New Cytotoxic Cyclic Peptide from the Marine Sponge-Associated sp. UR67.

A new cyclic hexapeptide, nocardiotide A (), together with three known compounds-tryptophan (), kynurenic acid (), and 4-amino-3-methoxy benzoic acid ()-were isolated and identified from the broth culture of sp. UR67 strain associated with the marine sponge sp. from the Red Sea.

Direct Pathway Cloning Combined with Sequence- and Ligation-Independent Cloning for Fast Biosynthetic Gene Cluster Refactoring and Heterologous Expression.

The need  for new pharmacological lead structures, especially against drug resistances, has led to a surge in natural product research and discovery. New biosynthetic gene cluster capturing methods to efficiently clone and heterologously express natural product pathways have thus been developed. Direct pathway cloning (DiPaC) is an emerging synthetic biology strategy that utilizes long-amplification PCR and HiFi DNA assembly for the capture and expression of natural product biosynthetic gene clusters.

Gauge-origin dependence in electronic g-tensor calculations.

We present a benchmark study on the gauge-origin dependence of the electronic g-tensor using data from unrestricted density functional theory calculations with the spin-orbit mean field ansatz. Our data suggest in accordance with previous studies that g-tensor calculations employing a common gauge-origin are sufficiently accurate for small molecules; however, for extended molecules, the introduced errors can become relevant and significantly exceed the basis set error. Using calculations with the spin-orbit mean field ansatz and gauge-including atomic orbitals as a reference, we furthermore show that the accuracy and reliability of common gauge-origin approaches in larger molecules depends strongly on the locality of the spin density distribution.

Chemo-enzymatic Total Synthesis of Oxosorbicillinol, Sorrentanone, Rezishanones B and C, Sorbicatechol A, Bisvertinolone, and (+)-Epoxysorbicillinol.

The sorbicillinoids are a large family of fungal natural products, many of which possess highly challenging molecular architectures. Depending on their individual structures they exhibit strong biological activities ranging from radical scavenging and anti-infective properties to cytotoxicity. Despite the resulting strong biomedical potential of these natural products and the interest of synthetic chemists owing to their fascinating structures, many sorbicillinoids are currently not synthetically accessible, thus hampering in-depth biological characterization and structural diversification.

Selected-Nuclei Method for the Computation of Hyperfine Coupling Constants within Second-Order Møller-Plesset Perturbation Theory.

We introduce a new ansatz to compute hyperfine coupling constants of selected nuclei at the level of second-order Møller-Plesset perturbation (MP2) and double-hybrid density functional theory with reduced computational effort, opening the route to the analyis of hyperfine coupling constants of large molecular structures. Our approach is based on a reformulation of the canonical MP2 term in atomic orbitals, thus exploiting the locality of electron correlation. We show that a perturbation-including integral screening reduces the scaling behavior of the number of significant two-electron integrals to sublinear.

Natural Product Potential of the Genus .

Actinomycetes are a relevant source of novel bioactive compounds. One of the pharmaceutically and biotechnologically important genera that attract natural products research is the genus mainly for its ability to produce a wide variety of secondary metabolites accounting for its wide range of biological activities. This review covers the literature from January 2015 until February 2018 making a complete survey of all the compounds that were isolated from the genus their biological activities, and natural sources, whenever applicable.

Accurate and Efficient Parallel Implementation of an Effective Linear-Scaling Direct Random Phase Approximation Method.

An efficient algorithm for calculating the random phase approximation (RPA) correlation energy is presented that is as accurate as the canonical molecular orbital resolution-of-the-identity RPA (RI-RPA) with the important advantage of an effective linear-scaling behavior (instead of quartic) for large systems due to a formulation in the local atomic orbital space. The high accuracy is achieved by utilizing optimized minimax integration schemes and the local Coulomb metric attenuated by the complementary error function for the RI approximation. The memory bottleneck of former atomic orbital (AO)-RI-RPA implementations ( Schurkus, H.

Reconstitution of Isotopically Labeled Ribosomal Protein L29 in the 50S Large Ribosomal Subunit for Solution-State and Solid-State NMR.

