Proteome-level assessment of origin, prevalence and function of leucine-aspartic acid (LD) motifs.

MOTIVATION: Leucine-aspartic acid (LD) motifs are short linear interaction motifs (SLiMs) that link paxillin family proteins to factors controlling cell adhesion, motility and survival. The existence and importance of LD motifs beyond the paxillin family is poorly understood. RESULTS: To enable a proteome-wide assessment of LD motifs, we developed an active learning based framework (LD motif finder; LDMF) that iteratively integrates computational predictions with experimental validation. Our analysis of the human proteome revealed a dozen new proteins containing LD motifs. We found that LD motif signalling evolved in unicellular eukaryotes more than 800 Myr ago, with paxillin and vinculin as core constituents, and nuclear export signal as a likely source of de novo LD motifs. We show that LD motif proteins form a functionally homogenous group, all being involved in cell morphogenesis and adhesion. This functional focus is recapitulated in cells by GFP-fused LD motifs, suggesting that it is intrinsic to the LD motif sequence, possibly through their effect on binding partners. Our approach elucidated the origin and dynamic adaptations of an ancestral SLiM, and can serve as a guide for the identification of other SLiMs for which only few representatives are known. AVAILABILITY AND IMPLEMENTATION: LDMF is freely available online at www.cbrc.kaust.edu.sa/ldmf; Source code is available at https://github.com/tanviralambd/LD/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Elemental Quantification and Residues Characterization of Wet Digested Certified and Commercial Carbon Materials.

Inductively coupled plasma optical emission spectroscopy (ICP-OES) is a common, relatively low cost, and straightforward analytical technique for the study of trace quantities of metals in solid materials, but its applicability to nanocarbons (e.g., graphene and nanotubes) has suffered from the lack of efficient digestion steps and certified reference materials (CRM). Here, various commercial and certified graphitic carbon materials were subjected to a "two-step" microwave-assisted acid digestion procedure, and the concentrations of up to 18 elements were analyzed by ICP-OES. With one exception (Sm), successful quantification of all certified elements in the two reference nanocarbons studied was achieved, hence validating the sample preparation approach used. The applicability of our "two-step" protocol was further confirmed for a commercial single-walled carbon nanotube sample. However, the digestion was markedly incomplete for all other commercial materials tested. Where possible, the digestion residues of the carbon materials analyzed (CRM included) were characterized to understand the structural changes that take place and how this may explain the challenge of disintegrating graphitic carbon. In this respect, it was found that solid state nuclear magnetic resonance holds considerable promise as a nonlocalized, easily interpretable, and reliable tool to access the efficient disintegration of these materials.

High Thermal Stability of La2O3- and CeO2-Stabilized Tetragonal ZrO2.

Catalyst support materials of tetragonal ZrO2, stabilized by either La2O3 (La2O3-ZrO2) or CeO2 (CeO2-ZrO2), were synthesized under hydrothermal conditions at 200 °C with NH4OH or tetramethylammonium hydroxide as the mineralizer. From in situ synchrotron powder X-ray diffraction and small-angle X-ray scattering measurements, the calcined La2O3-ZrO2 and CeO2-ZrO2 supports were nonporous nanocrystallites that exhibited rectangular shapes with a thermal stability of up to 1000 °C in air. These supports had an average size of ∼ 10 nm and a surface area of 59-97 m(2)/g. The catalysts Pt/La2O3-ZrO2 and Pt/CeO2-ZrO2 were prepared by using atomic layer deposition with varying Pt loadings from 6.3 to 12.4 wt %. Monodispersed Pt nanoparticles of ∼ 3 nm were obtained for these catalysts. The incorporation of La2O3 and CeO2 into the t-ZrO2 structure did not affect the nature of the active sites for the Pt/ZrO2 catalysts for the water-gas shift reaction.

Silica-Supported Cationic Gold(I) Complexes as Heterogeneous Catalysts for Regio- and Enantioselective Lactonization Reactions.

