Theoretical insight into the hydroxylamine oxidoreductase mechanism

The multiheme enzyme hydroxylamine oxidoreductase from the autotrophic bacteria Nitrosomonas europaea catalyzes the conversion of hydroxylamine to nitrite, with a complicate arrangement of heme groups in three subunits. As a distinctive feature, the protein has a covalent linkage between a tyrosyl residue of one subunit and a meso carbon atom of the heme active site of another. We studied the influence of this bond in the catalysis from a theoretical perspective through electronic structure calculations at the density functional theory level, starting from the crystal structure of the protein. Geometry optimizations of proposed reaction intermediates were used to calculate the dissociation energy of different nitrogen containing ligands, considering the presence and absence of the meso tyrosyl residue. The results indicate that the tyrosine residue enhances the binding of hydroxylamine, and increases the stability of a Fe^IIINO intermediate, while behaving indifferently in the Fe^IINO form. The calculations performed on model systems including neighboring aminoacids revealed the probable formation of a bidentate hydrogen bond between the Fe^IIIH₂O complex and Asp 257, in a high-spin aquo complex as the resting state. Characterization of non-planar heme distortions showed that the meso-substituent induces significant ruffling in the evaluated intermediates.     

Theoretical insight into the structural mechanism for the binding of vinblastine with tubulin

Vinblastine (VLB) is one of vinca alkaloids with high cytotoxicity toward cancer cells approved for clinical use. However, because of drug resistance, toxicity, and other side effects caused from the use of VLB, new vinca alkaloids with higher cytotoxicity toward cancer cells and other good qualities need to develop. One strategy is to further study and better understand the essence why VLB possesses the high cytotoxicity toward cancer cells. In present work, by using molecular simulation, molecular docking, density functional calculation, and the crystal structure of α,β-tubulin complex, we find two modes labeled in catharanthine moiety (CM) and vindoline moiety (VM) modes of VLB bound with the interface of α,β-tubulin to probe the essence why VLB has the high cytotoxicity toward cancer cells. In the CM mode, nine key residues B-Ser178, B-Asp179, B-Glu183, B-Tyr210, B-Asp226, C-Lys326, C-Asp327, C-Lys336, and C-Lys352 from the α,β-tubulin complex are determined as the active sites for the interaction of VLB with α,β-tubulin. Some of them such as B-Ser178, B-Glu183, B-Tyr210, B-Asp226, C-Lys326, C-Asp327, and C-Lys336 are newly identified as the active sites in present work. The affinity between VLB and the active pocket within the interface of α,β-tubulin is ?60.8 kJ mol^?1 in the CM mode. In the VM mode, that is a new mode established in present paper, nine similar key residues B-Lys176, B-Ser178, B-Asp179, B-Glu183, B-Tyr210, B-Asp226, C-Lys326, C-Asp327, and C-Lys336 from the α,β-tubulin complex are found as the active sites for the interaction with VLB. The difference is from one key residue C-Lys352 in the CM mode changed to the key residue B-Lys176 in the VM mode. The affinity between VLB and the active pocket within the interface of α,β-tubulin is ?96.3 kJ mol^?1 in the VM mode. Based on the results obtained in present work, and because VLB looks like two faces, composed of CM and VM both to have similar polar active groups, to interact with the active sites, we suggest double-faces sticking mechanism for the binding of VLB to the interface of α,β-tubulin. The double-faces sticking mechanism can be used to qualitatively explain high cytotoxicity toward cancer cells of vinca alkaloids including vinblastine, vincristine, vindestine, and vinorelbine approved for clinical use and vinflunine still in a phase III clinical trial. Furthermore, this mechanism will be applied to develop novel vinca alkaloids with much higher cytotoxicity toward cancer cells.     

Understanding the desensitizing mechanism of olefin in explosives: shear slide of mixed HMX-olefin systems

We simulated the shear slide behavior of typical mixed HMX-olefin systems and the effect of thickness of olefin layers (4–22 ?) on the behavior at a molecular level by considering two cases: bulk shear and interfacial shear. The results show that: (1) the addition of olefin into HMX can reduce greatly the shear sliding barriers relative to the pure HMX in the two cases, suggesting that the desensitizing mechanism of olefin is controlled dominantly by its good lubricating property; (2) the change of interaction energy in both systoles of shear slide is strongly dominated by van der Waals interaction; and (3) the thickness of olefin layers in the mixed explosives can influence its desensitizing efficiency. That is, the excessive thinness of olefin layers in the mixed explosive systems, for example, several angstroms, can lead to very high sliding barriers.     

