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Structures of set of serine-threonine and tyrosine kinases were investigated by the recently developed bioinformatics tool Local Spatial Patterns (LSP) alignment. We report a set of conserved motifs comprised mostly of hydrophobic residues. These residues are scattered throughout the protein sequence and thus were not previously detected by traditional methods. These motifs traverse the conserved protein kinase core and play integrating and regulatory roles. They are anchored to the F-helix, which acts as an organizing \"hub\" providing precise positioning of the key catalytic and regulatory elements. Consideration of these discovered structures helps to explain previously inexplicable results.

Epidermal cells of dark-grown plant seedlings reorient their cortical microtubule arrays in response to blue light from a net lateral orientation to a net longitudinal orientation with respect to the long axis of cells. The molecular mechanism underlying this microtubule array reorientation involves katanin, a microtubule severing enzyme, and a plant-specific microtubule associated protein called SPIRAL2. Katanin preferentially severs longitudinal microtubules, generating seeds that amplify the longitudinal array. Upon severing, SPIRAL2 binds nascent microtubule minus ends and limits their dynamics, thereby stabilizing the longitudinal array while the lateral array undergoes net depolymerization. To date, no experimental structural information is available for SPIRAL2 to help inform its mechanism. To gain insight into SPIRAL2 structure and function, we determined a 1.8 Å resolution crystal structure of the Arabidopsis thaliana SPIRAL2 C-terminal domain. The domain is composed of seven core α-helices, arranged in an α-solenoid. Amino-acid sequence conservation maps primarily to one face of the domain involving helices α1, α3, α5, and an extended loop, the α6-α7 loop. The domain fold is similar to, yet structurally distinct from the C-terminal domain of Ge-1 (an mRNA decapping complex factor involved in P-body localization) and, surprisingly, the C-terminal domain of the katanin p80 regulatory subunit. The katanin p80 C-terminal domain heterodimerizes with the MIT domain of the katanin p60 catalytic subunit, and in metazoans, binds the microtubule minus-end factors CAMSAP3 and ASPM. Structural analysis predicts that SPIRAL2 does not engage katanin p60 in a mode homologous to katanin p80. The SPIRAL2 structure highlights an interesting evolutionary convergence of domain architecture and microtubule minus-end localization between SPIRAL2 and katanin complexes, and establishes a foundation upon which structure-function analysis can be conducted to elucidate the role of this domain in the regulation of plant microtubule arrays.

Naegleria fowleri is a pathogenic, thermophilic, free-living amoeba which causes primary amebic meningoencephalitis (PAM). Penetrating the olfactory mucosa, the brain-eating amoeba travels along the olfactory nerves, burrowing through the cribriform plate to its destination: the brain’s frontal lobes. The amoeba thrives in warm, freshwater environments, with peak infection rates in the summer months and has a mortality rate of approximately 97%. A major contributor to the pathogen’s high mortality is the lack of sensitivity of N . fowleri to current drug therapies, even in the face of combination-drug therapy. To enable rational drug discovery and design efforts we have pursued protein production and crystallography-based structure determination efforts for likely drug targets from N . fowleri . The genes were selected if they had homology to drug targets listed in Drug Bank or were nominated by primary investigators engaged in N . fowleri research. In 2017, 178 N . fowleri protein targets were queued to the Seattle Structural Genomics Center of Infectious Disease (SSGCID) pipeline, and to date 89 soluble recombinant proteins and 19 unique target structures have been produced. Many of the new protein structures are potential drug targets and contain structural differences compared to their human homologs, which could allow for the development of pathogen-specific inhibitors. Five of the structures were analyzed in more detail, and four of five show promise that selective inhibitors of the active site could be found. The 19 solved crystal structures build a foundation for future work in combating this devastating disease by encouraging further investigation to stimulate drug discovery for this neglected pathogen.

Molecular mimicry between viral antigens and host proteins can produce cross-reacting antibodies leading to autoimmunity. The coronavirus SARS-CoV-2 causes COVID-19, a disease curiously resulting in varied symptoms and outcomes, ranging from asymptomatic to fatal. Autoimmunity due to cross-reacting antibodies resulting from molecular mimicry between viral antigens and host proteins may provide an explanation. Thus, we computationally investigated molecular mimicry between SARS-CoV-2 Spike and known epitopes. We discovered molecular mimicry hotspots in Spike and highlight two examples with tentative high autoimmune potential and implications for understanding COVID-19 complications. We show that a TQLPP motif in Spike and thrombopoietin shares similar antibody binding properties. Antibodies cross-reacting with thrombopoietin may induce thrombocytopenia, a condition observed in COVID-19 patients. Another motif, ELDKY, is shared in multiple human proteins, such as PRKG1 involved in platelet activation and calcium regulation, and tropomyosin, which is linked to cardiac disease. Antibodies cross-reacting with PRKG1 and tropomyosin may cause known COVID-19 complications such as blood-clotting disorders and cardiac disease, respectively. Our findings illuminate COVID-19 pathogenesis and highlight the importance of considering autoimmune potential when developing therapeutic interventions to reduce adverse reactions.

