scholarly journals Impact of Deuteration and Temperature on Furan Ring Dynamics

Molecules ◽  
2021 ◽  
Vol 26 (10) ◽  
pp. 2889
Author(s):  
Przemyslaw Dopieralski ◽  
Iryna V. Omelchenko ◽  
Zdzislaw Latajka
Keyword(s):  
Conformational Changes ◽  
Furan Ring ◽  
Computational Studies ◽  
Significant Progress ◽  
Dynamic Simulations ◽  
Cyclic Molecules ◽  
Ring Dynamics ◽  
Different Temperatures ◽  
Long Time ◽  
Shape And Size

Despite significant progress in conformational analysis of cyclic molecules, the number of computational studies is still limited while most of that available in the literature data have been obtained long time ago with outdated methods. In present research, we have studied temperature driven conformational changes of the furan ring at three different temperatures. Additionally, the effect of deuteration on the ring dynamics is discussed; in addition, the aromaticity indices following the Bird and HOMA schemes are computed along all trajectories. Our ab initio molecular dynamic simulations revealed that deuteration has changed the furan ring dynamics and the obvious consequences; in addition, the shape and size of molecule are expected to be different.

Current Challenges and Limitations in the Studies of Intrinsically Disordered Proteins in Neurodegenerative Diseases by Computer Simulations

2020 ◽  
Vol 17 ◽  
Author(s):  
Ibrahim Yagiz Akbayrak ◽  
Sule Irem Caglayan ◽  
Zilan Ozcan ◽  
Vladimir N. Uversky ◽  
Orkid Coskuner-Weber
Keyword(s):  
Neurodegenerative Diseases ◽  
Computer Simulations ◽  
Conformational Changes ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Computational Studies ◽  
Accurate Data ◽  
Aggregation Propensity ◽  
Intrinsically Disordered ◽  
Future Developments

: Experiments face challenges in the analysis of intrinsically disordered proteins in solution due to fast conformational changes and enhanced aggregation propensity. Computational studies complement experiments, being widely used in the analyses of intrinsically disordered proteins, especially those positioned at the centers of neurodegenerative diseases. However, recent investigations – including our own – revealed that computer simulations face significant challenges and limitations themselves. In this review, we introduced and discussed some of the scientific challenges and limitations of computational studies conducted on intrinsically disordered proteins. We also outlined the importance of future developments in the areas of computational chemistry and computational physics that would be needed for generating more accurate data for intrinsically disordered proteins from computer simulations. Additional theoretical strategies that can be developed are discussed herein.

scholarly journals The Odd Faces of Oligomers: The Case of TRAF2-C, A Trimeric C-Terminal Domain of TNF Receptor-Associated Factor

2021 ◽  
Vol 22 (11) ◽  
pp. 5871
Author(s):  
Almerinda Di Venere ◽  
Eleonora Nicolai ◽  
Velia Minicozzi ◽  
Anna Maria Caccuri ◽  
Luisa Di Paola ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Strong Dependence ◽  
Conformational Dynamics ◽  
Receptor Interaction ◽  
Tnf Receptor ◽  
Oligomeric State ◽  
Dynamic Simulations ◽  
Associated Factor ◽  
Terminal Domain

TNF Receptor Associated Factor 2 (TRAF2) is a trimeric protein that belongs to the TNF receptor associated factor family (TRAFs). The TRAF2 oligomeric state is crucial for receptor binding and for its interaction with other proteins involved in the TNFR signaling. The monomer-trimer equilibrium of a C- terminal domain truncated form of TRAF2 (TRAF2-C), plays also a relevant role in binding the membrane, causing inward vesiculation. In this study, we have investigated the conformational dynamics of TRAF2-C through circular dichroism, fluorescence, and dynamic light scattering, performing temperature-dependent measurements. The data indicate that the protein retains its oligomeric state and most of its secondary structure, while displaying a significative increase in the heterogeneity of the tyrosines signal, increasing the temperature from ≈15 to ≈35 °C. The peculiar crowding of tyrosine residues (12 out of 18) at the three subunit interfaces and the strong dependence on the trimer concentration indicate that such conformational changes mainly involve the contact areas between each pair of monomers, affecting the oligomeric state. Molecular dynamic simulations in this temperature range suggest that the interfaces heterogeneity is an intrinsic property of the trimer that arises from the continuous, asymmetric approaching and distancing of its subunits. Such dynamics affect the results of molecular docking on the external protein surface using receptor peptides, indicating that the TRAF2-receptor interaction in the solution might not involve three subunits at the same time, as suggested by the static analysis obtainable from the crystal structure. These findings shed new light on the role that the TRAF2 oligomeric state might have in regulating the protein binding activity in vivo.