Theoretical insights into the structures and mechanical properties of HMX/NQ cocrystal explosives and their complexes,and the influence of molecular ratios on their bonding energies

Molecular dynamics (MD) methods were employed to study the binding energies and mechanical properties of selected crystal planes of 1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane (HMX)/nitroguanidine (NQ) cocrystals at different molecular molar ratios. The densities and detonation velocities of the cocrystals at different molar ratios were estimated. The intermolecular interaction and bond dissociation energy (BDE) of the N–NO₂ bond in the HMX:NQ (1:1) complex were calculated using the B3LYP, MP2(full) and M06-2X methods with the 6-311++G(d,p) and 6-311++G(2df,2p) basis sets. The results indicated that the HMX/NQ cocrystal prefers cocrystalizing in a 1:1 molar ratio, and the cocrystallization is dominated by the (0 2 0) and (1 0 0) facets. The K, G, and E values of the ratio of 1:1 are smaller than those of the other ratios, and the 1:1 cocrystal has the best ductility. The N–NO₂ bond becomes stronger upon the formation of the intermolecular H-bonding interaction and the sensitivity of HMX decreases in the cocrystal. This sensitivity change in the HMX/NQ cocrystal originates not only from the formation of the intermolecular interaction but also from the increment of the BDE of N–NO₂ bond in comparison with isolated HMX. The HMX/NQ (1:1) cocrystal exhibits good detonation performance. Reduced density gradient (RDG) reveals the nature of cocrystallization. Analysis of the surface electrostatic potential further confirmed that the sensitivity decreases in complex (or cocrystal) in comparison with that in isolated HMX.

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Graphical Abstract Binding energies and mechanical properties of HMX/NQ cocrystals in different molecular molar ratios were studied using molecular dynamics methods. The origin of the sensitivity change in the HMX/NQ cocrystal originates from formation of intermolecular interactions and the bond dissociation energy increment of the N–NO₂ bond

     

Theoretical insights into the effects of molar ratios on stabilities,mechanical properties,and detonation performance of CL-20/HMX cocrystal explosives by molecular dynamics simulation

To research and estimate the effects of molar ratios on structures, stabilities, mechanical properties, and detonation properties of CL-20/HMX cocrystal explosive, the CL-20/HMX cocrystal explosive models with different molar ratios were established in Materials Studio (MS). The crystal parameters, structures, stabilities, mechanical properties, and some detonation parameters of different cocrystal explosives were obtained and compared. The molecular dynamics (MD) simulation results illustrate that the molar ratios of CL-20/HMX have a direct influence on the comprehensive performance of cocrystal explosive. The hardness and rigidity of the 1:1 cocrystal explosive was the poorest, while the plastic property and ductibility were the best, thus implying that the explosive has the best mechanical properties. Besides, it has the highest binding energy, so the stability and compatibility is the best. The cocrystal explosive has better detonation performance than HMX. In a word, the 1:1 cocrystal explosive is worth more attention and further research. This paper could offer some theoretical instructions and technological support, which could help in the design of the CL-20 cocrystal explosive.     

Theoretical insight into three disease-related benefits of migration

Migration (seasonal round-trip movement across relatively large distances) is common within the animal kingdom. This behaviour often incurs extreme costs in terms of time, energy, and/or survival. Climate, food, predation, and breeding are typically suggested as factors favouring the evolution of migration. Although disease regulation has also been considered, few studies consider it as the primary selective pressure for migration. Our aim was to determine, theoretically, under what conditions migration could reduce the long-term disease prevalence within a population, assuming the only benefits of migration are infection-related. We created two mathematical models, one where the population migrates annually and one where the entire population remains on the breeding ground year-round. In each we simulated disease transmission (frequency-dependent and density-dependent) and quantified eventual disease prevalence. In the migration model we varied the time spent migrating, disease-related migration mortality, and the overall migration mortality. When we compared results from the two models, we found that migration generally lowered disease prevalence. We found a population was healthier if it: (1) spent more time migrating (assuming no disease transmission during migration), (2) had higher disease-induced migration mortality, and (3) had an overall higher mortality when migrating (compared to not migrating). These results provide support for two previously proposed mechanisms by which migration can reduce disease prevalence (migratory escape and migratory cull), and also demonstrate that non-selective mortality during migration is a third mechanism. Our findings indicate that migration may be evolutionarily advantageous even if the only migratory benefit is disease control.     

