Stereochemical errors and their implications for molecular dynamics simulations

<p>Abstract</p> <p>Background</p> <p>Biological molecules are often asymmetric with respect to stereochemistry, and correct stereochemistry is essential to their function. Molecular dynamics simulations of biomolecules have increasingly become an integral part of biophysical research. However, stereochemical errors in biomolecular structures can have a dramatic impact on the results of simulations.</p> <p>Results</p> <p>Here we illustrate the effects that chirality and peptide bond configuration flips may have on the secondary structure of proteins throughout a simulation. We also analyze the most common sources of stereochemical errors in biomolecular structures and present software tools to identify, correct, and prevent stereochemical errors in molecular dynamics simulations of biomolecules.</p> <p>Conclusions</p> <p>Use of the tools presented here should become a standard step in the preparation of biomolecular simulations and in the generation of predicted structural models for proteins and nucleic acids.</p

Lateral opening in the intact β-barrel assembly machinery captured by cryo-EM

The β-barrel assembly machinery (BAM) is a ~203 kDa complex of five proteins (BamA-E) which is essential for viability in E. coli. BAM promotes the folding and insertion of β-barrel proteins into the outer membrane via a poorly understood mechanism. Several current models suggest that BAM functions through a ‘lateral gating’ motion of the β-barrel of BamA. Here we present a cryo-EM structure of the BamABCDE complex, at 4.9 Å resolution. The structure is in a laterally open conformation showing that gating is independent of BamB binding. We describe conformational changes throughout the complex, and interactions between BamA, B, D, and E and the detergent micelle that suggest communication between BAM and the lipid bilayer. Finally, using an enhanced reconstitution protocol and functional assays, we show that for the outer membrane protein OmpT, efficient folding in vitro requires lateral gating in BAM

E. coli metabolic protein aldehydealcohol dehydrogenase-E binds to the ribosome: a unique moonlighting action revealed

It is becoming increasingly evident that a high degree of regulation is involved in the protein synthesis machinery entailing more interacting regulatory factors. A multitude of proteins have been identified recently which show regulatory function upon binding to the ribosome. Here, we identify tight association of a metabolic protein aldehyde-alcohol dehydrogenase E (AdhE) with the E. coli 70S ribosome isolated from cell extract under low salt wash conditions. Cryo-EM reconstruction of the ribosome sample allows us to localize its position on the head of the small subunit, near the mRNA entrance. Our study demonstrates substantial RNA unwinding activity of AdhE which can account for the ability of ribosome to translate through downstream of at least certain mRNA helices. Thus far, in E. coli, no ribosome-associated factor has been identified that shows downstream mRNA helicase activity. Additionally, the cryo-EM map reveals interaction of another extracellular protein, outer membrane protein C (OmpC), with the ribosome at the peripheral solvent side of the 50S subunit. Our result also provides important insight into plausible functional role of OmpC upon ribosome binding. Visualization of the ribosome purified directly from the cell lysate unveils for the first time interactions of additional regulatory proteins with the ribosom

Mechanism of eIF6 release from the nascent 60S ribosomal subunit.

SBDS protein (deficient in the inherited leukemia-predisposition disorder Shwachman-Diamond syndrome) and the GTPase EFL1 (an EF-G homolog) activate nascent 60S ribosomal subunits for translation by catalyzing eviction of the antiassociation factor eIF6 from nascent 60S ribosomal subunits. However, the mechanism is completely unknown. Here, we present cryo-EM structures of human SBDS and SBDS-EFL1 bound to Dictyostelium discoideum 60S ribosomal subunits with and without endogenous eIF6. SBDS assesses the integrity of the peptidyl (P) site, bridging uL16 (mutated in T-cell acute lymphoblastic leukemia) with uL11 at the P-stalk base and the sarcin-ricin loop. Upon EFL1 binding, SBDS is repositioned around helix 69, thus facilitating a conformational switch in EFL1 that displaces eIF6 by competing for an overlapping binding site on the 60S ribosomal subunit. Our data reveal the conserved mechanism of eIF6 release, which is corrupted in both inherited and sporadic leukemias.Supported by a Federation of European Biochemical Societies Long term Fellowship (to FW), Specialist Programme from Bloodwise [12048] (AJW), the Medical Research Council [MC_U105161083] (AJW) and [U105115237] (RRK), Wellcome Trust strategic award to the Cambridge Institute for Medal Research [100140], Tesni Parry Trust (AJW), Ted’s Gang (AJW) and the Cambridge NIHR Biomedical Research Centre.This is the author accepted manuscript. The final version is available from Nature Publishing Group via http://dx.doi.org/10.1038/nsmb.311

The 2014-2015 Brazilian Mutual Phenomena campaign for the Jovian satellites and improved results for the 2009 events