Mechanical and tribological properties of ice-bonded abrasive polishing tools

2017 ◽  
Vol 233 (1) ◽  
pp. 132-144 ◽  
Author(s):  
S Rambabu ◽  
N Ramesh Babu
Keyword(s):  
Wear Rate ◽  
Coefficient Of Friction ◽  
Tribological Properties ◽  
Melting Rate ◽  
Wear Behaviour ◽  
Mechanical And Tribological Properties ◽  
Different Temperatures ◽  
Long Time ◽  
Polishing Tool ◽  
Hardness Coefficient

This article covers the efforts on characterising ice-bonded abrasive polishing tool in terms of the mechanical and tribological properties such as hardness, coefficient of friction, and wear rate. These studies were attempted on the tools prepared at different temperatures ranging from −10 °C to 0 °C with a view to identify the condition suitable to prepare ice-bonded abrasive polishing tool for effective polishing of Ti–6Al–4V alloy specimen. It also presents the methods adopted to determine various properties of ice-bonded abrasive polishing tool. Hardness was estimated from the measured penetration depth of cone shape indenter into the tool, coefficient of friction was determined from the change in power drawn by the motor rotating the tool mould, and wear behaviour of tool was assessed from the melting rate of the tool determined from the change in height of ice-bonded abrasive polishing tool at different stages of polishing. From the results of this study, it is clear that ice-bonded abrasive polishing tool prepared at −4 °C has possessed sufficient hardness, coefficient of friction, and reasonable wear rate suitable for polishing of Ti–6Al–4V specimens. This article also covers the details of low-temperature coolant supply unit developed to prepare the ice-bonded abrasive polishing tool at any desired temperature between 0 °C and −40 °C and thus to maintain it for a long time. Polishing studies with such ice-bonded abrasive polishing tool showed 72% improvement in finish after 90 min of polishing of Ti–6Al–4V specimen with tool, prepared at −4 °C.

scholarly journals Antlers Characterization for Identification of Deer Species (Family Cervidae) in Indonesia

2019 ◽  
Vol 4 (3) ◽  
pp. 97
Author(s):  
Donan Satria Yudha ◽  
M Zulfiqar Meizar Pratama ◽  
Rury Eprilurahman
Keyword(s):  
Principal Component Analysis ◽  
Principal Component ◽  
Morphological Characters ◽  
Main Beam ◽  
Size Measurement ◽  
Economic Values ◽  
Deer Species ◽  
Unique Character ◽  
Long Time ◽  
Shape And Size

There are five species of deer (family Cervidae) living in Indonesia today. Male deer possesses antlers, a unique character of male deer. Antlers have economic values for quite a long time. Antler’s growth is influenced by several factors, therefore each species of deer have its own unique antlers’ shape and size. Antler’s identification usually relies on size measurement and overall shape of complete antlers which still attach to the skull. It is difficult to identify shed, broken or individual antler. The purpose of the research is to understand antlers’ morphological characters on each species to become diagnostic characters. Specimens analysed were collections of LIPI and were analysed with Principal Component Analysis (PCA) using PAST3 software. The results showed each species of deer having their own unique antlers’ character, and so it can be used to determine the species of Indonesian deer. The important structures for identification are relief, pedicle, brow, bez, and main beam.

scholarly journals Characterisation and molecular dynamic simulations of J15 asparaginase from Photobacterium sp. strain J15.

2014 ◽  
Vol 61 (4) ◽  
Author(s):  
Mohd Adilin Yaacob ◽  
Wan Atiqah Najiah Wan Hasan ◽  
Mohd Shukuri Mohamad Ali ◽  
Raja Noor Zaliha Raja Abdul Rahman ◽  
Abu Bakar Salleh ◽  
...  
Keyword(s):  
Molecular Dynamic ◽  
Conformational Changes ◽  
Specific Activity ◽  
3D Structure ◽  
Coli Strain ◽  
Exchange Chromatography ◽  
Molecular Dynamic Simulations ◽  
Type I ◽  
Enzymatic Reactions ◽  
Dynamic Simulations

Genome mining revealed a 1011 nucleotide-long fragment encoding a type I L-asparaginase (J15 asparaginase) from the halo-tolerant Photobacterium sp. strain J15. The gene was overexpressed in pET-32b (+) vector in E. coli strain Rosetta-gami B (DE3) pLysS and purified using two-step chromatographic methods: Ni(2+)-Sepharose affinity chromatography and Q-Sepharose anion exchange chromatography. The final specific activity and yield of the enzyme achieved from these steps were 20 U/mg and 49.2%, respectively. The functional dimeric form of J15-asparaginase was characterised with a molecular weight of ~70 kDa. The optimum temperature and pH were 25°C and pH 7.0, respectively. This protein was stable in the presence of 1 mM Ni(2+) and Mg(2+), but it was inhibited by Mn(2+), Fe(3+) and Zn(2+) at the same concentration. J15 asparaginase actively hydrolysed its native substrate, l-asparagine, but had low activity towards l-glutamine. The melting temperature of J15 asparaginase was ~51°C, which was determined using denatured protein analysis of CD spectra. The Km, Kcat, Kcat/Km of J15 asparaginase were 0.76 mM, 3.2 s(-1), and 4.21 s(-1) mM(-1), respectively. Conformational changes of the J15 asparaginase 3D structure at different temperatures (25°C, 45°C, and 65°C) were analysed using Molecular Dynamic simulations. From the analysis, residues Tyr₂₄ , His₂₂, Gly₂₃, Val₂₅ and Pro₂₆ may be directly involved in the 'open' and 'closed' lid-loop conformation, facilitating the conversion of substrates during enzymatic reactions. The properties of J15 asparaginase, which can work at physiological pH and has low glutaminase activity, suggest that this could be a good candidate for reducing toxic effects during cancer treatment.

