Conformational Basis for Substrate Recruitment in Protein Tyrosine Phosphatase 10D

The coordinated activity of protein tyrosine phosphatases (PTPs) is crucial for the initiation, modulation, and termination of diverse cellular processes. The catalytic activity of this protein depends on a nucleophilic cysteine at the active site that mediates the hydrolysis of the incoming phosphotyrosine substrate. While the role of conserved residues in the catalytic mechanism of PTPs has been extensively examined, the diversity in the mechanisms of substrate recognition and modulation of catalytic activity suggests that other, less conserved sequence and structural features could contribute to this process. Here we describe the crystal structures of Drosophila melanogaster PTP10D in the apo form as well as in a complex with a substrate peptide and an inhibitor. These studies reveal the role of aromatic ring stacking interactions at the boundary of the active site of PTPs in mediating substrate recruitment. We note that phenylalanine 76, of the so-called KNRY loop, is crucial for orienting the phosphotyrosine residue toward the nucleophilic cysteine. Mutation of phenylalanine 76 to leucine results in a 60-fold decrease in the catalytic efficiency of the enzyme. Fluorescence measurements with a competitive inhibitor, p-nitrocatechol sulfate, suggest that Phe76 also influences the formation of the enzyme-substrate intermediate. The structural and biochemical data for PTP10D thus highlight the role of relatively less conserved residues in PTP domains in both substrate recruitment and modulation of reaction kinetics.

Highly efficient dialkylphosphate-mediated syntheses of hydantoins and a bicyclohydantoin under solvent-free conditions

Diversely substituted hydantoins have been synthesized by new strategy from cyanamide based precursor, that is, methyl N-cyano-N-alkyl/arylaminoacetate. Dialkylphosphates were employed as the mild reagent to hydrolyze and cyclize the substrate in one step to give quantitative yields of the desired products. Syntheses of multivalent hydantoins viz bis-hydantoin, bicyclohydantoin have potentially widened the scope and applicability of the present method. Solvent-free conditions and very easy work-up procedure make the reaction convenient and eco-friendly. Single crystal structures of some of the representative compounds are also reported. (C) 2011 Elsevier Ltd. All rights reserved.

Structure and temperature dependence of conductivity of Ag2.5Se‐Se composite

Rapid solidification of Ag‐53 at. % Se alloy resulted in the formation of a composite mixture of Ag2.5Se and Se. The microstructure consists of spherical Se grains of 2–20 μm size, randomly distributed in a matrix of Ag2.5 Se. The Se grains were found to be layered hexagonal while the Ag2.5 Se had an orthorhombic crystal structure. The unit cell size of this phase, however, was twice that reported for the equilibrium orthorhombic Ag2 Se compound. The conductivity σ variation with temperature in the range 80–320 K was found to be similar to that observed in degenerate semiconductors. The σ decreased from 295 Ω−1 cm−1 at room temperature to a saturation value of 70 Ω−1 cm−1 for temperatures <80 K. The results are discussed in terms of percolation conduction in the Ag2.5 Se phase.

Structural, electrical, and optical properties of as-grown and heat treated ultra-thin SnS films

The composition, structural, electrical, and optical properties of as-grown and heat treated tin-mono-sulfide (SnS) ultra-thin films have been studied. The ultra-thin SnS films were prepared on glass substrates by thermal resistive evaporation technique. All the SnS films contained nanocrystallites and exhibited p-type conductivity with a low Hall-mobility, <50 cm(2)/Vs. All these films are highly tin rich in nature and exhibited orthorhombic crystal structure. As compared to other films, the SnS films annealed at 300 degrees C showed a low electrical resistivity of similar to 36 Omega cm with an optical band gap of similar to 1.98 eV. The observed electrical and optical properties of all the films are discussed based on their composition and structural parameters. These nanocrystalline ultra-thin SnS films could be expected as a buffer layer for the development of tandem solar cell devices due to their low-resistivity and high absorbability with an optimum band gap. (C) 2011 Elsevier B.V. All rights reserved.

