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1.  Amyloid Properties of the Mouse Egg Zona Pellucida 
PLoS ONE  2015;10(6):e0129907.
The zona pellucida (ZP) surrounding the oocyte is an extracellular fibrillar matrix that plays critical roles during fertilization including species-specific gamete recognition and protection from polyspermy. The mouse ZP is composed of three proteins, ZP1, ZP2, and ZP3, all of which have a ZP polymerization domain that directs protein fibril formation and assembly into the three-dimensional ZP matrix. Egg coats surrounding oocytes in nonmammalian vertebrates and in invertebrates are also fibrillar matrices and are composed of ZP domain-containing proteins suggesting the basic structure and function of the ZP/egg coat is highly conserved. However, sequence similarity between ZP domains is low across species and thus the mechanism for the conservation of ZP/egg coat structure and its function is not known. Using approaches classically used to identify amyloid including conformation-dependent antibodies and dyes, X-ray diffraction, and negative stain electron microscopy, our studies suggest the mouse ZP is a functional amyloid. Amyloids are cross-β sheet fibrillar structures that, while typically associated with neurodegenerative and prion diseases in mammals, can also carry out functional roles in normal cells without resulting pathology. An analysis of the ZP domain from mouse ZP3 and ZP3 homologs from five additional taxa using the algorithm AmylPred 2 to identify amyloidogenic sites, revealed in all taxa a remarkable conservation of regions that were predicted to form amyloid. This included a conserved amyloidogenic region that localized to a stretch of hydrophobic amino acids previously shown in mouse ZP3 to be essential for fibril assembly. Similarly, a domain in the yeast protein α-agglutinin/Sag 1p, that possesses ZP domain-like features and which is essential for mating, also had sites that were predicted to be amyloidogenic including a hydrophobic stretch that appeared analogous to the critical site in mouse ZP3. Together, these studies suggest that amyloidogenesis may be a conserved mechanism for ZP structure and function across billions of years of evolution.
doi:10.1371/journal.pone.0129907
PMCID: PMC4456372  PMID: 26043223
2.  1,3,5-Tri-p-tolyl­pentane-1,5-diol 
In the title compound, C26H30O2, the central benzene ring forms dihedral angles of 14.85 (15) and 28.17 (14)° with the terminal benzene rings. The dihedral angle between the terminal benzene rings is 32.14 (13)°. The crystal packing exhibits two strong inter­molecular O—H⋯O hydrogen bonds, forming directed four-membered co-operative rings. A region of disordered electron density, most probably disordered ethyl acetate solvent mol­ecules, occupying voids of ca 519 Å3 for an electron count of 59, was treated using the SQUEEZE routine in PLATON [Spek (2009 ▶). Acta Cryst. D65, 148–155]. Their formula mass and unit-cell characteristics were not taken into account during refinement. The structure was refined as an inversion twin [absolute structure parameter = −0.3 (4)].
doi:10.1107/S160053681400018X
PMCID: PMC3998290  PMID: 24764851
3.  1,5-Bis(4-chloro­phen­yl)-3-(4-methyl­phen­yl)pentane-1,5-dione 
In the title mol­ecule, C24H20Cl2O2, the central methyl­benzene ring forms dihedral angles of 42.47 (10) and 34.34 (10)° with the terminal 4-chloro­phenyl fragments. The dihedral angle between the chloro­benzene rings is 34.45 (11)°. A weak intra­molecular C—H⋯O inter­action generates an S(6) ring motif. The crystal packing exhibits weak C—H⋯O hydrogen bonds and C—H⋯π inter­actions.
doi:10.1107/S1600536813024355
PMCID: PMC3790380  PMID: 24098202
4.  4-(2-Hy­droxy­phen­yl)-3,5-di­thia­hepta­ne­dioic acid 
In the crystal of the title compound, C11H12O5S2, mol­ecules are linked by O—H⋯O hydrogen bonds and C—H⋯O inter­actions, forming a three-dimensional network.
