UGSF

sharing their kinematic models and GPS data for comparison with the dynamic models, L. Wen for help with using his code, and three anonymous reviewers for their comments that substantially improved the manuscript. We are grateful to UNAVCO, Incorporated Research Institutions for Seismology, NSF-EarthScope, International GNSS Service, NASA, and countless researchers for facilitation and availability of geodetic and seismic data. The codes are available as a zip file as part of the supporting online material.

The limited knowledge we have about red algal genomes comes from the highly specialized extremophiles, Cyanidiophyceae. Here, we describe the first genome sequence from a mesophilic, unicellular red alga, Porphyridium purpureum. The 8,355 predicted genes in P. purpureum, hundreds of which are likely to be implicated in a history of horizontal gene transfer, reside in a genome of 19.7 Mbp with 235 spliceosomal introns. Analysis of light-harvesting complex proteins reveals a nuclear-encoded phycobiliprotein in the alga. We uncover a complex set of carbohydrate-active enzymes, identify the genes required for the methylerythritol phosphate pathway of isoprenoid biosynthesis, and find evidence of sexual reproduction. Analysis of the compact, function-rich genome of P. purpureum suggests that ancestral lineages of red algae acted as mediators of horizontal gene transfer between prokaryotes and photosynthetic eukaryotes, thereby significantly enriching genomes across the tree of photosynthetic life.

Starch, unlike hydrosoluble glycogen particles, aggregates into insoluble, semicrystalline granules. In photosynthetic eukaryotes, the transition to starch accumulation occurred after plastid endosymbiosis from a preexisting cytosolic host glycogen metabolism network. This involved the recruitment of a debranching enzyme of chlamydial pathogen origin. The latter is thought to be responsible for removing misplaced branches that would otherwise yield a water-soluble polysaccharide. We now report the implication of starch debranching enzyme in the aggregation of semicrystalline granules of single-cell cyanobacteria that accumulate both glycogen and starch-like polymers. We show that an enzyme of analogous nature to the plant debranching enzyme but of a different bacterial origin was recruited for the same purpose in these organisms. Remarkably, both the plant and cyanobacterial enzymes have evolved through convergent evolution, showing novel yet identical substrate specificities from a preexisting enzyme that originally displayed the much narrower substrate preferences required for glycogen catabolism.

Under the endosymbiont hypothesis, over a billion years ago a heterotrophic eukaryote entered into a symbiotic relationship with a cyanobacterium (the cyanobiont). This partnership culminated in the plastid that has spread to forms as diverse as plants and diatoms. However, why primary plastid acquisition has not been repeated multiple times remains unclear. Here, we report a possible answer to this question by showing that primary plastid endosymbiosis was likely to have been primed by the secretion in the host cytosol of effector proteins from intracellular Chlamydiales pathogens. We provide evidence suggesting that the cyanobiont might have rescued its afflicted host by feeding photosynthetic carbon into a chlamydiacontrolled assimilation pathway. PERSPECTIVE 8 of 15 The Plant Cell PERSPECTIVE Figure 4. Glycogen Metabolism Putative Effectors in Extant and Ancient Chlamydiales.

Plastid endosymbiosis defines a process through which a fully evolved cyanobacterial ancestor has transmitted to a eukaryotic phagotroph the hundreds of genes required to perform oxygenic photosynthesis, together with the membrane structures, and cellular compartment associated with this process. In this review, we will summarize the evidence pointing to an active role of Chlamydiales in metabolic integration of free living cyanobacteria, within the cytosol of the last common plant ancestor.

Type 1 isopentenyl diphosphate isomerase (IDI-1) has been crystallized in a new crystal form. After data collection from small thin needle-shaped crystals, a new monoclinic form of the studied protein was identified. In this article, the three crystal forms of IDI-1 (orthorhombic, monoclinic and trigonal) are compared.

The synthesis and enzyme inhibitor properties of reversible type B monoamine oxidase inhibitors are described. These compounds belong to the 5H-indeno[1,2-c]pyridazine family and possess a hydrophobic benzyloxy or 4,4,4-trifluorobutoxy side chain which, in contrast to a previous assignment, has been unambiguously located at C(8) of the heterocyclic moiety. Investigation of the regioisomeric structures establishes that substitution of the 5H-indeno[1,2-c]pyridazin-5-one core at C(7) vs C(8) dramatically influences the MAO-inhibiting properties of these compounds.

Using the SIBFA polarizable molecular mechanics procedure, we analyze the binding energy of a bimetallic Mg(II)/Zn(II) enzyme, isopentenyl diphosphate isomerase, to an inhibitor built up of a trianionic diphosphate and of a cationic ethyldimethylammonium (EDMA) moiety. The analyses are performed on the protein recognition site, which totals 13 residues, as well as on some "mutants" in which one selected residue is removed at a time. They are also carried out for the individual recognition sites, namely, EDMA, Mg(II), and Zn(II). Comparisons are done with ab initio quantum chemistry (QC) results on all considered sites, with different basis sets and at different levels of correlation. The SIBFA computations reproduce the evolutions of the QC interaction energies in the recognition site and its "mutants". For such sites, small (<2-3%) relative errors are found after the BSSE correction is done. Such close agreements can conceal, however, some shortcomings found in the individual binding sites, which QC energy decomposition analyses can identify. Figure 1. Representation of (a) the three-dimensional structure of IDI and (b) the molecular structure of the NIPP inhibitor.