An efficient method for the synthesis of heterogeneous gold catalysts has been developed. These catalysts were easily assembled from readily available silica materials and gold complexes. The heterogeneous catalysts exhibited superior reactivity in various reactions where protodeauration is the rate-limiting step. Dramatic enhancement in regio- and enantioselectivity was observed when compared to the homogeneous unsupported gold catalyst. The catalysts are easily recovered and recycled up to 11 times without loss of enantioselectivity.

Atomic layer deposition overcoating: tuning catalyst selectivity for biomass conversion.

The terraces, edges, and facets of nanoparticles are all active sites for heterogeneous catalysis. These different active sites may cause the formation of various products during the catalytic reaction. Here we report that the step sites of Pd nanoparticles (NPs) can be covered precisely by the atomic layer deposition (ALD) method, whereas the terrace sites remain as active component for the hydrogenation of furfural. Increasing the thickness of the ALD-generated overcoats restricts the adsorption of furfural onto the step sites of Pd NPs and increases the selectivity to furan. Furan selectivities and furfural conversions are linearly correlated for samples with or without an overcoating, though the slopes differ. The ALD technique can tune the selectivity of furfural hydrogenation over Pd NPs and has improved our understanding of the reaction mechanism. The above conclusions are further supported by density functional theory (DFT) calculations.

Tunable Solid Acid Catalyst Thin Films Prepared by Atomic Layer Deposition.

Solid acid catalysts, including zeolites and amorphous silica-aluminas (ASAs), are industrially important materials widely used in the fuel and petrochemical industries. The versatility of zeolites is due to the Brønsted acidity of the bridging hydroxyl and shape selectivity that can be tailored during and after synthesis. This is in contrast to amorphous silica-alumina, where tailoring acidity is a major challenge as the Brønsted acid structure in ASA is still debated. In both cases, however, the pore size and acidity cannot be tuned independently, and this is particularly limiting in the application of biomass conversion, where zeolite pores are too small for the molecules of interest. Herein, we present a method using atomic layer deposition (ALD) to prepare thin films of solid acid materials where the ratio of Brønsted to Lewis acid sites can be tuned precisely. This capability, combined with the sub-nm pore size control afforded by ALD yields a powerful and flexible method for synthesizing solid acid catalysts inside virtually any mesoporous host. We demonstrate the utility of these materials in two acid-catalyzed reactions relevant to biomass conversion: (1) Meerwein-Ponndorf-Verley-Oppenauer (MPVO) reaction and dehydration of fructose and (2) cascade reaction of glucose to 5-hydroxymethylfurfural. Finally, we propose a plausible structure for the Brønsted acid sites in our materials based on infrared spectroscopy and solid-state nuclear magnetic resonance measurements and density functional theory calculations and argue that this same structure might apply to conventional ASAs as well.

Anesthetic effects on the structure and dynamics of the second transmembrane domains of nAChR alpha4beta2.

Channel functions of the neuronal alpha4beta2 nicotinic acetylcholine receptor (nAChR), one of the most widely expressed subtypes in the brain, can be inhibited by volatile anesthetics. Our Na(+) flux experiments confirmed that the second transmembrane domains (TM2) of alpha4 and beta2 in 2:3 stoichiometry, (alpha4)(2)(beta2)(3), could form pentameric channels, whereas the alpha4 TM2 alone could not. The structure, topology, and dynamics of the alpha4 TM2 and (alpha4)(2)(beta2)(3) TM2 in magnetically aligned phospholipid bicelles were investigated using solid-state NMR spectroscopy in the absence and presence of halothane and isoflurane, two clinically used volatile anesthetics. (2)H NMR demonstrated that anesthetics increased lipid conformational heterogeneity. Such anesthetic effects on lipids became more profound in the presence of transmembrane proteins. PISEMA experiments on the selectively (15)N-labeled alpha4 TM2 showed that the TM2 formed transmembrane helices with tilt angles of 12 degrees +/-1 degrees and 16 degrees +/-1 degrees relative to the bicelle normal for the alpha4 and (alpha4)(2)(beta2)(3) samples, respectively. Anesthetics changed the tilt angle of the alpha4 TM2 from 12 degrees +/-1 degrees to 14 degrees +/-1 degrees , but had only a subtle effect on the tilt angle of the (alpha4)(2)(beta2)(3) TM2. A small degree of wobbling motion of the helix axis occurred in the (alpha4)(2)(beta2)(3) TM2. In addition, a subset of the (alpha4)(2)(beta2)(3) TM2 exhibited counterclockwise rotational motion around the helix axis on a time scale slower than 10(-4) s in the presence of anesthetics. Both helical tilting and rotational motions have been identified computationally as critical elements for ion channel functions. This study suggested that anesthetics could alter these motions to modulate channel functions.