Plant innate immunity: An updated insight into defense mechanism

Plants are invaded by an array of pathogens of which only a few succeed in causing disease. The attack by others is countered by a sophisticated immune system possessed by the plants. The plant immune system is broadly divided into two, viz. microbial-associated molecular-patterns-triggered immunity (MTI) and effector-triggered immunity (ETI). MTI confers basal resistance, while ETI confers durable resistance, often resulting in hypersensitive response. Plants also possess systemic acquired resistance (SAR), which provides long-term defense against a broad-spectrum of pathogens. Salicylic-acid-mediated systemic acquired immunity provokes the defense response throughout the plant system during pathogen infection at a particular site. Trans-generational immune priming allows the plant to heritably shield their progeny towards pathogens previously encountered. Plants circumvent the viral infection through RNA interference phenomena by utilizing small RNAs. This review summarizes the molecular mechanisms of plant immune system, and the latest breakthroughs reported in plant defense. We discuss the plant–pathogen interactions and integrated defense responses in the context of presenting an integral understanding in plant molecular immunity.     

Structure and evolution of neurexin genes: insight into the mechanism of alternative splicing

Neurexins are neuron-specific vertebrate proteins with hundreds of differentially spliced isoforms that may function in synapse organization. We now show that Drosophila melanogaster and Caenorhabditis elegans express a single gene encoding only an alpha-neurexin, whereas humans and mice express three genes, each of which encodes alpha- and beta-neurexins transcribed from separate promoters. The neurexin genes are very large (up to 1.62 Mb), with the neurexin-3 gene occupying almost 2% of human chromosome 14. Although invertebrate and vertebrate neurexins exhibit a high degree of evolutionary conservation, only vertebrate neurexins are subject to extensive alternative splicing that uses mechanisms ranging from strings of mini-exons to multiple alternative splice donor and acceptor sites. Consistent with their proposed role in synapse specification, neurexins thus have evolved from relatively simple genes in invertebrates to diversified genes in vertebrates with multiple promoters and extensive alternative splicing.     

Proteomics analysis reveals insight into the mechanism of H-Ras-mediated transformation

We implemented a proteomics approach to the systematical analysis of the alterations in the proteome of NIH3T3 cells transformed by oncogenic H-RasV12. Forty-four proteins associated with Ras-mediated transformation have been identified, and 28 proteins were not previously reported. RT-PCR analysis showed that approximately 44% of target proteins identified showed concomitant changes in mRNA abundance. A principal finding was the up-regulation of gankyrin, which was the first evidence to show that gankyrin pathway was implicated in Ras-activated transformation.     

Thermal properties of rhodopsin: insight into the molecular mechanism of dim-light vision

Rhodopsin has developed mechanisms to optimize its sensitivity to light by suppressing dark noise and enhancing quantum yield. We propose that an intramolecular hydrogen-bonding network formed by ～20 water molecules, the hydrophilic residues, and peptide backbones in the transmembrane region is essential to restrain thermal isomerization, the source of dark noise. We studied the thermal stability of rhodopsin at 55 °C with single point mutations (E181Q and S186A) that perturb the hydrogen-bonding network at the active site. We found that the rate of thermal isomerization increased by 1-2 orders of magnitude in the mutants. Our results illustrate the importance of the intact hydrogen-bonding network for dim-light detection, revealing the functional roles of water molecules in rhodopsin. We also show that thermal isomerization of 11-cis-retinal in solution can be catalyzed by wild-type opsin and that this catalytic property is not affected by the mutations. We characterize the catalytic effect and propose that it is due to steric interactions in the retinal-binding site and increases quantum yield by predetermining the trajectory of photoisomerization. Thus, our studies reveal a balancing act between dark noise and quantum yield, which have opposite effects on the thermal isomerization rate. The acquisition of the hydrogen-bonding network and the tuning of the steric interactions at the retinal-binding site are two important factors in the development of dim-light vision.     

New insight into the formation mechanism of imidazolium-based halide salts

By performing density functional theory calculations, the Menshutkin reaction between the N-methyl imidazole with chloroethane is reexamined to rationalize the experimental discovery. The calculated results show that the reaction proceeds via a S_N2 mechanism with a barrier of 119.1 kJ mol^-1 which is much lower than that reported in previous literature according to a five-membered transition state mechanism. Moreover, it is found that the barrier is further reduced to 98.1 kJ mol^-1 in toluene solution. The present result validates the experimental finding that the Menshutkin reaction for synthesizing N-alkyl imidazolium halide salts proceed smoothly at lower heating temperature.     