doi:10.1107/S1600536813012737
PMCID: PMC3685050  PMID: 23795069
5.  (E)-3-(4-Meth­oxy­phen­yl)-3-[3-(4-meth­oxy­phen­yl)-1H-pyrazol-1-yl]prop-2-enal 
In the title mol­ecule, C20H18N2O3, the pyrazole ring forms a dihedral angle of 2.2 (1)° with its meth­oxy­phenyl substituent and a dihedral angle of 67.2 (1)° with the benzene substituent on the propenal unit. In the crystal, mol­ecules are connected by weak C—H⋯O hydrogen bonds, forming R 2 2(26) and R 2 2(28) cyclic dimers that lie about crystallographic inversion centres. These dimers are further linked through C—H⋯O and C—H⋯N hydrogen bonds, forming C(8), C(9), C(10) and C(16) chain motifs. These primary motifs are further linked to form secondary C 2 2(15) chains and R 2 2(18) rings.
doi:10.1107/S1600536813007678
PMCID: PMC3629636  PMID: 23634123
6.  1-(2,4-Dinitro­phen­yl)-3-phenyl-4-phenyl­sulfanyl-1H-pyrazole 
In the title mol­ecule, C21H14N4O4S, the pyrazole ring forms dihedral angles of 45.6 (1), 87.7 (1) and 27.4 (1)° with the phenyl, sulfur-substituted benzene and nitro-substituted benzene rings, respectively. In the crystal, mol­ecules are connected by weak C—H⋯O and C—H⋯N hydrogen bonds into layers parallel to (010).
doi:10.1107/S1600536812036914
PMCID: PMC3470205  PMID: 23125649
7.  5-(2-Nitro-1-phenyl­but­yl)-4-phenyl-1,2,3-selenadiazole 
In the title compound, C18H17N3O2Se, the selenadiazole ring is planar [maximum deviation = 0.012 (2) Å for the ring C atom bearing the phenyl substituent]. The dihedral angle between the selenadiazole ring and the attached benzene ring is 46.5 (1)°. There is one short intra­molecular C—H⋯Se contact.
doi:10.1107/S1600536812007027
PMCID: PMC3297921  PMID: 22412724
8.  Ethyl 2-phenyl-3-(4-phenyl-1,2,3-selenadiazol-5-yl)-3-p-tolyl­propano­ate 
In the title compound, C26H24N2O2Se, the selenadiazole ring is essentially planar [maximum deviation = 0.004 (3) Å]. The dihedral angle between the selenadiazole ring and the attached benzene ring is 50.17 (1)°. The crystal packing is stabilized by inter­molecular C—H⋯N inter­actions.
doi:10.1107/S1600536811056017
PMCID: PMC3275202  PMID: 22347058
9.  Medicago PhosphoProtein Database: a repository for Medicago truncatula phosphoprotein data 
The ability of legume crops to fix atmospheric nitrogen via a symbiotic association with soil rhizobia makes them an essential component of many agricultural systems. Initiation of this symbiosis requires protein phosphorylation-mediated signaling in response to rhizobial signals named Nod factors. Medicago truncatula (Medicago) is the model system for studying legume biology, making the study of its phosphoproteome essential. Here, we describe the Medicago PhosphoProtein Database (MPPD; http://phospho.medicago.wisc.edu), a repository built to house phosphoprotein, phosphopeptide, and phosphosite data specific to Medicago. Currently, the MPPD holds 3,457 unique phosphopeptides that contain 3,404 non-redundant sites of phosphorylation on 829 proteins. Through the web-based interface, users are allowed to browse identified proteins or search for proteins of interest. Furthermore, we allow users to conduct BLAST searches of the database using both peptide sequences and phosphorylation motifs as queries. The data contained within the database are available for download to be investigated at the user’s discretion. The MPPD will be updated continually with novel phosphoprotein and phosphopeptide identifications, with the intent of constructing an unparalleled compendium of large-scale Medicago phosphorylation data.
doi:10.3389/fpls.2012.00122
PMCID: PMC3371616  PMID: 22701463
Medicago truncatula; phosphoproteome; ETD; CAD; proteomics
10.  1-(2-Naphth­yl)-3-phenyl-3-(4,5,6,7-tetra­hydro-1,2,3-benzoselenadiazol-4-yl)propan-1-one 
In the title compound, C25H22N2OSe, the fused six-membered cyclo­hexene ring of the 4,5,6,7-tetra­hydro-1,2,3-benzoselenadiazole group adopts a near half-chair conformation and the five-membered 1,2,3-selenadiazole ring is essentially planar (r.m.s. deviation = 0.004 Å). There are weak inter­molecular C—H⋯O and C—H⋯π inter­actions in the crystal structure. Inter­molecular π–π stacking is also observed between the naphthyl units, with a centroid–centroid distance of 3.529 (15) Å.
