Solution Structure Of Complex Research Articles

Solution and solid state structures of lanthanides(III) and uranyl(II) complexes of tripodal tris(2-pyridyl)-containing ligand on Ph3P(O) platform

Reaction of tris[2-(2′-pyridylmethoxy)phenyl]phosphine oxide (L) with f-element nitrates resulted in 1:1 complexes. The isolated complexes of ligand L with La(III), Eu(III), Tb(III), and U(VI) nitrates, and with La(III) chloride were studied in the solid state and solution by IR, Raman, and NMR spectroscopy, X-ray analysis, and also DFT calculations. Composition and structure of the complexes vary with lanthanide cation radius. According to the data of elemental analysis, vibrational spectroscopy, and X-ray diffraction, the ligand is coordinated in tridentate mode in crystalline La(III) and solid Eu(III) complexes: [Ln(OPO,N,Oeth-L)(H2O)(O,O-NO3)3], and in monodentate mode in crystalline complex [Tb(OPO-L)(H2O)2(O,O-NO3)3]. Nitrogen atoms of pyridine fragments of the ligand not involved in coordination produce intra- and intermolecular H-bonds with coordinated water molecules in the second coordination sphere of Ln(III). According to IR, NMR spectrometry, and DFT calculations, the structure of coordination polyhedron of the main species of Ln(III) complexes in acetonitrile solutions is retained including coordination of one of pyridine fragments in the second coordination sphere: [Ln{OPO,N,(N*),Oeth-L}(H2O)(O,O-NO3)3] and [Tb{OPO,(N*)-L}(H2O)2(O,O-NO3)3], where Ln = La, Eu, and N* is the nitrogen atom of pyridine fragment producing intramolecular H-bond with coordinated water molecule. According IR and Raman spectroscopy, ligand L is coordinated in bidentate mode in solid complex [UO2(OPO,N-L)(O,O-NO3)], and uncoordinated nitrogen atoms remain free. Solution structure of uranyl complex is labile and depends on solvent nature. Equilibria of complex species with variable coordination of nitrate ions, ligand L, and with probable involvement of water take place in CD3CN and CDCl3 solutions. Photophysical properties of the prepared Eu(III) and Tb(III) complexes were studied. The preliminary assessment of extraction properties of compound L was made. Stability of studied compounds in acetonitrile solutions was examined, and the structure of one of protolysis product of Eu(III) complex, [Eu(LH)(H2O)(NO3)4], was established by micro-IR and X-ray analysis.

Solid State and Solution Structures of Lanthanide Nitrate Complexes of Tris-(1-napthylphosphine oxide).

Coordination complexes of lanthanide metals with tris-1-naphthylphosphine oxide (Nap3PO, L) have not been previously reported in the literature. We describe here the formation of lanthanide(III) nitrate complexes Ln(NO3)3L4 (Ln = Eu to Lu) and the structures of [Ln(NO3)3L2]·2L (Ln = Eu, Dy, Ho, Er) and L. The core structure of the complexes is an eight-coordinate [Ln(NO3)3L2] with the third and fourth ligands H-bonded via their oxygen atoms to one of the naphthyl rings. The structures are compared with those of the analogous complexes of triphenylphosphine oxide and show that the Ln-O(P) bond in the Nap3PO complexes is slightly longer than expected on the basis of differences in coordination numbers. The reaction solutions, investigated by 31P and 13C NMR spectroscopy in CD3CN, show that coordination of L occurs across the lanthanide series, even though complexes can only be isolated from Eu onwards. Analysis of the 31P NMR paramagnetic shifts shows that there is a break in the solution structures with a difference between the lighter lanthanides (La-Eu) and heavier metals (Tb-Lu) which implies a minor difference in structures. The isolated complexes are very poorly soluble, but in CDCl3, NMR measurements show dissociation into [Ln(NO3)3L2] and 2L occurs.

Solution Structures of Two Different FRP-OCP Complexes as Revealed via SEC-SANS.

