Gray Spheres Research Articles

Computer Simulations on Phase Transitions in Ice

Ice has a very rich phase diagram (Petrenko and Whitworth 1999) as shown in Figure 1⇓. Up to now, sixteen crystalline phases have been identified experimentally. All crystalline phases except ice X consist of water molecules connected to four adjacent ones by hydrogen bonds. Broadly speaking, the crystalline phases of ice can be described as follows: the low-pressure forms ( P < ~1 GPa) consist of a unique hydrogen-bond network (1HBN). The high-pressure forms (~1 GPa < P < ~80 GPa) are made up of two interpenetrating networks (2HBN); they are often referred to as self-clathrates. Ice Ih and XI are prototypical forms of low-pressure ice with low density, and ice VII and VIII are those of high-pressure ices with high density. Figure 2⇓ shows atomic structures of ice XI and VIII, hydrogen-ordered phases. Between these prototypical phases, there are many complex phases. Figure 1. Phase diagram of ice. Tetrahedra denote water molecules connected to each other by hydrogen bonds represented by solid lines. In ice VI, VII, VIII, X, and XV, two interpenetrating lattices are distinguished by different colors of tetrahedra. Ice Ih, Ic, III, IV, V, VI, VII, and XII are hydrogen-disordered. Other phases are hydrogen-ordered. Ice X is a hydrogen-bond-symmetrized form. Figure 2. Atomic structures of (a) ice XI and (b) ice VIII. Small white and large gray spheres denote hydrogen and oxygen atoms, respectively. Ice XI is a hydrogen-ordered form of ice Ih, the most usual form of ice. Ice Ih is hexagonal ( P 63/ mmc ) and paraelectric. Ice XI is orthorhombic ( Cmc 21) and ferroelectric.For ice VIII, light and dark gray spheres represent two sublattices interpenetrating to each other. Ice VIII is a hydrogen-ordered form of ice VII. Ice VII is cubic ( Pn 3 m ) and …

Colour analysis on portable sphere for custom white balance with multiple illuminations

A novel, efficient white balancing technique is presented for images illuminated by multiple light sources. The existing portable two-dimensional grey reference colour chart has been replaced by a portable three-dimensional (3D) grey sphere to deal with multiple illuminant sources in the 3D real world. Experiments indicate that the proposed solution provides significantly better white balance results in the sense of both objective error measure and subjective visual quality.

Cover Picture: Directly Relating Gas‐Phase Cluster Measurements to Solution‐Phase Hydrolysis, the Absolute Standard Hydrogen Electrode Potential, and the Absolute Proton Solvation Energy (Chem. Eur. J. 24/2009)

AbstractA new method for measuring the absolute standard hydrogen electrode (SHE) potential is demonstrated by E. R. Williams et al. on page 5926 ff. Gaseous clusters containing one of nine different divalent metal ions and 24 water molecules (red and gray spheres) are reduced by thermally generated electrons. From reaction energies measured for nine different metal‐ion‐containing clusters, and other thermochemical data, an average absolute value for the SHE potential of +4.29±0.02 V is obtained. The cover image was created by Mariam ElNaggar.magnified image

Color Constancy Algorithms: Psychophysical Evaluation on a New Dataset

The estimation of the illuminant of a scene from a digital image has been the goal of a large amount of research in computer vision. Color constancy algorithms have dealt with this problem by defining different heuristics to select a unique solution from within the feasible set. The performance of these algorithms has shown that there is still a long way to go to globally solve this problem as a preliminary step in computer vision. In general, performance evaluation has been done by comparing the angular error between the estimated chromaticity and the chromaticity of a canonical illuminant, which is highly dependent on the image dataset. Recently, some workers have used high-level constraints to estimate illuminants; in this case selection is based on increasing the performance on the subsequent steps of the systems. In this paper the authors propose a new performance measure, the perceptual angular error. It evaluates the performance of a color constancy algorithm according to the perceptual preferences of humans, or naturalness (instead of the actual optimal solution) and is independent of the visual task. We show the results of a new psychophysical experiment comparing solutions from three different color constancy algorithms. Our results show that in more than half of the judgments the preferred solution is not the one closest to the optimal solution. Our experiments were performed on a new dataset of images acquired with a calibrated camera with an attached neutral gray sphere, which better copes with the illuminant variations of the scene.

