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  • 1
    Language: English
    Description: Geometric morphometrics commonly have been utilized to explore patterns of variation across a wide range of taxa. We present a geometric morphometric analysis of skull shape morphology for New World crocodilians of the genus Crocodylus, placing emphasis on studying variation within the Greater Antillean region of the Neotropics. It has been suggested that the major factor contributing to the modern diversity of Cuban (C. rhombifer) and American crocodiles (C. acutus) in the Greater Antilles is the result of ancient hybridization. Genetic studies found that mitochondrial DNA haplotypes for C. acutus in the Greater Antilles are actually more closely related to C. rhombifer than other American crocodiles throughout the Neotropics. To infer whether genetic relationships are correlated with morphological relationships, we use geometric morphometrics to assess shape variation and compare skull morphology to a reconstruction of a cytochrome-b gene phylogeny. Analysis of skull shape variation using geometric morphometrics of landmark data reveals three broad groups of New World Crocodylus within the given morphospace. Two of these groups correspond to present day Crocodylus whereas the other corresponds to fossil specimens of C. rhombifer. Within these groups, nearly all sub-groups correspond to our current taxonomic understanding of New World Crocodylus; except for the placement of Greater Antillean C. acutus, which clusters much closer to C. rhombifer. This further supports recent studies of Greater Antillean C. acutus dynamics and their genetic phylogenies, indicating a unique evolutionary history.
    Keywords: Crocodile ; Morphometrics ; Crocodylus ; Greater Antilles ; Antillean ; Crocodilians ; Morphospace ; Crocodylus acutus ; Crocodylus rhombifer
    Source: Texas Tech University
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  • 2
    Language: English
    In: 2014, Vol.9(10), p.e111531
    Description: Prolidases, metalloproteases that catalyze the cleavage of Xaa-Pro dipeptides, are conserved enzymes found in prokaryotes and eukaryotes. In humans, prolidase is crucial for the recycling of collagen. To further characterize the essential elements of this enzyme, we utilized the Escherichia coli prolidase, PepQ, which shares striking similarity with eukaryotic prolidases. Through structural and bioinformatic insights, we have extended previous characterizations of the prolidase active site, uncovering a key component for substrate specificity. Here we report the structure of E. coli PepQ, solved at 2.0 Å resolution. The structure shows an antiparallel, dimeric protein, with each subunit containing N-terminal and C-terminal domains. The C-terminal domain is formed by the pita-bread fold typical for this family of metalloproteases, with two Mg(II) ions coordinated by five amino-acid ligands. Comparison of the E. coli PepQ structure and sequence with homologous structures and sequences from a diversity of organisms reveals distinctions between prolidases from Gram-positive eubacteria and archaea, and those from Gram-negative eubacteria, including the presence of loop regions in the E. coli protein that are conserved in eukaryotes. One such loop contains a completely conserved arginine near the catalytic site. This conserved arginine is predicted by docking simulations to interact with the C-terminus of the substrate dipeptide. Kinetic analysis using both a charge-neutralized substrate and a charge-reversed variant of PepQ support this conclusion, and allow for the designation of a new role for this key region of the enzyme active site.
    Keywords: Research Article ; Biology And Life Sciences
    E-ISSN: 1932-6203
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  • 3
    Language: English
    In: Journal of Bacteriology, March, 2013, Vol.195(5-6), p.1346(10)
    Description: Y is the putative holin gene of the paradigm coliphage P2 and encodes a 93-amino-acid protein. Y is predicted to be an integral membrane protein that adopts an N-out C-in membrane topology with 3 transmembrane domains (TMDs) and a highly charged C-terminal cytoplasmic tail. The same features are observed in the canonical class I lambda holin, the S105 protein of phage lambda, which controls lysis by forming holes in the plasma membrane at a programmed time. S105 has been the subject of intensive genetic, cellular, and biochemical analyses. Although Y is not related to S105 in its primary structure, its characterization might prove useful in discerning the essential traits for holin function. Here, we used physiological and genetic approaches to show that Y exhibits the essential holin functional criteria, namely, allele-specific delayed-onset lethality and sensitivity to the energization of the membrane. Taken together, these results suggest that class I holins share a set of unusual features that are needed for their remarkable ability to program the end of the phage infection cycle with precise timing. However, Y holin function requires the integrity of its short cytoplasmic C-terminal domain, unlike for S105. Finally, instead of encoding a second translational product of Y as an antiholin, as shown for lambda S107, the P2 lysis cassette encodes another predicted membrane protein, LysA, which is shown here to have a Y-specific antiholin character.
