Structural analysis of inhibition of E. coli methionine aminopeptidase: implication of loop adaptability in selective inhibition of bacterial enzymes

<p>Abstract</p> <p>Background</p> <p>Methionine aminopeptidase is a potential target of future antibacterial and anticancer drugs. Structural analysis of complexes of the enzyme with its inhibitors provides valuable information for structure-based drug design efforts.</p> <p>Results</p> <p>Five new X-ray structures of such enzyme-inhibitor complexes were obtained. Analysis of these and other three similar structures reveals the adaptability of a surface-exposed loop bearing Y62, H63, G64 and Y65 (the YHGY loop) that is an integral part of the substrate and inhibitor binding pocket. This adaptability is important for accommodating inhibitors with variations in size. When compared with the human isozymes, this loop either becomes buried in the human type I enzyme due to an N-terminal extension that covers its position or is replaced by a unique insert in the human type II enzyme.</p> <p>Conclusion</p> <p>The adaptability of the YHGY loop in <it>E. coli </it>methionine aminopeptidase, and likely in other bacterial methionine aminopeptidases, enables the enzyme active pocket to accommodate inhibitors of differing size. The differences in this adaptable loop between the bacterial and human methionine aminopeptidases is a structural feature that can be exploited to design inhibitors of bacterial methionine aminopeptidases as therapeutic agents with minimal inhibition of the corresponding human enzymes.</p

Structural analysis of inhibition of E. coli methionine aminopeptidase: implication of loop adaptability in selective inhibition of bacterial enzymes

Background: Methionine aminopeptidase is a potential target of future antibacterial and anticancer drugs. Structural analysis of complexes of the enzyme with its inhibitors provides valuable information for structure-based drug design efforts. Results: Five new X-ray structures of such enzyme-inhibitor complexes were obtained. Analysis of these and other three similar structures reveals the adaptability of a surface-exposed loop bearing Y62, H63, G64 and Y65 (the YHGY loop) that is an integral part of the substrate and inhibitor binding pocket. This adaptability is important for accommodating inhibitors with variations in size. When compared with the human isozymes, this loop either becomes buried in the human type I enzyme due to an N-terminal extension that covers its position or is replaced by a unique insert in the human type II enzyme. Conclusion: The adaptability of the YHGY loop in E. coli methionine aminopeptidase, and likely in other bacterial methionine aminopeptidases, enables the enzyme active pocket to accommodate inhibitors of differing size. The differences in this adaptable loop between the bacterial and human methionine aminopeptidases is a structural feature that can be exploited to design inhibitors of bacterial methionine aminopeptidases as therapeutic agents with minimal inhibition of the corresponding human enzymes

Generation of Oligodendrocyte Progenitor Cells From Mouse Bone Marrow Cells.

Oligodendrocyte progenitor cells (OPCs) are a subtype of glial cells responsible for myelin regeneration. Oligodendrocytes (OLGs) originate from OPCs and are the myelinating cells in the central nervous system (CNS). OLGs play an important role in the context of lesions in which myelin loss occurs. Even though many protocols for isolating OPCs have been published, their cellular yield remains a limit for clinical application. The protocol proposed here is novel and has practical value; in fact, OPCs can be generated from a source of autologous cells without gene manipulation. Our method represents a rapid, and high-efficiency differentiation protocol for generating mouse OLGs from bone marrow-derived cells using growth-factor defined media. With this protocol, it is possible to obtain mature OLGs in 7-8 weeks. Within 2-3 weeks from bone marrow (BM) isolation, after neurospheres formed, the cells differentiate into Nestin+ Sox2+ neural stem cells (NSCs), around 30 days. OPCs specific markers start to be expressed around day 38, followed by RIP+O4+ around day 42. CNPase+ mature OLGs are finally obtained around 7-8 weeks. Further, bone marrow-derived OPCs exhibited therapeutic effect in shiverer (Shi) mice, promoting myelin regeneration and reducing the tremor. Here, we propose a method by which OLGs can be generated starting from BM cells and have similar abilities to subventricular zone (SVZ)-derived cells. This protocol significantly decreases the timing and costs of the OLGs differentiation within 2 months of culture

Functional Disparity of Three Pheromone-Binding Proteins to Different Sex Pheromone Components in Hyphantria cunea (Drury)

Hyphantria cunea (Drury) is a destructive invasive pest species in China that uses type II sex pheromone components. To date, however, the binding mechanisms of its sex pheromone components to their respective pheromone-binding proteins (HcunPBPs 1/2/3) have not been explored. In the current study, all three HcunPBPs were expressed in the antennae of both sexes. The prokaryotic expression and ligand binding assays were employed to study the binding of the moth\u27s four sex pheromone components, including two aldehydes and two epoxides, and 24 plant volatiles to the HcunPBPs. Our results showed that the abilities of these HcunPBPs to bind to the aldehydes were significantly different from binding to the epoxides. These three HcunPBPs also selectively bind to some of the plant volatiles tested. Our molecular docking results indicated that some crucial hydrophobic residues might play a role in the binding of HcunPBPs to their sex pheromone components. Three HcunPBPs have different selectivities for pheromone components with both major and minor structural differences. Our study provides a fundamental insight into the olfactory mechanism of moths at the molecular level, especially for moth species that use various type II pheromone components