Progress in astrometry and orbital modelling of planetary moons in the last decade enabled better determinations of their orbits. These studies need accurate positions spread over extended periods. We present the results of the 2014-2015 Brazilian campaign for 40 mutual events from 47 observed light curves by the Galilean satellites plus one eclipse of Amalthea by Ganymede. We also reanalysed and updated results for 25 mutual events observed in the 2009 campaign. All telescopes were equipped with narrow-band filters centred at 889 nm with a width of 15 nm to eliminate the scattered light from Jupiter. The albedos' ratio was determined using images before and after each event. We simulated images of moons, umbra, and penumbra in the sky plane, and integrated their fluxes to compute albedos, simulate light curves and fit them to the observed ones using a chi-square fitting procedure. For that, we used the complete version of the Oren-Nayer reflectance model. The relative satellite positions mean uncertainty was 11.2 mas ($\sim$35 km) and 10.1 mas ($\sim$31 km) for the 2014-2015 and 2009 campaigns respectively. The simulated and observed \textsc{ascii} light curve files are freely available in electronic form at the \textit{Natural Satellites DataBase} (NSDB). The 40/25 mutual events from our 2014-2015/2009 campaigns represent a significant contribution of 17%/15% in comparison with the PHEMU campaigns lead by the IMCCE. Besides that, our result for the eclipse of Amalthea is only the 4$^{th}$ such measurement ever published after the three ones observed by the 2014-2015 international PHEMU campaign. Our results are suitable for new orbital/ephemeris determinations for the Galilean moons and Amalthea.Comment: 14 pages, 8 figures and 5 table

Antigenic response to CT-P13 and infliximab originator in inflammatory bowel disease patients shows similar epitope recognition

Funding Information: Declaration of personal interests: JG received consultancy fees and/or research support from Pfizer, Merck, Biogen, Celltrion, and Samsung Bioepis. TD received fees for scientific advice and/or research support from Pfizer/Hospira, Amgen, MSD, Biogen, Roche, and Samsung Bioepis. IR was the lead investigator in a MSD sponsored prospective observational study, consultant/speaker at scientific meetings sponsored by MSD, AbbVie, Falk Ferring, Janssen, and received support to participate in scientific meetings from MSD, AbbVie, Falk, Ferring, Norgine, Hospira, Pharmakern, Janssen. JEF received unrestricted research grants or acted as a speaker for AbbVie, Ache, Amgen, Biogen, BMS, Janssen, Lilly, MSD, Novartis, Pfizer, Roche, UCB. PLL has been a speaker and/or advisory board member: Abb-Vie, EGIS, Falk Pharma GmbH, Ferring, Genetech, Jansen, Kyowa Hakko Kirin Pharma, Mitsubishi Tanabe Pharma Corporation, MSD, Otsuka Pharma, Pharmacosmos, Pfizer, Roche, Shire and Takeda and has received unrestricted research grant: AbbVie, MSD, and Pfizer. Funding Information: Declaration of personal interests: JG received consultancy fees and/or research support from Pfizer, Merck, Biogen, Celltrion, and Samsung Bioepis. TD received fees for scientific advice and/or research support from Pfizer/Hospira, Amgen, MSD, Biogen, Roche, and Samsung Bioepis. IR was the lead investigator in a MSD sponsored prospective observational study, consultant/speaker at scientific meetings sponsored by MSD, AbbVie, Falk Ferring, Janssen, and received support to participate in scientific meetings from MSD, AbbVie, Falk, Ferring, Norgine, Hospira, Pharmakern, Janssen. JEF received unrestricted research grants or acted as a speaker for AbbVie, Ache, Amgen, Biogen, BMS, Janssen, Lilly, MSD, Novartis, Pfizer, Roche, UCB. PLL has been a speaker and/or advisory board member: AbbVie, EGIS, Falk Pharma GmbH, Ferring, Genetech, Jansen, Kyowa Hakko Kirin Pharma, Mitsubishi Tanabe Pharma Corporation, MSD, Otsuka Pharma, Pharmacosmos, Pfizer, Roche, Shire and Takeda and has received unrestricted research grant: AbbVie, MSD, and Pfizer. Declaration of funding interests: This work was supported by grants from Fundação para a Ciência e Tecnologia, HIVERA ERA-NET HIVERA/0002/2013 and PTDC/QEQ-MED/4412/2014 to J.G. Funding Information: Declaration of funding interests: This work was supported by grants from Fundac©ão para a Ciência e Tecnologia, HIVERA ERA-NET HIVERA/0002/2013 and PTDC/QEQ-MED/4412/2014 to J.G. Publisher Copyright: © 2018 John Wiley & Sons LtdAim: To test the cross-immunogenicity of anti-CT-P13 IBD patients’ sera to CT-P13/infliximab originator and the comparative antigenicity evoked by CT-P13/infliximab originator sera. Methods: Sera of patients with IBD with measurable anti-CT-P13 antibodies were tested for their cross-reactivity to 5 batches of infliximab originator and CT-P13. Anti-drug antibody positive sera from treated patients were used to compare antigenic epitopes. Results: All 42 anti-CT-P13 and 37 anti-infliximab originator IBD sera were cross-reactive with infliximab originator and CT-P13 respectively. Concentration of anti-drug antibodies against infliximab originator or CT-P13 were strongly correlated both for IgG1 and IgG4 (P < 0.001). Anti-CT-P13 sera of patients with IBD (n = 32) exerted similar functional inhibition on CT-P13 or infliximab originator TNF binding capacity and showed reduced binding to CT-P13 in the presence of five different batches of CT-P13 and infliximab originator. Anti-CT-P13 and anti-infliximab originator IBD sera selectively enriched phage-peptides from the VH (CDR1 and CDR3) and VL domains (CDR2 and CDR3) of infliximab. Sera reactivity detected major infliximab epitopes in these regions of infliximab in 60%-79% of patients, and no significant differences were identified between CT-P13 and infliximab originator immunogenic sera. Minor epitopes were localised in framework regions of infliximab with reduced antibody reactivity shown, in 30%-50% of patients. Monoclonal antibodies derived from naïve individuals and ADA-positive IBD patients treated with CT-P13 provided comparable epitope specificity to five different batches of CT-P13 and infliximab originator. Conclusions: These results strongly support a similar antigenic profile for infliximab originator and CT-P13, and point toward a safe switching between the two drugs in anti-drug antibody negative patients.publishersversionpublishe