Photosynthetic organisms have established photoprotective mechanisms in order to dissipate excess light energy into heat, which is commonly known as non-photochemical quenching. Cyanobacteria utilize the orange carotenoid protein (OCP) as a high-light sensor and quencher to regulate the energy flow in the photosynthetic apparatus. Triggered by strong light, OCP undergoes conformational changes to form the active red state (OCPR). In many cyanobacteria, the back conversion of OCP to the dark-adapted state is assisted by the fluorescence recovery protein (FRP). However, the exact molecular events involving OCP and its interaction with FRP remain largely unraveled so far due to their metastability. Here, we use small-angle neutron scattering combined with size exclusion chromatography (SEC-SANS) to unravel the solution structures of FRP-OCP complexes using a compact mutant of OCP lacking the N-terminal extension (∆NTEOCPO) and wild-type FRP. The results are consistent with the simultaneous presence of stable 2:2 and 2:1 FRP-∆NTEOCPO complexes in solution, where the former complex type is observed for the first time. For both complex types, we provide ab initio low-resolution shape reconstructions and compare them to homology models based on available crystal structures. It is likely that both complexes represent intermediate states of the back conversion of OCP to its dark-adapted state in the presence of FRP, which are of transient nature in the photocycle of wild-type OCP. This study demonstrates the large potential of SEC-SANS in revealing the solution structures of protein complexes in polydisperse solutions that would otherwise be averaged, leading to unspecific results.

Integrative solution structure of PTBP1-IRES complex reveals strong compaction and ordering with residual conformational flexibility

RNA-binding proteins (RBPs) are crucial regulators of gene expression, often composed of defined domains interspersed with flexible, intrinsically disordered regions. Determining the structure of ribonucleoprotein (RNP) complexes involving such RBPs necessitates integrative structural modeling due to their lack of a single stable state. In this study, we integrate magnetic resonance, mass spectrometry, and small-angle scattering data to determine the solution structure of the polypyrimidine-tract binding protein 1 (PTBP1/hnRNP I) bound to an RNA fragment from the internal ribosome entry site (IRES) of the encephalomyocarditis virus (EMCV). This binding, essential for enhancing the translation of viral RNA, leads to a complex structure that demonstrates RNA and protein compaction, while maintaining pronounced conformational flexibility. Acting as an RNA chaperone, PTBP1 orchestrates the IRES RNA into a few distinct conformations, exposing the RNA stems outward. This conformational diversity is likely common among RNP structures and functionally important. Our approach enables atomic-level characterization of heterogeneous RNP structures.

Complexation between Dendritic Polyelectrolytes and Amphiphilic Surfactants: The Impact of Surfactant Concentration and Hydrophobicity

The solution structure of complexes composed of the cationic dendrimer, anionic surfactants, and their counterions is studied by molecular dynamics simulations using the bead–spring coarse-grained model. We identify that depending on the surfactant concentration and hydrophobicity the system exists in three structural regimes. In the first regime surfactant molecules are noncooperatively absorbed by the dendrimer. Here, the pervaded volume of the dendrimer and the bulk solution contain loosely distributed unimeric surfactants and counterions. In the second regime hydrophobic attractions between surfactant tails give rise to cooperative binding. The absorbed surfactants self-assembly into multichain micellar-like aggregates, whereas the bulk solution consists of separate unimers. In the third regime the surfactants form multichain aggregates both within the interior of the dendrimer and in the bulk. Our data indicate that self-assembly of the absorbed surfactants affects the dendrimer conformations as compared to its neutral counterpart. In the case of noncooperative binding the dendritic polyelectrolyte swells due to the osmotic pressure exerted by the absorbed unimers and counterions. In the regimes characterized by cooperative binding and pronounced self-aggregation of the encapsulated surfactants swelling of the dendrimer is suppressed. This is attributed to a reduction of the osmotic pressure inside the macromolecule due to the ion exchange phenomenon appearing as a result of strong Coulomb attractions between charged monomers of the dendrimer and the encapsulated micellar aggregates. We also find that aggregate formation affects the overall charge accumulated in the dendrimer. In particular, for the dendrimer loaded with massive aggregates, we report the charge inversion effect which transforms the cationic dendrimer into an anionic dendrimer–surfactant complex. Our results provide molecular insights into self-assembly of supramolecular complexes and controlled absorption of guest surfactant molecules in dendrimer-based host–guest systems.

