Proteotronics

Alfinito, Eleonora; Pousset, J.; Reggiani, L.

doi:10.1201/b18966

Cited by 19 publications

(24 citation statements)

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“…The cut-off radius RC is a free parameter, whose tuning produces a graph more connected at increasing values [3].…”

Section: Topological Descriptionmentioning

confidence: 99%

“…To formulate this expression, we notice that the observed impedance variation is well reproduced by an RC parallel circuit [3,31], here i,j and i,j represent the resistivity and the dielectric constants of the link connecting two neighbor bricks [14]. The shape size of the equivalent element is resumed by Si.j, with dimension inverse of a length and which depends on the distance between the bricks and the interaction radius.…”

Section: Electrical Descriptionmentioning

confidence: 99%

“…The process is repeated for different frequencies and/or RC values. In such a way, we are able to produce two kinds of spectra, the frequency and the interaction spectra [3,11,31].…”

Section: Electrical Descriptionmentioning

confidence: 99%

“…Medicine is addressing more and more efforts toward prevention, personalization of cure and the search of less invasive and point-of-care diagnostic methods. Accordingly, the development of new analysis techniques and therapies is a challenging task for researches belonging to all the branches of science, from biology to informatics and from physics and chemistry to engineering [1][2][3][4].…”

Section: Introductionmentioning

confidence: 99%

“…This paper proposes a theoretical/computational approach, within the emergent science of Proteotronics [3] as a novel tool to reproduce chemical affinity in aptamer-ligand complexes. It is able to interpret the electrical responses observed in experiments [8][9][10][11][12][13], and to be predictive of novel results.…”

Section: Introductionmentioning

confidence: 99%

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Hierarchy and Assortativity as New Tools for Binding-Affinity Investigation: The Case of the TBA Aptamer-Ligand Complex

Cataldo

Alfinito

Reggiani

2017

IEEE Trans.on Nanobioscience

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Aptamers are single stranded DNA, RNA, or peptide sequences having the ability to bind several specific targets (proteins, molecules as well as ions). Therefore, aptamer production and selection for therapeutic and diagnostic applications is very challenging. Usually, they are generated in vitro, although computational approaches have been recently developed for the in silico production. Despite these efforts, the mechanism of aptamer-ligand formation is not completely clear, and producing high-affinity aptamers is still quite difficult. This paper aims to develop a computational model able to describe aptamer-ligand affinity. Topological tools, such as the conventional degree distribution, the rank-degree distribution (hierarchy), and the node assortativity are employed. In doing so, the macromolecules tertiary-structures are mapped into appropriate graphs. These graphs reproduce the main topological features of the macromolecules, by preserving the distances between amino acids (nucleotides). Calculations are applied to the thrombin binding aptamer (TBA), and the TBA-thrombin complex produced in the presence of Na or K. The topological analysis is able to detect several differences between complexes obtained in the presence of the two cations, as expected by previous investigations. These results support graph analysis as a novel computational tool for testing affinity. Otherwise, starting from the graphs, an electrical network can be obtained by using the specific electrical properties of amino acids and nucleobases. Therefore, a further analysis concerns with the electrical response, revealing that the resistance is sensitively affected by the presence of sodium or potassium, thus suggesting resistance as a useful physical parameter for testing binding affinity.

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“…The cut-off radius RC is a free parameter, whose tuning produces a graph more connected at increasing values [3].…”

Section: Topological Descriptionmentioning

confidence: 99%

Section: Electrical Descriptionmentioning

confidence: 99%

“…The process is repeated for different frequencies and/or RC values. In such a way, we are able to produce two kinds of spectra, the frequency and the interaction spectra [3,11,31].…”

Section: Electrical Descriptionmentioning

confidence: 99%