98,515 research outputs found
Salacia krigsneri Lombardi
No full textSalacia krigsneri Lombardi — J.A. Lombardi 6687, Brazil (HRCB); 26S rDNA HM230067, ITS rDNA HM230112, matK HM230159, trnL intron HM230205, trnL-F spacer HM230250;Published as part of Coughenour, Jennifer M., Simmons, Mark P., Lombardi, Julio A., Yakobson, Kendra & Archer, Robert H., 2011, Phylogeny of Celastraceae subfamily Hippocrateoideae inferred from morphological characters and nuclear and plastid loci, pp. 320-330 in Molecular Phylogenetics and Evolution 59 (2) on page 328, DOI: 10.1016/j.ympev.2011.02.017, http://zenodo.org/record/515569
De Novo Design And Characterization Of A Protein Binding An Abiotic Tetranuclear Zinc Cluster
No full textThe protein matrix finely tunes metal cofactor geometry and reactivity, despite the limited number of ligands.[1] De novo protein design is particularly appealing in gaining new insights on the concurring interactions providing specific functions.[2] While there has been considerable progress in designing proteins that bind mononuclear as well as multinuclear metal cofactors,[3-5] the design of tetranuclear clusters with oxygen-rich environments has not been accomplished. Here, we describe our recent work on the design, structural and spectroscopic characterization of tetra-Zn2+ carboxylate-bridged clusters. The distorted cube-like structure is deeply inserted into the hydrophobic core of a four-helix bundle scaffold, and largely stabilized by a fully connected hydrogen-bonded network, unprecedented in protein design, consisting of 16 polar side chains. By varying the metal-bridging and the interfacial residues in the bundle, we show that subtle changes (in the order of few angstroms) have a great impact on the coordination geometry, as well as oligomeric state and stability. The crystal structures of the first four analogues confirm the validity of the design process in two cases, and define general rules for subsequent designs.[6] Three of these newly designed proteins have been fully characterized by CD and NMR spectroscopies. Solution studies strongly suggest that the desired structure is achieved also in the apo state, providing evidence that the peptide is able to actively impart the designed geometry to the metal cluster.[7]
In perspective, such abiotic tetra-Zn2+ cluster will be adopted as catalyst for both complex transesterification, and hydrolysis reactions.[8] It may also constitute the basis for the construction of the first de novo designed oxygen evolving complex, by replacing zinc with designated redox-active metals.
[1] O. Maglio, F. Nastri, A. Lombardi, in Ioninc Interactions in Natural and Synthetic Macromolecules (Eds.: A. Ciferri, A. Perico), John Wiley & Sons, Inc., Hoboken, NJ, USA, 2012, pp. 361–450.
[2] F. Yu, V. M. Cangelosi, M. L. Zastrow, M. Tegoni, J. S. Plegaria, A. G. Tebo, C. S. Mocny, L. Ruckthong, H. Qayyum, V. L. Pecoraro, Chem. Rev. 2014, 114, 3495–3578.
[3] F. Nastri, M. Chino, O. Maglio, A. Bhagi-Damodaran, Y. Lu, A. Lombardi, Chem. Soc. Rev. 2016, 45, 5020–5054.
[4] A. F. Peacock, Curr. Opin. Chem. Biol. 2016, 31, 160–165.
[5] M. Chino, L. Leone, G. Zambrano, F. Pirro, D. D’Alonzo, V. Firpo, D. Aref, L. Lista, O. Maglio, F. Nastri,
A. Lombardi, Biopolymers 2018, e23107.
[6] S.Q. Zhang, M. Chino, L. Liu, Y. Tang, X. Hu, W. F. DeGrado, A. Lombardi, J. Am. Chem. Soc. 2018, 140, 1294–1304.
[7] M. Chino, S.Q. Zhang, F. Pirro, L. Leone, O. Maglio, A. Lombardi, W. F. DeGrado, Biopolymers 2018, under review.
[8] T. Ohshima, Chem. Pharm. Bull. (Tokyo) 2016, 64, 523–539
FIGURE 1. Salacia juradoi Cornejo & Lombardi. A in Salacia juradoi (Celastraceae), a new species from coastal Ecuador
No full textFIGURE 1. Salacia juradoi Cornejo & Lombardi. A, Terminal branchlet with petioles and leaf bases, adaxial view; B, A leafy ramiflorous branch, abaxial view; C, Light-orange mature flowers and flower buds; D, Light-green mature flowers from a same population; E, Immature fruit; F, Mature fruit. Photographs taken from the holotype, X. Cornejo 9359 (GUAY).Published as part of Cornejo, Xavier & Lombardi, Julio A., 2021, Salacia juradoi (Celastraceae), a new species from coastal Ecuador, pp. 125-130 in Phytotaxa 524 (2) on page 126, DOI: 10.11646/phytotaxa.524.2.8, http://zenodo.org/record/564211
Effects of malingering in self-report measures: A scenario analysis approach
No full textIn many psychological questionnaires (i.e., personnel selection surveys
and diagnostic tests) the collected samples often include fraudulent records. This
confronts the researcher with the crucial problem of biases yielded by the usage
of standard statistical models. In this paper we generalize a recent combinato-
rial perturbation procedure, called SGR (Sample Generation by Replacements;
[Lombardi et al., 2004]), to the analysis of structured malingering scenarios for
dichotomous data. Combinatorial aspects of the approach are discussed and an
application to a simple data set on the drug addiction domain is presented. Fi-
nally, the close relationships with Monte Carlo simulation studies are explored
Doctoral Consortium of the 12th AI*IA Symposium on Artificial Intelligence 2012, AIxIA-DC 2012: proceedings of the Doctoral Consortium of the 12th Symposium of the Italian Association for Artificial Intelligence Rome, Italy, June 15, 2012
No full text
Simicratea sp. nov.(?) Coughenour & Simmons & Lombardi & Yakobson & Archer 2011
No full textSimicratea sp. nov. (?) — Luke & Luke 4747, Kenya (K); 26S rDNA HM230105, ITS rDNA HM230152, matK HM230198, trnL intron HM230244, trnL-F spacer HM230287;Published as part of Coughenour, Jennifer M., Simmons, Mark P., Lombardi, Julio A., Yakobson, Kendra & Archer, Robert H., 2011, Phylogeny of Celastraceae subfamily Hippocrateoideae inferred from morphological characters and nuclear and plastid loci, pp. 320-330 in Molecular Phylogenetics and Evolution 59 (2) on page 328, DOI: 10.1016/j.ympev.2011.02.017, http://zenodo.org/record/515569
Pristimera sp. nov. Coughenour & Simmons & Lombardi & Yakobson & Archer 2011
No full textPristimera sp. nov. — R.H. Archer et al. 2948, Madagascar (CS); 26S rDNA HM230094, ITS rDNA HM230142, matK HM230187, trnL intron HM230233, trnL-F spacer HM230277;Published as part of Coughenour, Jennifer M., Simmons, Mark P., Lombardi, Julio A., Yakobson, Kendra & Archer, Robert H., 2011, Phylogeny of Celastraceae subfamily Hippocrateoideae inferred from morphological characters and nuclear and plastid loci, pp. 320-330 in Molecular Phylogenetics and Evolution 59 (2) on page 327, DOI: 10.1016/j.ympev.2011.02.017, http://zenodo.org/record/515569
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