Dynamics of protein-protein encounter: a Langevin equation approach with reaction patches

We study the formation of protein-protein encounter complexes with a Langevin equation approach that considers direct, steric and thermal forces. As three model systems with distinctly different properties we consider the pairs barnase:barstar, cytochrome c:cytochrome c peroxidase and p53:MDM2. In each case, proteins are modeled either as spherical particles, as dipolar spheres or as collection of several small beads with one dipole. Spherical reaction patches are placed on the model proteins according to the known experimental structures of the protein complexes. In the computer simulations, concentration is varied by changing box size. Encounter is defined as overlap of the reaction patches and the corresponding first passage times are recorded together with the number of unsuccessful contacts before encounter. We find that encounter frequency scales linearly with protein concentration, thus proving that our microscopic model results in a well-defined macroscopic encounter rate. The number of unsuccessful contacts before encounter decreases with increasing encounter rate and ranges from 20-9000. For all three models, encounter rates are obtained within one order of magnitude of the experimentally measured association rates. Electrostatic steering enhances association up to 50-fold. If diffusional encounter is dominant (p53:MDM2) or similarly important as electrostatic steering (barnase:barstar), then encounter rate decreases with decreasing patch radius. More detailed modeling of protein shapes decreases encounter rates by 5-95 percent. Our study shows how generic principles of protein-protein association are modulated by molecular features of the systems under consideration. Moreover it allows us to assess different coarse-graining strategies for the future modelling of the dynamics of large protein complexes

Towards the implementation of the environmental and economic doctrine of energy sector development: an environmental and economic assessment of public-private partnerships in decarbonization

The disruption of the energy system at the global and local levels requires an intensification of public policy in this area to respond quickly to changes. Strategic planning and public policy changes are needed to ensure the sustainability of the energy sector. In the short term, improving energy security should be a priority for many countries. Natural gas will be essential in balancing electricity on the road to decarbonization. The transition to renewable energy sources can achieve natural gas self-sufficiency. The article analyzes the directions of energy security and normative and legal regulation in the energy sector. It is established that the main direction of transition to decarbonization in an unstable external environment is public-private partnership mechanisms. The introduction of this mechanism provides benefits for all interested parties. In order to choose the most effective form of public-private partnership, a flowchart of analysis and evaluation of environmental and economic efficiency was developed. This flowchart applies to decarbonization projects and considers regional features of the energy sector and differences in readiness for the transition to the decarbonization of different countries. Limitations of the model application are the imperfect regulatory framework and the high instability of the external environment. The main objective is to simplify the procedures for attracting investment in the energy sector and reduce the time for project preparation and submission, which will help to implement the most effective projects in the short term and make the transition to decarbonization in the long term

Evaluating the Effect of Substrates on the Stability of the Bacterial Luminescent System during Co-Immobilization in the Starch Gel

This study presents the evaluation of the effect of the substrates: tetradecanal and NADH on the activity of the coupled enzyme system NAD(P)H: FMN oxidoreductase – luciferase during co-immobilization and long-term storage.Участие в IX Международной молодежной научной конференции «Физика. Техно-логии. Инновации. ФТИ-2022» поддержано Красноярским краевым фондом науки

Dopant-induced 2D-3D transition in small Au-containing clusters: DFT-global optimisation of 8-atom Au-Ag nanoalloys

A genetic algorithm (GA) coupled with density functional theory (DFT) calculations is used to perform global optimisations for all compositions of 8-atom Au–Ag bimetallic clusters. The performance of this novel GA-DFT approach for bimetallic nanoparticles is tested for structures reported in the literature. New global minimum structures for various compositions are predicted and the 2D–3D transition is located. Results are explained with the aid of an analysis of the electronic density of states. The chemical ordering of the predicted lowest energy isomers are explained via a detailed analysis of the charge separation and mixing energies of the bimetallic clusters. Finally, dielectric properties are computed and the composition and dimensionality dependence of the electronic polarizability and dipole moment is discussed, enabling predictions to be made for future electric beam deflection experiments

Predicting DNA-Binding Specificities of Eukaryotic Transcription Factors

Today, annotated amino acid sequences of more and more transcription factors (TFs) are readily available. Quantitative information about their DNA-binding specificities, however, are hard to obtain. Position frequency matrices (PFMs), the most widely used models to represent binding specificities, are experimentally characterized only for a small fraction of all TFs. Even for some of the most intensively studied eukaryotic organisms (i.e., human, rat and mouse), roughly one-sixth of all proteins with annotated DNA-binding domain have been characterized experimentally. Here, we present a new method based on support vector regression for predicting quantitative DNA-binding specificities of TFs in different eukaryotic species. This approach estimates a quantitative measure for the PFM similarity of two proteins, based on various features derived from their protein sequences. The method is trained and tested on a dataset containing 1 239 TFs with known DNA-binding specificity, and used to predict specific DNA target motifs for 645 TFs with high accuracy