doi:10.1107/S1600536811027103
PMCID: PMC3213465  PMID: 22091044
11.  3-(4-Methyl­phen­yl)-1-phenyl-3-(4,5,6,7-tetra­hydro-1,2,3-benzoselenadiazol-4-yl)propan-1-one 
In the title compound, C22H22N2OSe, the fused six-membered ring of the 4,5,6,7-tetra­hydro­benzo[d][1,2,3] selenadiazole group adopts a near to envelope (E form) conformation and the five-membered 1,2,3-selenadiazole ring is essentially planar (r.m.s. deviation = 0.0059 Å). In the crystal, adjacent mol­ecules are inter­linked through weak inter­molecular C—H⋯π inter­actions.
doi:10.1107/S160053681102174X
PMCID: PMC3151998  PMID: 21837060
12.  4-{(4-Chloro­phen­yl)[4-(4-methyl­phen­yl)-1,2,3-selenadiazol-5-yl]meth­yl}-4,5,6,7-tetra­hydro-1,2,3-benzoselenadiazole 
In the title compound, C22H19ClN4Se2, the mean plane of the non-fused selenadiazole ring forms dihedral angles of 54.20 (16)° and 70.48 (11)°, respectively, with the essentially planar [maximum deviations of 0.025 (5) and 0.009 (2) Å, respectively] methyl­phenyl and chloro­phenyl substituents. The tetra­hydro-1,2,3-benzoselenadiazole group is disordered over two sets of sites with a refined occupancy ratio of 0.802 (5):0.198 (5). In the crystal, weak inter­molecular C—H⋯N inter­actions are observed.
doi:10.1107/S160053681101751X
PMCID: PMC3120601  PMID: 21754802
13.  Spectral Analysis and Crystal Structures of 4-(4-Methylphenyl)-6-Phenyl-2,3,3a, 4-Tetrahydro-1H-Pyrido[3,2,1-jk]Carbazole and 4-(4-Methoxyphenyl)-6-Phenyl-2,3,3a, 4-Tetrahydro-1H-Pyrido[3,2,1-jk]Carbazole 
ISRN organic chemistry  2011;2011:541082.
The crystal structures of 4-(4-methylphenyl)-6-phenyl-2,3,3a,4-tetrahydro-1H-pyrido[3,2,1-jk]carbazole (IIa) and 4-(4-methoxyphenyl)-6-phenyl-2,3,3a,4-tetrahydro-1H-pyrido[3,2,1-jk]carbazole (IIb) were elucidated by single crystal X-ray diffraction. Compound (IIa), C28H25N, crystallizes in the triclinic system, space group P-1, with a = 8.936(2) Å, b = 10.490(1) Å, c = 11.801(1) Å, α = 102.69(5)°,  β = 103.27(3)°, γ = 93.80(1)°, and Z = 2. The compound (IIb), C28H25NO, crystallizes in the monoclinic system, space group P21/a, with a = 11.376(5) Å, b = 14.139(3) Å, c = 13.237(4) Å, β = 97.41(3)°, and Z = 4. In both the structures, the pyrido ring adopts a twist boat conformation and the carbazole molecule has the twisted envelope structure with C3 and C13 at the flap. No classical hydrogen bonds are observed in the crystal structures. Details of the preparation, structures, and spectroscopic properties of the new compounds are discussed.
doi:10.5402/2011/541082
PMCID: PMC3767200  PMID: 24052824
14.  (E)-3-(4-Chloro­phen­yl)-3-[3-(4-chloro­phen­yl)-1H-pyrazol-1-yl]prop-2-enal 
In the title compound, C18H12Cl2N2O, the pyrazole ring is almost planar [r.m.s. deviation = 0.002 Å] while the two chloro­phenyl rings are twisted out from the plane of the pyrazole ring, making dihedral angles of 5.3 (1) and 65.34 (4)°. In the crystal, centrosymmetric R 2 2(24) dimers are formed about crystallographic inversion centres through a pair of C—H⋯Cl inter­actions. These dimers are further linked through a C—H⋯O hydrogen bond, forming a C(8) chain extending along the a axis. C—H⋯π inter­actions are also observed.