Background Soybean is an extensively utilized oilseed crop, and improved cultivars and cultivation efficiency of soybean have contributed to the increased use of soybean in edible oil applications. The food industry necessitates the development of soybean oil with an optimized balance of polyunsaturated and saturated fatty acids to meet both nutritional requirements and industrial applications. Results This study aimed to elucidate the protein structure and functional characterization of a novel allele of KASII-A derived from an EMS-induced mutant line and assess its potential as a genetic resource for developing soybean cultivars with elevated saturated fatty acid composition. Sequence variation in the KASII-A gene was evaluated for PE1544 (~ 16.1% palmitic acid composition), an EMS-induced mutant with high-palmitic acid. A single-nucleotide polymorphism was identified in the KASII-A gene of PE1544, resulting in an amino acid substitution from Gly309 to Asp309. Comparative analysis of three-dimensional protein structures revealed that Gly309 plays a critical role in stabilizing the catalytic residue in the KASII-A active site. Co-segregation analysis revealed that the novel allele was recessive to KASII-A and was associated with high-palmitic acid composition. Furthermore, we analyzed the F 2 population derived from the cross between the high-stearic acid line with homozygous recessive sacpd-c allele and PE1544. The F 2 progeny with both mutations exhibited a lower stearic acid composition compared to the single sacpd-c mutant. Notably, the F 2 progeny with both mutations exhibited a similar ratio of polyunsaturated to saturated fatty acids (P/S index) compared to the single sacpd-c mutant. These findings suggest that KASII-A regulates the palmitic acid and stearic acid composition regardless of the total composition of saturated fatty acids in the single sacpd-c mutant. Comprehensively, the regulation of KASII-A in the single sacpd-c mutant is effective for the development of soybean oil with an ideal P/S index by regulating the content of palmitic and stearic acid while maintaining high-saturated fatty acids. Conclusion These results suggest that the conversion of palmitic acid to stearic acid is impaired due to the loss-of-function of KASII-A, indicating that the novel allele of KASII-A plays a crucial role in this biochemical conversion in soybean.

RNA viruses are the fastest evolving known biological entities. Consequently, the sequence similarity between homologous viral proteins disappears quickly, limiting the usability of traditional sequence-based phylogenetic methods in the reconstruction of relationships and evolutionary history among RNA viruses. Protein structures, however, typically evolve more slowly than sequences, and structural similarity can still be evident, when no sequence similarity can be detected. Here, we used an automated structural comparison method, homologous structure finder, for comprehensive comparisons of viral RNA-dependent RNA polymerases (RdRps). We identified a common structural core of 231 residues for all the structurally characterized viral RdRps, covering segmented and non-segmented negative-sense, positive-sense, and double-stranded RNA viruses infecting both prokaryotic and eukaryotic hosts. The grouping and branching of the viral RdRps in the structure-based phylogenetic tree follow their functional differentiation. The RdRps using protein primer, RNA primer, or self-priming mechanisms have evolved independently of each other, and the RdRps cluster into two large branches based on the used transcription mechanism. The structure-based distance tree presented here follows the recently established RdRp-based RNA virus classification at genus, subfamily, family, order, class and subphylum ranks. However, the topology of our phylogenetic tree suggests an alternative phylum level organization.

Antifreeze proteins (AFPs) enhance the survival of organisms inhabiting cold environments by affecting the formation and/or structure of ice. We report the crystal structure of the first multi-domain AFP that has been characterized. The two ice binding domains are structurally similar. Each consists of an irregular β-helix with a triangular cross-section and a long α-helix that runs parallel on one side of the β-helix. Both domains are stabilized by hydrophobic interactions. A flat plane on the same face of each domain's β-helix was identified as the ice binding site. Mutating any of the smaller residues on the ice binding site to bulkier ones decreased the antifreeze activity. The bulky side chain of Leu174 in domain A sterically hinders the binding of water molecules to the protein backbone, partially explaining why antifreeze activity by domain A is inferior to that of domain B. Our data provide a molecular basis for understanding differences in antifreeze activity between the two domains of this protein and general insight on how structural differences in the ice-binding sites affect the activity of AFPs.

