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11 results on '"De Ruvo, Micol"'

8. Mathematical Modeling and Experimental Validation of the Spatial Distribution of Boron in the Root of Arabidopsis thaliana Identify High Boron Accumulation in the Tip and Predict a Distinct Root Tip Uptake Function.

Author

Akie Shimotohno, Naoyuki Sotta, Takafumi Sato, De Ruvo, Micol, Marée, Athanasius F. M., Grieneisen, Verônica A., and Toru Fujiwara

Subjects
BORON, ARABIDOPSIS thaliana, PLANT root physiology, BIOACCUMULATION in plants, PLANT nutrients, MICRONUTRIENTS, MATHEMATICAL models, PHYSIOLOGY
Abstract

Boron, an essential micronutrient, is transported in roots of Arabidopsis thaliana mainly by two different types of transporters, BORs and NIPs (nodulin26-like intrinsic proteins). Both are plasma membrane localized, but have distinct transport properties and patterns of cell type-specific accumulation with different polar localizations, which are likely to affect boron distribution. Here, we used mathematical modeling and an experimental determination to address boron distributions in the root. A computational model of the root is created at the cellular level, describing the boron transporters as observed experimentally. Boron is allowed to diffuse into roots, in cells and cell walls, and to be transported over plasma membranes, reflecting the properties of the different transporters. The model predicts that a region around the quiescent center has a higher concentration of soluble boron than other portions. To evaluate this prediction experimentally, we determined the boron distribution in roots using laser ablation-inductivity coupled plasmamass spectrometry. The analysis indicated that the boron concentration is highest near the tip and is lower in the more proximal region of the meristem zone, similar to the pattern of soluble boron distribution predicted by the model. Our model also predicts that upward boron flux does not continuously increase from the root tip toward the mature region, indicating that boron taken up in the root tip is not efficiently transported to shoots. This suggests that root tip-absorbed boron is probably used for local root growth, and that instead it is the more mature root regions which have a greater role in transporting boron toward the shoots. [ABSTRACT FROM AUTHOR]

Published
2015
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10. Modules identification in protein structures: the topological and geometrical solutions

Author

Almerinda Di Venere, Daniele Santoni, Paola Paci, Luisa Di Paola, Alessandro Giuliani, Setareh Tasdighian, Giampiero Mei, Pasquale Palumbo, Micol De Ruvo, Tasdighian, S, Di Paola, L, De Ruvo, M, Paci, P, Santoni, D, Palumbo, P, Mei, G, Di Venere, A, and Giuliani, A

Subjects
Models, Molecular, Protein Conformation, General Chemical Engineering, Respiratory chain, Library and Information Sciences, Topology, Electron Transport, Protein structure, Azurin, Protein Interaction Mapping, Computer Simulation, Protein Interaction Domains and Motifs, Adjacency matrix, Settore BIO/10, Databases, Protein, Mathematics, Quantitative Biology::Biomolecules, Sequence, Contact Network, Computational Biology, Proteins, Graph theory, General Chemistry, Spectral clustering, Computer Science Applications, Dynamics, Structural biology, Graph Theory, Pseudomonas aeruginosa, Amino acids, Structure (composition)
Abstract

The identification of modules in protein structures has major relevance in structural biology, with consequences in protein stability and functional classification, adding new perspectives in drug design. In this work, we present the comparison between a topological (spectral clustering) and a geometrical (k-means) approach to module identification, in the frame of a multiscale analysis of the protein architecture principles. The global consistency of an adjacency matrix based technique (spectral clustering) and a method based on full rank geometrical information (k-means) give a proof-of-concept of the relevance of protein contact networks in structure determination. The peculiar "small-world" character of protein contact graphs is established as well, pointing to average shortest path as a mesoscopic crucial variable to maximize the efficiency of within-molecule signal transmission. The specific nature of protein architecture indicates topological approach as the most proper one to highlight protein functional domains, and two new representations linking sequence and topological role of aminoacids are demonstrated to be of use for protein structural analysis. Here we present a case study regarding azurin, a small copper protein implied in the Pseudomonas aeruginosa respiratory chain. Its pocket molecular shape and its electron transfer function have challenged the method, highlighting its potentiality to catch jointly the structure and function features of protein structures through their decomposition into modules.

Published
2014

11. Characterizing protein shape by a volume distribution asymmetry index

Author

Micol De Ruvo, Daniele Santoni, Nicola Arrigo, Luisa Di Paola, Paola Paci, Filippo Castiglione, and Alessandro Giuliani

Subjects
Protein contact network, Mass distribution, Topological indices, media_common.quotation_subject, Mathematical analysis, Principal component analysis, Biomedical Engineering, Health Informatics, Space (mathematics), Linear discriminant analysis, Asymmetry, Attractor, Turn (geometry), Computer Science (miscellaneous), Asymmetry Index, Protein shape, Mathematics, media_common
Abstract

A fully quantitative shape index relying upon the asymmetry of mass distribution of protein molecules along the three space dimensions is proposed. Multidimensional statistical analysis, based on principal component extraction and subsequent linear discriminant analysis, showed the presence of three major ‘attractor forms’ roughly correspondent to rod-like, discoidal and spherical shapes. This classification of protein shapes was in turn demonstrated to be strictly connected with topological features of proteins, as emerging from complex network invariants of their contact maps.

Published
2012

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