Search

We calculate the thermal and conformational states of the spike glycoprotein (S-protein) of SARS-CoV-2 at seven temperatures ranging from 3°C to 95°C by all-atom molecular dynamics (MD) µs-scale simulations with the objectives to understand the structural variations on the temperatures and to determine the potential phase transition while trying to correlate such findings of the S-protein with the observed properties of the SARS-CoV2. Our simulations revealed the following thermal properties of the S-protein: 1) It is structurally stable at 3°C, agreeing with observations that the virus stays active for more than two weeks in the cold supply chain; 2) Its structure varies more significantly at temperature values of 60°C–80°C; 3) The sharpest structural variations occur near 60°C, signaling a plausible critical temperature nearby; 4) The maximum deviation of the receptor-binding domain at 37°C, corroborating the anecdotal observations that the virus is most infective at 37°C; 5) The in silico data agree with reported experiments of the SARS-CoV-2 survival times from weeks to seconds by our clustering approach analysis. Our MD simulations at µs scales demonstrated the S-protein’s thermodynamics of the critical states at around 60°C, and the stable and denatured states for temperatures below and above this value, respectively.

We have computed the low energy minima for the two endomorphin peptides, N-acetyl-Tyr-Pro-Trp-Phe-NHCH3 (endomorphin 1) and Tyr-Pro-Phe-Phe-NHCH3 (endomorphin 2) in aqueous solution. These peptides block pain without inducing the harmful side effects of the opiates that bind to the same mu opiate receptor but have short half lives. From over 1000 starting conformations for each peptide, we find less than 200 low energy structures whose conformational energies were ≤ 5 kcal/mole of the energy of the global minimum. The most probable conformations calculated using the Boltzmann distribution for both peptides were similar to one another. Using the letter representation for backbone conformational states, these most probable structures were D A E E for endomorphin 1 and E A E E for endomorphin 2. Both of these structures form reverse turns at Pro 2-Trp (Phe) 3 resulting in the juxtaposition of the aromatic rings of Tyr 1 and Phe 4. The Trp residue of endomorphin 1 points to the back of the reverse turn. These features may be useful in the design of non-peptide analogues that will have longer half-lives than the peptides. [ABSTRACT FROM AUTHOR]

Background: Ion channels form a varied class of integral membrane proteins involved in the regulation of fundamental cellular processes. The structural and functional diversity of ion channels, as well as their participation in the vital systems of the body causes an increased interest in their study. The importance of research of channels' structures is underscored by the identification of numerous "channelopathies", caused by ion channel mutations. However, the complex molecular architecture of eukaryotic ion channels, which include large non-membrane domains, is often an obstacle to structural studies by experimental methods. Thus, only еру atomic X-ray structure of the pentameric ligand-dependent mammalian channel of the serotonin 5-HT3 receptor (pdb id 4PIR) and the Cryo-EM structure (pdb id 6BE1) are known at the present. Based on the available experimental data on this channel, the conformational state of this channel cannot be determined. In this regard, the aim of this study was to compare and analyze the structure of serotonin 5-HT3 receptor and its models, built by modeling homology. Methods: Structures with pdb id 2BG9, 4AQ9 for modeling 5-HT3 receptor closed and open conformations respectively were used as templates for modeling. We used the model of water TIP4P/2005 which suffciently well describes the liquid and crystal states. The cutoff radius for nonvalent interaction was 1.8 nm. The calculations ran as an NPT ensemble. To maintain constant temperature and pressure, we used the stochastic dynamics thermostat and Berendsen barostat. We placed the ion channels molecules at the nodes of a hexagonal lattice and rotated them about their axes through random angles. The simulations ran in the software package Gromacs 4.6.7. We specified the initial velocities of atoms using a random number generator with the Maxwell distribution. Results: The obtained models of open and closed channels of 5-HT3 receptor differ in the area of the internal threshold: the pore radius in this area is greater in open conformation models, compared with the closed conformation model and the structure of 5-HT3 receptor (4PIR). In the membrane part of the 5-HT3 receptor and the model of the closed conformation, the oxygen of the hydroxyl groups of threonine in the M2 helices form the area of the minimum radius of the pores. Conclusion: According to the molecular dynamics data obtained by us, hydrated sodium ions are unable to pass through this section of the channel 5-HT3 of the receptor. Thus, the data obtained suggest that the structure of the 5-HT3 receptor (pdb id 4PIR) is more consistent with the closed conformation. The work was carried out with the financial support of the Russian Foundation for basic research, agreement № 16-34-60252. The MD research has been carried out using the equipment of the shared research facilities of HPC computing resources at Lomonosov Moscow State University. This work structural analysis has been carried out using computing resources of the federal collective usage center Complex for Simulation and Data Processing for Mega-science Facilities at NRC “Kurchatov Institute”(ministry subvention under agreement RFMEFI62117X0016), http://ckp.nrcki.ru/.

