Mutational Basin-Hopping: Combined Structure and Sequence Optimization for Biomolecules.

The study of energy landscapes has led to a good understanding of how and why proteins and nucleic acids adopt their native structure. Through evolution, sequences have adapted until they exhibit a strongly funneled energy landscape, stabilizing the native fold. Design of artificial biomolecules faces the challenge of creating similar stable, minimally frustrated, and functional sequences. Here we present a biminimization approach, mutational basin-hopping, in which we simultaneously use global optimization to optimize the energy and a target function describing a desired property of the system. This optimization of structure and sequence is a generalized basin-hopping method and produces an efficient design process, which can target properties such as binding affinity or solubility

Biological resources of the Fabaceae family in the Cretaceous south of Russia as a source of starting material for drought-resistance selection

The aim of this work is the study of biological resources of the genera Medicago and Trifolium species in Cretaceous South of the Central Russian Upland as the most valuable in genetic and economic term

An experimental investigation into resonance dry grinding of hardened steel and nickel alloys with element of MQL

Current policies on environmental issues put extra pressures on manufacturing processes to be resource efficient and eco-friendly. However, in grinding processes, large amounts of cutting fluids are used. These fluids are not environmental friendly thus require proper management before disposal with associated cost. Hence, this work sets to explore low-frequency vibration in grinding in order to improve coolant application in conventional grinding at the first stage with the aim to introduce this into high efficiency deep grinding (HEDG) at latter stage. An attempt is made to grind nickel alloys with minimum quantity lubricant (MQL) as oppose to flood cooling. To achieve this with minimum alterations to the machine tool, a piezo-driven workpiece holder was developed for surface grinding. This simple innovative workpiece holder allowed oscillating during actual grinding process. However, this paper presents the results of low-frequency oscillatory grinding in dry and near-dry conditions. The response of the machine tool spindle unit is presented alongside with the workpiece holder response. In this investigation, hardened steels and nickel alloys were ground with vibration assistance. The grinding forces are illustrated together with the surface finish. The wheel performance is given in terms of grinding ratio

Disordered Structural Ensembles of Vasopressin and Oxytocin and Their Mutants

Vasopressin and oxytocin are intrinsically disordered cyclic nonapeptides belonging to a family of neurohypophysial hormones. Although unique in their functions, these peptides differ only by two residues and both feature a tocin ring formed by the disulfide bridge between first and sixth cysteine residues. This sequence and structural similarity are experimentally linked to oxytocin agonism at vasopressin receptors and vasopressin antagonism at oxytocin receptors. Yet single- or double-residue mutations in both peptides have been shown to have drastic impacts on their activities at either receptor, and possibly the ability to bind to their neurophysin carrier protein. In this study we perform molecular dynamics simulations of the unbound native and mutant sequences of the oxytocin and vasopressin hormones to characterize their structural ensembles. We classify the subpopulations of these structural ensembles on the basis of the distributions of radius of gyration and secondary structure and hydrogen-bonding features of the canonical tocin ring and disordered tail region. We then relate the structural changes observed in the unbound form of the different hormone sequences to experimental information about peptide receptor binding, and more indirectly, carrier protein binding affinity, receptor activity, and protease degradation. This study supports the hypothesis that the structural characteristics of the unbound form of an IDP can be used to predict structural or functional preferences of its functional bound form

Finding New Genes for Non-Syndromic Hearing Loss through an In Silico Prioritization Study

At present, 51 genes are already known to be responsible for Non-Syndromic hereditary Hearing Loss (NSHL), but the knowledge of 121 NSHL-linked chromosomal regions brings to the hypothesis that a number of disease genes have still to be uncovered. To help scientists to find new NSHL genes, we built a gene-scoring system, integrating Gene Ontology, NCBI Gene and Map Viewer databases, which prioritizes the candidate genes according to their probability to cause NSHL. We defined a set of candidates and measured their functional similarity with respect to the disease gene set, computing a score () that relies on the assumption that functionally related genes might contribute to the same (disease) phenotype. A Kolmogorov-Smirnov test, comparing the pair-wise distribution on the disease gene set with the distribution on the remaining human genes, provided a statistical assessment of this assumption. We found at a p-value that the former pair-wise is greater than the latter, justifying a prioritization strategy based on the functional similarity of candidate genes respect to the disease gene set. A cross-validation test measured to what extent the ranking for NSHL is different from a random ordering: adding 15% of the disease genes to the candidate gene set, the ranking of the disease genes in the first eight positions resulted statistically different from a hypergeometric distribution with a p-value and a power. The twenty top-scored genes were finally examined to evaluate their possible involvement in NSHL. We found that half of them are known to be expressed in human inner ear or cochlea and are mainly involved in remodeling and organization of actin formation and maintenance of the cilia and the endocochlear potential. These findings strongly indicate that our metric was able to suggest excellent NSHL candidates to be screened in patients and controls for causative mutations

Thrombin Receptor Agonist Peptide as a Novel Antiulcerogenic Factor

peer reviewe

Biological resources of the Fabaceae family in the Cretaceous south of Russia as a source of starting material for drought-resistance selection

The aim of this work is the study of biological resources of the genera Medicago and Trifolium species in Cretaceous South of the Central Russian Upland as the most valuable in genetic and economic term

Thrombin receptor agonist peptide immobilized in microspheres stimulates reparative processes in rats with gastric ulcer

The effect of synthetic thrombin receptor (PAR1) agonist peptide encapsulated in microspheres made of lactic and glycolic acid copolymer on tissue reparation was studied in rats with acetate-induced ulcer. PAR1 agonist peptide was immobilized in biodegraded lactic and glycolic acid microspheres by double emulgation, the kinetics of peptide release was analyzed, and the dynamics of ulcer healing was studied in experimental (administration of microspheres with the peptide into the stomach) and two control groups (administration of saline or spheres without peptide). Thrombin receptor agonist peptide gradually released from lactic and glycolic acid microspheres into the stomach shortened the inflammation phase and shifted the proliferation phase to the earlier period, thus accelerating healing of experimental ulcers in rats