Structural Characterization of Protein-Protein Complexes by Integrating Computational Docking with Small-angle Scattering Data

X-ray crystallography and NMR can provide detailed structural information of protein-protein complexes, but technical problems make their application challenging in the high-throughput regime. Other methods such as small-angle X-ray scattering (SAXS) are more promising for large-scale application, but at the cost of lower resolution, which is a problem that can be solved by complementing SAXS data with theoretical simulations. Here, we propose a novel strategy that combines SAXS data and accurate protein-protein docking simulations. The approach has been benchmarked on a large pool of known structures with synthetic SAXS data, and on three experimental examples. The combined approach (pyDockSAXS) provided a significantly better success rate (43% for the top 10 predictions) than either of the two methods alone. Further analysis of the influence of different docking parameters made it possible to increase the success rates for specific cases, and to define guidelines for improving the data-driven protein-protein docking protocols.     

BacA Is Essential for Bacteroid Development in Nodules of Galegoid,but not Phaseoloid,Legumes

BacA is an integral membrane protein, the mutation of which leads to increased resistance to the antimicrobial peptides bleomycin and Bac7_1-35 and a greater sensitivity to SDS and vancomycin in Rhizobium leguminosarum bv. viciae, R. leguminosarum bv. phaseoli, and Rhizobium etli. The growth of Rhizobium strains on dicarboxylates as a sole carbon source was impaired in bacA mutants but was overcome by elevating the calcium level. While bacA mutants elicited indeterminate nodule formation on peas, which belong to the galegoid tribe of legumes, bacteria lysed after release from infection threads and mature bacteroids were not formed. Microarray analysis revealed almost no change in a bacA mutant of R. leguminosarum bv. viciae in free-living culture. In contrast, 45 genes were more-than 3-fold upregulated in a bacA mutant isolated from pea nodules. Almost half of these genes code for cell membrane components, suggesting that BacA is crucial to alterations that occur in the cell envelope during bacteroid development. In stark contrast, bacA mutants of R. leguminosarum bv. phaseoli and R. etli elicited the formation of normal determinate nodules on their bean host, which belongs to the phaseoloid tribe of legumes. Bacteroids from these nodules were indistinguishable from the wild type in morphology and nitrogen fixation. Thus, while bacA mutants of bacteria that infect galegoid or phaseoloid legumes have similar phenotypes in free-living culture, BacA is essential only for bacteroid development in indeterminate galegoid nodules.Bacteria of the family Rhizobiaceae are alphaproteobacteria, which form a species-specific symbiotic relationship with leguminous plants. Plants release flavonoids that typically induce the synthesis of lipochitooligosaccharides by rhizobia, which in turn initiate a signaling cascade in the plant, leading to nodule formation (34). Rhizobia become trapped by curling root hairs, which they enter via infection threads that grow and ramify into the root cortex, where newly induced meristematic cells form the nodule (34). Bacteria are released from infection threads and engulfed by a plant-derived symbiosome membrane. In galegoid legumes (a clade in the subfamily Papilionoideae, such as Medicago, Pisum, or Vicia), which form indeterminate nodules that have a persistent meristem, bacteria undergo the endoreduplication of their chromosome, resulting in dramatic increases in size, shape, and DNA content to become terminally differentiated bacteroids (32). However, in phaseoloid legumes (e.g., lotus, bean, and soybean), which form determinate nodules with a transient meristem, bacteria do not undergo endoreduplication and therefore do not enlarge substantially. These bacteroids retain a normal DNA content and can regrow after isolation from nodules (32). The endoreduplication of bacteroids is controlled by the plant, and it is believed that nodule-specific cysteine-rich (NCR) peptides, which are made in indeterminate, but not in determinate, nodules, may be responsible for inducing and maintaining bacteroid development (31, 32). Finally, mature bacteroids receive dicarboxylic acids from the plant, which they use as a carbon, reductant, and energy source for the reduction of N₂ to ammonia (38). The ammonia is secreted to the plant, where it is assimilated into amino acids or ureides, depending on the legume, for export to the shoot.Sinorhizobium meliloti BacA protein was the first bacterial factor identified to be essential for bacteroid development (15). More recently, it also has been shown to be essential for the Mesorhizobium-Astragalus symbiosis (42). S. meliloti elicits the formation of indeterminate nodules on alfalfa, and while S. meliloti bacA null mutants induce nodule formation, bacteria lyse soon after endocytosis but prior to bacteroid differentiation (15, 20). BacA is a cytoplasmic membrane protein that shares 64% identity with SbmA from Escherichia coli (15, 25). SbmA/BacA proteins belong to the ATP binding cassette (ABC) superfamily and share sequence similarity with a family of eukaryotic peroxisomal membrane proteins, including the human adrenoleukodystrophy protein, which is required for the efficient transport of very-long-chain fatty acids (VLCFAs) out of the cytoplasm (9). Consistent with this, S. meliloti BacA is required for the complete modification of lipid A with VLCFAs (9). However, since S. meliloti mutants, which are directly involved in the biosynthesis of VLCFA-modified lipid A, show bacteroid abnormalities but still can form a successful alfalfa symbiosis, the effect of BacA on lipid A VLCFA modification does not fully account for its essential role in bacteroid development (10, 11, 16). Strains mutated in bacA also have an increased resistance to the glycopeptide bleomycin, a low-level resistance to aminoglycoside antibiotics, and an increased sensitivity to ethanol, sodium dodecyl sulfate (SDS), and deoxycholate relative to the sensitivities of the parent strain (12, 18, 25). More recently it has been shown that an S. meliloti bacA null mutant has an increased resistance to a truncated form of a eukaryotic proline-rich peptide, Bac7_1-16, and was unable to accumulate a fluorescently labeled form of this peptide (28). This finding, combined with the increased resistance of an S. meliloti bacA null mutant to bleomycin, led to the hypothesis that BacA is itself a putative peptide transporter (BacA mediated) or able to alter the activity of such a transporter (BacA influenced) (11, 15, 18, 28).As the increased resistance of the S. meliloti bacA null mutant to bleomycin and Bac7_1-16 appears to be independent of the VLCFA modification of lipid A (11, 28), this suggested that either BacA-mediated or BacA-influenced peptide uptake into S. meliloti plays a role in bacteroid development. Since indeterminate galegoid nodules contain hundreds of NCR peptides, whereas determinate phaseoloid nodules lack these host peptides (31), we considered it important to assess the role of BacA in bacteroid development during the formation of both nodule types.Here, we show that bacA mutants of Rhizobium leguminosarum bv. viciae strains 3841 and A34 failed to develop bacteroids and did not fix nitrogen in indeterminate pea (Pisum sativum) nodules. However, bacA mutants of both R. leguminosarum bv. phaseoli 4292 and Rhizobium etli CE3 formed normal bacteroids and fixed nitrogen at wild-type rates in determinate bean (Phaseolus vulgaris) nodules. This is consistent with BacA being a key component of bacteroid development in indeterminate galegoid nodules that is not required for functional bacteroid formation in determinate phaseoloid nodules.     