A Computational Investigation on the Connection between Dynamics Properties of Ribosomal Proteins and Ribosome Assembly

Assembly of the ribosome from its protein and RNA constituents has been studied extensively over the past 50 years, and experimental evidence suggests that prokaryotic ribosomal proteins undergo conformational changes during assembly. However, to date, no studies have attempted to elucidate these conformational changes. The present work utilizes computational methods to analyze protein dynamics and to investigate the linkage between dynamics and binding of these proteins during the assembly of the ribosome. Ribosomal proteins are known to be positively charged and we find the percentage of positive residues in r-proteins to be about twice that of the average protein: Lys+Arg is 18.7% for E. coli and 21.2% for T. thermophilus. Also, positive residues constitute a large proportion of RNA contacting residues: 39% for E. coli and 46% for T. thermophilus. This affirms the known importance of charge-charge interactions in the assembly of the ribosome. We studied the dynamics of three primary proteins from E. coli and T. thermophilus 30S subunits that bind early in the assembly (S15, S17, and S20) with atomic molecular dynamic simulations, followed by a study of all r-proteins using elastic network models. Molecular dynamics simulations show that solvent-exposed proteins (S15 and S17) tend to adopt more stable solution conformations than an RNA-embedded protein (S20). We also find protein residues that contact the 16S rRNA are generally more mobile in comparison with the other residues. This is because there is a larger proportion of contacting residues located in flexible loop regions. By the use of elastic network models, which are computationally more efficient, we show that this trend holds for most of the 30S r-proteins

EMDataBank.org: unified data resource for CryoEM

Cryo-electron microscopy reconstruction methods are uniquely able to reveal structures of many important macromolecules and macromolecular complexes. EMDataBank.org, a joint effort of the Protein Data Bank in Europe (PDBe), the Research Collaboratory for Structural Bioinformatics (RCSB) and the National Center for Macromolecular Imaging (NCMI), is a global ‘one-stop shop’ resource for deposition and retrieval of cryoEM maps, models and associated metadata. The resource unifies public access to the two major archives containing EM-based structural data: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural data of macromolecules and macromolecular complexes by the wider scientific community

Tratamiento de efluentes acuosos contaminados con compuestos organoclorados

[ES] Los compuestos organoclorados son un tipo de residuos que han adquirido especial relevancia en los últimos tiempos, debido a sus características tóxicas y peligrosas, tanto para el medio ambiente como para los seres humanos. Su especial peligrosidad ha potenciado la búsqueda de alternativas para su tratamiento en las distintas corrientes donde se presentan. En este artículo se describe la problemática real de este tipo de compuestos, se exponen los principales contaminantes y se muestra una visión general de las alternativas para la eliminación de estos organoclorados de corrientes acuosas, detallándose en profundidad una de las alternativas de eliminación consideradas: la hidrodecloración catalítica en fase acuosa.Padilla Vivas, B.; Díez Sanz, FV.; Ordóñez García, S. (2005). Tratamiento de efluentes acuosos contaminados con compuestos organoclorados. 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