Evidence That Two Enzyme-derived Histidine Ligands Are Sufficient for Iron Binding and Catalysis by Factor Inhibiting HIF (FIH)

A 2-His-1-carboxylate triad of iron binding residues is present in many non-heme iron oxygenases including the Fe(II) and 2-oxoglutarate (2OG)-dependent dioxygenases. Three variants (D201A, D201E, and D201G) of the iron binding Asp-201 residue of an asparaginyl hydroxylase, factor inhibiting HIF (FIH), were made and analyzed. FIH-D201A and FIH-D201E did not catalyze asparaginyl hydroxylation, but in the presence of a reducing agent, they displayed enhanced 2OG turnover when compared with wild-type FIH. Turnover of 2OG by FIH-D201A was significantly stimulated by the addition of HIF-1alpha(786-826) peptide. Like FIH-D201A and D201E, the D201G variant enhanced 2OG turnover but rather unexpectedly catalyzed asparaginyl hydroxylation. Crystal structures of the FIH-D201A and D201G variants in complex with Fe(II)/Zn(II), 2OG, and HIF-1alpha(786-826/788-806) implied that only two FIH-based residues (His-199 and His-279) are required for metal binding. The results indicate that variation of 2OG-dependent dioxygenase iron-ligating residues as a means of functional assignment should be treated with caution. The results are of mechanistic interest in the light of recent biochemical and structural analyses of non-heme iron and 2OG-dependent halogenases that are similar to the FIH-D201A/G variants in that they use only two His-residues to ligate iron.

Crystal structure of a putative lysostaphin peptidase from Vibrio cholerae.

Peptidoglycan (PGN) constitutes the cell walls of virtually all bacteria, making it a target of the innate immune system. PGN is a polymer of alternating {Beta} (1{yields}4) linked N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc), crossbridged by oligopeptide stems. Lysotaphin type enzymes are believed to cleave the glycl-glycine and glycyl-alanine bonds that occur in glycine-rich cross-bridges. Lysostaphins represent potential anti staphylococcal agents. Specifically, they can eradicate S.aureus nasal colonization in the rat model and are effective in treating methicillin-resistant S. aureus endophthalmitis in rabbits. These enzymes belong to the metalloendopeptidase family and possess a conserved HXH active site motif.

Molecular Mechanism of Allosteric Substrate Activation in a Thiamine Diphosphate-dependent Decarboxylase

Thiamine diphosphate-dependent enzymes are involved in a wide variety of metabolic pathways. The molecular mechanism behind active site communication and substrate activation, observed in some of these enzymes, has since long been an area of debate. Here, we report the crystal structures of a phenylpyruvate decarboxylase in complex with its substrates and a covalent reaction intermediate analogue. These structures reveal the regulatory site and unveil the mechanism of allosteric substrate activation. This signal transduction relies on quaternary structure reorganizations, domain rotations, and a pathway of local conformational changes that are relayed from the regulatory site to the active site. The current findings thus uncover the molecular mechanism by which the binding of a substrate in the regulatory site is linked to the mounting of the catalytic machinery in the active site in this thiamine diphosphate-dependent enzyme.