    Keywords: Bacteriophage Lambda -- Research ; Membrane Proteins -- Research
    ISSN: 0021-9193
    Source: Cengage Learning, Inc.
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  • 4
    Language: English
    In: Biophysical Journal, 29 January 2013, Vol.104(2), pp.572a-572a
    Keywords: Biology
    ISSN: 0006-3495
    E-ISSN: 1542-0086
    Source: ScienceDirect Journals (Elsevier)
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  • 5
    Language: English
    In: FEBS Letters, 01 November 2013, Vol.587(21), pp.3464-3470
    Description: We illuminate the metabolism and the cell-signaling activities of inositol pyrophosphates, by showing that regulation of yeast cyclin-kinase by 1-InsP is not conserved for mammalian CDK5, and by kinetically characterizing Ddp1p/DIPP-mediated dephosphorylation of 1-InsP , 5-InsP and InsP . Each phosphatase exhibited similar values for every substrate (range: 35–148 nM). The rank order of values (1-InsP 〉 5-InsP = InsP ) was identical for each enzyme, although DIPP1 was 10- to 60-fold more active than DIPP2α/β and DIPP3α/β. We demonstrate InsP dephosphorylation preferentially progresses through 1-InsP . Conversely, we conclude that the more metabolically and functionally significant steady-state route of InsP synthesis proceeds via 5-InsP .
    Keywords: Nudix ; Diphosphoinositol ; Phosphohydrolase ; Cdk5rap1 ; Biology ; Chemistry ; Anatomy & Physiology
    ISSN: 0014-5793
    E-ISSN: 1873-3468
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  • 6
    In: Chemical Communications, 2012, Vol.48(92), pp.11292-11294
    Description: We synthesised analogues of diphosphoinositol polyphosphates (PP-InsPs) in which the diphosphate is replaced by an -phosphonoacetic acid (PA) ester. Structural analysis revealed that 5-PA-InsP 5 mimics 5-PP-InsP 5 binding to the kinase domain of PPIP5K2; both molecules were phosphorylated by the enzyme. PA-InsPs are promising candidates for further studies into the biology of PP-InsPs.
    Keywords: Chemistry;
    ISSN: 1359-7345
    E-ISSN: 1364-548X
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  • 7
    Language: English
    In: PLoS ONE, Oct 29, 2014, Vol.9(10)
    Description: Prolidases, metalloproteases that catalyze the cleavage of Xaa-Pro dipeptides, are conserved enzymes found in prokaryotes and eukaryotes. In humans, prolidase is crucial for the recycling of collagen. To further characterize the essential elements of this enzyme, we utilized the Escherichia coli prolidase, PepQ, which shares striking similarity with eukaryotic prolidases. Through structural and bioinformatic insights, we have extended previous characterizations of the prolidase active site, uncovering a key component for substrate specificity. Here we report the structure of E. coli PepQ, solved at 2.0 #197; resolution. The structure shows an antiparallel, dimeric protein, with each subunit containing N-terminal and C-terminal domains. The C-terminal domain is formed by the pita-bread fold typical for this family of metalloproteases, with two Mg(II) ions coordinated by five amino-acid ligands. Comparison of the E. coli PepQ structure and sequence with homologous structures and sequences from a diversity of organisms reveals distinctions between prolidases from Gram-positive eubacteria and archaea, and those from Gram-negative eubacteria, including the presence of loop regions in the E. coli protein that are conserved in eukaryotes. One such loop contains a completely conserved arginine near the catalytic site. This conserved arginine is predicted by docking simulations to interact with the C-terminus of the substrate dipeptide. Kinetic analysis using both a charge-neutralized substrate and a charge-reversed variant of PepQ support this conclusion, and allow for the designation of a new role for this key region of the enzyme active site.