Nuclear magnetic resonance evidence for retention of a lamellar membrane phase with curvature in the presence of large quantities of the HIV fusion peptide.

The HIV fusion peptide (HFP) is a biologically relevant model system to understand virus/host cell fusion. (2)H and (31)P NMR spectroscopies were applied to probe the structure and motion of membranes with bound HFP and with a lipid headgroup and cholesterol composition comparable to that of membranes of host cells of HIV. The lamellar phase was retained for a variety of highly fusogenic HFP constructs as well as a non-fusogenic HFP construct and for the influenza virus fusion peptide. The lamellar phase is therefore a reasonable structure for modeling the location of HFP in lipid/cholesterol dispersions. Relative to no HFP, membrane dispersions with HFP had faster (31)P transverse relaxation and faster transverse relaxation of acyl chain (2)H nuclei closest to the lipid headgroups. Relative to no HFP, mechanically aligned membrane samples with HFP had broader (31)P signals with a larger fraction of unoriented membrane. The relaxation and aligned sample data are consistent with bilayer curvature induced by the HFP which may be related to its fusion catalytic function. In some contrast to the subtle effects of HFP on a host-cell-like membrane composition, an isotropic phase was observed in dispersions rich in phosphatidylethanolamine lipids and with bound HFP.

Four-alpha-helix bundle with designed anesthetic binding pockets. Part II: halothane effects on structure and dynamics.

As a model of the protein targets for volatile anesthetics, the dimeric four-alpha-helix bundle, (Aalpha(2)-L1M/L38M)(2), was designed to contain a long hydrophobic core, enclosed by four amphipathic alpha-helices, for specific anesthetic binding. The structural and dynamical analyses of (Aalpha(2)-L1M/L38M)(2) in the absence of anesthetics (another study) showed a highly dynamic antiparallel dimer with an asymmetric arrangement of the four helices and a lateral accessing pathway from the aqueous phase to the hydrophobic core. In this study, we determined the high-resolution NMR structure of (Aalpha(2)-L1M/L38M)(2) in the presence of halothane, a clinically used volatile anesthetic. The high-solution NMR structure, with a backbone root mean-square deviation of 1.72 A (2JST), and the NMR binding measurements revealed that the primary halothane binding site is located between two side-chains of W15 from each monomer, different from the initially designed anesthetic binding sites. Hydrophobic interactions with residues A44 and L18 also contribute to stabilizing the bound halothane. Whereas halothane produces minor changes in the monomer structure, the quaternary arrangement of the dimer is shifted by about half a helical turn and twists relative to each other, which leads to the closure of the lateral access pathway to the hydrophobic core. Quantitative dynamics analyses, including Modelfree analysis of the relaxation data and the Carr-Purcell-Meiboom-Gill transverse relaxation dispersion measurements, suggest that the most profound anesthetic effect is the suppression of the conformational exchange both near and remote from the binding site. Our results revealed a novel mechanism of an induced fit between anesthetic molecule and its protein target, with the direct consequence of protein dynamics changing on a global rather than a local scale. This mechanism may be universal to anesthetic action on neuronal proteins.

Four-alpha-helix bundle with designed anesthetic binding pockets. Part I: structural and dynamical analyses.