Crystal Structure of Bacteriophage T4 5′ Nuclease in Complex with a Branched DNA Reveals How Flap Endonuclease-1 Family Nucleases Bind Their Substrates

Bacteriophage T4 RNase H, a flap endonuclease-1 family nuclease, removes RNA primers from lagging strand fragments. It has both 5' nuclease and flap endonuclease activities. Our previous structure of native T4 RNase H (PDB code 1TFR) revealed an active site composed of highly conserved Asp residues and two bound hydrated magnesium ions. Here, we report the crystal structure of T4 RNase H in complex with a fork DNA substrate bound in its active site. This is the first structure of a flap endonuclease-1 family protein with its complete branched substrate. The fork duplex interacts with an extended loop of the helix-hairpin-helix motif class 2. The 5' arm crosses over the active site, extending below the bridge (helical arch) region. Cleavage assays of this DNA substrate identify a primary cut site 7-bases in from the 5' arm. The scissile phosphate, the first bond in the duplex DNA adjacent to the 5' arm, lies above a magnesium binding site. The less ordered 3' arm reaches toward the C and N termini of the enzyme, which are binding sites for T4 32 protein and T4 45 clamp, respectively. In the crystal structure, the scissile bond is located within the double-stranded DNA, between the first two duplex nucleotides next to the 5' arm, and lies above a magnesium binding site. This complex provides important insight into substrate recognition and specificity of the flap endonuclease-1 enzymes.

Color constancy in natural scenes with and without an explicit illuminant cue

Observers can generally make reliable judgments of surface color in natural scenes despite changes in an illuminant that is out of view. This ability has sometimes been attributed to observers' estimating the spectral properties of the illuminant in order to compensate for its effects. To test this hypothesis, two surface-color-matching experiments were performed with images of natural scenes obtained from high-resolution hyperspectral images. In the first experiment, the sky illuminating the scene was directly visible to the observer, and its color was manipulated. In the second experiment, a large gray sphere was introduced into the scene so that its illumination by the sun and sky was also directly visible to the observer, and the color of that illumination was manipulated. Although the degree of color constancy varied across this and other variations of the images, there was no reliable effect of illuminant color. Even when the sky was eliminated from view, color constancy did not worsen. Judging surface color in natural scenes seems to be independent of an explicit illuminant cue.

Color constancy in natural scenes independent of an explicit illuminant cue

The ability of observers to make reliable judgments of surface color despite changes in an illuminant (&#x201C;color constancy&#x201D;) has sometimes been attributed to their estimating the spectral properties of the illuminant in order to discount its effects. To test how information about the illuminant contributes to surface-color judgments, observers' performance in two surface-color-matching experiments with natural scenes, acquired with a high-resolution hyperspectral imaging system, was subjected to a multivariate analysis of variance. In the first experiment, the sky was directly visible to the observer, and its color was varied. In the second experiment, a large gray sphere was introduced into the scene so that its illumination by the sun and sky was directly visible to the observer and the color of that illumination was varied. Although observers' surface-color matches varied across conditions, there was no reliable effect of the illuminant cue. Even when the sky was invisible, performance did not worsen. Judging surface color in natural scenes seems not to require knowledge of the illuminant.

Folding in a crowd

![][1] Crowding molecules (gray spheres) force a WW domain into compaction. THIRUMALAI/NAS Proteins fold better in a crowd, as predicted by a biophysical model from Margaret Cheung, Dmitri Klimov, and D. Thirumalai (University of Maryland, College Park, MD). Interactions between a

Dual Function for a Unique Site within the β2I Domain of Integrin αMβ2

Integrin activation has been postulated to occur in part via conformational changes in the I domain of the beta subunit (the betaI domain), especially near the F-alpha(7) loop, in response to "inside-out" signaling. However, direct evidence for a role of the F-alpha(7) loop in ligand binding and activity modulation is still lacking. Here, we report our finding that the F-alpha(7) loop (residues 344-358) within the beta(2)I domain has dual functions in ligand binding by alpha(M)beta(2). On the one hand, it supports intercellular adhesion molecule 1 (ICAM-1) binding to alpha(M)beta(2) directly as part of a recognition interface formed by five noncontiguous segments (Pro(192)-Glu(197), Asn(213)-Glu(220), Leu(225)-Leu(230), Ser(324)-Thr(329), and Glu(344)-Asp(348)) on the apex of the beta(2)I domain. On the other hand, it controls the open and closed conformation of the alpha(M)beta(2) receptor, thereby indirectly affecting alpha(M)beta(2) binding to other ligands. Switching the five constituent sequences of the ICAM-1-binding site within the beta(2)I domain to their beta(1) counterparts destroyed ICAM-1 binding but had no effect on the gross conformations of the receptor. Of the five ICAM-1 binding-defective mutants, four had normal or even stronger interaction with Fg and C3bi, as reported in our previous study. Synthetic peptides derived from the identified site inhibited alpha(M)beta(2)-ICAM-1 interaction and supported direct binding to ICAM-1. Most importantly, perturbation of the F-alpha(7) loop caused conformational changes within the beta(2)I domain, which was further propagated to other regions of alpha(M)beta(2). Altogether, our data demonstrate that inside-out signaling could modulate ligand binding directly by changing the ligand-binding pocket per se and/or indirectly by inducing multiple conformational changes within the receptor.