Isolierte und deponierte Cluster

The present work deals with different semiempirical potentials to the global optimization of transition and noble metal clusters. The three energetically lowest isomers of gold and silver clusters with up to 150 atoms have been determined. For structural and energetical comparison, additional computations have been performed on nickel and copper systems. The results confirm the applicability of the embedding functions even to the smallest metal particles. In order to determine general cluster properties, we have introduced structural and energetical descriptors such as stability function, moments of inertia, radial distribution of distances, similarity function quantifying the similarity to different fcc and icosahedral fragments, and how much a cluster of N atoms can be considered as made of a N-1 - atom cluster plus one additional atom. When possible, comparison was made to ab initio and experimental results. While copper, nickel and silver clusters show very similar structural and energetical properties, gold clusters differ markedly from those systems. In contrast to the regular icosahedral cluster growth observed for Ni and Cu, and the decahedral for Ag, the gold particles show irregular growth with predominant low-symmetric lowest-energy isomers, and no preferred structural pattern. The second part of this study concerns dynamical processes of deposition of clusters on metal surfaces. The cluster-cluster interactions were followed from the Low Energy Cluster Beam, using a newly developed Molecular Dynamics algorithm, simulating the experimental procedure. It was found that applying even little kinetic energy to the clusters leads to the formation of diverse (meta)stable products. The cluster molecules emerged from the collision processes had relatively short lifetimes, and were crucially dependent on the initial orientation of the impacting clusters. Deposition of clusters on substrates was carried out using particularly stable and particularly unstable copper cluster structures. The results showed that at low impact energies the structure of the smallest deposited cluster, Cu13 , remained preserved on the surface up to relatively high impact energy of 0.5 eV/atom, where it collapsed on the surface forming a monolayer. Similar behavior was observed for the particularly unstable Cu18. The final products of the cluster deposition depended on all parameters of the deposition process, i.e., impact energy, cluster size, relative orientation and position.Die vorliegende Arbeit beschäftigt sich mit der Anwendung verschiedener semiempirischer Potentiale zur globalen Optimierung von Übergangs- und Edelmetall-Clustern. Es wurden die drei energetisch niedrigsten Isomere von Gold- und Silber-Clustern mit bis zu 150 Atomen bestimmt. Um die Strukturen und Energien vergleichen zu können, wurden zusätzliche Berechnungen mit Nickel- und Kupfer-Systemen durchgeführt. Die Ergebnisse bestätigen die Anwendbarkeit der Embedding-Funktionen auf kleinste Metallpartikel. Um allgemeine Cluster-Eigenschaften bestimmen zu können, wurden strukturelle und energetische Deskriptoren eingeführt, wie zum Beispiel Stabilitätsfunktion, Massenträgheitsmoment, Radiale Verteilungsfunktion oder Ähnlichkeitsfunktion, welche die Ähnlichkeit von verschiedenen fcc und ikosaedrischen Fragmenten quantifziert und inwiefern ein Cluster (bestehend) aus N Atomen als ein Cluster aus N - 1 Atomen plus ein zusätzliches Atom betrachtet werden kann. Wenn möglich wurde mit ab initio und experimentellen Ergebnissen verglichen. Während Cu-, Ni-, und Ag-Cluster sehr ähnliche strukturelle und energetische Eigenschaften zeigen, unterscheiden sich Au-Cluster erheblich von diesen Systemen. Im Gegensatz zu dem regelmäßigen ikosaedralen Cluster-Wachstum, welches für Ni und Cu beobachtet wurde, und dem dekaedralen Wachstum für Ag zeigen die Au-Partikel unregelmäßiges Wachstum, das zu vorwiegend niedrigsymmetrischen Isomeren führt. In diesem Fall bevorzugen die Au-Partikel keine bestimmten Wachstumsmuster. Der zweite Teil dieser Arbeit bezieht sich auf dynamische Prozesse der Deponierung von Clustern auf metallenen Oberflächen. Die Cluster-Cluster-Wechselwirkungen wurden dem Low Energy Cluster Beam-Experiment (LECB) nachgeahmt, in dem man einen Molecular Dynamics Algorithmus entwickelt hat, der die experimentelle Prozedur simuliert. Man fand heraus, dass selbst niedrige kinetische Anfangsenergie der Cluster zur Bildung von verschiedenen (meta)stabilen Produkten führt. Die Cluster-Moleküle, welche aus dem Kollisionsprozess entstehen, sind relativ kurzlebig, und hängen entscheidend von der ursprünglichen Orientierung der zusammenstoßenden Cluster ab. Die Deponierung von Clustern auf Oberflächen wurde mithilfe von besonders stabilen, bzw. instabilen Strukturen von Kupfer-Clustern durchgeführt. Diese Ergebnisse zeigen, dass bei niedrigen Anfangsenergien die Struktur des kleinsten deponierten Clusters, Cu13 , auf der Oberfläche erhalten bleibt. Bei höheren Anfangsenergien von 0.5 eV/Atom bildet das Cluster eine Monoschicht auf der Oberfläche. Ein ähnliches Verhalten wurde mit dem besonders instabilen Cu18 Cluster beobachtet. Die Endprodukte der Cluster-Deponierung hängen von allen Parametern des Deponierungsprozesses ab, wie Anfangsenergie, Clustergröße, relativer Orientierung, und Position