The four-alpha-helix bundle mimics the transmembrane domain of the Cys-loop receptor family believed to be the protein target for general anesthetics. Using high resolution NMR, we solved the structure (Protein Data Bank ID: 2I7U) of a prototypical dimeric four-alpha-helix bundle, (Aalpha(2)-L1M/L38M)(2,) with designed specific binding pockets for volatile anesthetics. Two monomers of the helix-turn-helix motif form an antiparallel dimer as originally designed, but the high-resolution structure exhibits an asymmetric quaternary arrangement of the four helices. The two helices from the N-terminus to the linker (helices 1 and 1') are associated with each other in the dimer by the side-chain ring stacking of F12 and W15 along the long hydrophobic core and by a nearly perfect stretch of hydrophobic interactions between the complementary pairs of L4, L11, L18, and L25, all of which are located at the heptad e position along the helix-helix dimer interface. In comparison, the axes of the two helices from the linker to the C-terminus (helices 2 and 2') are wider apart from each other, creating a lateral access pathway around K47 from the aqueous phase to the center of the designed hydrophobic core. The site of the L38M mutation, which was previously shown to increase the halothane binding affinity by approximately 3.5-fold, is not part of the hydrophobic core presumably involved in the anesthetic binding but shows an elevated transverse relaxation (R(2)) rate. Qualitative analysis of the protein dynamics by reduced spectral density mapping revealed exchange contributions to the relaxation at many residues in the helices. This observation was confirmed by the quantitative analysis using the Modelfree approach and by the NMR relaxation dispersion measurements. The NMR structures and Autodock analysis suggest that the pocket with the most favorable amphipathic property for anesthetic binding is located between the W15 side chains at the center of the dimeric hydrophobic core, with the possibility of two additional minor binding sites between the F12 and F52 ring stacks of each monomer. The high-resolution structure of the designed anesthetic-binding protein offers unprecedented atomistic details about possible sites for anesthetic-protein interactions that are essential to the understanding of molecular mechanisms of general anesthesia.

Residual dipolar coupling measurements of transmembrane proteins using aligned low-q bicelles and high-resolution magic angle spinning NMR spectroscopy.

Bicelles are a major medium form to produce weak alignment of soluble proteins for residual dipolar coupling (RDC) measurements. The obstacle to using the same type of bicelles for transmembrane proteins with solution-state NMR spectroscopy is the loss of signals due to the adhesion or penetration of the proteins into large bicelles, resulting in slow protein tumbling. In this study, weak alignment of the second and third transmembrane domains (TM23) of the human glycine receptor (GlyR) was achieved in low-q bicelles (q = DMPC/DHPC). Although protein-free bicelles with such low q would likely show isotropic properties, the insertion of TM23 induced weakly preferred orientations so that the RDC of the embedded protein can be measured. The extent of the alignment increased but the TM23 signal intensity decreased when q was varied from 0.19 to 0.60. A q of 0.50 was found to be an optimal compromise between alignment and the signal-to-noise ratio. In each pair of NMR experiments for RDC measurements, the same sample and pulse sequence were used, with one being performed at high-resolution magic-angle spinning to obtain pure J-couplings without RDC. A meaningful structure refinement in bicelles was possible by iteratively fitting the experimental RDCs to the back-calculated RDCs using the high-resolution NMR structure of GlyR TM23 in trifluoroethanol as the starting template. Combination of this method with the conventional high-resolution NMR in membrane mimicking mixtures of water and organic solvents offers an attractive way to derive structural information for membrane proteins in their native environment.

Anesthetic modulation of protein dynamics: insight from an NMR study.