The reaction of [Os6(CO)18] with [(SPPh2)2NH]: Facile rearrangement of the metal framework

The reaction of [Os₆(CO)₁₈] 1 with [(SPPh₂)₂NH] in the presence of Me₃NO produces a purple compound characterized spectroscopically and by X-ray crystallography, as [HOs₆(CO)₁₇(SPPh₂)₂N] 2. The structure shows the hexanuclear fragment to have suffered a geometrical rearrangement to give a metal framework that can be described as an edge-bridged tetrahedron with an additional terminal osmium atom bonded to one of the bridged metal atoms. The ligand acts as a bimetallic tetraconnective unit through both sulphur atoms between two non-bonded osmium atoms.     

Regulation of cAMP-dependent Protein Kinases: THE HUMAN PROTEIN KINASE X (PrKX) REVEALS THE ROLE OF THE CATALYTIC SUBUNIT αH-αI LOOP*

cAMP-dependent protein kinases are reversibly complexed with any of the four isoforms of regulatory (R) subunits, which contain either a substrate or a pseudosubstrate autoinhibitory domain. The human protein kinase X (PrKX) is an exemption as it is inhibited only by pseudosubstrate inhibitors, i.e. RIα or RIβ but not by substrate inhibitors RIIα or RIIβ. Detailed examination of the capacity of five PrKX-like kinases ranging from human to protozoa (Trypanosoma brucei) to form holoenzymes with human R subunits in living cells shows that this preference for pseudosubstrate inhibitors is evolutionarily conserved. To elucidate the molecular basis of this inhibitory pattern, we applied bioluminescence resonance energy transfer and surface plasmon resonance in combination with site-directed mutagenesis. We observed that the conserved αH-αI loop residue Arg-283 in PrKX is crucial for its RI over RII preference, as a R283L mutant was able to form a holoenzyme complex with wild type RII subunits. Changing the corresponding αH-αI loop residue in PKA Cα (L277R), significantly destabilized holoenzyme complexes in vitro, as cAMP-mediated holoenzyme activation was facilitated by a factor of 2–4, and lead to a decreased affinity of the mutant C subunit for R subunits, significantly affecting RII containing holoenzymes.     