A novel insight into the mechanism of mammalian selenoprotein synthesis

The amino acid selenocysteine is encoded by UGA, usually a stop codon, thus requiring a specialized machinery to enable its incorporation into selenoproteins. The machinery comprises the tRNA^Sec, a 3′-UTR mRNA stem–loop termed SElenoCysteine Insertion Sequence (SECIS), which is mandatory for recoding UGA as a Sec codon, the SECIS Binding Protein 2 (SBP2), and other proteins. Little is known about the molecular mechanism and, in particular, when, where, and how the SECIS and SBP2 contact the ribosome. Previous work by others used the isolated SECIS RNA to address this question. Here, we developed a novel approach using instead engineered minimal selenoprotein mRNAs containing SECIS elements derivatized with photoreactive groups. By cross-linking experiments in rabbit reticulocyte lysate, new information could be gained about the SBP2 and SECIS contacts with components of the translation machinery at various translation steps. In particular, we found that SBP2 was bound only to the SECIS in 48S pre-initiation and 80S pretranslocation complexes. In the complex where the Sec-tRNA^Sec was accommodated to the A site but transpeptidation was blocked, SBP2 bound the ribosome and possibly the SECIS element as well, and the SECIS had flexible contacts with the 60S ribosomal subunit involving several ribosomal proteins. Altogether, our findings led to broadening our understanding about the unique mechanism of selenocysteine incorporation in mammals.     

The reaction of artemisinin with hemin: a further insight into the mechanism

The mechanism of action of trioxane antimalarial drugs is still largely controversial and warrants further investigation. We report here on the direct reaction of artemisinin with hemin, carried out in DMSO, in the absence of reducing agents. The reaction was analysed, independently, by visible spectroscopy, HPLC-ESI/MS and ¹H NMR. Two isomeric artemisinin-hemin long-lived adducts are unambiguously detected. Eventual degradation of the porphyrin ring and loss of the Soret band are observed as well. Implications of the present results for the mechanism of action of artemisinin-based antimalarials are discussed.     

A new insight into mercurized hemoglobin aggregation mechanism

Coagulation of bovine oxyhemoglobin in the presence of mercuric acetate in concentrations within a range including concentrations exceeding those required to block the single pair of thiol groups of the protein has been investigated in Tris-acetate buffer. The values of initial coagulation rate plotted against mercury-to-hemoglobin molar ratio give curves exhibiting a clear break points at ratios corresponding to full blocking of the mentioned thiol groups. Larger amounts of mercury reagents producing enhanced protein coagulation effect depend approximately quadratically on the mercury concentration. Interaction of the excess mercuric ions with some mercury-binding sites located on or near the dimer-dimer contact surfaces of the protein producing stronger coagulation effect is suggested.     

New insight into the oncogenic mechanism of the retroviral oncoprotein Tax

Human T cell leukemia virus type 1 (HTLV-1), an etiological factor that causes adult T cell leukemia and lymphoma (ATL), infects over 20 million people worldwide. About 1 million of HTLV-1-infected patients develop ATL, a highly aggressive non-Hodgkin's lymphoma without an effective therapy. The pX region of the HTLV-1 viral genome encodes an oncogenic protein, Tax, which plays a central role in transforming CD4+ T lymphocytes by deregulating oncogenic signaling pathways and promoting cell cycle progression. Expression of Tax following viral entry is critical for promoting survival and proliferation of human T cells and is required for initiation of oncogenesis. Tax exhibits diverse functions in host cells, and this oncoprotein primarily targets IκB kinase complex in the cytoplasm, resulting in persistent activation of NF-κB and upregulation of its responsive gene expressions that are crucial for T cell survival and cell cycle progression. We here review recent advances for the pathological roles of Tax in modulating IκB kinase activity. We also discuss our recent observation that Tax connects the IκB kinase complex to autophagy pathways. Understanding Tax-mediated pathogenesis will provide insights into development of new therapeutics in controlling HTLV-1- associated diseases.     

Myosin I: A new insight into the mechanism and cellular significance of actin-based motility

From our work on brush border myosin I structure, activity, regulation, and function, we can begin to understand the significance of the diversification of myosin proteins. While myosin I and II proteins retain conserved elements of structure that may dictate their similar mechanisms of motility and actin-activated MgATPase activity, their unique structures may provide the basis for the distinct localization and regulation of the two myosin types. How does the tropomyosin-inhibited actin-binding site of myosin I differ from that of the tropomyosin-activated myosin II actin-binding site? What elements of the sites of interaction of the 110K-protein and calmodulin contribute to the conserved, light-chain dependent coupling of MgATPase activity to translocation and which confer the novel calcium regulation of dissociation in vitro? It seems that the evolutionary demand for diversification of cellular motility functions has been met, at least in the actin-based system, by the evolution of isoforms tailored in structure, activity, regulation, and localization to serve complementary needs.     