Mistic (membrane integrating sequence for translation of integral membrane protein constructs) comprises the four-alpha-helix bundle scaffold found in the transmembrane domains of the Cys-loop receptors that are plausible targets for general anesthetics. Nuclear magnetic resonance (NMR) studies of anesthetic halothane interaction with Mistic in dodecyl phosphocholine (DPC) micelles provide an experimental basis for understanding molecular mechanisms of general anesthesia. Halothane was found to interact directly with Mistic, mostly in the interfacial loop regions. Although the presence of halothane had little effect on Mistic structure, (15)N NMR relaxation dispersion measurements revealed that halothane affected Mistic's motion on the microsecond-millisecond time scale. Halothane shifted the equilibrium of chemical exchange in some residues and made the exchange faster or slower in comparison to the original state in the absence of halothane. The motion on the microsecond-millisecond time scale in several residues disappeared in response to the addition of halothane. Most of the residues experiencing halothane-induced dynamics changes also exhibited profound halothane-induced changes in chemical shift, suggesting that dynamics modification of these residues might result from their direct interaction with halothane molecules. Allosteric modulation by halothane also contributed to dynamics changes, as reflected in residues I52 and Y82 where halothane introduction brought about dynamics changes but not chemical shift changes. The study suggests that inhaled general anesthetics could act on proteins via altering protein motion on the microsecond-millisecond time scale, especially motion in the flexible loops that link different alpha helices. The validation of anesthetic effect on protein dynamics that are potentially correlated with protein functions is a critical step in unraveling the mechanisms of anesthetic action on proteins.

Helical polymer 1/infinity[P2Se6(2-)]: strong second harmonic generation response and phase-change properties of its K and Rb salts.

The selenophosphates A2P2Se6 (A = K, Rb) crystallize in the chiral trigonal space group P3121, with a = 7.2728(9) A, c = 18.872(4) A, and Z = 3 at 298(2) K and a = 14.4916(7) A, c = 18.7999(17) A, and Z = 12 at 173(2) K for K+ salt and a = 7.2982(5) A, c = 19.0019(16) A, and Z = 3 at 100(2) K for Rb+ salt. The A2P2Se6 feature parallel one-dimensional helical chains of 1/infinity[P2Se62-] which depict an oxidative polymerization of the ethane-like [P2Se6]4- anion. On cooling well below room temperature K2P2Se6 exhibits a displacive phase transition to a crystallographic subgroup and forms a superstructure with a cell doubling along the a- and b-axes. The Rb analogue does not exhibit the phase transition. The compounds are air stable and show reversible glass-crystal phase-change behavior with a band gap red shift of 0.11 and 0.22 eV for K+ and Rb+ salts, respectively. Raman spectroscopy, 31P magic angle spinning solid-state NMR, and pair distribution function (PDF) analysis for crystalline and glassy K2P2Se6 give further understanding of the phase transition and the local structure of the amorphous state. K2P2Se6 exhibits excellent mid-IR transparency and a strong second harmonic generation (SHG) response. The SHG response is type-I phase-matchable and in the wavelength range of 1000-2000 nm was measured to be 50 times larger than that of the commercially used material AgGaSe2. Glassy K2P2Se6 also exhibits an SHG response without the application of electric field poling. In connection with the NLO properties the thermal expansion coefficients for K2P2Se6 are reported.

The role of hydroxyl group acidity on the activity of silica-supported secondary amines for the self-condensation of n-butanal.

The catalytic activity of secondary amines supported on mesoporous silica for the self-condensation of n-butanal to 2-ethylhexenal can be altered significantly by controlling the Brønsted acidity of M--OH species present on the surface of the support. In this study, M--OH (M=Sn, Zr, Ti, and Al) groups were doped onto the surface of SBA-15, a mesoporous silica, prior to grafting secondary propyl amine groups on to the support surface. The catalytic activity was found to depend critically on the synthesis procedure, the nature and amount of metal species introduced and the spatial separation between the acidic sites and amine groups. DFT analysis of the reaction pathway indicates that, for weak Brønsted acid groups, such as Si--OH, the rate-limiting step is C--C bond formation, whereas for stronger Brønsted acid groups, such as Ti and Al, hydrolysis of iminium species produced upon C--C bond formation is the rate-limiting step. Theoretical analysis shows further that the apparent activation energy decreases with increasing Brønsted acidity of the M--OH groups, consistent with experimental observation.

Shape-selective sieving layers on an oxide catalyst surface.

