Background: Streptococcus pneumoniae Neuraminidase A (NanA) is a multi-domain protein anchored to the bacterial surface. Upstream of the catalytic domain of NanA is a domain that conforms to the sialic acid-recognising CBM40 family of the CAZY (carbohydrate-active enzymes) database. This domain has been identified to play a critical role in allowing the bacterium to promote adhesion and invasion of human brain microvascular endothelial cells, and hence may play a key role in promoting bacterial meningitis. In addition, the CBM40 domain has also been reported to activate host chemokines and neutrophil recruitment during infection. Results: Crystal structures of both apo- and holo- forms of the NanA CBM40 domain (residues 121 to 305), have been determined to 1.8 Å resolution. The domain shares the fold of other CBM40 domains that are associated with sialidases. When in complex with α2,3- or α2,6-sialyllactose, the domain is shown to interact only with the terminal sialic acid. Significantly, a deep acidic pocket adjacent to the sialic acid-binding site is identified, which is occupied by a lysine from a symmetry-related molecule in the crystal. This pocket is adjacent to a region that is predicted to be involved in protein-protein interactions. Conclusions: The structural data provide the details of linkage-independent sialyllactose binding by NanA CBM40 and reveal striking surface features that may hold the key to recognition of binding partners on the host cell surface. The structure also suggests that small molecules or sialic acid analogues could be developed to fill the acidic pocket and hence provide a new therapeutic avenue against meningitis caused by S. pneumoniae.

ABSTRACT

Low molecular weight peptides derived from the breakdown of crystallins have been reported in adult human lenses. The proliferation of these LMW peptides coincides with the earliest stages of cataract formation, suggesting that the protein cleavages involved may contribute to the aggregation and insolubilization of crystallins. This study reports the identification of 238 endogenous LMW crystallin peptides from the cortical extracts of four human lenses representing young, middle and old-age human lenses. Analysis of the peptide terminal amino acids showed that Lys and Arg were situated at the C-terminus with significantly higher frequency compared to other residues, suggesting that trypsin-like proteolysis may be active in the lens cortical fiber cells. Selected reaction monitoring analysis of an endogenous αA-crystallin peptide (αA57-65) showed that the concentration of this peptide in the human lens increased gradually to middle age, after which the rate of αA57-65 formation escalated significantly. Using 2D gel electrophoresis/nanoLC-ESI-MS/MS, 12 protein complexes of 40–150 kDa consisting of multiple crystallin components were characterized from the water soluble cortical extracts of an adult human lens. The detection of these protein complexes suggested the possibility of crystallin cross-linking, with these complexes potentially acting to stabilize degraded crystallins by sequestration into water soluble complexes. Proteins 2015; 83:1878–1886. © 2015 Wiley Periodicals, Inc.

Drosophila melanogaster is a model organism that has been instrumental in understanding the circadian clock at different levels. A range of studies on the anatomical and neurochemical properties of clock neurons in the fly led to a model of interacting neural circuits that control circadian behavior. Here we focus on recent research on the dynamics of the multiple communication pathways between clock neurons, and, particularly, on how the circadian timekeeping system responds to changes in environmental conditions.

Metallo-β-lactamases are the latest resistance mechanism of pathogenic and opportunistic bacteria against carbapenems, considered as last resort drugs. The worldwide spread of genes coding for these enzymes, together with the lack of a clinically useful inhibitor, have raised a sign of alarm. Inhibitor design has been mostly impeded by the structural diversity of these enzymes. Here we provide a critical review of mechanistic studies of the three known subclasses of metallo-β-lactamases, analyzed at the light of structural and mutagenesis investigations.

RSUME (for RWD-domain-containing sumoylation enhancer), RWDD3 gene, was identified from a pituitary tumor cell with increased tumorigenic and angiogenic potential, and has higher expression in cerebellum, pituitary, heart, kidney, liver, pancreas, adrenal gland and prostate. RSUME is induced by cellular stress like hypoxia and heat shock, and is increased in pituitary tumors, in gliomas and in VHL tumors. Seven splicing forms have been described. Two of them correspond to non-coding RNAs and the other five possess an RWD domain in the N-terminus and differ in their C-terminal end.

Although identified in the 1960’s, interest in autophagy has significantly increased in the past decade with notable research efforts oriented at understanding as to how this multi-protein complex operates and is regulated. Autophagy is commonly defined as a “self-eating” process evolved by eukaryotic cells to recycle senescent organelles and expired proteins, which is significantly increased during cellular stress responses. In addition, autophagy can also play important roles during human diseases, such as cancer, neurodegenerative and autoimmune disorders.