基于代谢组的厌氧氨氧化菌群对温度的响应机制

【背景】在环境工程领域中,大多数耐冷菌从活性污泥中分离得到。了解活性污泥菌群对低温的响应有助于耐冷菌的驯化培养。【目的】以厌氧氨氧化污泥菌群作为研究对象,研究温度对厌氧氨氧化菌群代谢通路与代谢产物的影响,以期初步阐释厌氧氨氧化菌群低温响应机理。【方法】在25°C与35°C条件下驯化培养厌氧氨氧化污泥,研究温度对反应器脱氮效能、菌群活性与生长以及群落结构的影响,通过代谢组学比较两个温度下厌氧氨氧化菌群代谢物丰度以及代谢通路活性。【结果】虽然低温导致厌氧氨氧化菌群CO_2固定、TCA循环与丙酮酸代谢的下调,进而导致氮去除活性以及增长速率显著下降,但菌群RNA合成水平、腐胺与信号分子合成上调,从而通过转录调控、调控膜脂组成与改变膜结构的方式,调控菌群代谢以适应低温环境。【结论】从分子机理的角度探究了厌氧氨氧化污泥菌群适应低温环境的生理机制,首次阐释了腐胺与信号分子在污泥菌群适应低温过程中的重要作用。     

Theoretical insights into the AIE mechanism of assembles

Fluorophores in aggregated state are commonly used in optoelectronic devices, and the molecular packing are complex and diverse, including crystal, amorphous aggregate in solution, thin film, ordered supramolecular assemblies, and highly ordered cell membrane. In addition, the luminous behavior of the aggregated state can be precisely regulated by external stimuli such as hydrostatic pressure. In this review, we summarize the representative progress on the application of multiscale modeling protocol to illustrate the underlying mechanism of fluorescent emission of organic dyes in different assembles. The aim is to obtain the molecular packing in different forms of assembles and then to understand their underlying mechanism of stimuli-responsive fluorescent behavior at the molecular level. This is essential for the rational design, synthesis, and efficient application of fluorescent dyes.     

Structural insight into the rotational switching mechanism of the bacterial flagellar motor

The bacterial flagellar motor can rotate either clockwise (CW) or counterclockwise (CCW). Three flagellar proteins, FliG, FliM, and FliN, are required for rapid switching between the CW and CCW directions. Switching is achieved by a conformational change in FliG induced by the binding of a chemotaxis signaling protein, phospho-CheY, to FliM and FliN. FliG consists of three domains, FliG(N), FliG(M), and FliG(C), and forms a ring on the cytoplasmic face of the MS ring of the flagellar basal body. Crystal structures have been reported for the FliG(MC) domains of Thermotoga maritima, which consist of the FliG(M) and FliG(C) domains and a helix E that connects these two domains, and full-length FliG of Aquifex aeolicus. However, the basis for the switching mechanism is based only on previously obtained genetic data and is hence rather indirect. We characterized a CW-biased mutant (fliG(ΔPAA)) of Salmonella enterica by direct observation of rotation of a single motor at high temporal and spatial resolution. We also determined the crystal structure of the FliG(MC) domains of an equivalent deletion mutant variant of T. maritima (fliG(ΔPEV)). The FliG(ΔPAA) motor produced torque at wild-type levels under a wide range of external load conditions. The wild-type motors rotated exclusively in the CCW direction under our experimental conditions, whereas the mutant motors rotated only in the CW direction. This result suggests that wild-type FliG is more stable in the CCW state than in the CW state, whereas FliG(ΔPAA) is more stable in the CW state than in the CCW state. The structure of the TM-FliG(MC)(ΔPEV) revealed that extremely CW-biased rotation was caused by a conformational change in helix E. Although the arrangement of FliG(C) relative to FliG(M) in a single molecule was different among the three crystals, a conserved FliG(M)-FliG(C) unit was observed in all three of them. We suggest that the conserved FliG(M)-FliG(C) unit is the basic functional element in the rotor ring and that the PAA deletion induces a conformational change in a hinge-loop between FliG(M) and helix E to achieve the CW state of the FliG ring. We also propose a novel model for the arrangement of FliG subunits within the motor. The model is in agreement with the previous mutational and cross-linking experiments and explains the cooperative switching mechanism of the flagellar motor.