doi:10.1107/S1600536810035646
PMCID: PMC2983380  PMID: 21587573
15.  (E)-3-Phenyl-3-(3-phenyl-1H-1-pyrazol­yl)-2-propenal 
In the title compound C18H14N2O, the pendant rings make dihedral angles of 66.1 (1)° and 13.9 (1) with the central ring. In the crystal, two mol­ecules form a cyclic centrosymmetric R 2 2(22) dimer through pairs of C—H⋯O bonds. These dimers are further connected into zigzag chains extending along the b axis through C—H⋯π and C—H⋯O inter­actions.
doi:10.1107/S1600536810004332
PMCID: PMC2983577  PMID: 21580344
16.  (E)-3-(4-Bromo­phen­yl)-3-[3-(4-bromo­phen­yl)-1H-pyrazol-1-yl]prop-2-enal 
There are two crystallographically independent mol­ecules in the asymmetric unit of the title compound, C18H12Br2N2O. In each mol­ecule, one of the bromo­phenyl rings lies almost in the plane of pyrazole unit [dihedral angles of 5.8 (3)° in the first mol­ecule and and 5.1 (3)° in the second] while the other ring is approximately perpendicular to it [dihedral angles of 80.3 (3) and 76.5 (3)°]. The crystal packing shows inter­molecular C—H⋯O inter­actions. The crystal studied was a racemic twin.
doi:10.1107/S1600536809054749
PMCID: PMC2979980  PMID: 21579715
17.  A preliminary assessment of PM10 and TSP concentrations in Tuticorin, India 
The respirable particulate matter (RPM; PM10) and total suspended particulate matter (TSP) concentrations in ambient air in Tuticorin, India, were preliminarily estimated. Statistical analyses on so-generated database were performed to infer frequency distributions and to identify dominant meteorological factor affecting the pollution levels. Both the RPM and TSP levels were well below the permissible limits set by the US Environmental Protection Agency. As expected, lognormal distribution always fit the data during the study period. However, fit with the normal was also acceptable except for very few seasons. The RPM concentrations ranged between 20.9 and 198.2 μg/m3, while the TSP concentrations varied from 51.5 to 333.3 μg/m3 during the study period. There was a better correlation between PM10–100 and TSP concentrations than that of PM10 (RPM) and TSP concentrations, but the correlation of RPM fraction was also acceptable. It was found that wind speed was the most important meteorological factor affecting the concentrations of the pollutants of present interest. Significant seasonal variations in the pollutant concentrations of present interest were found at 5% significance level except for TSP concentrations in the year 2006.
doi:10.1007/s11869-009-0055-x
PMCID: PMC2860090  PMID: 20495598
ANOVA; Coal-fired power station; Correlation; Frequency distribution; RPM; Seasonal variation; TSP
18.  3-(4-Chloro­phen­yl)-1-[(E)-1-(4-chloro­phen­yl)-2-(4-methyl­phenyl­sulfan­yl)ethen­yl]-4-(4-methyl­phenyl­sulfan­yl)-1H-pyrazole 
In the title compound, C31H24Cl2N2S2, the pyrazole ring adopts planar conformation with a maximum deviation of 0.002 (2) Å. The chloro­phenyl rings are twisted out of the plane of the pyrazole ring by 75.1 (1) and 39.5 (1)°. The crystal packing is controlled by weak intermolecular C—H⋯π interactions.
doi:10.1107/S1600536809043293
PMCID: PMC2971206  PMID: 21578467
19.  Agrobacterium-Mediated Transient Gene Expression and Silencing: A Rapid Tool for Functional Gene Assay in Potato 
PLoS ONE  2009;4(6):e5812.
Potato is the third most important food crop worldwide. However, genetic and genomic research of potato has lagged behind other major crops due to the autopolyploidy and highly heterozygous nature associated with the potato genome. Reliable and technically undemanding techniques are not available for functional gene assays in potato. Here we report the development of a transient gene expression and silencing system in potato. Gene expression or RNAi-based gene silencing constructs were delivered into potato leaf cells using Agrobacterium-mediated infiltration. Agroinfiltration of various gene constructs consistently resulted in potato cell transformation and spread of the transgenic cells around infiltration zones. The efficiency of agroinfiltration was affected by potato genotypes, concentration of Agrobacterium, and plant growth conditions. We demonstrated that the agroinfiltration-based transient gene expression can be used to detect potato proteins in sub-cellular compartments in living cells. We established a double agroinfiltration procedure that allows to test whether a specific gene is associated with potato late blight resistance pathway mediated by the resistance gene RB. This procedure provides a powerful approach for high throughput functional assay for a large number of candidate genes in potato late blight resistance.