Current challenges in the field of structural genomics point to the need for new tools and technologies for obtaining structures of macromolecular protein complexes. Here, we present an integrative computational method that uses molecular modelling, ion mobility-mass spectrometry (IM-MS) and incomplete atomic structures, usually from X-ray crystallography, to generate models of the subunit architecture of protein complexes. We begin by analyzing protein complexes using IM-MS, and by taking measurements of both intact complexes and sub-complexes that are generated in solution. We then examine available high resolution structural data and use a suite of computational methods to account for missing residues at the subunit and/or domain level. High-order complexes and sub-complexes are then constructed that conform to distance and connectivity constraints imposed by IM-MS data. We illustrate our method by applying it to multimeric protein complexes within the Escherichia coli replisome: the sliding clamp, (beta2), the gamma complex (gamma3deltadelta'), the DnaB helicase (DnaB6) and the Single-Stranded Binding Protein (SSB4).

The monoclinic rare-earth metal(III) bromide oxoarsenates(III) RE5Br3[AsO3]4 of the A-type (RE = La and Ce) crystallize in the space group C2/c with the lattice parameters a = 1834.67(9) pm, b = 553.41(3) pm, c = 1732.16(9) pm and β = 107.380(3)° for La5Br3[AsO3]4 and a = 1827.82(9) pm, b = 550.67(3) pm, c = 1714.23(9) pm and β = 107.372(3)° for Ce5Br3[AsO3]4 with Z = 4, while, for the B-type (RE = Pr, Nd and Sm–Tb), they prefer the space group P2/c with lattice parameters from a = 881.23(5) pm, b = 547.32(3) pm, c = 1701.14(9) pm and β = 90.231(3)° for Pr5Br3[AsO3]4 to a = 875.71(5) pm, b = 535.90(3) pm, c = 1643.04(9) pm and β = 90.052(3)° for Tb5Br3[AsO3]4 with Z = 2. The closely related rare-earth metal(III) bromide oxoarsenates(III) RE3Br2[AsO3][As2O5] crystallize in the triclinic space group P1¯ with lattice parameters from a = 539.15(4) pm, b = 870.68(6) pm, c = 1092.34(8), α = 90.661(2)°, β = 94. 792(2)° and γ = 90.223(2)° for Dy3Br2[AsO3][As2O5] to a = 533.56(4) pm, b = 869.61(6) pm, c = 1076.70(8), α = 90.698(2)°, β = 94.785(2)° and γ = 90.053(2)° for Yb3Br2[AsO3][As2O5] with Z = 2. All three structures have the same building units with [REO8]13− and [REO4Br4]9− polyhedra as well as isolated ψ1-tetrahedral [AsO3]3− anions in common, with the exception that, in the latter two, ψ1-[AsO3]3− tetrahedra linked by a corner form a pyroanionic [As2O5]4− entity. A- and B-type differ in the stacking sequence of their 2∞[(RE3)Ot4/1(Br1)v1/2(Br2)e3/3]6.5− layers. While the former have an ABC sequence, the latter exhibit an AAA variant. In the triclinic structures, the (RE3)3+ sites are thinned out, while the As3+ sites are simultaneously enriched, resulting in the mentioned condensed units.

Background In modern structural bioinformatics, comparison of molecular structures aimed to identify and assess similarities and differences between them is one of the most commonly performed procedures. It gives the basis for evaluation of in silico predicted models. It constitutes the preliminary step in searching for structural motifs. In particular, it supports tracing the molecular evolution. Faced with an ever-increasing amount of available structural data, researchers need a range of methods enabling comparative analysis of the structures from either global or local perspective. Results Herein, we present a new, superposition-independent method which processes pairs of RNA 3D structures to identify their local similarities. The similarity is considered in the context of structure bending and bonds’ rotation which are described by torsion angles. In the analyzed RNA structures, the method finds the longest continuous segments that show similar torsion within a user-defined threshold. The length of the segment is provided as local similarity measure. The method has been implemented as LCS-TA algorithm (Longest Continuous Segments in Torsion Angle space) and is incorporated into our MCQ4Structures application, freely available for download from http://www.cs.put.poznan.pl/tzok/mcq/ . Conclusions The presented approach ties torsion-angle-based method of structure analysis with the idea of local similarity identification by handling continuous 3D structure segments. The first method, implemented in MCQ4Structures, has been successfully utilized in RNA-Puzzles initiative. The second one, originally applied in Euclidean space, is a component of LGA (Local-Global Alignment) algorithm commonly used in assessing protein models submitted to CASP. This unique combination of concepts implemented in LCS-TA provides a new perspective on structure quality assessment in local and quantitative aspect. A series of computational experiments show the first results of applying our method to comparison of RNA 3D models. LCS-TA can be used for identifying strengths and weaknesses in the prediction of RNA tertiary structures.