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Penta-coordinated phosphorus structure analysis on kinases

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Science China Chemistry 2004年第5期47卷 420-427页

作者： LI Wu MA Yuan zhao yufen Key Lab of Bioorganic Phosphorus Chemistry and Chemical Biology of Ministry of Education Department of Chemistry School of Life Sciences Tsinghua University Beijing 100084 China Key Lab of Bioorganic Phosphorus Chemistry and Chemical Biology of Ministry of Education Department of Chemistry School of Life Sciences Tsinghua University Beijing 100084 China Key Lab of Bioorganic Phosphorus Chemistry and Chemical Biology of Ministry of Education Department of Chemistry School of Life Sciences Tsinghua University Beijing 100084 China

In this paper, based on the known crystal structures of Square Pyramid (SP) and Trigonal Bipyramid (TBP) penta-coordinated phosphorus compounds containing amino acid side chains, such as amino, carboxyl, hydroxyl or thiol, a software designed to survey the P(5)-Structure of phosphorylated proteins. By this software, it was found that 382 of 398 phos- phorus-related kinases (96%) from current PDB could go through the penta-coordinated phos- phorus transition state or intermediate. For example, in protein 1HE8, amino group in Lysine16 was within 3.58 ?from the phosphorus atom, and a potential TBP structure consisting GNP2 and NZ could be overlapped with an authentic TBP with an RMSD value of 0.71 ?.

关键词： penta-coordinated phosphorus structures, kinases.

Prebiotic Chemistry in Aqueous Environment:A Review of Peptide Synthesis and Its Relationship with Genetic Code

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Chinese Journal of Chemistry 2021年第8期39卷 2264-2272页

作者： Jianxi Ying Ruiwen Ding Yan Liu yufen zhao Institute of Drug Discovery Technology Ningbo UniversityNo.818 Fenghua RoadNingboZhejiang 315211China Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences Ningbo UniversityNo.818 Fenghua RoadNingboZhejiang 315211China College of Chemistry and Chemical Engineering Xiamen UniversityNo.422Siming South RoadXiamenFujian 361005China

Prebiotic peptide synthesis and the origin of the genetic code are central issues concerning the origin of *** question of how they are possibly correlated on the primordial Earth remains perplexing,although numerous experiments have been carried out to explain the prebiotic chemistry of peptide synthesis and the genetic code *** purpose of this article is to review the chemical reactions occurred during the synthesis of peptides and the origin of the genetic code in the early Earth aqueous ***,we attempt to review their relationship as *** last,from our perspective,the chiral properties of biomolecules should be taken into account in the prebiotic chemical scenarios,which may contribute to some breakthroughs in the further research of this field.

关键词： Amino acids Peptides Molecular evolution Prebiotic chemistry Genetic code origin

Research progresses of artificial nucleic acid cleavage agents

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Chinese Science Bulletin 2000年第22期45卷 2017-2028页

作者： Rong Wan Gang zhao Jing Chen yufen zhao Tsinghua Univ Dept Chem State Key Lab Bioorgan Phosphorus Chem Educ Minist ChinaSch Life Sci & Engn Beijing 100084 Peoples R China

Artificial nucleic acid cleavage agents have attracted close attention because they play important roles in biochemistry and molecular biology. According to the cleavage mechanism of nucleic acid, they are divided into three types, namely free radical, phosphodiester bond hydrolysis and elimination cleavage agents. In this review, a series of cleavage agents, including the site- and sequence-specific ones, are illustrated, and some suggestions for the future researches in this field are also put forward.

关键词： nucleic acid cleavage agents site-and sequence-specific cleavage agents free radical phosphodiester bond hydrolysis elimination.

