Correction: In Silico Generation of Peptides by Replica Exchange Monte Carlo: Docking-Based Optimization of Maltose-Binding-Protein Ligands.

[This corrects the article DOI: 10.1371/journal.pone.0133571.].

Designing High-Affinity Peptides for Organic Molecules by Explicit Solvent Molecular Dynamics.

Short peptides offer a cheap alternative to antibodies for developing sensing units in devices for concentration measurement. We here describe a computational procedure that allows designing peptides capable of binding with high affinity a target organic molecule in aqueous or nonstandard solvent environments. The algorithm is based on a stochastic search in the space of the possible sequences of the peptide, and exploits finite temperature molecular dynamics simulations in explicit solvent to check if a proposed mutation improves the binding affinity or not. The procedure automatically produces peptides which form thermally stable complexes with the target. The estimated binding free energy reaches the 13 kcal/mol for Irinotecan anticancer drug, the target considered in this work. These peptides are by construction solvent specific; namely, they recognize the target only in the solvent in which they have been designed. This feature of the algorithm calls for applications in devices in which the peptide-based sensor is required to work in denaturants or under extreme conditions of pressure and temperature.

In Silico Generation of Peptides by Replica Exchange Monte Carlo: Docking-Based Optimization of Maltose-Binding-Protein Ligands.

Short peptides can be designed in silico and synthesized through automated techniques, making them advantageous and versatile protein binders. A number of docking-based algorithms allow for a computational screening of peptides as binders. Here we developed ex-novo peptides targeting the maltose site of the Maltose Binding Protein, the prototypical system for the study of protein ligand recognition. We used a Monte Carlo based protocol, to computationally evolve a set of octapeptides starting from a polialanine sequence. We screened in silico the candidate peptides and characterized their binding abilities by surface plasmon resonance, fluorescence and electrospray ionization mass spectrometry assays. These experiments showed the designed binders to recognize their target with micromolar affinity. We finally discuss the obtained results in the light of further improvement in the ex-novo optimization of peptide based binders.

Atomic force microscopy based nanoassay: a new method to study α-Synuclein-dopamine bioaffinity interactions.

Intrinsically Disordered Proteins (IDPs) are characterized by the lack of well-defined 3-D structure and show high conformational plasticity. For this reason, they are a strong challenge for the traditional characterization of structure, supramolecular assembly and biorecognition phenomena. We show here how the fine tuning of protein orientation on a surface turns useful in the reliable testing of biorecognition interactions of IDPs, in particular α-Synuclein. We exploited atomic force microscopy (AFM) for the selective, nanoscale confinement of α-Synuclein on gold to study the early stages of α-Synuclein aggregation and the effect of small molecules, like dopamine, on the aggregation process. Capitalizing on the high sensitivity of AFM topographic height measurements we determined, for the first time in the literature, the dissociation constant of dopamine-α-Synuclein adducts.

Interactions of iron-sulfur clusters with small peptides: insights into early evolution.

Favoring the stability of iron-sulfur clusters in hydrothermal vents could have been important for the origin of life. It has been postulated that small "nest" peptides with lengths between 3 and 6 residues could have been important to stabilize early iron-sulfur clusters. We present theoretical calculations exploring the sequence and conformational spaces of short peptides able to bind with high affinity the iron-sulfur cluster Fe(4)S(4). Our results indicate that it is unlikely to form stable complexes between Fe(4)S(4) and small peptides at the core of hydrothermal vents. The formation of these complexes is instead favored for peptides of at least 8 residues as they diffused together with the Fe(4)S(4) clusters toward lower temperature regions within the vent-associated temperature gradients.

Designing Short Peptides with High Affinity for Organic Molecules: A Combined Docking, Molecular Dynamics, And Monte Carlo Approach.

