Individually double minimum-distance definition of protein–RNA binding residues and application to structure-based prediction

Identifying protein–RNA binding residues is essential for understanding the mechanism of protein–RNA interactions. So far, rigid distance thresholds are commonly used to define protein–RNA binding residues. However, after investigating 182 non-redundant protein–RNA complexes, we find that it would be unsuitable for a certain amount of complexes since the distances between proteins and RNAs vary widely. In this work, a novel definition method was proposed based on a flexible distance cutoff. This method can fully consider the individual differences among complexes by setting a variable tolerance limit of protein–RNA interactions, i.e. the double minimum-distance by which different distance thresholds are achieved for different complexes. In order to validate our method, a comprehensive comparison between our flexible method and traditional rigid methods was implemented in terms of interface structure, amino acid composition, interface area and interaction force, etc. The results indicate that this method is more reasonable because it incorporates the specificity of different complexes by extracting the important residues lost by rigid distance methods and discarding some redundant residues. Finally, to further test our double minimum-distance definition strategy, we developed a classifier to predict those binding sites derived from our new method by using structural features and a random forest machine learning algorithm. The model achieved a satisfactory prediction performance and the accuracy on independent data sets reaches to 85.0%. To the best of our knowledge, it is the first prediction model to define positive and negative samples using a flexible cutoff. So the comparison analysis and modeling results have demonstrated that our method would be a very promising strategy for more precisely defining protein–RNA binding sites.     

Total synthesis of (+)-brefeldin A

(+)-Brefeldin A was synthesized through an efficient route, which features (1) construction of the five-membered ring from a Crimmins aldol via tandem Li-I exchange and carbanion-mediated cyclization with concurrent removal of the chiral auxiliary, (2) introduction of the lower side chain (C10 to C16) via a Rh-catalyzed Michael addition of a vinyl boronic acid, (3) stereoselective reduction of the C7 ketone with SmI2, and (4) a 2-methyl-6-nitrobenzoic anhydride-mediated (Shiina) lactonization.     

ent‐Kaurane Diterpenoids from Isodon phyllostachys

Phytochemical investigation of the medicinal plant Isodon phyllostachys led to the isolation of four new ent‐kaurane diterpenoids, phyllostacins F–I ( 1 – 4 , resp.), together with 11 known compounds, rosthorin A ( 5 ), rabdoternin C ( 6 ), enmenol ( 7 ), oridonin ( 8 ), lasiocarpanin ( 9 ), xerophilusin B ( 10 ), ponicidin ( 11 ), macrocalin B ( 12 ), phyllostachysin A ( 13 ), sculponeatin C ( 14 ), and macrocalyxoformin E ( 15 ). The structures of the new compounds were established by spectroscopic methods, including extensive 1D‐ and 2D‐NMR analyses. Compounds 1, 2, 7, 10 , and 13 were evaluated for their inhibitory activity against K562 and HepG2 cell lines.     

基于单模光纤的非对称熔锥型零耦合器结构的理论模型与实验研究

我们报道了一种新型非对称熔锥型零耦合器结构的理论模型,采用椭圆近似的方法得到了零耦合器渐变区和束腰区的横截面的变化函数,并在实验中得到了验证.     

变量核分数次积分在Hardy空间的有界性

§ 1　 Introduction and main resultsLet Sn- 1 be the unitsphere in Rn(n≥ 2 ) equipped with normalized Lebesgue measure dσ= dσ(z′) .We say that a functionΩ(x,z) defined on Rn× Rnbelongs to L∞ (Rn)× Lr(Sn- 1 )(r≥ 1 ) ,ifΩ(x,z) satisfies the following two conditions,(i) for any x,z∈Rnandλ>0 ,there hasΩ(x,λz) =Ω(x,z) ;(ii)‖Ω‖L∞(Rn)× Lr(Sn- 1) :=supx∈ Rn∫Sn- 1|Ω(x,z′) | rdσ(z′) 1 / r<∞ .For 0 <α相似文献   