Exploring the binding mechanism of thioflavin-T to the β-amyloid peptide by blind docking method

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Science China Chemistry 2012年第1期55卷 112-117页

作者： zhao DeSheng CHEN YongXiang LIU Qian zhao yufen LI YanMei Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology(Ministry of Education) Department of ChemistryTsinghua UniversityBeijing 100084China

Using blind dock method,we find that thioflavin-T(ThT) can bind to both monomers and fibrils of the full-length β-amyloid peptide(Aβ1-42) and has a higher binding affinity to the *** is shown that the hydrophobic interaction between the ligand(ThT) and substrate(Aβ1-42) are stronger than hydrogen ***,ThT tends to be located near the C-terminus of Aβ monomer through hydrophobic and electrostatic interactions,while it tends to contact the residues Met35 and Gly27 of the fibril surface mainly through hydrophobic ***,according to the docking results and ThT fluorescence assay,a kinetic equation is proposed to deduce the aggregation rate coefficient of Aβ1-42.

关键词： ThT Aβ1-42 autodock aggregation kinetic equation

Studies on the DNA binding and cleavage activity of a synthesized polyamide containing dipeptide Ser-His

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Science China Chemistry 2007年第6期50卷 806-811页

作者： ZHANG Zhen NIU MingYu JU Yong zhao yufen Key Laboratory of Bioorganic Phosphorous Chemistry&Chemical Biology Ministry of Education Department of ChemistryTsinghua UniversityBeijing 100084China

The DNA binding and cleavage activity of a synthetic polyamide containing dipeptide Ser-His has been investigated by spectroscopic techniques,such as electronic absorbance and circular dichroism(CD)spectropolarimetry,as well as gel *** results show that the molecule has a strong interaction with DNA and can improve DNA-cleavage ability about 100 fold as compared with single dipeptide Ser-His.

关键词： polyamide DNA binding affinity spectroscopy DNA cleavage

Mechanism of intramolecular mixed anhydride formation as intermediates in the reactions of N-phosphorylamino-acids──An MNDO research

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Chinese Science Bulletin 1998年第11期43卷 917-921页

作者： ZHONG Rugang zhao yufen DAI Qianhuan Bioorganic Phosphorus Chemistry Laboratory Department of ChemistryTsinghua UniversityBeijing 100022China Center for Chemistry and Bioengineering of Cancer Research Beijing Poly technic UniversityBeijing 100022China.

N-phosphoryl-α-amino acids can react to form esters, peptides, phosphoryl ester-exchanged products and phosphoryl group migration products under mild conditions, which are very important in researches on arohebiont. It has been proposed that intramolecular mixed carboxylic-phosphoric anhydrides (IMCPAs) might be the common intermediates of the reactions, which are difficult to be experimentally observed because of their high activity. In this note, it has been revealed, by means of MNDO, that the IMCPAs are situated at the relatively minimal points of the potential surface and can form in a non-synchronous concerted reaction pathway that passes through a transition state with a hydrogen-bond-bridge structure. The results give a successful explanation to the structure and formation of IMCPAs and their ability to promote the various reactions mentioned above.

关键词： N-phosphorylamino-acid intramolecular mixed anhydride mechanism MNDO.

Investigation of Reaction Mechanism of Amino Acids and Phosphorus Trichloride by 31P NMR and ESI-MS/MS

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Chinese Journal of Chemistry 2011年第6期29卷 1173-1179页

作者： Guo, Yanchun Cao Shuxia Xie, Yali Zong, Xiangkun zhao, yufen Key Laboratory of Chemical Biology and Organic Chemistry Department of Chemistry Zhengzhou University Zhengzhou Henan 450052 China College of Chemistry and Chemical Engineering and The Key Laboratory for Chemical Biology of Fujian Province Xiamen University Xiamen Fujian 361005 China Key Laboratory for Bioorganic Phosphorus Chemistry of Ministry of Education Department of Chemistry School of Life Sciences and Engineering Tsinghua University Beijing 100084 China

The reaction of amino acids and phosphorus trichloride in THF was studied by 31P NMR tracing and ESI-MS/MS. A series of hydridophoranes and cyclic dipeptides were obtained. The reaction presented interesting diversity and the reaction mechanism was proposed. The mechanism suggests that phosphorus plays an important role in the synthesis of amino acid hydridophorane and cyclic dipeptides. The results also show that 31P NMR and ESI-MS/MS are useful tools for the investigation of reaction mechanism.