Modular development of deep potential for complex solid solutions

The multicomponent oxide solid solution is a versatile platform to tune the delicate balance between competing spin, charge, orbital, and lattice degrees of freedom for materials design and discovery. The development of compositionally complex oxides with superior functional properties has been largely empirical and serendipitous, in part due to the exceedingly complex chemistry and structure of solid solutions that span a range of length scales. The usage of classical molecular dynamics (MD), a powerful statistical method, in computer-aided materials design has not yet reached the same level of sophistication as that in computer-aided drug design because of the limited availability and accuracy of classical force fields for solids. Here, we introduce the strategy of ``modular development of deep potential'' (ModDP) that enables a systematic development and improvement of deep-neural-network-based model potential, termed as deep potential, for complex solid solutions with minimum human intervention. The converged training database associated with an end-member material is treated as an independent module and is reused to train the deep potential of solid solutions via a concurrent learning procedure. We apply ModDP to obtain classical force fields of two technologically important solid solutions, ${\mathrm{Pb}}_{x}{\mathrm{Sr}}_{1\ensuremath{-}x}{\mathrm{TiO}}_{3}$ and ${\mathrm{Hf}}_{x}{\mathrm{Zr}}_{1\ensuremath{-}x}{\mathrm{O}}_{2}$. For both materials' systems, a single model potential is capable of predicting various properties of solid solutions including temperature-driven and composition-driven phase transitions over a wide range of compositions. In particular, the deep potential of ${\mathrm{Pb}}_{x}{\mathrm{Sr}}_{1\ensuremath{-}x}{\mathrm{TiO}}_{3}$ reproduces a few known topological textures such as polar vortex lattice and electric dipole waves in ${\mathrm{PbTiO}}_{3}/{\mathrm{SrTiO}}_{3}$ superlattices, paving the way for MD investigations on the dynamics of topological structures in response to external stimuli. MD simulations of ${\mathrm{Hf}}_{x}{\mathrm{Zr}}_{1\ensuremath{-}x}{\mathrm{O}}_{2}$ reveal a substantial impact of composition variation on both the phase transition temperature and the nature of the high-temperature nonpolar phase.

Contribution of Molecular Dynamics in pNMR for the Structural Determination of AnV and AnVI Complexes in Solution.

In this study, we propose to use classical molecular dynamics (MD) coupled with 1H NMR spectroscopy to study the conformations of different actinyl AnVI (An = U, Np, and Pu) and AnV (An = Np) complexes with tetra-ethyl dyglicolamide (TEDGA) ligands in order to have a better representation of such complexes in solution. Molecular dynamics simulations showed its effectiveness in interpreting the experiments by the calculation of geometric factors needed for the determination of magnetic properties of these complexes. We demonstrated that different conformations of the AnV and AnVI complexes with TEDGA exist in solution with different coordination modes, which is experimentally confirmed by 1H NMR and EXAFS spectroscopies. Furthermore, MD simulations provide additional insights into the structures of complexes in solution since conformations with fast exchanges, which are not accessible from NMR experiments, have been observed by MD simulations.

Study on ionic association behavior in sodium nitrate solution

Raman spectroscopy combined with component analysis and molecular dynamics simulation were used to study chemical species and their transformation in aqueous sodium solutions. Study shows that the characteristic vibrational frequency of nitrate ions (ν1-NO3-) blue-shifted from 1043.9 to 1046.9 cm−1, and the full width at half maximum increased from 6.8 to 10.8 cm−1 as the concentration increasing. When water/salt molar ratio (WSR) > 30, the relative concentration (RC) of free hydrated ions and solvent shared ion pair accounts for the vast majority, and there is almost no contact ion pair in solution. When WSR less than 30, due to the continuous reduction of the number of water molecules, the hydrated water molecules around the sodium ions and nitrate ions begin to decrease, and solvent shared ion pair or contact ion pair gradually forms. Sodium ions and nitrate ions mainly exist in a monodentate coordination. When WSR > 160, both the relative concentration of contact ion pair and complex structure is close to 0. This work proves that a lower RC of complex structure in solution, a smaller supersaturation of the solution is achieved, meaning aqueous sodium nitrate solution is easier to nucleate crystals.