Neuropeptide Y4 receptor has the most significant effect on body weight and fat mass in its physiological functions, and the activation of Y4 receptor has explicit role on losing weight. The Y4 receptor has been successfully applied in the development of anti‐obesity agent, thus representing a potential therapeutic target for obesity treatment. Here, we reported the first discovery of small molecule agonists targeting Y4 receptor: three Y4 receptor models with active and inactive conformations were built, each model was submitted following structure‐based virtual screening, and finally six hits were identified as Y4 receptor agonists. These results confirm the reliability of the constructed Y4 receptor models and the proposed computational strategy for investigating novel Y4 receptor agonists. These new small molecule Y4 receptor agonists will contribute to the further development of Y4 agonists as potential therapeutics and functional probes. [ABSTRACT FROM AUTHOR]

Chitosan–based biomaterials with a low molecular weight (LMW) have been drawn attention due to the promising applications in the pharmaceutical and food fields. For this reason, the aim of this work was to study the effect of two distinct depolymerization pathways on the chitosan physicochemical properties. Chitosan was submitted to depolymerization reaction to obtain chitosan with low molecular weight (LMW), using the oxidative pathway (H 2 O 2) and the acid pathway (HCl). The molecular weight reduction was investigated by kinetic study and chain scission mechanism. Chitosan characterization was performed according to its viscosimetric average molecular weight and deacetylation degree, respectively, through the viscosimetric method and proton nuclear magnetic resonance spectroscopy (1H NMR). The structural integrity was evaluated by Fourier transform infrared (FTIR) and energy dispersive spectroscopy (EDS). The crystalline and thermal properties were investigated, respectively, by X–ray diffraction (XRD) spectroscopy and thermogravimetric (TGA)/ differential thermal (DTA)/ differential scanning calorimetry (DSC) analysis. The water–chitosan interaction study was used to estimate the chitosan solubility. The results pointed out that both pathways resulted in chitosan with low molecular weight (<50 kDa). Moreover, the structural integrity of chitosan polymeric chains was preserved after depolymerization by oxidative pathway, while the acid pathway modified the polymer chain arrangement. Therefore, the chemical pathways resulted in two distinct low molecular weight chitosans, which allows different applications in food science. Unlabelled Image • Acidic and oxidative treatments reduced the molecular weight of chitosan (<50 kDa). • Both depolymerization reactions followed a mixed order reaction. • The depolymerization reactions reduced the crystalline domains. • The oxidative pathway induced minor structural changes. • The acid pathway induced structural alterations by formation of –NH3+Cl− salts. [ABSTRACT FROM AUTHOR]

The interaction between doxorubicin (Dox) and bovine serum albumin (BSA) complex with gold nanoparticles (AuNPs) was investigated by optical spectroscopy. The optical absorption of Dox and BSA solutions was studied. The formation of Dox–BSA complexes with a binding constant K = 7.56 × 106 M−2 and the number of binding sites n = 2 was found out. With pH 6.9, the concentration of complexes is an order of magnitude lower than the concentration of unbound antibiotic molecules. Optical absorption in solutions of Dox–BSA conjugates in the presence of AuNPs undergoes a significant rearrangement, which manifests the changes in the magnitude of the hydrophobic interaction of BSA with Dox, changes in the conformational state of antibiotic, and, as a consequence, a plasmon-induced change in the mechanism of complex formation. The aggregation of the Dox–AuNPs conjugate depends on the presence and concentration of BSA and in the case of formation of the Dox–BSA complex is minimal. [ABSTRACT FROM AUTHOR]