Conference tweeting rule frustrates ecologists

Nature 524, 7566 (2015). doi:10.1038/524391f

Author: Chris Woolston

Complaints ensued when attendees at an ecology meeting were asked to get permission before live-tweeting.

Evolution: Gene transfer in complex cells

Nature 524, 7566 (2015). doi:10.1038/nature15205

Authors: John M. Archibald

A comparative genomic study shows that, during evolution, nucleus-containing cells acquired DNA from bacteria primarily by endosymbiosis — the uptake and integration of one cell by another. See Article p.427

Endosymbiotic origin and differential loss of eukaryotic genes

Nature 524, 7566 (2015). doi:10.1038/nature14963

Authors: Chuan Ku, Shijulal Nelson-Sathi, Mayo Roettger, Filipa L. Sousa, Peter J. Lockhart, David Bryant, Einat Hazkani-Covo, James O. McInerney, Giddy Landan & William F. Martin

Chloroplasts arose from cyanobacteria, mitochondria arose from proteobacteria. Both organelles have conserved their prokaryotic biochemistry, but their genomes are reduced, and most organelle proteins are encoded in the nucleus. Endosymbiotic theory posits that bacterial genes in eukaryotic genomes entered the eukaryotic lineage via organelle ancestors.

Sidekick 2 directs formation of a retinal circuit that detects differential motion

Nature 524, 7566 (2015). doi:10.1038/nature14682

Authors: Arjun Krishnaswamy, Masahito Yamagata, Xin Duan, Y. Kate Hong & Joshua R. Sanes

In the mammalian retina, processes of approximately 70 types of interneurons form specific synapses on roughly 30 types of retinal ganglion cells (RGCs) in a neuropil called the inner plexiform layer. Each RGC type extracts salient features from visual input, which are sent deeper into the brain for further processing. The specificity and stereotypy of synapses formed in the inner plexiform layer account for the feature-detecting ability of RGCs. Here we analyse the development and function of synapses on one mouse RGC type, called the W3B-RGC. These cells have the remarkable property of responding when the timing of the movement of a small object differs from that of the background, but not when they coincide. Such cells, known as local edge detectors or object motion sensors, can distinguish moving objects from a visual scene that is also moving. We show that W3B-RGCs receive strong and selective input from an unusual excitatory amacrine cell type known as VG3-AC (vesicular glutamate transporter 3). Both W3B-RGCs and VG3-ACs express the immunoglobulin superfamily recognition molecule sidekick 2 (Sdk2), and both loss- and gain-of-function studies indicate that Sdk2-dependent homophilic interactions are necessary for the selectivity of the connection. The Sdk2-specified synapse is essential for visual responses of W3B-RGCs: whereas bipolar cells relay visual input directly to most RGCs, the W3B-RGCs receive much of their input indirectly, via the VG3-ACs. This non-canonical circuit introduces a delay into the pathway from photoreceptors in the centre of the receptive field to W3B-RGCs, which could improve their ability to judge the synchrony of local and global motion.

Cell mixing induced by myc is required for competitive tissue invasion and destruction

Nature 524, 7566 (2015). doi:10.1038/nature14684

Authors: Romain Levayer, Barbara Hauert & Eduardo Moreno

Cell–cell intercalation is used in several developmental processes to shape the normal body plan. There is no clear evidence that intercalation is involved in pathologies. Here we use the proto-oncogene myc to study a process analogous to early phase of tumour expansion: myc-induced cell competition. Cell competition is a conserved mechanism driving the elimination of slow-proliferating cells (so-called ‘losers’) by faster-proliferating neighbours (so-called ‘winners’) through apoptosis and is important in preventing developmental malformations and maintain tissue fitness. Here we show, using long-term live imaging of myc-driven competition in the Drosophila pupal notum and in the wing imaginal disc, that the probability of elimination of loser cells correlates with the surface of contact shared with winners. As such, modifying loser–winner interface morphology can modulate the strength of competition. We further show that elimination of loser clones requires winner–loser cell mixing through cell–cell intercalation. Cell mixing is driven by differential growth and the high tension at winner–winner interfaces relative to winner–loser and loser–loser interfaces, which leads to a preferential stabilization of winner–loser contacts and reduction of clone compactness over time. Differences in tension are generated by a relative difference in F-actin levels between loser and winner junctions, induced by differential levels of the membrane lipid phosphatidylinositol (3,4,5)-trisphosphate. Our results establish the first link between cell–cell intercalation induced by a proto-oncogene and how it promotes invasiveness and destruction of healthy tissues.