ANALYSIS OF HIDDEN ATTRACTORS OF NON-EQUILIBRIUM FRACTAL-FRACTIONAL CHAOTIC SYSTEM WITH ONE SIGNUM FUNCTION

In 2017, Atangana proposed more generalized operators depending on two parameters: one is fractional order (FO) and other is fractal dimension. The novel operators are defined with three different kernels. These operators produced excellent dynamics of the chaotic systems. In this paper, the Caputo fractal-fractional operator is used to explore a chaotic system which contains only one signum function. The existence theory is developed by using the fixed-point result of Leray–Schauder to prove that the considered chaotic system possesses at least one solution. The proposed chaotic system has a unique solution, according to Banach’s fixed-point theorem. We demonstrate that the suggested chaotic system is Ulam–Hyres (UH) stable under the novel operator of power law kernel by employing nonlinear functional analysis. The Adams–Bashforth technique is used to evaluate the numerical outcomes of the considered model. We show the complex structure of numerical solutions for different FO and fractal dimension values.

Solution structure of a thrombin binding aptamer complex with a non-planar platinum(ii) compound.

Thrombin Binding Aptamer (TBA) is a monomolecular well-defined two G-tetrad antiparallel G-quadruplex DNA that inhibits the activity of human α-thrombin. In this report, we synthesized a quasi-cross-shaped platinum(ii) compound (L′2LPt) with one cyclometalated and two carbene ligands. We found L′2LPt has selective affinity to bind the TBA G-quadruplex. A fibrinogen clotting assay revealed that L′2LPt can abrogate the inhibitory activity of TBA against thrombin. We solved the 1 : 1 L′2LPt–TBA complex structure by NMR, which revealed a unique self-adaptive property of L′2LPt upon binding to TBA. In the complex, a carbene ligand of L′2LPt rotates to pair with the cyclometalated ligand to form a plane stacking over half of the TBA G-tetrad and covered by lateral TT loops. It is notable that the heavy atom Pt stays out of the G-tetrad. Meanwhile, the other carbene ligand remains relatively perpendicular and forms a hydrogen bond with a guanine to anchor the L′2LPt position. This structure exhibits a quasi-cross-shaped Pt(ii) compound bound to the G-quadruplex with an unusual “wall-mounted” binding mode. Our structures provide insights into the specific recognition of antiparallel G-quadruplex DNA by a self-adaptive Pt(ii) compound and useful information for the design of selective G-quadruplex targeting non-planar molecules.

Solution Structure of Ternary Complex of Berberine Bound to a dGMP-Fill-In Vacancy G-Quadruplex Formed in the PDGFR-β Promoter.

The G-quadruplexes (G4s) formed in the PDGFR-β gene promoter are transcriptional modulators and amenable to small-molecule targeting. Berberine (BER), a clinically important natural isoquinoline alkaloid, has gained increasing attention due to its potential as anticancer drug. We previously showed that the PDGFR-β gene promoter forms a unique vacancy G4 (vG4) that can be filled in and stabilized by guanine metabolites, such as dGMP. Herein, we report the high-resolution NMR structure of a ternary complex of berberine bound to the dGMP-fill-in PDGFR-β vG4 in potassium solution. This is the first small-molecule complex structure of a fill-in vG4. This ternary complex has a 2:1:1 binding stoichiometry with a berberine molecule bound at each the 5'- and 3'-end of the 5'-dGMP-fill-in PDGFR-β vG4. Each berberine recruits the adjacent adenine residue from the 5'- or 3'-flanking sequence to form a "quasi-triad plane" that covers the external G-tetrad of the fill-in vG4, respectively. Significantly, berberine covers and stabilizes the fill-in dGMP. The binding of berberine involves both π-stacking and electrostatic interactions, and the fill-in dGMP is covered and well-protected by berberine. The NMR structure can guide rational design of berberine analogues that target the PDGFR-β vG4 or dGMP-fill-in vG4. Moreover, our structure provides a molecular basis for designing small-molecule guanine conjugates to target vG4s.

Electronic Structure of Ytterbium(III) Solvates-a Combined Spectroscopic and Theoretical Study.

