A protein domain interaction interface database: InterPare.

BACKGROUND: Most proteins function by interacting with other molecules. Their interaction interfaces are highly conserved throughout evolution to avoid undesirable interactions that lead to fatal disorders in cells. Rational drug discovery includes computational methods to identify the interaction sites of lead compounds to the target molecules. Identifying and classifying protein interaction interfaces on a large scale can help researchers discover drug targets more efficiently. DESCRIPTION: We introduce a large-scale protein domain interaction interface database called InterPare http://interpare.net. It contains both inter-chain (between chains) interfaces and intra-chain (within chain) interfaces. InterPare uses three methods to detect interfaces: 1) the geometric distance method for checking the distance between atoms that belong to different domains, 2) Accessible Surface Area (ASA), a method for detecting the buried region of a protein that is detached from a solvent when forming multimers or complexes, and 3) the Voronoi diagram, a computational geometry method that uses a mathematical definition of interface regions. InterPare includes visualization tools to display protein interior, surface, and interaction interfaces. It also provides statistics such as the amino acid propensities of queried protein according to its interior, surface, and interface region. The atom coordinates that belong to interface, surface, and interior regions can be downloaded from the website. CONCLUSION: InterPare is an open and public database server for protein interaction interface information. It contains the large-scale interface data for proteins whose 3D-structures are known. As of November 2004, there were 10,583 (Geometric distance), 10,431 (ASA), and 11,010 (Voronoi diagram) entries in the Protein Data Bank (PDB) containing interfaces, according to the above three methods. In the case of the geometric distance method, there are 31,620 inter-chain domain-domain interaction interfaces and 12,758 intra-chain domain-domain interfaces

Synthesis of mesoporous zeolites in fluoride media with structure-directing multiammonium surfactants

Mesoporous zeolite beta in pure-silica form and its analogues, including aluminosilicate, stannosilicate, and titanosilicate, were synthesized at near-neutral pH in the presence of fluoride ion as a mineralizer and piperidinium-functionalized multiammonium surfactant as a zeolite structure-directing agent (SDA). During hydrothermal synthesis, the surfactant headgroup generated zeolite beta frameworks with a thickness of 9 nm while numerous surfactant molecules were self-organized to form a nanosponge-like mesostructure in a disordered manner. The mesopores generated after calcination to remove the surfactant were highly uniform and further tailored with diameters in the range of 3.2–4.5 nm according to the surfactant tail lengths. MFI zeolite was also synthesized with a nanosheet morphology using C16H33[sbnd]N+(CH3)2[sbnd]C6H12[sbnd]N+(CH3)2[sbnd]C6H13 as the SDA in fluoride media. The zeolite samples obtained in this manner exhibited remarkably enhanced thermal stability, Brønsted acid strength, and hydrophobic nature compared to those synthesized at a high pH using OH− as the mineralizer due to the reduced defect sites, as confirmed by 29Si MAS NMR and FT-IR measurements. Due to these advantages, the mesoporous zeolite beta obtained in the fluoride media exhibited high catalytic activity in esterification of oleic acid with methanol. © 2016 Elsevier Inc.7

Sulfonium-based organic structure-directing agents for microporous aluminophosphate synthesis

Sulfur-centered phenyl, n-butyl, p-tolyl, and benzyl sulfoniums and sulfides were tested as organic structure-directing agents (SDAs) for the synthesis of crystalline microporous aluminophosphates (AlPOs) over various ranges of gel compositions, hydrothermal treatment temperatures, and crystallization times. Among the investigated compounds, triphenylsulfonium gave single-phase products of ATS-type AlPO and silicoaluminophosphate. Other sulfoniums yielded only non-porous, dense crystalline AlPOs. On the other hand, diaryl sulfides gave a tiny amount of AFI-type AlPO amid tridymite and amorphous phases. Based on the results, it was found to be reasonable that weakly basic sulfide could hardly act as a zeotype SDA due to the low protonation to sulfonium at the present synthesis pH. © 2019 Elsevier Inc. All rights reserved.11sciescopu

Enhancing indoor building occupant safety in the built environment: Assessing the validity of social force modeling for simulating physical distancing behaviors

Facility managers play a key role in ensuring the safety of occupants in indoor environments, particularly in the event of a disaster. Pedestrian Simulation Models, such as the Social Force Model (SFM), are essential for simulating pedestrian behavior and evaluating safety measures in complex indoor environments. These models help to identify potential hazards and bottlenecks. However, concerns about the accuracy of the SFM in reproducing physical distance, particularly during the COVID-19 pandemic, have raised doubts about its reliability, but little attention has been paid to the validity of the SFM in analyzing human movement in indoor environments. Our study rigorously evaluates the applicability of SFM for simulating physical distancing behavior in indoor environments, using trajectory data from building occupants during the COVID-19 peak. The investigation compares standard SFM with Pandemic SFM, which is customized for physical distancing. The results clearly demonstrate the superior performance of Pandemic-SFM in replicating indoor occupant movement, particularly in crowded spaces. Sensitivity analysis highlights the importance of accurately modeling physical distancing, particularly during infectious disease outbreaks. These findings hold great promise for improving occupant behavior simulation models, especially in indoor building environments, and provide scientific evidence to guide safety improvements during pandemics