Triclabendazole: An Intriguing Case of Co-existence of Conformational and Tautomeric Polymorphism

The crystal polymorphism of the anthelmintic drug, triclabendazole (TCB), is described. Two anhydrates (Forms I and II), three solvates, and an amorphous form have been previously mentioned. This study reports the crystal structures of Forms I (1) and II (2). These structures illustrate the uncommon phenomenon of tautomeric polymorphism. TCB exists as two tautomers A and B. Form I (Z'=2) is composed of two molecules of tautomer A while Form II (Z'=1) contains a 1:1 mixture of A and B. The polymorphs are also characterized by using other solid-state techniques (differential scanning calorimetry (DSC), thermal gravimetric analysis (TGA), PXRD, FT-IR, and NMR spectroscopy). Form I is the higher melting form (m.p.: 177 degrees C, Delta Hf=approximate to 105 +/- 4 Jg-1) and is the more stable form at room temperature. Form II is the lower melting polymorph (m.p.: 166 degrees C, Delta Hf=approximate to 86 +/- 3 Jg-1) and shows high kinetic stability on storage in comparison to the amorphous form but it transforms readily into Form I in a solution-mediated process. Crystal structure analysis of co-crystals 3-11 further confirms the existence of tautomeric polymorphism in TCB. In 3 and 11, tautomer A is present whereas in 4-10 the TCB molecule exists wholly as tautomer B. The DFT calculations suggest that the optimized tautomers A and B have nearly the same energies. Single point energy calculations reveal that tautomer A (in Form I) exists in two low-energy conformations, whereas in Form II both tautomers A and B exist in an unfavorable high-energy conformation, stabilized by a five-point dimer synthon. The structural and thermodynamic features of 1-11 are discussed in detail. Triclabendazole is an intriguing case in which tautomeric and conformational variations co-exist in the polymorphs.

Asparagine and glutamine differ in their propensities to form specific side chain-backbone hydrogen bonded motifs in proteins

Short range side chain-backbone hydrogen bonded motifs involving Asn and Gln residues have been identified from a data set of 1370 protein crystal structures (resolution = 1.5 angstrom). Hydrogen bonds involving residues i - 5 to i + 5 have been considered. Out of 12,901 Asn residues, 3403 residues (26.4%) participate in such interactions, while out of 10,934 Gln residues, 1780 Gln residues (16.3%) are involved in these motifs. Hydrogen bonded ring sizes (Cn, where n is the number of atoms involved), directionality and internal torsion angles are used to classify motifs. The occurrence of the various motifs in the contexts of protein structure is illustrated. Distinct differences are established between the nature of motifs formed by Asn and Gln residues. For Asn, the most highly populated motifs are the C10 (COdi .NHi + 2), C13 (COdi .NHi + 3) and C17 (NdHi .COi - 4) structures. In contrast, Gln predominantly forms C16 (COei .NHi - 3), C12 (NeHi .COi - 2), C15 (NeHi .COi - 3) and C18 (NeHi .COi - 4) motifs, with only the C18motif being analogous to the Asn C17structure. Specific conformational types are established for the Asn containing motifs, which mimic backbone beta-turns and a-turns. Histidine residues are shown to serve as a mimic for Asn residues in side chain-backbone hydrogen bonded ring motifs. Illustrative examples from protein structures are considered. Proteins 2012; (c) 2011 Wiley Periodicals, Inc.