The wide range of optical and magnetic properties of lanthanide(III) ions is associated with their intricate electronic structures which, in contrast to lighter elements, is characterized by strong relativistic effects and spin-orbit coupling. Nevertheless, computational methods are now capable of describing the ladder of electronic energy levels of the simpler trivalent lanthanide ions, as well as the lowest energy term of most of the series. The electronic energy levels result from electron configurations that are first split by spin-orbit coupling into groups of energy levels denoted by the corresponding Russell-Saunders terms. Each of these groups are then split by the ligand field into the actual electronic energy levels known as microstates or sometimes mJ levels. The ligand-field splitting directly informs on the coordination geometry and is a valuable tool for determining the structure and thus correlating the structure and properties of metal complexes in solution. The issue with lanthanide complexes is that the determination of complex structures from ligand-field splitting remains a very challenging task. In this paper, the optical spectra-absorption, luminescence excitation, and luminescence emission-of ytterbium(III) solvates were recorded in water, methanol, dimethyl sulfoxide (DMSO), and N,N-dimethylformamide (DMF). The electronic energy levels, that is, the microstates, were resolved experimentally. Subsequently, density functional theory calculations were used to model the structures of the solvates, and ab initio relativistic complete active space self-consistent field calculations (CASSCF) were employed to obtain the microstates of the possible structures of each solvate. By comparing the experimental and theoretical data, it was possible to determine both the coordination number and solution structure of each solvate. In water, methanol, and N,N-dimethylformamide, the solvates were found to be eight-coordinated and have a square antiprismatic coordination geometry. In DMSO, the speciation was found to be more complicated. The robust methodology developed for comparing experimental spectra and computational results allows the solution structures of homoleptic lanthanide complexes to be determined.

Modelling finger propagation in elasto-rigid channels

Abstract

Fast Sparse Grid Simulations of Fifth Order WENO Scheme for High Dimensional Hyperbolic PDEs

The weighted essentially non-oscillatory (WENO) schemes, especially the fifth order WENO schemes, are a popular class of high order accurate numerical methods for solving hyperbolic partial differential equations (PDEs). However when the spatial dimensions are high, the number of spatial grid points increases significantly. It leads to large amount of operations and computational costs in the numerical simulations by using nonlinear high order accuracy WENO schemes such as a fifth order WENO scheme. How to achieve fast simulations by high order WENO methods for high spatial dimension hyperbolic PDEs is a challenging and important question. In the literature, sparse-grid technique has been developed as a very efficient approximation tool for high dimensional problems. In a recent work [Lu, Chen and Zhang, Pure and Applied Mathematics Quarterly, 14 (2018) 57-86], a third order finite difference WENO method with sparse-grid combination technique was designed to solve multidimensional hyperbolic equations including both linear advection equations and nonlinear Burgers’ equations. Numerical experiments showed that WENO computations on sparse grids achieved comparable third order accuracy in smooth regions of the solutions and nonlinear stability as that for computations on regular single grids. In application problems, higher than third order WENO schemes are often preferred in order to efficiently resolve the complex solution structures. In this paper, we extend the approach to higher order WENO simulations specifically the fifth order WENO scheme. A fifth order WENO interpolation is applied in the prolongation part of the sparse-grid combination technique to deal with discontinuous solutions. Benchmark problems are first solved to show that significant CPU times are saved while both fifth order accuracy and stability of the WENO scheme are preserved for simulations on sparse grids. The fifth order sparse grid WENO method is then applied to kinetic problems modeled by high dimensional Vlasov based PDEs to further demonstrate large savings of computational costs by comparing with simulations on regular single grids. Several open problems are discussed at last.

Insights into Solution Structures of Photosynthetic Protein Complexes from Small-Angle Scattering Methods

High-resolution structures of photosynthetic pigment–protein complexes are often determined using crystallography or cryo-electron microscopy (cryo-EM), which are restricted to the use of protein crystals or to low temperatures, respectively. However, functional studies and biotechnological applications of photosystems necessitate the use of proteins isolated in aqueous solution, so that the relevance of high-resolution structures has to be independently verified. In this regard, small-angle neutron and X-ray scattering (SANS and SAXS, respectively) can serve as the missing link because of their capability to provide structural information for proteins in aqueous solution at physiological temperatures. In the present review, we discuss the principles and prototypical applications of SANS and SAXS using the photosynthetic pigment–protein complexes phycocyanin (PC) and Photosystem I (PSI) as model systems for a water-soluble and for a membrane protein, respectively. For example, the solution structure of PSI was studied using SAXS and SANS with contrast matching. A Guinier analysis reveals that PSI in solution is virtually free of aggregation and characterized by a radius of gyration of about 75 Å. The latter value is about 10% larger than expected from the crystal structure. This is corroborated by an ab initio structure reconstitution, which also shows a slight expansion of Photosystem I in buffer solution at room temperature. In part, this may be due to conformational states accessible by thermally activated protein dynamics in solution at physiological temperatures. The size of the detergent belt is derived by comparison with SANS measurements without detergent match, revealing a monolayer of detergent molecules under proper solubilization conditions.