A highly selective fluorescent chemosensor for Cu2+ based on a diarylethene with a 2,1,3‐benzoxadiazole unit

A novel photochromic diarylethene containing a 2,1,3‐benzoxadiazole structure has been synthesized and its multicontrollable fluorescence properties have been systematically studied by the stimulation of light and metal ions. The compound exhibited favorable photochromism and fluorescent switching properties. Furthermore, it can serve as a fluorescent chemosensor for highly selective recognition of Cu²⁺ in aqueous acetonitrile. When triggered by Cu²⁺, it displayed a remarkable blue shift from 594 to 524 nm (70 nm) with a significant fluorescence color change from yellow to bright green. As a result, a logic circuit has also been constructed on the basis of light and chemical stimulation.     

From submodule categories to preprojective algebras

Let \(S(n)\) be the category of invariant subspaces of nilpotent operators with nilpotency index at most \(n\) . Such submodule categories have been studied already in 1934 by Birkhoff, they have attracted a lot of attention in recent years, for example in connection with some weighted projective lines (Kussin, Lenzing, Meltzer). On the other hand, we consider the preprojective algebra \(\Pi _n\) of type \(\mathbb {A}_n\) ; the preprojective algebras were introduced by Gelfand and Ponomarev, they are now of great interest, for example they form an important tool to study quantum groups (Lusztig) or cluster algebras (Geiss, Leclerc, Schröer). We are going to discuss the connection between the submodule category \(\mathcal {S}(n)\) and the module category \(\hbox {mod}\;\Pi _{n-1}\) of the preprojective algebra \(\Pi _{n-1}\) . Dense functors \(\mathcal {S}(n) \rightarrow \hbox {mod}\;\Pi _{n-1}\) are known to exist: one has been constructed quite a long time ago by Auslander and Reiten, recently another one by Li and Zhang. We will show that these two functors are full, dense, objective functors with index \(2n\) , thus \(\hbox {mod}\;\Pi _{n-1}\) is obtained from \(\mathcal {S}(n)\) by factoring out an ideal which is generated by \(2n\) indecomposable objects. As a byproduct we also obtain new examples of ideals in triangulated categories, namely ideals \(\mathcal {I}\) in a triangulated category \(\mathcal {T}\) which are generated by an idempotent such that the factor category \(\mathcal {T}/\mathcal {I}\) is an abelian category.     

Elimination of dispersion effect in a white-light scanning interferometer by using a spectral analyzer

Optical Review - A general equation of the interference signal of white-light scanning interferometer (WSI) and its Fourier transform are derived. Based on these equations, a new method for...     

Highly selective fluorescent recognition of glutathione by using a water soluble binaphthyl aldehyde

A water soluble binaphthyl-based aldehyde was designed and synthesized. This compound in combination with Zn(OAc)₂ is found to exhibit greatly enhanced fluorescence in the presence of GSH in aqueous solution (pH = 7.5) but give little or no fluorescence enhancement in the presence of cysteine, homocysteine and other amino acids. This remarkable selectivity makes this probe potentially useful for the analysis of the biologically important GSH.     

Catalysis of Extracellular Deamination by a FAD-Linked Oxidoreductase after Prodrug Maturation in the Biosynthesis of Saframycin A

The biosynthesis of antibiotics in bacteria is usually believed to be an intracellular process, at the end of which the matured compounds are exported outside the cells. The biosynthesis of saframycin A (SFM-A), an antitumor antibiotic, requires a cryptic fatty acyl chain to guide the construction of a pentacyclic tetrahydroisoquinoline scaffold; however, the follow-up deacylation and deamination steps remain unknown. Herein we demonstrate that SfmE, a membrane-bound peptidase, hydrolyzes the fatty acyl chain to release the amino group; and SfmCy2, a secreted oxidoreductase covalently associated with FAD, subsequently performs an oxidative deamination extracellularly. These results not only fill in the missing steps of SFM-A biosynthesis, but also reveal that a FAD-binding oxidoreductase catalyzes an unexpected deamination reaction through an unconventional extracellular pathway in Streptmyces bacteria.