Helix and hairpin nucleation in short peptides using centrally positioned conformationally constrained dipeptide segments

The effect of incorporation of a centrally positioned Ac(6)c-Xxx segment where Xxx = (L)Val/(D)Val into a host oligopeptide composed of L-amino acid residues has been investigated. Studies of four designed octapeptides Boc-Leu-Phe-Val-Ac(6)c-Xxx-Leu-Phe-Val-OMe (Xxx = (D)Val 1, (L)Val 2) Boc-Leu-Val-Val-Ac(6)c-Xxx-Leu-Val-Val-OMe (Xxx = (D)Val 3, (L)Val 4) are reported. Diagnostic nuclear Overhouse effects characteristic of hairpin conformations are observed for Xxx = (D)Val peptides (1 and 3) while continuous helical conformation characterized by sequential NiH <-> Ni+1H NOEs are favored for Xxx = (L)Val peptides (2 and 4) in methanol solutions. Temperature co-efficient of NH chemical shifts are in agreement with distinctly different conformational preferences upon changing the configuration of the residue at position 5. Crystal structures of peptides 2 and 4 (Xxx = (L)Val) establish helical conformations in the solid state, in agreement with the structures deduced from NMR data. The results support the design principle that centrally positioned type I beta-turns may be used to nucleate helices in short peptides, while type I' beta-turns can facilitate folding into beta-hairpins.

Segregation into Chiral Enantiomeric Conformations of an Achiral Molecule by Concomitant Polymorphism

An analogue of the green fluorescent protein (GFP) luminophore crystallizes from a methanol solution impregnated with dichloromethane, into a pair of chiral crystals. Thermal analysis, fluorescence emission studies, and crystal packing analysis show that the two crystals are different materials. The two polymorphs arise from the rotation of a monosubstituted benzene ring about a C-N bond which results in the formation of two strong bifurcated C-H center dot center dot center dot O intermolecular bonds to oxygen O(6). The color difference has been ascribed to a difference in the packing of the two crystal forms. Theoretical studies supported by low temperature NMR show low kinetic energy barriers (similar to 10 kJ mol(-1)) separating the asymmetric units of the two crystal structures, suggesting that the driving force for the polymorphism could be the result of packing of two different asymmetric units.

Structural characterization of folded pentapeptides containing centrally positioned beta(R)Val, gamma(R)Val and gamma(S)Val residues

A cylindrical pore of similar to 7.5 angstrom diameter containing a one-dimensional water wire, within the confines of a hydrophobic channel lined with the valine side chain, has been observed in crystals of the peptide Boc-D-Pro-Aib-Val-Aib-Val-OMe (1) (Raghavender et al., 2009, 2010). The synthesis and structural characterization in crystals of three backbone homologated analogues Boc-D-Pro-Aib-beta(3)(R) Val-Aib-Val-OMe (2), Boc-D-Pro-Aib-gamma(4)(R)Val-Aib-Val-OMe (3), Boc-D-Pro-Aib-gamma(4)(S)Val-Aib-Val-OMe (4) are described. Crystal structures of peptides 2, 3 and 4 reveal close-packed arrangements in which no pore was formed. In peptides 2 and 3 the N-terminus D-Pro-Aib segment adopted conformations closely related to Type II' beta-turns, while residues 2-4 form one turn of an alpha beta right-handed C-11 helix in 2 and an alpha gamma C-12 helix in 3. In peptide 4, a continuous left-handed helical structure was observed with the D-Pro-Aib segment forming a Type III' beta-turn, followed by one turn of a left-handed alpha gamma C-12 helix. (C) 2012 Elsevier Ltd. All rights reserved.

Gel Sculpture: Moldable, Load-Bearing and Self-Healing Non-Polymeric Supramolecular Gel Derived from a Simple Organic Salt

An easy access to a library of simple organic salts derived from tert-butoxycarbonyl (Boc)-protected L-amino acids and two secondary amines (dicyclohexyl- and dibenzyl amine) are synthesized following a supramolecular synthon rationale to generate a new series of low molecular weight gelators (LMWGs). Out of the 12 salts that we prepared, the nitrobenzene gel of dicyclohexylammonium Boc-glycinate (GLY.1) displayed remarkable load-bearing, moldable and self-healing properties. These remarkable properties displayed by GLY.1 and the inability to display such properties by its dibenzylammonium counterpart (GLY.2) were explained using microscopic and rheological data. Single crystal structures of eight salts displayed the presence of a 1D hydrogen-bonded network (HBN) that is believed to be important in gelation. Powder X-ray diffraction in combination with the single crystal X-ray structure of GLY.1 clearly established the presence of a 1D hydrogen-bonded network in the xerogel of the nitrobenzene gel of GLY.1. The fact that such remarkable properties arising from an easily accessible (salt formation) small molecule are due to supramolecular (non-covalent) interactions is quite intriguing and such easily synthesizable materials may be useful in stress-bearing and other applications.