关键词： 31P NMR ESI-MS/MS mechanism amino acid phosphorus trichloride

Appraisal of an oligomerization behavior of unprotected carbohydrates induced by phosphorus reagent

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Science China Chemistry 2018年第2期61卷 243-250页

作者： Hang Yuan Xu Yang Peng Chen Yan Liu Guo Tang yufen zhao Department of Chemical Biology College of Chemistry and Chemical Engineering Key Laboratory for Chemical Biology of Fujian ProvinceXiamen University Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology Ministry of Education Department of Chemistry Tsinghua University

In this article, a novel oligomerization behavior of unprotected monosaccharides was discovered in a one-pot reaction induced by phosphorus reagent at room temperature. The inherent characteristics of the oligomerization reaction were dissected in detail by mass spectrometry based method combined with NMR technology. It was found that the main glycosidic bonding pattern is (1→6) linkage with 66% regioselectivity for each step. The ratio of α-(1→6) and β-(1→6) glycosidic bonds formed is around 1:1. The reactivity of 1-OH group from aldoses and the driving force from penta-coordinated phosphorus intermediates are the two critical factors for the oligomerization, according to the monitoring experiments by ESI-MS and NMR. Besides, the oligomerization reaction has good compatibility for various aldoses and could expand to O-glycosylated modification of peptides in vitro. The above results will provide a novel enlightenment to develop more convenient and higher-efficient methods for the synthesis of oligosaccharide library.

关键词： organic phosphorus activation oligosaccharide oligomerization one-pot unprotected synthesis

Theoretical investigation on the elusive biomimetic iron(Ⅲ)-iodosylarene chemistry: An unusual hydride transfer triggers the Ritter reaction

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Chinese Chemical Letters 2021年第12期32卷 3857-3861页

作者： Lanping Gao Xiaolu Chen Dongru Sun Hua zhao yufen zhao Wonwoo Nam Yong Wang Institute of Drug Discovery Technology Ningbo UniversityNingbo 315211China Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences Ningbo UniversityNingbo 3152UChina Department of Chemistry and Nano Science Ewha Womans UniversitySeoul 03760Korea

Introduction of iodosylarnes into biomimetic nonheme chemistry has made great achievement on identification of the subtle metal-oxygen reaction intermediates. However, after more than three decades of experimental and theoretical efforts the nature of the metal-iodosylarene adducts and the related dichotomous one-oxidant/multiple-oxident controversy have remained a matter of speculation. Herein, we report a theoretical study of the structure-activity relationship of the noted iron(Ⅲ)-iodsylarene complex,FeⅢ(Ph IO)(OTf)3(1), in oxygenation of cyclohexene. The calculated results revealed that 1 behaves like a chameleon by adapting its roles as a 2 e-oxidant or an oxygen donor, as a response to the regioselective attack of the C–H bond and the C=C bond. The oxidative C–H bond activation by 1 was found, for the first time, to proceed via a novel hydride transfer process to form a cyclohexene carbonium intermediate,such non-rebound step triggers the Ritter reaction to uptake an acetonitrile molecule to form the amide product, or proceeds with the rebound of the hydroxyl group return to the solvent cage to form the hydroxylated product. While in the C=C bond activation, 1 is a normal oxygen donor and shows two-state reactivity to present the epoxide product via a direct oxygen atom transfer mechanism. These mechanistic findings fit and explain the famous Valentine’s experiments and enrich the non-rebound scenario in bioinorganic chemistry.

关键词： Reaction mechanism DFT calculations Metal-iodosylbenzene Ritter reaction Olefin oxidation