After the first introduction of π aromaticity in chemistry to explain the bonding, structure, and reactivity of benzene and its derivatives, this concept was further applied to many other compounds featuring other types of aromaticity (i.e., σ, δ). Thus far, there have been no reports on d-AO-based spherical σ aromaticity. Here, we predict a highly stable bare Ce6O8 cluster of a spherical shape using evolutionary algorithm USPEX and DFT + U calculations. Natural bond orbital analysis, adaptive natural density partitioning algorithm, electron localization function, and partial charge plots demonstrate that bare Ce6O8 cluster exhibits d-AO spherical σ aromaticity, thus explaining its exotic geometry and stability. Ce6O8 complex plays an important role in many reactions and is known to exist in many forms, such as in NH4[Ce6(μ3O)5(μ3OH)3(μ2-C6H5COO)9(NO3)3(DMF)3]*DMF*H2O compound, which is prepared under room temperature, and acts as an oxidizing agent. © 2015 Wiley Periodicals, Inc.

A highly stable bare Ce6O8 cluster of a spherical shape is predicted using evolutionary algorithm and DFT + U calculations. Natural bond orbital analysis, adaptive natural density partitioning algorithm, electron localization function, and partial charge plots demonstrate that the bare Ce6O8 cluster exhibits a unique 6c2e chemical bonding, thus, explaining its exotic geometry and stability.

A causal relation connecting aromaticity with the current aromaticity descriptors used in the literature and compliant with a quantum mechanics theoretical background is described. © 2015 Wiley Periodicals, Inc.

A concise description of Kekulé's historical origin of aromaticity and the current state of the field is given. Still, space is left for a discussion about the existence of aromaticity's quantum mechanical foundation. Quantum multimolecular polyhedra (QMP), based on density functions sets attached to QMP vertices, collective QMP distances, QSPR fundamental equation, and aromaticity descriptors are proposed as a way to construct an equation able to estimate aromaticity via expectation values of Hermitian operators.

The main role of voltage-gated proton channels (Hv1) is to extrude protons from the intracellular milieu when, mediated by different cellular processes, the H+ concentration increases. Hv1 are exquisitely selective for protons and their structure is homologous to the voltage sensing domain (VSD) of other voltage-gated ion channels like sodium, potassium, and calcium channels. In clear contrast to the classical voltage-dependent channels, Hv1 lacks a pore domain and thus permeation necessarily occurs through the voltage sensing domain.

Coupling of transcription and alternative splicing via regulation of the transcriptional elongation rate is a well-studied phenomenon. Template features that act as roadblocks for the progression of RNA polymerase II comprise histone modifications and variants, DNA-interacting proteins and chromatin compaction. These may affect alternative splicing decisions by inducing pauses or decreasing elongation rate that change the time-window for splicing regulatory sequences to be recognized. Herein we discuss the evidence supporting the influence of template structural modifications on transcription and splicing, and provide insights about possible roles of non-B DNA conformations on the regulation of alternative splicing.

Considering the worldwide incidence of well characterized demyelinating disorders such as Multiple Sclerosis (MS) and the increasing number of pathologies recently found to involve hypomyelinating factors such as micronutrient deficits, elucidating the molecular basis of central nervous system (CNS) demyelination, remyelination and hypomyelination becomes essential to the development of future neuroregenerative therapies. In this context, this review discusses novel findings on the contribution of galectin-3 (Gal-3), transferrin (Tf) and iron to the processes of myelination and remyelination and their potentially positive regulation of oligodendroglial precursor cell (OPC) differentiation.