New porous materials such as zeolites, metal-organic frameworks and mesostructured oxides are of immense practical utility for gas storage, separations and heterogeneous catalysis. Their extended pore structures enable selective uptake of molecules or can modify the product selectivity (regioselectivity or enantioselectivity) of catalyst sites contained within. However, diffusion within pores can be problematic for biomass and fine chemicals, and not all catalyst classes can be readily synthesized with pores of the correct dimensions. Here, we present a novel approach that adds reactant selectivity to existing, non-porous oxide catalysts by first grafting the catalyst particles with single-molecule sacrificial templates, then partially overcoating the catalyst with a second oxide through atomic layer deposition. This technique is used to create sieving layers of Al(2)O(3) (thickness, 0.4-0.7 nm) with 'nanocavities' (<2 nm in diameter) on a TiO(2) photocatalyst. The additional layers result in selectivity (up to 9:1) towards less hindered reactants in otherwise unselective, competitive photocatalytic oxidations and transfer hydrogenations.

31P solid state NMR studies of metal selenophosphates containing [P2Se6]4-, [P4Se10]4-, [PSe4]3-, [P2Se7]4-, and [P2Se9]4- ligands.

31P solid-state nuclear magnetic resonance (NMR) spectra of 12 metal-containing selenophosphates have been examined to distinguish between the [P(2)Se(6)](4-), [PSe(4)](3-), [P(4)Se(10)](4-), [P(2)Se(7)](4-), and [P(2)Se(9)](4-) anions. There is a general correlation between the chemical shifts (CSs) of anions and the presence of a P[bond]P. The [P(2)Se(6)](4-) and [P(4)Se(10)](4-) anions both contain a P[bond]P and resonate between 25 and 95 ppm whereas the [PSe(4)](3-), [P(2)Se(7)](4-), and [P(2)Se(9)](4-) anions do not contain a P[bond]P and resonate between -115 and -30 ppm. The chemical shift anisotropies (CSAs) of compounds containing [PSe(4)](3-) anions are less than 80 ppm, which is significantly smaller than the CSAs of any of the other anions (range: 135-275 ppm). The smaller CSAs of the [PSe(4)](3-) anion are likely due to the unique local tetrahedral symmetry of this anion. Spin-lattice relaxation times (T(1)) have been determined for the solid compounds and vary between 20 and 3000 s. Unlike the CS, T(1) does not appear to correlate with P-P bonding. (31)P NMR is also shown to be a good method for impurity detection and identification in the solid compounds. The results of this study suggest that (31)P NMR will be a useful tool for anion identification and quantitation in high-temperature melts.

APSe6 (A = K, Rb, and Cs): Polymeric selenophosphates with reversible phase-change properties.

The ternary alkali selenophosphates KPSe6 and RbPSe6 crystallize in the polar orthorhombic space group Pca2(1) with a = 11.7764(17) A, b = 6.8580(10) A, c = 11.4596(16) A, and Z = 4 for RbPSe6. CsPSe6 crystallizes in the monoclinic space group P2/n with a = 6.877(3) A, b = 12.713(4) A, c = 11.242(4) A, beta = 92.735(7) degrees, and Z = 4. All compounds feature the one-dimensional infinite chain of [PSe2(Se)4-], where each P atom is connected with Se4(2-) bridge. These compounds show reversible glass-crystal transition, and 31P NMR data suggest that crystallization and infinite [PSe(6-)] chain formation are coupled processes.

Investigation of longitudinal 31P relaxation in metal selenophosphate compounds.

Molten salt syntheses yield a rich variety of metal selenophosphate compounds which have a wide range of 31P T(1) longitudinal relaxation times (20-3000 s). There is a qualitative positive correlation between squared dipolar couplings and 1/T(1), suggesting that these interactions contribute to relaxation. However, two of the compounds, K(2)CdP(2)Se(6) and Rb(2)CdP(2)Se(6), have T(1) which are significantly shorter than what is expected from dipolar couplings. The ESR spectra of these compounds show the presence of unpaired electrons which may accelerate the rate of 31P relaxation. The importance of relaxation in application of (31)P NMR to these systems is demonstrated in analysis of the mixture of crystalline products formed in a Ag(4)P(2)Se(6) synthesis. At short relaxation delays, the NMR intensities are non-quantitative and overestimate the concentration of an Ag(7)PSe(6) impurity.