Nitric Oxide Mediates the Glutamate-dependent Pathway for Neurotransmission in Sepia officinalis Chromatophore Organs

Chromatophore organs are complex and unique structures responsible for the variety of body coloration patterns used by cephalopods to communicate and camouflage. They are formed by a pigment-containing cytoelastic sacculus, surrounded by muscle fibers directly innervated from the brain. Muscle contraction and relaxation are responsible for expansion and retraction of the pigment-containing cell. Their functioning depends on glutamate and Phe-Met-Arg-Phe-NH₂-related peptides, which induce fast and slow cell expansion, respectively, and 5-hydroxytryptamine, which induces retraction. Apart from these three substances and acetylcholine, which acts presynaptically, no other neuroactive compounds have so far been found to be involved in the neuroregulation of chromatophore physiology, and the detailed signaling mechanisms are still little understood. Herein, we disclose the role of nitric oxide (NO) as mediator in one of the signaling pathways by which glutamate activates body patterning. NO and nitric-oxide synthase have been detected in pigment and muscle fibers of embryo, juvenile, and adult chromatophore organs from Sepia officinalis. NO-mediated Sepia chromatophore expansion operates at slower rate than glutamate and involves cGMP, cyclic ADP-ribose, and ryanodine receptor activation. These results demonstrate for the first time that NO is an important messenger in the long term maintenance of the body coloration patterns in Sepia.     

Self-assembling SAS-6 Multimer Is a Core Centriole Building Block

Centrioles are conserved microtubule-based organelles with 9-fold symmetry that are essential for cilia and mitotic spindle formation. A conserved structure at the onset of centriole assembly is a “cartwheel” with 9-fold radial symmetry and a central tubule in its core. It remains unclear how the cartwheel is formed. The conserved centriole protein, SAS-6, is a cartwheel component that functions early in centriole formation. Here, combining biochemistry and electron microscopy, we characterize SAS-6 and show that it self-assembles into stable tetramers, which serve as building blocks for the central tubule. These results suggest that SAS-6 self-assembly may be an initial step in the formation of the cartwheel that provides the 9-fold symmetry. Electron microscopy of centrosomes identified 25-nm central tubules with repeating subunits and show that SAS-6 concentrates at the core of the cartwheel. Recombinant and native SAS-6 self-oligomerizes into tetramers with ∼6-nm subunits, and these tetramers are components of the centrosome, suggesting that tetramers are the building blocks of the central tubule. This is further supported by the observation that elevated levels of SAS-6 in Drosophila cells resulted in higher order structures resembling central tubule morphology. Finally, in the presence of embryonic extract, SAS-6 tetramers assembled into high density complexes, providing a starting point for the eventual in vitro reconstruction of centrioles.     

Importancia de la determinación de variantes en el número de copias en neonatos con aneuploidías autosómicas

Introduction:

Aneuploidies are frequent genetic disorders in clinical practice. However, little is known about other genetic variants that may influence the final phenotype.

Objective:

To determine the variations in the number of copies and regions with homozygosity greater than 0.5% or larger than 10 Mb in newborns with autosomal aneuploidies.

Materials and methods:

We performed a chromosomal microarray analysis on newborns with autosomal aneuploidies (n=7), trisomy 21 (n=5), and trisomy 18 (n=2) evaluated at the Hospital Antonio Lorena and Hospital Regional of Cusco, Perú, during 2018.

Results:

We found pathogenic and probably pathogenic variants in the number of copies in other genomic regions different to chromosomes 21 or 18 in two neonates. Additionally, we found two variants bigger than 500 kpb of unknown pathogenicity.

Conclusions:

Although the number of analyzed individuals was small, it is important to highlight that we found other variants in the number of copies that have been described in association with neurodevelopmental disorders, congenital anomalies, deafness, and short/ tall stature, among others, in almost half of them, which will probably impact the phenotype negatively in patients with aneuploidies.     

Regulation of myocardial substrate metabolism during increased energy expenditure: insights from computational studies

In response to exercise, the heart increases its metabolic rate severalfold while maintaining energy species (e.g., ATP, ADP, and Pi) concentrations constant; however, the mechanisms that regulate this response are unclear. Limited experimental studies show that the classic regulatory species NADH and NAD+ are also maintained nearly constant with increased cardiac power generation, but current measurements lump the cytosol and mitochondria and do not provide dynamic information during the early phase of the transition from low to high work states. In the present study, we modified our previously published computational model of cardiac metabolism by incorporating parallel activation of ATP hydrolysis, glycolysis, mitochondrial dehydrogenases, the electron transport chain, and oxidative phosphorylation, and simulated the metabolic responses of the heart to an abrupt increase in energy expenditure. Model simulations showed that myocardial oxygen consumption, pyruvate oxidation, fatty acids oxidation, and ATP generation were all increased with increased energy expenditure, whereas ATP and ADP remained constant. Both cytosolic and mitochondrial NADH/NAD+ increased during the first minutes (by 40% and 20%, respectively) and returned to the resting values by 10-15 min. Furthermore, model simulations showed that an altered substrate selection, induced by either elevated arterial lactate or diabetic conditions, affected cytosolic NADH/NAD+ but had minimal effects on the mitochondrial NADH/NAD+, myocardial oxygen consumption, or ATP production. In conclusion, these results support the concept of parallel activation of metabolic processes generating reducing equivalents during an abrupt increase in cardiac energy expenditure and suggest there is a transient increase in the mitochondrial NADH/NAD+ ratio that is independent of substrate supply.