Through the Looking Glass: Chiral Recognition of Substrates and Products at the Active Sites of Racemases and Epimerases

Unlike most enzymes, which exhibit stereospecific substrate binding, racemases and epimerases bind and catalyze the reversible interconversion of enantiomeric and epimeric pairs of substrates. Over the past 15 years, a growing number of racemase and epimerase structures have been solved, furnishing insights into the nature of chiral recognition of substrates by these enzymes. Those enzymes catalyzing stereoinversion of a carbon acid substrate through a direct 1,1-proton transfer mechanism all bind their substrates in a mirror-image packing orientation. This does not apply generally to racemases and epimerases that use other mechanisms, such as NADH-dependent epimerases that employ a “flipping” mechanism. In general, polar groups are bound and fixed at the three binding determinants on the protein defining a pseudo-mirror plane, while nonpolar groups may be mobile. The hydrogen atoms on each stereocenter are positioned antipodal with respect to the pseudo-mirror plane, making a two-base mechanism imperative. Recognition that mirror-image packing is the common binding mode for enantiomeric or epimeric substrates of these enzymes should inform modelling/docking studies and protein engineering.     

α-Helix-Mimetic Foldamers for Targeting HIV-1 TAR RNA

An oligopyridylamide-based foldamer approach has been employed to target HIV TAR RNA-TAT assembly as a model system to study RNA-protein interactions. The oligopyridylamide scaffold adopts a constrained conformation which presents surface functionalities at distinct spatial locations and mimic the chemical features of the secondary structure of proteins. We have designed a library of oligopyridylamides containing diverse surface functionalities which mimic the side chain residues of the TAT protein domain. The interaction of TAR RNA and TAT plays a pivotal role in facilitating HIV replication. The library was screened using various fluorescent based assays to identify antagonists of the TAR RNA-TAT complex. A tricationic oligopyridylamide ADH-19, possessed the highest affinity towards TAR and efficiently inhibited the TAR RNA-TAT interaction with apparent K_d of 4.1±1.0 μm . Spectroscopic studies demonstrated that ADH-19 interacts with the bulge and the lower bulge regions of TAR RNA, the domains important for TAT interaction. ADH-19 demonstrated appreciable in vivo efficacy (IC₅₀=25±1 μm ) by rescuing TZM-bl cells infected with the pseudovirus HIV-1HXB-2.     

芳香大分子和超分子螺旋管构筑及其功能

疏溶剂作用、氢键、静电作用、卤键和配位作用等非共价键作用力都可以用于控制芳香大分子和超分子的折叠和螺旋,由此形成的芳香聚合物螺旋管内径尺寸相对固定,内穴深度可调,作为主体分子可以识别或包结多种客体分子,通过络合能够产生手性诱导与传递和跨膜输送功能,也能够促进有机化学转化等。本文综述了由芳香砌块构筑的这类大分子和超分子螺旋管的构筑和功能。首先介绍了通过不同策略形成管状结构的背景,以及超分子和大分子方法的特点,着重介绍了由芳香酰胺、酰肼、三唑和乙炔重复链段的不同低聚物分子形成的分子管,并总结了形成超分子管的自组装策略,最后讨论了长高分子管的合成挑战以及这种结构独特的结构家族的新的潜在应用。     

An Adaptive Hydrogen-Bonded Organic Framework for the Exclusive Recognition of p-Xylene

Separation of xylene isomers is one of the most important but most challenging and energy-intensive separation processes in the petrochemical industry. Here, we report an adaptive hydrogen-bonded organic framework (HOF-29) constructed from a porphyrin based organic building block 4,4′,4′′,4′′′-(porphyrin-5,10,15,20-tetrayl) tetrabenzonitrile (PTTBN), exhibiting the exclusive molecular recognition of p-xylene (pX) over its isomers of o-xylene (oX) and m-xylene (mX), as clearly demonstrated in the single crystal structure transformation and ¹H NMR studies. Single crystal structure studies show that single-crystal-to-single-crystal transformation from the as-synthesized HOF-29 to the pX exclusively included HOF-29⊃pX is triggered by the encapsulation of pX molecules, accompanied by sliding of the 2D layers and local distortion of the ligand, which provides multiple C−H⋅⋅⋅π interactions.     

When Molecules Meet in Water-Recent Contributions of Supramolecular Chemistry to the Understanding of Molecular Recognition Processes in Water

Molecular recognition processes in water differ from those in organic solvents in that they are mediated to a much greater extent by solvent effects. The hydrophobic effect, for example, causes molecules that only weakly interact in organic solvents to stay together in water. Such water-mediated interactions can be very efficient as demonstrated by many of the synthetic receptors discussed in this review, some of which have substrate affinities matching or even surpassing those of natural binders. However, in spite of considerable success in designing such receptors, not all factors determining their binding properties in water are fully understood. Existing concepts still provide plausible explanations why the reorganization of water molecules often causes receptor-substrate interactions in water to be strongly exothermic rather than entropically favored as predicted by the classical view of the hydrophobic effect.     