Extent of Structural Asymmetry in Homodimeric Proteins: Prevalence and Relevance

Most homodimeric proteins have symmetric structure. Although symmetry is known to confer structural and functional advantage, asymmetric organization is also observed. Using a non-redundant dataset of 223 high-resolution crystal structures of biologically relevant homodimers, we address questions on the prevalence and significance of asymmetry. We used two measures to quantify global and interface asymmetry, and assess the correlation of several molecular and structural parameters with asymmetry. We have identified rare cases (11/223) of biologically relevant homodimers with pronounced global asymmetry. Asymmetry serves as a means to bring about 2:1 binding between the homodimer and another molecule; it also enables cellular signalling arising from asymmetric macromolecular ligands such as DNA. Analysis of these cases reveals two possible mechanisms by which possible infinite array formation is prevented. In case of homodimers associating via non-topologically equivalent surfaces in their tertiary structures, ligand-dependent mechanisms are used. For stable dimers binding via large surfaces, ligand-dependent structural change regulates polymerisation/depolymerisation; for unstable dimers binding via smaller surfaces that are not evolutionarily well conserved, dimerisation occurs only in the presence of the ligand. In case of homodimers associating via interaction surfaces with parts of the surfaces topologically equivalent in the tertiary structures, steric hindrance serves as the preventive mechanism of infinite array. We also find that homodimers exhibiting grossly symmetric organization rarely exhibit either perfect local symmetry or high local asymmetry. Binding of small ligands at the interface does not cause any significant variation in interface asymmetry. However, identification of biologically relevant interface asymmetry in grossly symmetric homodimers is confounded by the presence of similar small magnitude changes caused due to artefacts of crystallisation. Our study provides new insights regarding accommodation of asymmetry in homodimers.

Structural and Mutational Studies on Substrate Specificity and Catalysis of Salmonella typhimurium D-Cysteine Desulfhydrase

Salmonella typhimurium DCyD (StDCyD) is a fold type II pyridoxal 5' phosphate (PLP)-dependent enzyme that catalyzes the degradation of D-Cys to H2S and pyruvate. It also efficiently degrades beta-chloro-D-alanine (beta CDA). D-Ser is a poor substrate while the enzyme is inactive with respect to L-Ser and 1-amino-1-carboxy cyclopropane (ACC). Here, we report the X-ray crystal structures of StDCyD and of crystals obtained in the presence of D-Cys, beta CDA, ACC, D-Ser, L-Ser, D-cycloserine (DCS) and L-cycloserine (LCS) at resolutions ranging from 1.7 to 2.6 angstrom. The polypeptide fold of StDCyD consisting of a small domain (residues 48-161) and a large domain (residues 1-47 and 162-328) resembles other fold type II PLP dependent enzymes. The structures obtained in the presence of D-Cys and beta CDA show the product, pyruvate, bound at a site 4.0-6.0 angstrom away from the active site. ACC forms an external aldimine complex while D- and L-Ser bind non-covalently suggesting that the reaction with these ligands is arrested at C alpha proton abstraction and transimination steps, respectively. In the active site of StDCyD cocrystallized with DCS or LCS, electron density for a pyridoxamine phosphate (PMP) was observed. Crystals soaked in cocktail containing these ligands show density for PLP-cycloserine. Spectroscopic observations also suggest formation of PMP by the hydrolysis of cycloserines. Mutational studies suggest that Ser78 and Gln77 are key determinants of enzyme specificity and the phenolate of Tyr287 is responsible for C alpha proton abstraction from D-Cys. Based on these studies, a probable mechanism for the degradation of D-Cys by StDCyD is proposed.

