new ALMA Band 7 H2O 515-422 data at 325 GHz, and supplementary 22 GHz H2O 616 - 523 VLA observations, are used to better constrain the parameter space in the excitation modelling of the water lines. Results:We detect 183 GHz H2O and 325 GHz water emission towards the two compact nuclei at the center of Arp 220, being brighter in Arp 220 West. The emission at these two frequencies is compared to previous single-dish data and does not show evidence of variability. The 183 and 325 GHz lines show similar spectra and kinematics, but the 22 GHz profile is significantly different in both nuclei due to a blend with an NH3 absorption line. Conclusions:Our findings suggest that the most likely scenario to cause the observed water emission in Arp 220 is a large number of independent masers originating from numerous star-forming regions.
| S-EPMC5687566 | biostudies-literature
Project description:Bartonella henselae is a recently recognized pathogenic bacterium associated with cat scratch disease, bacillary angiomatosis, and bacillary peliosis. This study describes the cloning, sequencing, and characterization of an antigenic autotransporter gene from B. henselae. A cloned 6.0-kb BclI-EcoRI DNA fragment expresses a 120-kDa B. henselae protein immunoreactive with 21.2% of sera from patients positive for B. henselae immunoglobulin G antibodies by indirect immunofluorescence, with 97.3% specificity and no cross-reactivity with antibodies against various other organisms. DNA sequencing of the clone revealed one open reading frame of 4,320 bp with a deduced amino acid sequence that shows homology to the family of autotransporters. The autotransporters are a group of proteins that mediate their own export through the outer membrane and consist of a passenger region, the alpha-domain, and an outer membrane transporter region, the beta-domain. The passenger domain shows homology to a family of pertactin-like adhesion proteins and contains seven, nearly identical 48-amino-acid repeats not found in any other bacterial or Bartonella DNA sequences. The passenger alpha-domain has a calculated molecular mass of 117 kDa, and the transporter beta-domain has a calculated molecular mass of 36 kDa. The clone expresses a 120-kDa protein and a protein that migrates at approximately 38 kDa exclusively in the outer membrane protein fraction, suggesting that the 120-kDa passenger protein remains associated with the outer membrane after cleavage from the 36-kDa transporter.
| S-EPMC2168282 | biostudies-literature
Project description:ARP/wARP is a software suite to build macromolecular models in X-ray crystallography electron density maps. Structural genomics initiatives and the study of complex macromolecular assemblies and membrane proteins all rely on advanced methods for 3D structure determination. ARP/wARP meets these needs by providing the tools to obtain a macromolecular model automatically, with a reproducible computational procedure. ARP/wARP 7.0 tackles several tasks: iterative protein model building including a high-level decision-making control module; fast construction of the secondary structure of a protein; building flexible loops in alternate conformations; fully automated placement of ligands, including a choice of the best-fitting ligand from a 'cocktail'; and finding ordered water molecules. All protocols are easy to handle by a nonexpert user through a graphical user interface or a command line. The time required is typically a few minutes although iterative model building may take a few hours.
| S-EPMC2582149 | biostudies-literature
Project description:Recent developments in cryogenic electron microscopy (cryo-EM) have enabled structural studies of large macromolecular complexes at resolutions previously only attainable using macromolecular crystallography. Although a number of methods can already assist in de novo building of models into high-resolution cryo-EM maps, automated and reliable map interpretation remains a challenge. Presented here is a systematic study of the accuracy of models built into cryo-EM maps using ARP/wARP. It is demonstrated that the local resolution is a good indicator of map interpretability, and for the majority of the test cases ARP/wARP correctly builds 90% of main-chain fragments in regions where the local resolution is 4.0?Å or better. It is also demonstrated that the coordinate accuracy for models built into cryo-EM maps is comparable to that of X-ray crystallographic models at similar local cryo-EM and crystallographic resolutions. The model accuracy also correlates with the refined atomic displacement parameters.
| S-EPMC7869898 | biostudies-literature
Project description:Antiserum to the Borrelia burgdorferi arthritis-related protein, Arp, has been shown to prevent or reduce arthritis in immunodeficient mice. To directly investigate the requirement for this lipoprotein in the generation of Lyme arthritis, we utilized targeted deletion to generate a B. burgdorferi clone that lacked only the arp gene locus. Infection of Lyme disease-susceptible C3H/HeN mice with the arp deletion mutant demonstrated significantly reduced tibiotarsal joint swelling during the first 6 weeks of infection compared to a wild-type control. The severity of joint swelling was restored to wild-type levels in mice infected with an arp mutant clone complemented in cis. Interestingly, the reduced swelling of joint tissues exhibited by mice infected with the arp deletion mutant did not directly correspond to reduced underlying arthritis. Histopathology data at 2 weeks postinfection showed some reduction in arthritis severity caused by the arp mutant clone; however, by 8 weeks, no significant difference was observed between joint tissues infected by the wild-type or arp mutant clones. The spirochete load in the joint tissues of mice infected with the arp mutant was found to be greater than that exhibited by the wild-type control. Our findings demonstrate that this lipoprotein contributes to the generation of early-onset joint swelling and suggests that arp expression has a negative secondary effect on total spirochete numbers in joint tissues.
| S-EPMC3911854 | biostudies-literature
Project description:An Arabidopsis thaliana cDNA encoding an analogue, referred to as Arp for apurinic endonuclease-redox protein, of the human redox factor REF has been cloned. Arp stimulates in vitro DNA-binding activity of the human transcription factor Jun and Fos by the reduction of a cysteine residue located in the DNA-binding domain. Based on amino acid sequence homology, this redox activity is probably confined to the small internal domain of the Arp protein. In analogy to REF, we show that the Arabidopsis Arp protein also functions as an apurinic/apyrimidinic class II endonuclease. This base-free endonuclease activity resides in the carboxyl-terminal domain, and this part of the protein has significant sequence similarity to bacterial (Escherichia coli exonuclease III and Streptococcus pneumoniae exonuclease A) and animal (Drosophila Rrp1 and human REF/HAP) apurinic/apyrimidinic endonucleases. The amino-terminal domain of the Arp protein is highly charged and apparently increases the affinity of the protein for DNA. Therefore, the Arabidopsis Arp protein is multifunctional and may be involved both in DNA repair and in the regulation of transcription.
| S-EPMC43564 | biostudies-other