PtZn Intermetallic Compound Nanoparticles in Mesoporous Zeolite Exhibiting High Catalyst Durability for Propane Dehydrogenation

© 2021 American Chemical Society.A PtZn alloy nanoparticle catalyst for propane dehydrogenation was synthesized by simple coimpregnation of Pt(NH3)4(NO3)2 with Zn(NO3)2 onto a mesoporous material, which was built with siliceous MFI zeolite nanosheets. This mesoporous zeolite-supported PtZn catalyst exhibited high activity and selectivity with remarkably long catalytic lifetime compared with other PtZn catalysts loaded on γ-alumina, MCM-48 mesoporous silica, silica gel, and bulk MFI zeolite. When measured under a high-purity propane flow at 580 °C, the PtZn/mesoporous zeolite catalyst with metal loadings of 0.7 wt % Pt and 0.7 wt % Zn lasted for more than 20 days before the propane conversion decreased to half of its initial value. In comparison, other PtZn catalysts were deactivated almost completely within a few days. Atomic-resolution scanning transmission electron microscopic analysis revealed that the mesoporous zeolite contained finely dispersed Pt1Zn1 intermetallic compound-type alloy nanoparticles, which could effectively suppress catalyst deactivation. The mesoporous structure and the surface silanol groups of the MFI zeolite are suggested to play an important role in promoting the formation of intermetallic alloy nanoparticles.11Nsciescopu

The Atom of Evolution

The main mechanism of evolution is that biological entities change, are selected, and reproduce. We propose a different concept in terms of the main agent or atom of evolution: in the biological world, not an individual object, but its interactive network is the fundamental unit of evolution. The interaction network is composed of interaction pairs of information objects that have order information. This indicates a paradigm shift from 3D biological objects to an abstract network of information entities as the primary agent of evolution. It forces us to change our views about how organisms evolve and therefore the methods we use to analyze evolution.clos

Dimensional accuracy, mechanical property, and optical stability of zirconia orthodontic bracket according to yttria proportions

Abstract This in vitro study evaluated comprehensively the performances of zirconia brackets with varying yttria proportions in manufacturing advanced orthodontic brackets. Three experimental groups of zirconia brackets were fabricated using yttria-stabilized zirconia (YSZ) materials with different yttria proportions—3 mol% yttria (3Y-YSZ), 4 mol% yttria (4Y-YSZ), and 5 mol% yttria (5Y-YSZ) (Tosoh Ceramic, Japan). A polycrystalline alumina ceramic bracket (3M™ Clarity™ Advanced, MBT 0.022-in. slot) was employed as the control group. Morphological properties, including slot surface structure and dimensions, were examined using scanning electron microscopy and surface profiler analysis. Manufacturing accuracy was assessed with root mean square calculations of trueness and precision. Mechanical properties were tested, encompassing static and kinetic frictional resistance (FR) and fracture strength. Optical stability was evaluated through 20,000 cycles of thermocycling and a 7-day immersion in various coloring agents. Within the limitations of this study, zirconia brackets containing 3 to 5 mol% YSZ presented enhanced reliability in terms of dimensional accuracy and demonstrated favorable optical stability. Notably, owing to its advantageous mechanical properties, the 3Y-YSZ variant showed remarkable potential as an advanced material for fabricating orthodontic brackets

Oxygen activation on the interface between Pt nanoparticles and mesoporous defective TiO2 during CO oxidation

© 2019 Author(s).Platinum-based heterogeneous catalysts are mostly used in various commercial chemical processes because of their high catalytic activity, influenced by the metal/oxide interaction. To design rational catalysts with high performance, it is crucial to understand the relationship between the metal-oxide interface and the reaction pathway. Here, we investigate the role of oxygen defect sites in the reaction mechanism for CO oxidation using Pt nanoparticles supported on mesoporous TiO2 catalysts with oxygen defects. We show an intrinsic correlation between the catalytic reactivity and the local properties of titania with oxygen defects (i.e., Ti3+ sites). In situ infrared spectroscopy observations of the Pt/mesoporous TiO2-x catalyst indicate that an oxygen molecule bond can be activated at the perimeter between the Pt and an oxygen vacancy in TiO2 by neighboring CO molecules on the Pt surface before CO oxidation begins. The proposed reaction pathways for O2 activation at the Pt/TiO2-x interface based on density functional theory confirm our experimental findings. We suggest that this provides valuable insight into the intrinsic origin of the metal/support interaction influenced by the presence of oxygen vacancies, which clarifies the pivotal role played by the support11sciescopu