The High Resolution Crystal Structure of a Native Thermostable Serpin Reveals the Complex Mechanism Underpinning the Stressed to Relaxed Transition

Serpins fold into a native metastable state and utilize a complex conformational change to inhibit target proteases. An undesirable result of this conformational flexibility is that most inhibitory serpins are heat sensitive, forming inactive polymers at elevated temperatures. However, the prokaryote serpin, thermopin, from Thermobifida fusca is able to function in a heated environment. We have determined the 1.8 A x-ray crystal structure of thermopin in the native, inhibitory conformation. A structural comparison with the previously determined 1.5 A structure of cleaved thermopin provides detailed insight into the complex mechanism of conformational change in serpins. Flexibility in the shutter region and electrostatic interactions at the top of the A beta-sheet (the breach) involving the C-terminal tail, a unique structural feature of thermopin, are postulated to be important for controlling inhibitory activity and triggering conformational change, respectively, in the native state. Here we have discussed the structural basis of how this serpin reconciles the thermodynamic instability necessary for function with the stability required to withstand elevated temperatures.

Competitive Inhibitors of Mycobacterium tuberculosis Ribose-5-phosphate Isomerase B Reveal New Information about the Reaction Mechanism

Ribose-5-phosphate isomerase (Rpi), an important enzyme in the pentose phosphate pathway, catalyzes the interconversion of ribulose 5-phosphate and ribose 5-phosphate. Two unrelated isomerases have been identified, RpiA and RpiB, with different structures and active site residues. The reaction catalyzed by both enzymes is thought to proceed via a high energy enediolate intermediate, by analogy to other carbohydrate isomerases. Here we present studies of RpiB from Mycobacterium tuberculosis together with small molecules designed to resemble the enediolate intermediate. The relative affinities of these inhibitors for RpiB have a different pattern than that observed previously for the RpiA from spinach. X-ray structures of RpiB in complex with the inhibitors 4-phospho-d-erythronohydroxamic acid (K(m) 57 microm) and 4-phospho-d-erythronate (K(i) 1.7 mm) refined to resolutions of 2.1 and 2.2 A, respectively, allowed us to assign roles for most active site residues. These results, combined with docking of the substrates in the position of the most effective inhibitor, now allow us to outline the reaction mechanism for RpiBs. Both enzymes have residues that can catalyze opening of the furanose ring of the ribose 5-phosphate and so can improve the efficiency of the reaction. Both enzymes also have an acidic residue that acts as a base in the isomerization step. A lysine residue in RpiAs provides for more efficient stabilization of the intermediate than the corresponding uncharged groups of RpiBs; this same feature lies behind the more efficient binding of RpiA to 4-phospho-d-erythronate.