Solid-state nuclear magnetic resonance (NMR) has recently emerged as a method of choice to study structural and dynamic properties of large biomolecular complexes at atomic resolution. Indeed, recent technological and methodological developments have enabled the study of ever more complex systems in the solid-state. However, to explore multicomponent protein complexes by NMR, specific labeling schemes need to be developed that are dependent on the biological question to be answered.

Base-Independent DNA Base-Excision Repair of 8-Oxoguanine.

Living organisms protect their genome from gene mutation by excising damaged DNA bases. Here, 8-oxoguanine (8OG) is one of the most abundant DNA lesions. In bacteria the base excision is catalyzed by the enzyme formamidopyrimidine-DNA- glycosylase (Fpg), for which two different orientations of 8OG binding into the active site of Fpg have been proposed: syn- and anti-conformation.

Direct Pathway Cloning (DiPaC) to unlock natural product biosynthetic potential.

Specialized metabolites from bacteria are an important source of inspiration for drug development. The genes required for the biosynthesis of such metabolites in bacteria are usually organized in so-called biosynthetic gene clusters (BGCs). Using modern bioinformatic tools, the wealth of genomic data can be scanned for such BGCs and the expected products can often structurally be predicted in silico.

A Pericyclic Reaction Cascade in Leporin Biosynthesis.

All roads lead to Rome: The biosynthesis of the leporins in Aspergillus sp. involves an unprecedented pericyclic reaction cascade. The enzyme LepI directs the periselectivity of a [4+2] cycloaddition towards a hetero-Diels-Alder reaction outcome to give the leporin molecular scaffold.

Tyrosine-1 of RNA Polymerase II CTD Controls Global Termination of Gene Transcription in Mammals.

The carboxy-terminal domain (CTD) of RNA polymerase (Pol) II is composed of a repetition of YSPTSPS heptads and functions as a loading platform for protein complexes that regulate transcription, splicing, and maturation of RNAs. Here, we studied mammalian CTD mutants to analyze the function of tyrosine1 residues in the transcription cycle. Mutation of 3/4 of the tyrosine residues (YFFF mutant) resulted in a massive read-through transcription phenotype in the antisense direction of promoters as well as in the 3' direction several hundred kilobases downstream of genes.

Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the Translation Elongation Factor EF-P.

Ribosomes synthesizing proteins containing consecutive proline residues become stalled and require rescue via the action of uniquely modified translation elongation factors, EF-P in bacteria, or archaeal/eukaryotic a/eIF5A. To date, no structures exist of EF-P or eIF5A in complex with translating ribosomes stalled at polyproline stretches, and thus structural insight into how EF-P/eIF5A rescue these arrested ribosomes has been lacking. Here we present cryo-EM structures of ribosomes stalled on proline stretches, without and with modified EF-P.

Ubiquitome Analysis Reveals PCNA-Associated Factor 15 (PAF15) as a Specific Ubiquitination Target of UHRF1 in Embryonic Stem Cells.

Ubiquitination is a multifunctional posttranslational modification controlling the activity, subcellular localization and stability of proteins. The E3 ubiquitin ligase ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1) is an essential epigenetic factor that recognizes repressive histone marks as well as hemi-methylated DNA and recruits DNA methyltransferase 1. To explore enzymatic functions of UHRF1 beyond epigenetic regulation, we conducted a comprehensive screen in mouse embryonic stem cells to identify novel ubiquitination targets of UHRF1 and its paralogue UHRF2.

Distance-including rigorous upper bounds and tight estimates for two-electron integrals over long- and short-range operators.

We introduce both rigorous and non-rigorous distance-dependent integral estimates for four-center two-electron integrals derived from a distance-including Schwarz-type inequality. The estimates are even easier to implement than our so far most efficient distance-dependent estimates [S. A.

Expanding the Structural Space of Ribosomal Peptides: Autocatalytic N-Methylation in Omphalotin Biosynthesis.

Tail-Me: The N-methylation of backbone amide bonds in peptide natural products was thought to be exclusive to non-ribosomal peptides. A newly discovered methylation mechanism now brings this structural feature into the world of ribosomal peptides, thereby significantly expanding the structural diversity of ribosomally synthesized and post-translationally modified peptides (RiPPs).