Crystallographic Study of Novel Transthyretin Ligands Exhibiting Negative-Cooperativity between Two Thyroxine Binding Sites

Background: Transthyretin (TTR) is a homotetrameric serum and cerebrospinal fluid protein that transports thyroxine (T4) and retinol by binding to retinol binding protein. Rate-limiting tetramer dissociation and rapid monomer misfolding and disassembly of TTR lead to amyloid fibril formation in different tissues causing various amyloid diseases. Based on the current understanding of the pathogenesis of TTR amyloidosis, it is considered that the inhibition of amyloid fibril formation by stabilization of TTR in native tetrameric form is a viable approach for the treatment of TTR amyloidosis. Methodology and Principal Findings: We have examined interactions of the wtTTR with a series of compounds containing various substitutions at biphenyl ether skeleton and a novel compound, previously evaluated for binding and inhibiting tetramer dissociation, by x-ray crystallographic approach. High resolution crystal structures of five ligands in complex with wtTTR provided snapshots of negatively cooperative binding of ligands in two T4 binding sites besides characterizing their binding orientations, conformations, and interactions with binding site residues. In all complexes, the ligand has better fit and more potent interactions in first T4 site i.e. (AC site) than the second T4 site (BD site). Together, these results suggest that AC site is a preferred ligand binding site and retention of ordered water molecules between the dimer interfaces further stabilizes the tetramer by bridging a hydrogen bond interaction between Ser117 and its symmetric copy. Conclusion: Novel biphenyl ether based compounds exhibit negative-cooperativity while binding to two T4 sites which suggests that binding of only single ligand molecule is sufficient to inhibit the TTR tetramer dissociation.

Polymorphism and tautomeric preference in fenobam and the utility of NLO response to detect polymorphic impurities

Crystal structures of polymorphs and solvatomorphs of the potential anxiolytic drug fenobam exhibit an exclusive preference for one of the two possible tautomeric structures. A novel methodology based on nonlinear optical response has been successfully employed to detect the presence of a polymorphic impurity in a mixture of polymorphs.

Polymorphs and hydrates of Etoricoxib, a selective COX-2 inhibitor

The crystal structures of two polymorphs and two polymorphic hemihydrates of Etoricoxib are reported. Etoricoxib is a non-steroidal anti-inflammatory drug (NSAID) that is a selective inhibitor of COX-2. It is used in the treatment of various types of inflammation, pain and fever. Clas et al. have reported four polymorphs (labeled I through IV) and two solvates (hemi-and sesquihydrate) of the API in US patent 6,441,002 (Clas et al, US patent 6,441,002, 2002). However, no crystal structures have been reported for any of these forms. A comparison was made between the PXRD patterns reported in patent `002 and the powder spectra simulated from single crystal data. The two polymorphs characterized here correspond to form I and form IV of the patent. Form II of the patent could not be obtained by us with a variety of experimental conditions. Form III of the patent corresponds to hemihydrate II of this study. Form III is therefore not a polymorph of form I and form IV. What we have termed hemihydrate I in this study is obtained under a wide variety of conditions and it is also the only hemihydrate reported as such in the patent. Because the Etoricoxib molecule contains no conventional hydrogen bond donors, there cannot be any strong hydrogen bonds in the crystal structures of forms I and IV. The packing is accordingly characterized by weak hydrogen bonds of the C-H center dot center dot center dot O=S and C-H center dot center dot center dot N type. Thermal data were collected for form I, form IV and hemihydrate I to shed some light on relative stabilities. PXRD diffractograms show the transformation of form IV to form I at elevated temperature, indicating that form I is more stable than form IV. However, this transformation occurs only in samples of form IV that contain some form I; it does not occur in pure form IV. The formation of the two hemihydrates could follow from the known tendency of an acceptor-rich molecule to crystallize as a hydrate.