The Hidden Nematic Fluctuations in the Triclinic (Ca0.85La0.15)10(Pt3As8)(Fe2As2)5 Superconductor Revealed by Ultrafast Optical Spectroscopy

We reported the quasiparticle relaxation dynamics of an optimally doped triclinic iron-based superconductor (Ca$_{0.85}$La$_{0.15}$)$_{10}$(Pt$_3$As$_8$)(Fe$_2$As$_2$)$_5$ with bulk $T_c$ = 30 K using polarized ultrafast optical pump-probe spectroscopy. Our results reveal anisotropic transient reflectivity induced by nematic fluctuations develops below $T_{nem}$ $\approx$ 120 K and persists in the superconducting states. Measurements under high pump fluence reveal three distinct, coherent phonon modes at frequencies of 1.6, 3.5, and 4.7 THz, corresponding to $A_{1g}(1)$, $E_g$, and $A_{1g}(2)$ modes, respectively. The high-frequency $A_{1g}(2)$ mode corresponds to the $c$-axis polarized vibrations of FeAs planes with a nominal electron-phonon coupling constant $\lambda _{A_{1g}(2)}$ $\approx$ 0.139 $\pm$ 0.02. Our findings suggest that the superconductivity and nematic state are compatible but competitive at low temperatures, and the $A_{1g}$ phonons play an important role in the formation of Cooper pairs in (Ca$_{0.85}$La$_{0.15}$)$_{10}$(Pt$_3$As$_8$)(Fe$_2$As$_2$)$_5$.Comment: 6 pages, 3 figures and Supplemental Material

Frequent occurrence of unreduced gametes in Triticum turgidum-Aegilops tauschii hybrids.

Abstract Spontaneous chromosome doubling via union of unreduced (2n) gametes has been thought to be the way that common wheat (Triticum aestivum L.) was originated from the hybridization of T. turgidum L. with Ae. tauschii Cosson. Previous works have observed unreduced gametes in F 1 hybrids of Ae. tauschii with six of the eight T. turgidum subspecies. It is not clear, however, whether the formation of these unreduced gametes is a norm in the F 1 hybrids. In the present study, we tried to answer this question by assessing the occurrence frequency of unreduced gametes in 115 T. turgidum-Ae. tauschii hybrid combinations, involving 76 genotypes of seven T. turgdium subspecies and 24 Ae. tauschii accessions. Our data show that these hybrid combinations differed significantly (P B 0.01, F = 11.40) in selfed seedset, an indicator for production of unreduced gametes. This study clearly showed that meiotic restitution genes are widely distributed within T. turgidum. However, significant differences were found between as well as within T. turgidum subspecies and in the interaction of the T. turgidum genotypes with those of Ae. taushii. The possible application of the meiotic restitution genes from T. turgidum in production of double haploids is also discussed

Systems Chemical Genetics-Based Drug Discovery: Prioritizing Agents Targeting Multiple/Reliable Disease-Associated Genes as Drug Candidates

Genetic disease genes are considered a promising source of drug targets. Most diseases are caused by more than one pathogenic factor; thus, it is reasonable to consider that chemical agents targeting multiple disease genes are more likely to have desired activities. This is supported by a comprehensive analysis on the relationships between agent activity/druggability and target genetic characteristics. The therapeutic potential of agents increases steadily with increasing number of targeted disease genes, and can be further enhanced by strengthened genetic links between targets and diseases. By using the multi-label classification models for genetics-based drug activity prediction, we provide universal tools for prioritizing drug candidates. All of the documented data and the machine-learning prediction service are available at SCG-Drug (http://zhanglab.hzau.edu.cn/scgdrug)

A simulation study on the measurement of D0-D0bar mixing parameter y at BES-III

We established a method on measuring the \dzdzb mixing parameter $y$ for BESIII experiment at the BEPCII $e^+e^-$ collider. In this method, the doubly tagged $\psi(3770) \to D^0 \overline{D^0}$ events, with one $D$ decays to CP-eigenstates and the other $D$ decays semileptonically, are used to reconstruct the signals. Since this analysis requires good $e/\pi$ separation, a likelihood approach, which combines the $dE/dx$, time of flight and the electromagnetic shower detectors information, is used for particle identification. We estimate the sensitivity of the measurement of $y$ to be 0.007 based on a $20fb^{-1}$ fully simulated MC sample.Comment: 6 pages, 7 figure