    Keywords: Collagen – Analysis ; Proteases – Analysis ; Escherichia Coli – Analysis
    ISSN: 1932-6203
    Source: Cengage Learning, Inc.
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  • 8
    Language: English
    In: Journal of bacteriology, March 2013, Vol.195(6), pp.1346-55
    Description: Y is the putative holin gene of the paradigm coliphage P2 and encodes a 93-amino-acid protein. Y is predicted to be an integral membrane protein that adopts an N-out C-in membrane topology with 3 transmembrane domains (TMDs) and a highly charged C-terminal cytoplasmic tail. The same features are observed in the canonical class I lambda holin, the S105 protein of phage lambda, which controls lysis by forming holes in the plasma membrane at a programmed time. S105 has been the subject of intensive genetic, cellular, and biochemical analyses. Although Y is not related to S105 in its primary structure, its characterization might prove useful in discerning the essential traits for holin function. Here, we used physiological and genetic approaches to show that Y exhibits the essential holin functional criteria, namely, allele-specific delayed-onset lethality and sensitivity to the energization of the membrane. Taken together, these results suggest that class I holins share a set of unusual features that are needed for their remarkable ability to program the end of the phage infection cycle with precise timing. However, Y holin function requires the integrity of its short cytoplasmic C-terminal domain, unlike for S105. Finally, instead of encoding a second translational product of Y as an antiholin, as shown for lambda S107, the P2 lysis cassette encodes another predicted membrane protein, LysA, which is shown here to have a Y-specific antiholin character.
    Keywords: Bacteriolysis ; Bacteriophage P2 ; Viral Proteins -- Chemistry
    ISSN: 00219193
    E-ISSN: 1098-5530
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  • 9
    Language: English
    In: Journal of Broadcasting & Electronic Media, 02 April 2016, Vol.60(2), pp.213-230
    Description: The relationship between children's TV consumption and literacy outcomes is currently unclear, as past research has identified both linear and curvilinear trends. One explanation for the contradictory results is the varying content children consume; specifically, researchers have argued that research-based educational TV programming should be positively related to literacy outcomes whereas non research-based programming should be negatively related to literacy outcomes (what we refer to as the validated curriculum hypothesis). To test this hypothesis, students in grades 4 and 5 N = 120) completed a survey assessing educational TV consumption and leisure reading/writing behaviors. The results upheld the validated curriculum hypothesis and revealed several key moderators including composite TV consumption and parents' reading behavior.
    Keywords: Education ; Journalism & Communications
    ISSN: 0883-8151
    E-ISSN: 1550-6878
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  • 10
    Language: English
    In: Cell, 06 June 2013, Vol.153(6), pp.1354-1365
    Description: The GroEL/ES chaperonin system is required for the assisted folding of many proteins. How these substrate proteins are encapsulated within the GroEL-GroES cavity is poorly understood. Using symmetry-free, single-particle cryo-electron microscopy, we have characterized a chemically modified mutant of GroEL (EL43Py) that is trapped at a normally transient stage of substrate protein encapsulation. We show that the symmetric pattern of the GroEL subunits is broken as the GroEL -ring apical domains reorient to accommodate the simultaneous binding of GroES and an incompletely folded substrate protein (RuBisCO). The collapsed RuBisCO folding intermediate binds to the lower segment of two apical domains, as well as to the normally unstructured GroEL C-terminal tails. A comparative structural analysis suggests that the allosteric transitions leading to substrate protein release and folding involve concerted shifts of GroES and the GroEL apical domains and C-terminal tails. Cryo-EM captures protein encapsulation by the GroEL/ES chaperone, the first step in protein folding, showing that it involves an intermediate conformation in which the 7-fold symmetry of the GroEL/ES ring is broken and the flexible GroEL C-terminal tails bind the nonnative folding intermediate.
    Keywords: Biology
    ISSN: 0092-8674
    E-ISSN: 1097-4172
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