О решении задачи маршрутизации транспорта с помощью подвижного генетического алгоритма

Abstract. The article describes an approach to solving the vehicle routing problem based on a fluid ge-netic algorithm. Fluid genetic algorithms differ from classical ones by a more flexible coding scheme for solutions, which is relevant for problems with a complex solution structure. The article presents a mathematical formulation of the problem. The authors proposed two variants of encoding individuals, as well as an algorithm for recalculating the probabilities that form a chromosome in a fluid genetic al-gorithm. The proposed approach is compared with other existing approaches. The conducted research suggests that the use of fluid genetic algorithms to solve the vehicle routing problem is possible. The obtained results are correct, however, the algorithm works too slowly on a big data, and the resulting solution turns out to be significantly worse than the solution obtained by the classical genetic algorithm. The article discusses possible solutions to the problems encountered. This paper is an expanded version of the work presented at the conference "Mathematics and Interdisciplinary Research 2021" [1].

Structural Studies on Different Ligand Binding Ability of Sialoadhesin Using Molecular Modeling Techniques

Siglecs are the major homologous subfamily of I-type lectins with an ability to recognize sialylated glycans. Siglecs are attractive therapeutic targets because of their endocytic properties, ability to modulate receptor signaling and cell-type specific expression pattern. Sialoadhesin (Sn/Siglec-1/CD169), a member of the Siglec family expressed on subsets of resident and inflammatory macrophages and involves in modulation of inflammation and immunity. In this work, 3-D structure of human Siglec-1 (hSiglec-1) was predicted based on X-ray crystallo-graphically determined structure of mouse Siglec-1[mSiglec-1(PDB ID: 1QFP)] using molecular modeling techniques. The structure of complexes in solution of hSiglec-1 with ligands, glycopeptide and 3′-sialyllactose were predicted using a novel docking technique comprising of repeated cycles of molecular dynamics and energy minimization. Calculation of the free energies of binding of complexes suggested that glycopeptide can form stable complex with dissociation constant value of 3.31 μM whereas complex formation of 3′-sialyllactose with the protein in aqueous medium is thermodynamically unfavorable. The structural analysis of theses complexes represent the functional recognition interactions of this protein with the bound sugar molecule and as such provide detailed information about functional roles of such sugar binding protein.

High order semi-Lagrangian discontinuous Galerkin method coupled with Runge-Kutta exponential integrators for nonlinear Vlasov dynamics

In this paper, we propose a semi-Lagrangian discontinuous Galerkin method coupled with Runge-Kutta exponential integrators (SLDG-RKEI) for nonlinear Vlasov dynamics. The commutator-free Runge-Kutta (RK) exponential integrators (EI) were proposed by Celledoni, et al. (FGCS, 2003). In the nonlinear transport setting, the RKEI can be used to decompose the evolution of the nonlinear transport into a composition of a sequence of linearized dynamics. The resulting linearized transport equations can be solved by the semi-Lagrangian (SL) discontinuous Galerkin (DG) method proposed in Cai, et al. (JSC, 2017). The proposed method can achieve high order spatial accuracy via the SLDG framework, and high order temporal accuracy via the RK EI. Due to the SL nature, the proposed SLDG-RKEI method is not subject to the CFL condition, thus they have the potential in using larger time-stepping sizes than those in the Eulerian approach. Inheriting advantages from the SLDG method, the proposed SLDG-RKEI schemes are mass conservative, positivity-preserving, have no dimensional splitting error, perform well in resolving complex solution structures, and can be evolved with adaptive time stepping sizes. We show the performance of the SLDG-RKEI algorithm by classical test problems for the nonlinear Vlasov-Poisson system, as well as the Guiding center Vlasov model. Though that it is not our focus of this paper to explore the SLDG-RKEI scheme for nonlinear hyperbolic conservation laws that develop shocks, we show some preliminary results on schemes' performance on the Burgers' equation.