Determination of the second critical end point in silicate-H 2O systems using high-pressure and high-temperature X-ray radiography

To determine the second critical end point in silicate-H 2O systems, a new method for the direct observations of immiscible fluids has been developed using a synchrotron X-ray radiography technique. High-pressure and high-temperature experiments were carried out with a Kawai-type, double-stage, multi-anvil high-pressure apparatus (SPEED-1500) installed at BL04B1, SPring-8, Japan. The Sr-plagioclase (SrAl 2Si 2O 8)-H 2O system was used as an illustrative example. A new sample container composed of a metal (Pt) tube with a pair of lids, made of single crystal diamonds, was used under pressures between 3.0 and 4.3 GPa, and temperatures up to ∼1600°C. The sample in the container could be directly observed through the diamond lids with X-ray radiography. At around 980 to 1060°C and pressures between 3.0 and 4.0 GPa, light gray spherical bubbles moving upward through the dark gray matrix were observed. The light gray spheres that absorb less X-rays represent an aqueous fluid, whereas the dark gray matrix represents a silicate melt. These two immiscible phases (aqueous fluid and silicate melt) were observed up to 4.0 GPa. At 4.3 GPa, no bubbles were observed. These observations suggest that the second critical end point in the Sr-plagioclase-H 2O system occurs at around 4.2 ± 0.2 GPa and 1020 ± 50°C. Our new technique can be applied to the direct observations of various systems with two coexisting fluids under deep mantle conditions.

Structural genomics of Pyrococcus furiosus: X-ray crystallography reveals 3D domain swapping in rubrerythrin.

Structural genomics of Pyrococcus furiosus: X-ray crystallography reveals 3D domain swapping in rubrerythrin.

Molecular Basis of the Differences in Binding Properties of the Highly Related C-type Lectins DC-SIGN and L-SIGN to Lewis X Trisaccharide and Schistosoma mansoni Egg Antigens

The dendritic cell-specific C-type lectin DC-SIGN functions as a pathogen receptor that recognizes Schistosoma mansoni egg antigens through its major glycan epitope Galbeta1,4(Fucalpha1,3)GlcNAc (Lex). Here we report that L-SIGN, a highly related homologue of DC-SIGN found on liver sinusoidal endothelial cells, binds to S. mansoni egg antigens but not to the Lex epitope. L-SIGN does bind the Lewis antigens Lea, Leb, and Ley, similar as DC-SIGN. A specific mutation in the carbohydrate recognition domain of DC-SIGN (V351G) abrogates binding to all Lewis antigens. In L-SIGN Ser363 is present at the corresponding position of Val351 in DC-SIGN. Replacement of this Ser into Val resulted in a "gain of function" L-SIGN mutant that binds to Lex, and shows increased binding to the other Lewis antigens. These data indicate that Val351 is important for the fucose specificity of DC-SIGN. Molecular modeling and docking of the different Lewis antigens in the carbohydrate recognition domains of L-SIGN, DC-SIGN, and their mutant forms, demonstrate that Val351 in DC-SIGN creates a hydrophobic pocket that strongly interacts with the Fucalpha1,3/4-GlcNAc moiety of the Lewis antigens. The equivalent amino acid residue Ser363 in L-SIGN creates a hydrophilic pocket that prevents interaction with Fucalpha1,3-GlcNAc in Lex but supports interactions with the Fucalpha1,4-GlcNAc moiety in Lea and Leb antigens. These data demonstrate for the first time that DC-SIGN and L-SIGN differ in their carbohydrate binding profiles and will contribute to our understanding of the functional roles of these C-type lectin receptors, both in recognition of pathogen and self-glycan antigens.

Adsorption chemistry of sulfur dioxide in hydrated Na-Y zeolite.

Exceptional resistance to sulfur poisoning of the Na–Y zeolite arises from the localization of adsorbed sulfur dioxide on the zeolite in the presence of water. The work shows that Rietveld refinement of guest molecules is a powerful method to determine positions and states of different molecules co-adsorbed on a zeolite (see picture; H2SO3 in yellow (S) and large red spheres (O); zeolite framework in small red (O) and gray (Si or Al) spheres; large gray sphere is the Na cation).

Supramolecular chirality: a reporter of structural memory.

Supramolecular chirality: a reporter of structural memory.

Crystal structure of the Escherichia coli SbmC protein that protects cells from the DNA replication inhibitor microcin B17.

Crystal structure of the Escherichia coli SbmC protein that protects cells from the DNA replication inhibitor microcin B17.