We present a method for designing artificial receptors capable of binding with high affinity to a chosen target organic molecule. The primary sequence of the peptide is optimized to maximize its binding affinity. Our algorithm builds on a combination of molecular dynamics, semiflexible docking, and replica exchange Monte Carlo and performs simultaneous sampling in sequence and conformational spaces carefully selecting the degree of flexibility in the mutated peptides. The approach is used to design a decapeptide able to bind efavirenz. The calculated binding energy of the designed peptide (approximately -12 kcal/mol) was confirmed experimentally by fluorescence measurements. NMR spectroscopy confirmed the interactions between the peptide and the efavirenz molecule predicted by the algorithm.

Bioavailability of metal ions and evolutionary adaptation.

The evolution of life on earth has been a long process that began nearly 3,5 x 109 years ago. In their initial moments, evolution was mainly influenced by anaerobic environments; with the rise of O2 and the corresponding change in bioavailability of metal ions, new mechanisms of survival were created. Here we review the relationships between ancient atmospheric conditions, metal ion bioavailability and adaptation of metals homeostasis during early evolution. A general picture linking geochemistry, biochemistry and homeostasis is supported by the reviewed literature and is further illustrated in this report using simple database searches.

Estudio de la Variabilidad de la Frecuencia Cardiaca Mediante el Análisis de recurrencia Visual / I study of the Variability of the Heart Frequency By means of the Analysis of Visual

Se aplicaron varios métodos relacionados con la implementación del análisis de recurrencia visual a un grupo de 10 registros de señales RR obtenidas a partir de una señal de RR de 24 horas de duración de un sujeto sano voluntario del sexo masculino. En particular la utilización de la función de información mutua y del método de los falsos vecinos mostraron que la señal posee una elevada dimensión de inmersión , por esta razón se descarta la posibilidad de que la señal posea una dinámica de caos clásico. Esto está en correspondencia con resultados ya alcanzados en la literatura [14]. En general, en los gráficos de recurrencia se aprecia la presencia de cierta estructura en las señales RR estudiadas, este resultado se confirma con las mediciones de entropía espacio-temporal (aproximadamente 50 por ciento para todas las señales observadas). Conclusiones: i) consideramos que el análisis de recurrencia visual puede ser una herramienta util para explorar la estructura de las señales de variabilidad de la frecuencia cardíaca y su posible alteracion en algunas enfermedades(AU)

Analysis of the photoplethysmographic signal by means of the decomposition in principal components.

We study the plethysmographic signal using principal component analysis (PCA). By decomposing the signal using this method, we are able to regenerate it again, preserving in the process the functional relationships between the components. We have also found the relative contributions of each specific component to the signal. First return maps have been made for the series of residues of the decomposition. Further analysis using spectral methods has shown that the residues have a 1/f -like structure, which confirms the presence and conservation of this component in the signal and its relative independence with respect to the oscillating component (Hernández et al 2000 Rev. Cubana Inform. Medica 1 5). Our conclusions are that: (i) PCA is a good method to decompose the plethysmographic signal since it preserves the functional relationships in the variables, and this could be potentially useful in finding new clinically relevant indices; (ii) the 1/f process of the plethysmographic signal is preserved in the residues of the decomposed signal when PCA is used; (iii) clinically relevant parameters can potentially be obtained from photoplethysmographic signals when PCA is used.

Complejidad y codificación en RNAs no codificadores / Complexity and code in RNAs non codifiers

La estructura de la información presente en las regiones genéticas no codificadoras aún está muy poco caracterizada. En este trabajo se plantea como objetivo fundamental hacer una recodificación de estas secuencias y utilizar medidas teórico-informacionales de análisis, como la entropía de Shannon y la complejidad de Lempel-Ziv, para caracterizar estos datos. La complejidad de Lempel-Ziv mostró un patrón similar no aleatorio en secuencias no codificadoras de diferentes organismos; con medidas derivadas de la entropía de Shannon se obtuvieron evidencias de patrones que hacen posible un tipo de codificación diferente al código de tripletes clásico planteado para secuencias codificadoras(AU)