Cholinergic deficit is a characteristic factor of several pathologies, such as myasthenia gravis, some types of congenital myasthenic syndromes, and Alzheimer's Disease. Two molecular targets for its treatment are acetylcholinesterase (AChE) and nicotinic acetylcholine receptor (nAChR). In previous studies, we found that caffeine behaves as a partial nAChR agonist and confirmed that it inhibits AChE. Here, we present new bifunctional caffeine derivatives consisting of a theophylline ring connected to amino groups by different linkers. All of them were more potent AChE inhibitors than caffeine. Furthermore, although some of them also activated muscle nAChR as partial agonists, not all of them stabilized nAChR in its desensitized conformation. To understand the molecular mechanism underlying these results, we performed docking studies on AChE and nAChR. The nAChR agonist behavior of the compounds depends on their accessory group, whereas their ability to stabilize the receptor in a desensitized state depends on the interactions of the linker at the binding site. Our results show that the new compounds can inhibit AChE and activate nAChR with greater potency than caffeine and provide further information on the modulation mechanisms of pharmacological targets for the design of novel therapeutic interventions in cholinergic deficit.

In yeast, transcription of ribosomal DNA (rDNA) by RNA polymerase I (Pol I) is regulated by unique mechanisms acting at the level of the enzyme. Under stress situations such as starvation, Pol I hibernates through dimerization. When growth conditions are restored, dimer disassembly and Rrn3 binding drive enzyme activation and subsequent recruitment to rDNA. [ABSTRACT FROM AUTHOR]

The enzymatic decomposition of film materials based on chitosan with inclusions of cephalosporin antibiotics on a substrate impregnated with Ringer-Locke’s solution was studied. The introduction of antibiotics led to a decrease in the rate of the enzymatic decomposition of chitosan, as in the case of chitosan lysis in the presence of aminoglycoside antibiotics. A possible reason for the decrease in the rate of the enzymatic decomposition of chitosan is suppression of polyelectrolyte swelling in the presence of low-molecular electrolytes including medicinal agents. The introduction of drugs in the chitosan-based film is a potential method for selectively decreasing the rate of enzymatic hydrolysis of chitosan for increasing the service life of the film material on a wound surface. [ABSTRACT FROM AUTHOR]

Computing the absolute free energy of a macromolecule's structural state, F, is a challenging problem of high relevance. This study presents a method that computes F using only information from an unperturbed simulation of the macromolecule in the relevant conformational state, ensemble, and environment. Absolute free energies produced by this method, dubbed Valuation of Local Configuration Integral with Dynamics (VALOCIDY), enable comparison of alternative states. For example, comparing explicitly solvated and vaporous states of amino acid side-chain analogs produces solvation free energies in good agreement with experiments. Also, comparisons between alternative conformational states of model heptapeptides (including the unfolded state) produce free energy differences in agreement with data from μs molecular-dynamics simulations and experimental propensities. The potential of using VALOCIDY in computational protein design is explored via a small design problem of stabilizing a β-turn structure. When VALOCIDY-based estimation of folding free energy is used as the design metric, the resulting sequence folds into the desired structure within the atomistic force field used in design. The VALOCIDY-based approach also recognizes the distinct status of the native sequence regardless of minor details of the starting template structure, in stark contrast with a traditional fixed-backbone approach. © 2013 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Abstract: This study investigates whether Raman spectroscopy combined with multivariate analysis (MVA) enables a rapid and direct differentiation between two classes of conformational states, i.e., native-like and non-native proteins, in freeze-dried formulations. A data set comprising of 99 spectra, both from native-like and various types of non-native freeze-dried protein formulations, was obtained by freeze-drying lactate dehydrogenase (LDH) as model protein under various conditions. Changes in the secondary structure in the solid freeze-dried proteins were determined through visual interpretation of the blank corrected second derivative amide I band in the ATR-FTIR spectra (further called FTIR spectra) and served as an independent reference to assign class labels. Exploratory analysis and supervised classification, using Principal Components Analysis (PCA) and Partial Least Squares – Linear Discriminant Analysis (PLS–LDA), respectively, revealed that Raman spectroscopy is with 95% accuracy able to correctly discriminate between native-like and non-native states in the tested freeze-dried LDH formulations. Backbone (i.e., amide III) and side chain sensitive spectral regions proved important for making the discrimination between both classes. As discrimination was not influenced by the spectral signals from the tested excipients, there was no need for blank corrections. The Raman model may allow direct and automated analysis of the investigated quality attribute, opening possibilities for a real time and in-line quality indication as a future step. However, the sensitivity of the method should be further investigated and where possible improved. [Copyright &y& Elsevier]