scholarly journals Heat Exchanger for Bio-Digester under Thermophilic Range

2019 ◽  
Vol 5 ◽  
pp. 79-88
Author(s):  
Prajwal Sapkota ◽  
Laxman Poudel
Keyword(s):  
Heat Exchanger ◽  
Anaerobic Digestion ◽  
Heat Exchangers ◽  
Heating System ◽  
Gas Production ◽  
Cow Dung ◽  
Digestion Rate ◽  
Digestion Process ◽  
Different Temperatures ◽  
Long Time

Bio-gas has been one of the sources of renewable energy and has been used from long time. It is produced by the anaerobic digestion or decomposition of organic compounds and has different process. The digestion process is carried out by bacteria present in the waste and it is highly dependent on the bacteria which work differently on different temperatures. The rate of anaerobic digestion is highest at hemophilic temperature (55°C). Similarly, it is moderate at mesophilic temperature (35°C) and is lowest at psychrophilic (below 20°C). Thus, to attain the highest digestion rate a thermophilic heating system has beend eveloped. The heating system uses five heat exchangers to heat the influent at digester which is of 35m3 volume, to maintain temperature at 56°C. The volume of bio-gas production from this system which uses cow dung as digestingmaterial is about 28 m3 per day.

Characterizing the interaction modes of PAR4 receptor with agonist and antagonist by molecular simulation approach

2019 ◽  
Vol 18 (02) ◽  
pp. 1950008
Author(s):  
Nan Lu ◽  
Fancui Meng ◽  
Jing Yuan ◽  
Lei Liu ◽  
Yanshi Wang ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Molecular Design ◽  
Binding Free Energy ◽  
Structural Characteristics ◽  
Principal Component ◽  
Activation Mechanism ◽  
Binding Modes ◽  
Dynamic Simulations ◽  
Extracellular Region ◽  
Agonist And Antagonist

Protease-activated receptor 4 (PAR4) is a promising target for antiplatelet therapy. In this study, homology modeling and molecular docking methods were used to investigate the binding modes of PAR4 agonists and antagonists. The outcomes show that agonists have good docking scores, and they also form more hydrogen bonds with PAR4 than antagonists. To reveal the different conformational changes caused by agonist and antagonist, molecular dynamic simulations were carried out on three selected PAR4 systems. Simulation results show that PAR4 activation involves breaking interactions of 3–7 lock switch (Try157 and Tyr322) and ionic lock switch (Arg188 and Asp173), and formation of transmission switch among Tyr161, Asn300 and Phe296. In addition, principal component analysis (PCA) indicates that the major change for agonist bound system takes place in the intracellular region while that for antagonist bound system is in the extracellular region. The binding free energy of BMS-986120 is much lower than AYPGKF, suggesting high affinity of antagonist. Moreover, the electronegative aspartic residues Asp230 and Asp235 at ECL2 are important for PAR4 binding to agonist. Clarifying the PAR4 structural characteristics may be helpful to understand the activation mechanism, giving insights into the molecular design and discovery of novel potential PAR4 antagonists in the future.

scholarly journals 14C Dating of Fire-Damaged Mortars from Medieval Finland

Radiocarbon ◽  
2012 ◽  
Vol 54 (3-4) ◽  
pp. 915-931 ◽  
Author(s):  
Alf Lindroos ◽  
Lior Regev ◽  
Markku Oinonen ◽  
Åsa Ringbom ◽  
Jan Heinemeier
Keyword(s):  
14C Dating ◽  
Carbon And Oxygen Isotopes ◽  
Fire Event ◽  
Oxygen Isotope Ratios ◽  
Hydrolysis Process ◽  
Carbon And Oxygen Isotope ◽  
Different Temperatures ◽  
Long Time ◽  
Original Construction ◽  
Soluble Carbonate

This study focuses on radiocarbon dating of mortars that have withstood city fires and display visible fire damage effects. Some fire-damaged and undamaged original Medieval mortars from the same site have also been tested. The mortars were heated at different temperatures and then analyzed using the same preparation procedures as in 14C dating of mortars to see what kind of changes the heating would introduce to the mineralogy, chemistry, and the carbon and oxygen isotope ratios. We found that decarbonation during heating starts at ∼600 ° and recarbonation starts as soon as the temperature drops. Already after a few days, most of the lost CO2 has been replaced with atmospheric CO2. The renewed carbonates are readily soluble in the acid hydrolysis process and their carbon and oxygen isotopes have a light signature. Fire-damaged historical mortars display the same features. If a long time has elapsed between hardening of the original mortar and the fire, the new carbonates have 14C concentrations that point to the fire event rather than to the building event. In several cases, the fire-damaged mortars have an easily soluble carbonate fraction with a 14C age that could be related to a major fire event, but still most of the soluble carbonate yields a 14C age that seems like a reasonable age for the original construction.

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