Open Shell organic radicals are principal species involved in many diverse areas such as combustion, photochemistry, and polymer chemistry. Computational studies of such species with an accurate method like coupled-cluster with single and double and perturbative triple (CCSD(T)) may be restricted to systems of modest size due to the steep computational scaling of the method. Herein, we assess the accuracy of extrapolated CCSD(T) energies determined using the connectivity-based hierarchy (CBH) method on medium to large sized radicals. In our method, an MP2 calculation on the target radical is coupled with CCSD(T) energies of fragments determined uniquely by our hierarchy to perform accurate extrapolations. A careful assessment is done with a robust CBH-rad49 test set comprising of 49 diverse cyclic and acyclic radicals with a variety of functional groups. We demonstrate that the extrapolation method with CBH-2 or CBH-3 is sufficient to obtain sub-kcal accuracy. ROMP2 and PMP2 calculations with both Pople-style and Dunning-style basis-sets resulted in mean absolute errors for CCSD(T) extrapolation (full CCSD(T)—extrapolated CCSD(T)) within 0.5 kcal/mol. Further speedup for such CCSD(T) extrapolations are obtained with ROHF-based RI-MP2 calculations. Challenging systems with (a) high ring strain, (b) delocalized character, and (c) spin contamination are identified and analyzed in detail. Finally, we apply our extrapolation method on 10 larger radicals containing 10−15 heavy atoms, where accurate CCSD(T) energies are obtained at a fractional cost of full CCSD(T) calculations. © 2015 Wiley Periodicals, Inc.

Highly accurate extrapolated coupled-cluster with single and double and perturbative triple (CCSD(T)) energies were obtained using the Connectivity-Based Hierarchy method for medium to large sized radicals. A careful assessment was performed with a robust test set comprised of 49 diverse radicals including challenging systems with high ring strain and spin contamination. The most expensive calculation is MP2 on the entire radical, thereby breaking the existing bottleneck for calculating CCSD(T) energies of large open-shell organic molecules.

ABSTRACT

It has been suggested that proteins have substructures, called foldons, which can cooperatively fold into the native structure. However, several prior investigations define foldons in various ways, citing different foldon characteristics, thereby making the concept of a foldon ambiguous. In this study, we perform a Gō model simulation and analyze the characteristics of substructures that cooperatively fold into the native-like structure. Although some results do not agree well with the experimental evidence due to the simplicity of our coarse-grained model, our results strongly suggest that cooperatively folding units sometimes organize a partially overlapped and hierarchical structure. This view makes us easy to interpret some different proposal about the foldon as a difference of the hierarchical structure. On the basis of this finding, we present a new method to assign foldons and their hierarchy, using structural and sequence information. The results show that the foldons assigned by our method correspond to the intermediate structures identified by some experimental techniques. The new method makes it easy to predict whether a protein folds sequentially into the native structure or whether some foldons fold into the native structure in parallel. Proteins 2015; 83:1900–1913. © 2015 Wiley Periodicals, Inc.

ABSTRACT

Protein structure refinement during CASP11 by the Feig group was described. Molecular dynamics simulations were used in combination with an improved selection and averaging protocol. On average, modest refinement was achieved with some targets improved significantly. Analysis of the CASP submission from our group focused on refinement success versus amount of sampling, refinement of different secondary structure elements and whether refinement varied as a function of which group provided initial models. The refinement of local stereochemical features was examined via the MolProbity score and an updated protocol was developed that can generate high-quality structures with very low MolProbity scores for most starting structures with modest computational effort. Proteins 2015. © 2015 Wiley Periodicals, Inc.

The Continuum in the variation of the X-Z bond length change from blue-shifting to red-shifting through zero- shifting in the X-Z---Y complex is inevitable. This has been analyzed by ab-initio molecular orbital calculations using Z= Hydrogen, Halogens, Chalcogens, and Pnicogens as prototypical examples. Our analysis revealed that, the competition between negative hyperconjugation within the donor (X-Z) molecule and Charge Transfer (CT) from the acceptor (Y) molecule is the primary reason for the X-Z bond length change. Here, we report that, the proper tuning of X- and Y-group for a particular Z- can change the blue-shifting nature of X-Z bond to zero-shifting and further to red-shifting. This observation led to the proposal of a continuum in the variation of the X-Z bond length during the formation of X-Z---Y complex. The varying number of orbitals and electrons available around the Z-atom differentiates various classes of weak interactions and leads to interactions dramatically different from the H-Bond. Our explanations based on the model of anti-bonding orbitals can be transferred from one class of weak interactions to another. We further take the idea of continuum to the nature of chemical bonding in general. © 2015 Wiley Periodicals, Inc.

Red- and blue- shift in the X-Z bonds during the X-Z---Y complex formation has been analyzed. A continuum in the X-Z bond length is observed for various classes of weak bonds such as H-bonds, halogen-bonds, chalcogen-bonds, and pnicogen-bonds. The balance between negative hyperconjugation within the X-Z molecule and charge transfer from Y-group provides a working model to explain the observations. The definition of the continuum in the weak (X-Z---Y) interactions is profitably extended to include strong (Z-Y) chemical bonds as well.