Current cancer treatments still remain ineffective and cause side effects which ruinously affect healthy cells. Among new promising anticancer drugs, special attention is paid to the ribonucleases (RNases) which possess selective cytotoxicity against malignant cells. It is found that besides enzymatic activity conformational state of RNase molecules plays a role in the anticancer activity. Balnase, a new RNase from Bacillus altitudinis, is a close homolog of Bacillus pumilus RNase (binase) which selectively kills malignant cells expressing oncogenes KIT, ras, AML1/ETO, and FLT3. Earlier, homogeneous sample of balnase was obtained. Here, we have characterized structural organization of balnase. It was shown that it is a natural dimer. The enzyme has the same conformational state as binase but balnase dimers are less stable. [ABSTRACT FROM AUTHOR]

Abstract: The interaction of 18-methoxycoronaridine (18-MC) with nicotinic acetylcholine receptors (AChRs) was compared with that for ibogaine and phencyclidine (PCP). The results established that 18-MC: (a) is more potent than ibogaine and PCP inhibiting (±)-epibatidine-induced AChR Ca2+ influx. The potency of 18-MC is increased after longer pre-incubation periods, which is in agreement with the enhancement of [3H]cytisine binding to resting but activatable Torpedo AChRs, (b) binds to a single site in the Torpedo AChR with high affinity and inhibits [3H]TCP binding to desensitized AChRs in a steric fashion, suggesting the existence of overlapping sites. This is supported by our docking results indicating that 18-MC interacts with a domain located between the serine (position 6′) and valine (position 13′) rings, and (c) inhibits [3H]TCP, [3H]ibogaine, and [3H]18-MC binding to desensitized AChRs with higher affinity compared to resting AChRs. This can be partially attributed to a slower dissociation rate from the desensitized AChR compared to that from the resting AChR. The enthalpic contribution is more important than the entropic contribution when 18-MC binds to the desensitized AChR compared to that for the resting AChR, and vice versa. Ibogaine analogs inhibit the AChR by interacting with a luminal domain that is shared with PCP, and by inducing desensitization. [Copyright &y& Elsevier]

Electron transfer in the molecular complex donor-polymer-acceptor type was investigated. The carbon chain, which has two possible conformations (homogeneous and dimerized), was taken as polymer. The theoretical model, which described the electron transfer process in such type of the systems, was proposed. The probability of detection of the electron on the each subsequent unit, if originally was located on the first unit, was theoretically investigated. Two types of the electron transfer were revealed. [ABSTRACT FROM AUTHOR]

Abstract: The metal ions in insulin hexamer play a crucial role in the T to R conformational transitions. We have determined the crystal structures of 2Mn2+, 1Rb1+ and 4Ni2+ human arg-insulin and compared them with the 2Zn2+ structure. The first two structures exist in the T3R3f state like the native 2Zn2+ arg-insulin, while the 4Ni2+ adopts a T6 conformation. The metal coordination is found to be tetrahedral in all the structures except that of nickel where a dual octahedral and tetrahedral coordination is found at one site. Rubidium occupies only one of the high affinity metal binding sites. The metal induced structural changes observed, have been explained. [Copyright &y& Elsevier]