PfKsgA1 functions as a transcription initiation factor and interacts with the N-terminal region of the mitochondrial RNA polymerase of Plasmodium falciparum

The small mitochondrial genome (mtDNA) of the malaria parasite is known to transcribe its genes polycistonically, although promoter element(s) have not yet been identified. An unusually large Plasmodium falciparum candidate mitochondrial phage-like RNA polymerase (PfmtRNAP) with an extended N-terminal region is encoded by the parasite nuclear genome. Using specific antibodies against the enzyme, we established that PfmtRNAP was targeted exclusively to the mitochondrion and interacted with mtDNA. Phylogenetic analysis showed that it is part of a separate apicomplexan clade. A search for PfmtRNAP-associated transcription initiation factors using sequence homology and in silico protein–protein interaction network analysis identified PfKsgA1. PfKsgA1 is a dual cytosol- and mitochondrion-targeted protein that functions as a small subunit rRNA dimethyltransferase in ribosome biogenesis. Chromatin immunoprecipitation showed that PfKsgA1 interacts with mtDNA, and in vivo crosslinking and pull-down experiments confirmed PfmtRNAP-PfKsgA1 interaction. The ability of PfKsgA1 to serve as a transcription initiation factor was demonstrated by complementation of yeast mitochondrial transcription factor Mtf1 function in Rpo41-driven in vitro transcription. Pull-down experiments using PfKsgA1 and PfmtRNAP domains indicated that the N-terminal region of PfmtRNAP interacts primarily with the PfKsgA1 C-terminal domain with some contacts being made with the linker and N-terminal domain of PfKsgA1. In the absence of full-length recombinant PfmtRNAP, solution structures of yeast mitochondrial RNA polymerase Rpo41 complexes with Mtf1 or PfKsgA1 were determined by small-angle X-ray scattering. Protein interaction interfaces thus identified matched with those reported earlier for Rpo41-Mtf1 interaction and overlaid with the PfmtRNAP-interfacing region identified experimentally for PfKsgA1. Our results indicate that in addition to a role in mitochondrial ribosome biogenesis, PfKsgA1 has an independent function as a transcription initiation factor for PfmtRNAP.

Solution Structure of the Detergent-Photosystem II Core Complex Investigated by Small-Angle Scattering Techniques.

Albeit achieving the X-ray diffraction structure of dimeric photosystem II core complexes (dPSIIcc) at the atomic resolution, the nature of the detergent belt surrounding dPSIIcc remains ambiguous. Therefore, the solution structure of the whole detergent-protein complex of dPSIIcc of Thermosynechococcus elongatus (T. elongatus) solubilized in n-dodecyl-ß-d-maltoside (ßDM) was investigated by a combination of small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) with contrast variation. First, the structure of dPSIIcc was studied separately in SANS experiments using a contrast of 5% D2O. Guinier analysis reveals that the dPSIIcc solution is virtually free of aggregation in the studied concentration range of 2-10 mg/mL dPSIIcc, and characterized by a radius of gyration of 62 Å. A structure reconstitution shows that dPSIIcc in buffer solution widely retains the crystal structure reported by X-ray free electron laser studies at room temperature with a slight expansion of the entire protein. Additional SANS experiments on dPSIIcc samples in a buffer solution containing 75% D2O provide information about the size and shape of the whole detergent-dPSIIcc. The maximum position of P(r) function increases to 68 Å, i.e., it is about 6 Å larger than that of dPSIIcc only, thus indicating the presence of an additional structure. Thus, it can be concluded that dPSIIcc is surrounded by a monomolecular belt of detergent molecules under appropriate solubilization conditions. The homogeneity of the ßDM-dPSIIcc solutions was also verified using dynamic light scattering. Complementary SAXS experiments indicate the presence of unbound detergent micelles by a separate peak consistent with a spherical shape possessing a radius of about 40 Å. The latter structure also contributes to the SANS data but rather broadens the SANS curve artificially. Without the simultaneous inspection of SANS and SAXS data, this effect may lead to an apparent underestimation of the size of the PS II-detergent complex. The formation of larger unbound detergent aggregates in solution prior to crystallization may have a significant effect on the crystal formation or quality of the ßDM-dPSIIcc.