Heme oxygenase-1 (HO-1) inhibition is associated with antitumor activity. Imidazole-based analogues show effective and selective inhibitory potency of HO-1. In this work, five single-crystal structures of four imidazole-based compounds are presented, with an in-depth structural analysis. In order to study the influence of the conformation of the ligands on binding to protein, conformational data from crystallography are compared with quantum mechanics analysis and molecular docking studies. Molecular docking of imidazole-based analogues in the active site of HO-1 is in good agreement with the experimental structures. Inhibitors interact with the heme cofactor and a hydrophobic pocket (Met34, Phe37, Val50, Leu147 and Phe214) in the HO-1 binding site. An alternate binding mode can be hypothesized for some inhibitors in the series.

The synthesis and enzyme inhibitor properties of reversible type B monoamine oxidase inhibitors are described. These compounds belong to the 5H-indeno[1,2-c]pyridazine family and possess a hydrophobic benzyloxy or 4,4,4-trifluorobutoxy side chain which, in contrast to a previous assignment, has been unambiguously located at C(8) of the heterocyclic moiety. Investigation of the regioisomeric structures establishes that substitution of the 5H-indeno[1,2-c]pyridazin-5-one core at C(7) vs C(8) dramatically influences the MAO-inhibiting properties of these compounds.

Customary practice in predicting 3D structures of protein-protein complexes is employment of various docking methods when the structures of separate monomers are known a priori. The alternative approach, i.e. the template-based prediction with pure sequence information as a starting point, is still considered as being inferior mostly due to presumption that the pool of available structures of protein-protein complexes, which can serve as putative templates, is not sufficiently large. Recently, however, several labs have developed databases containing thousands of 3D structures of protein-protein complexes, which enable statistically reliable testing of homology-based algorithms. In this paper we report the results on homology-based modeling of 3D structures of protein complexes using alignments of modified sequence profiles. The method, called HOMology-BAsed COmplex Prediction (HOMBACOP), has two distinctive features: (I) extra weight on aligning interfacial residues in the dynamical programming algorithm, and (II) increased gap penalties for the interfacial segments. The method was tested against our recently developed ProtCom database and against the Boston University protein-protein BENCHMARK. In both cases, models generated were compared to the models built on basis of customarily protein structure initiative (PSI)-BLAST sequence alignments. It was found that existence of homologous (by the means of PSI-BLAST) templates (44% of cases) enables both methods to produce models of good quality, with the profiles method outperforming the PSI-BLAST models (with respect to the percentage of correctly predicted residues on the complex interface and fraction of native interfacial contacts). The models were evaluated according to the CAPRI assessment criteria and about two thirds of the models were found to fall into acceptable and medium-quality categories. The same comparison of a larger set of 463 protein complexes showed again that profiles generate better models. We further demonstrate, using our ProtCom database, the suitability of the profile alignment algorithm in detecting remote homologues between query and template sequences, where the PSI-BLAST method fails.

We report the first assessment of blind predictions of water positions at protein-protein interfaces, performed as part of the critical assessment of predicted interactions (CAPRI) community-wide experiment. Groups submitting docking predictions for the complex of the DNase domain of colicin E2 and Im2 immunity protein (CAPRI Target 47), were invited to predict the positions of interfacial water molecules using the method of their choice. The predictions-20 groups submitted a total of 195 models-were assessed by measuring the recall fraction of water-mediated protein contacts. Of the 176 high-or medium-quality docking models-a very good docking performance per se-only 44% had a recall fraction above 0.3, and a mere 6% above 0.5. The actual water positions were in general predicted to an accuracy level no better than 1.5 Å , and even in good models about half of the contacts represented false positives. This notwithstanding, three hotspot interface water positions were quite well predicted, and so was one of the water positions that is believed to stabilize the loop that confers specificity in these complexes. Overall the best interface water predictions was achieved by groups that also produced highquality docking models, indicating that accurate modelling of the protein portion is a determinant factor. The use of established molecular mechanics force fields, coupled to sampling and optimization procedures also seemed to confer an advantage. Insights gained from this analysis should help improve the prediction of protein-water interactions and their role in stabilizing protein complexes.

Clostridium perfringens phospholipase C (CpPLC), also called α-toxin, is the main virulence factor for gas gangrene in humans. The lipase activity serves the bacterium to generate lipid signals in the host eukaryotic cell, and ultimately to degrade the host cell membranes. Several previous reports indicated that CpPLC was specific for phosphatidylcholine and sphingomyelin. Molecular docking studies described in this paper predict favorable interactions of the CpPLC active site with other phospholipids, e.g. phosphatidylethanolamine, phosphatidylinositol and, to a lesser extent, phosphatidylglycerol. On the basis of these predictions, we have performed experimental studies showing α-toxin to degrade all the phospholipids mentioned above. The molecular docking data also provide an explanation for the observed lower activity of CpPCL on sphingomyelin as compared to the glycerophospholipids.

Cationic lipids have been extensively used as carriers of biologically active molecules (nucleic acids, peptides and proteins) into cells. Recent data provided evidence that cationic lipids are not just inert transporters but do activate specific cellular cascades. This review illustrates these activating properties with a few examples. Cell activation raises the question of which receptors are involved. Some cationic lipids seem to satisfy specific structural requirements of Toll-like receptors (TLR4) as they activate TLR4-dependent pathways. However, cationic lipids display a large structural diversity and it is likely that they are also recognized by receptors with a broader specificity. Alternatives are proposed and discussed to explain this broad specificity.