doi:10.1371/journal.pone.0005812
PMCID: PMC2686102  PMID: 19503835
20.  3,3′-(p-Phenyl­ene)bis­(3,4-dihydro-2H-1,3-benzoxazine) 
Mol­ecules of the title compound, C22H20N2O2, are situated on crystallographic centres of symmetry. The oxazinane ring adopts a sofa conformation. Mol­ecules are linked into cyclic centrosymmetric dimers via C—H⋯O hydrogen bonds with the motif R 2 2(6). In addition to the C—H⋯O inter­actions, the crystal structure is also stabilized by C—H⋯π inter­actions.
doi:10.1107/S1600536809005790
PMCID: PMC2968457  PMID: 21582236
21.  (E)-3-(4-Methyl­phen­yl)-3-[3-(4-methyl­phen­yl)-1H-pyrazol-1-yl]-2-propenal 
In the title compound, C20H18N2O, the pyrazole ring adopts a planar conformation. The C—N bond lengths in the pyrazole ring are shorter than a standard C—N single bond (1.443 Å), but longer than a standard double bond (1.269 Å), indicating electron delocalization. The propenal group assumes an extended conformation. Inter­molecular C—H⋯O hydrogen bonds connect mol­ecules into cyclic centrosymmetric R 2 2(26) dimers, which are cross-linked via C—H⋯π inter­actions.
doi:10.1107/S1600536808034697
PMCID: PMC2959754  PMID: 21581097
22.  4-(Cyclo­hexyl­sulfan­yl)-1-[(E)-2-(cyclo­hexyl­sulfan­yl)-1-phenyl­ethen­yl]-3-phenyl-1H-pyrazole 
In the title compound, C29H34N2S2, the pyrazole ring is planar and both cyclo­hexane rings adopt chair conformations. The dihedral angles between the pyrazole ring and the two benzene rings are 59.9 (2) and 19.8 (2)°. The conformation and packing of the mol­ecules in the unit cell are stabilized by a weak intra­molecular C—H⋯S and C—H⋯N interactions, in addition to van der Waals forces.
doi:10.1107/S1600536808033126
PMCID: PMC2959566  PMID: 21580994
23.  1-(2,4-Dinitro­phenyl)-3-(4-methyl­phenyl)-4-phenyl­sulfanyl-1H-pyrazole 
In the title compound, C22H16N4O4S, the dihedral angles between the pyrazole ring and the pendant aromatic rings are 26.2 (1), 41.1 (1) and 89.5 (1)°. In the crystal structure, an intermolecular C—H⋯N bond helps to establish the packing. A short C⋯C contact of 3.110 (12) Å is observed between the C atom of the pyrazole CH group and one of the α-C atoms of the 4-methyl­phenyl ring.
doi:10.1107/S160053680803122X
PMCID: PMC2959740  PMID: 21580957
24.  4-(4-Chloro­phenyl­sulfan­yl)-1-[(E)-2-(4-chloro­phenyl­sulfan­yl)-1-phenyl­ethen­yl]-3-phenyl-1H-pyrazole 
In the title compound, C29H20Cl2N2S2, the pyrazole ring adopts a planar conformation. The chlorophenyl rings are twisted from the pyrazole ring at angles of 52.74 (14) and 29.92 (13)°, respectively. The crystal structure is stabilized by C—H⋯N and C—H⋯π inter­actions.
doi:10.1107/S1600536808031231
PMCID: PMC2959571  PMID: 21580921
25.  1-[(E)-2-Formyl-1-(4-methyl­phen­yl)ethen­yl]-3-(4-methyl­phen­yl)pyrazole-4-carbaldehyde 
In the crystal structure of the title compound, C21H18N2O2, mol­ecules are linked through C—H⋯O inter­actions. Two symmetry-related mol­ecules form a cyclic centrosymmetric R 2 2(20) dimer. These dimers are further connected into chains running along the b axis.
doi:10.1107/S1600536808027694
PMCID: PMC2959333  PMID: 21201101

Results 1-25 (28)