Protein-mediated RNA folding governs sequence-specific interactions between rotavirus genome segments.

Segmented RNA viruses are ubiquitous pathogens, which include influenza viruses and rotaviruses. A major challenge in understanding their assembly is the combinatorial problem of a non-random selection of a full genomic set of distinct RNAs. This process involves complex RNA-RNA and protein-RNA interactions, which are often obscured by non-specific binding at concentrations approaching in vivo assembly conditions.

The two-pore channel TPC1 is required for efficient protein processing through early and recycling endosomes.

Two-pore channels (TPCs) are localized in endo-lysosomal compartments and assumed to play an important role for vesicular fusion and endosomal trafficking. Recently, it has been shown that both TPC1 and 2 were required for host cell entry and pathogenicity of Ebola viruses. Here, we investigate the cellular function of TPC1 using protein toxins as model substrates for distinct endosomal processing routes.

Methylation of DNA Ligase 1 by G9a/GLP Recruits UHRF1 to Replicating DNA and Regulates DNA Methylation.

DNA methylation is an essential epigenetic mark in mammals that has to be re-established after each round of DNA replication. The protein UHRF1 is essential for this process; it has been proposed that the protein targets newly replicated DNA by cooperatively binding hemi-methylated DNA and H3K9me2/3, but this model leaves a number of questions unanswered. Here, we present evidence for a direct recruitment of UHRF1 by the replication machinery via DNA ligase 1 (LIG1).

Stereoselective Total Synthesis of Bisorbicillinoid Natural Products by Enzymatic Oxidative Dearomatization/Dimerization.

Natural products are a virtually inexhaustible source of small molecules with spectacular molecular architectures and biomedical potential. Their structural complexity generates formidable challenges to total synthesis but often also precludes time- and resource-efficient, stereoselective synthetic access. Biosynthetically, nature frequently uses dimerization and oligomerization reactions to produce highly challenging frameworks from simple starting materials.

Small Molecules for Early Endosome-Specific Patch Clamping.

To resolve the subcellular distribution of endolysosomal ion channels, we have established a novel experimental approach to selectively patch clamp Rab5 positive early endosomes (EE) versus Rab7/LAMP1-positive late endosomes/lysosomes (LE/LY). To functionally characterize ion channels in endolysosomal membranes with the patch-clamp technique, it is important to develop techniques to selectively enlarge the respective organelles. We found here that two small molecules, wortmannin and latrunculin B, enlarge Rab5-positive EE when combined but not Rab7-, LAMP1-, or Rab11 (RE)-positive vesicles.

Patch-clamp technique to characterize ion channels in enlarged individual endolysosomes.

According to proteomics analyses, more than 70 different ion channels and transporters are harbored in membranes of intracellular compartments such as endosomes and lysosomes. Malfunctioning of these channels has been implicated in human diseases such as lysosomal storage disorders, neurodegenerative diseases and metabolic pathologies, as well as in the progression of certain infectious diseases. As a consequence, these channels have engendered very high interest as future drug targets.

Low-scaling first-order properties within second-order Møller-Plesset perturbation theory using Cholesky decomposed density matrices.

An efficient implementation of energy gradients and of hyperfine coupling constants in second-order Møller-Plesset perturbation theory (MP2) is presented based on our fully atomic orbital (AO)-based approach. For the latter, an unrestricted AO-based MP2 formulation is introduced. A reduction in the dependency of the computational efficiency on the size of the basis set is achieved by a Cholesky decomposition and the prefactor is reduced by the resolution-of-the-identity approximation.

Complete Genome Sequence of Subsp. , A Rich Source of Novel Natural Product (Bio-)Chemistry.

The soil dwelling actinomycete strain subsp. is the producer of the antiviral antibiotics kistamicin A and B. Genome sequencing and bioinformatic analysis revealed the presence of the kistamycin biosynthetic gene cluster responsible for the formation of these non-ribosomal peptides as well as an impressive number of yet uncharacterized biosynthetic pathways.