基于改进的DenseNet-BC对少数民族服饰的识别

随着信息技术的发展，数字技术越来越多地应用于民族文化数字化保护，民族服饰的数字化及分类问题也日益受关注。相比一般服饰，少数民族服饰具有更多的细节特征信息，对其进行分类识别具有很大挑战。选用卷积神经网络DenseNet-BC作为基础网络结构，设计并使用了多尺度密集连接单元，用不同大小的卷积提取不同尺度的特征信息，以提高网络的学习能力；此外，为进一步提高网络的鲁棒性，提出一种局部和全局注意力机制方法进行分类识别。实验结果表明，改进的DenseNet-BC模型对少数民族服饰的识别准确率达95.18%，较ResNet-18、ResNet-34和DenseNet模型的识别准确率分别提升了3.84%、2.27%和1.18%。改进的DenseNet-BC模型具有更好的特征提取能力，能够提取更多的细节特征信息，一定程度上解决了普通模型提取特征尺度单一、特征丰富度低的问题。     

Investigation on the chiral recognition mechanism between verteporfin and cholate salts by capillary electrophoresis

In this article, capillary electrophoresis was applied to investigate the chiral recognition mechanism for the enantioseparation on a well‐known second‐generation photodynamic therapy drug of benzoporphyrin derivative monoacid ring A, that is, verteporfin. In our previous study, cholate salts have been studied as the chiral selectors, which can realize baseline separation of the four verteporfin isomers. Aiming to reveal the chiral recognition mechanism, the separation effect of several kinds of chiral selectors was discussed. According to the results and references, the chiral separation mechanism of this system was concluded: the analytes selectively combine with the chiral micelles, that is, dynamic H‐bonds interactions occur between the hydroxyl groups on the outer side of the cholate micelles and the ester/carboxy groups of the four isomers. In addition, the role of dimethyl formamide as an organic modifier was also researched, including reducing the effective mobility of the analytes and mobility of electroosmotic flow, and preventing them from adsorbing to the capillary wall and self‐aggregating of verteporfin, which are pretty beneficial for separation. The method used in this article provides a direct and reliable solution to study the mechanism of chiral separation.     

Bifunctional RNA-Targeting Deoxyribozyme Nanodevice as a Potential Theranostic Agent

Theranostic approaches rely on simultaneous diagnostic of a disease and its therapy. Here, we designed a DNA nanodevice, which can simultaneously report the presence of a specific RNA target through an increase in fluorescence and cleave it. High selectivity of RNA target recognition under near physiological conditions was achieved. The proposed approach can become a basis for the design of DNA nanomachines and robots for diagnostics and therapy of viral infections, cancer, and genetic disorders.     

Plasmon Coupling Enhanced Micro-Spectroscopy and Imaging for Sensitive Discrimination of Membrane Domains of a Single Cell

Different cell membrane domains play different roles in many cell processes, and the discrimination of these domains is of considerable importance for the elucidation of cellular functions. However, the strategies available for distinguishing these cell membrane domains are limited. A novel technique called plasmon coupling enhanced micro-spectroscopy and imaging to discriminate basal and lateral membrane domains of a single cell combines the application of an additional plasmonic silver film for surface plasmon (SP) excitation to selectively excite and enhance the basal membranes in the near-field with directional enhanced microscopic imaging and spectroscopy. The SP and critical evanescent fields are induced upon excitation through a silver-coated semitransparent coverslip at the surface plasmon resonance and critical angles, respectively. The basal and lateral membrane domains located within the SP and critical evanescent fields can be selectively excited and distinguished by adjusting the incident angle of laser irradiation. Moreover, the brighter images and more intense spectra of membrane-targeting fluorescence-Raman probes under directional excitation than in conventional EPI mode allow clear identification of the membrane domains.     

Molecular Interrogation to Crack the Case of O-GlcNAc

The O-linked β-N-acetylglucosamine (O-GlcNAc) modification, termed O-GlcNAcylation, is an essential and dynamic post-translational modification in cells. O-GlcNAc transferase (OGT) installs this modification on serine and threonine residues, whereas O-GlcNAcase (OGA) hydrolyzes it. O-GlcNAc modifications are found on thousands of intracellular proteins involved in diverse biological processes. Dysregulation of O-GlcNAcylation and O-GlcNAc cycling enzymes has been detected in many diseases, including cancer, diabetes, cardiovascular and neurodegenerative diseases. Here, recent advances in the development of molecular tools to investigate OGT and OGA functions and substrate recognition are discussed. New chemical approaches to study O-GlcNAc dynamics and its potential roles in the immune system are also highlighted. It is hoped that this minireview will encourage more research in these areas to advance the understanding of O-GlcNAc in biology and diseases.