On the unknown proteins of eukaryotic proteomes

In order to study unknown proteins on a large scale, a reference system has been set up for the three major eukaryotic lineages, built with 36 proteomes as taxonomically diverse as possible. Proteins from 362 eukaryotic proteomes with no known homologue in this set were then analyzed, focusing noteworthy on singletons, that is, on unknown proteins with no known homologue in their own proteome. Consistently, according to Uniprot, for a given species, no more than 12% of the singletons thus found are known at the protein level. Also, since they rely on the information found in the alignment of homologous sequences, predictions of AlphaFold2 for their tridimensional structure are usually poor. In the case of metazoan species, the number of singletons seems to increase as a function of the evolutionary distance from the reference system. Interestingly, no such trend is found in the cases of viridiplantae and fungi, as if the timescale on which singletons are added to proteomes were different in metazoa and in other eukaryotic kingdoms. In order to confirm this phenomenon, further studies of proteomes closer to those of the reference system are however needed.Comment: 11 pages, 5 figure

Discrete breathers in nonlinear network models of proteins

We introduce a topology-based nonlinear network model of protein dynamics with the aim of investigating the interplay of spatial disorder and nonlinearity. We show that spontaneous localization of energy occurs generically and is a site-dependent process. Localized modes of nonlinear origin form spontaneously in the stiffest parts of the structure and display site-dependent activation energies. Our results provide a straightforward way for understanding the recently discovered link between protein local stiffness and enzymatic activity. They strongly suggest that nonlinear phenomena may play an important role in enzyme function, allowing for energy storage during the catalytic process.Comment: 4 pages, 5 figures. Minor change

Slow energy relaxation of macromolecules and nano-clusters in solution

Many systems in the realm of nanophysics from both the living and inorganic world display slow relaxation kinetics of energy fluctuations. In this paper we propose a general explanation for such phenomenon, based on the effects of interactions with the solvent. Within a simple harmonic model of the system fluctuations, we demonstrate that the inhomogeneity of coupling to the solvent of the bulk and surface atoms suffices to generate a complex spectrum of decay rates. We show for Myoglobin and for a metal nano-cluster that the result is a complex, non-exponential relaxation dynamics.Comment: 5 pages, 3 figure

Макроекономічні проблеми інфляції в умовах економічної трансформації

Розглянуто проблему інфляції як фундаментальну проблему для розвитку будь-якої країни. Стверджено, що в економічній науці не існує єдиних підходів щодо суті цього явища, причин появи і наслідків, а також основних напрямів боротьби з інфляцією. Макроекономічний інфляційний вплив на економіку має свою специфіку в умовах формування ринкових відносин країн перехідної економіки (наприклад, України). З застосуванням методології функціонального аналізу, системного підходу та аналогії проаналізовано причини і наслідки інфляції, антиінфляційну політику, яка проводиться в умовах ринкової економіки. Особливу увагу звернено на макроекономічні проблеми інфляції в економіці сучасної України. Зроблено висновки про необхідність проведення виважених як політичних, так і економічних рішень, від яких залежить майбутнє економіки нашої держави.Рассмотрена проблема инфляции как фундаментальную проблему для развития любой страны. Утверждено, что в экономической науке не существует единых подходов к сути этого явления, причин появления и последствий, а также основных направлений борьбы с инфляцией. Макроэкономический инфляционное воздействие на экономику имеет свою специфику в условиях формирования рыночных отношений стран переходной экономики (например, Украина). Применение методологии функционального анализа, системного подхода и аналогии проанализированы анализируются причины и последствия инфляции, антиинфляционную политику, которая проводится в условиях рыночной экономики. Особое внимание обращено на макроэкономические проблемы инфляции в экономике современной Украины. Сделаны выводы о необходимости проведения взвешенных как политических, так и экономических решений, от которых зависит будущее экономики государства.Inflation is a fundamental problem for the development of any country. There are no common approaches to the nature, causes and consequences of this phenomenon and the ways of its reduction in economics. Macroeconomical inflation impact on the economy has its own distinctive aspects in terms of the building of marketing relationships in the countries with transition economy (Ukraine, for example). Using methods of functional analysis, system analysis and analogy method the causes and consequences of inflation as well as antiinflationary policy conducted in a market economy are analyzed in the article. Special attention is paid to macro-economical problems of inflation in the economy of modern Ukraine. The conclusion about the necessity of making the deliberated political and economical decisions that affect the future economy of our country is made

Functional modes of proteins are among the most robust ones

It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result should prove helpful in the context of several applications proposed recently, like for solving difficult molecular replacement problems or for fitting atomic structures into low-resolution electron density maps. Moreover, it may also pave the way for the development of methods allowing to predict such motions accurately.Comment: 4 pages, 5 figure