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Survey on Interactive Theorem Proving Based Concurrent Program Verification

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Ruan Jian Xue Bao/Journal of Software 2024年第9期35卷

作者： Wang, Zhong-Ye Wu, shu-shu cao, Qin-Xiang School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China

Concurrent programs and systems are usually highly efficient and respond faster than serial systems, making them widely used in practice. However, concurrent programs and systems are often prone to error, which could bring fatal consequences in real world applications. Moreover, the non-determinism brought by concurrency is a major difficulty in the verification of concurrent programs. With formal verification, people could use interactive theorem provers to rigorously prove the correctness of a concurrent program. This study presents several correctness criteria for concurrent programs, which can be verified by interactive theorem proof techniques. The criteria include Hoare triple, linearizability, contextual refinement, and logical atomicity. Researchers usually use program logic to verify programs in an interactive theorem prover. This study summarizes the usage of concurrent separation logic, rely-guarantee-based logic, and relational Hoare logic in concurrent program verifications. It also surveys existing foundational verification tools and verification results by these techniques. © 2024 Chinese Academy of Sciences. All rights reserved.

关键词： Formal verification

Effect of Calcium Cation on Thermophilic Acylamino Acid-releasing Enzyme Ape1547 from Aeropyrum pernix K1

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Chemical Research in Chinese Universities 2009年第4期25卷 513-517页

作者： ZHOU Jun XIE gui-qiu cao shu-gui GAO Ren-jun Key Laboratory for Molecular Enzymology and Engineering Ministry of Education School of Pharmaceutical Sciences Jilin University Changchun 130021 P. R. China

The gene of enzyme（Ape1547） was cloned from hyperthermophilic archaeon Aeropyrum pernix K1 and expressed in Escherichia *** effect of calcium cation on the properties of Ape1547 was ***1547 exhibits both peptidase activity and esterase *** fluorescence spectrum shows that calcium cation quenches the fluorescence of the enzyme through static quenching mechanism,indicating that calcium cation was bound to the *** on the study of calcium cation on CD ellipticity of Ape1547 by circular dichroism,we concluded that the change of enzyme structure induced by calcium cation may be responsible for the change of enzyme *** cation has dual effects on Ape1547：it could activate the enzyme activity when its concentration was 0.1 mol/L,and the enzyme had the highest activity;however,when its concentration was higher than 0.2 mol/L,the enzyme activity was *** results indicate that the activity center of peptidase activity might involve more amino acid residues than that of esterase activity.

关键词： Acylamino acid-releasing enzyme Aeropyrum pernix K1 Conformational change Calcium cation

Expression and Characterization of a Thermostable Acyl-peptide Releasing Enzyme ST0779 from Sulfolobus tokodaii

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Chemical Research in Chinese Universities 2012年第5期28卷 851-855页

作者： LI Rong ZHANG Fei cao shu-gui XIE gui-qiu GAO Ren-jun Key Laboratory for Molecular Enzymology and Engineering Ministry of EducationCollege of Life ScienceJilin UniversityChangehun 130012P.R.China College of Pharmacy Jilin UniversityChangchun 130021P.R.China

Acyl-peptide releasing enzyme（AARE） belongs to a serine peptidase family and catalyzes the NH2-terminal hydrolysis of Nα-acylpeptides to release Nα-acylated amino acids. ORF0779（ORF=open reading frame） from thermophilic archaea Sulfolobus tokodaii（ST0779） was cloned and expressed in E. coli BL21 and the expressed protein was identified as a thermostable AARE. The target protein could be optimally overexpressed in E. coli at 30 °C for 8 h with 0.1 mmol/L isopropyl β-dthiogalactoside（IPTG）. The crude enzyme was heated at 70 °C for 30 min, and then the target protein could account for above 40% of the total protein. The purification fold was 27 and the enzyme showed both esterase activity and peptidase activity. The optimal temperature and pH for ST0779 were 70 °C and 8.0 when Ac-Ala3 was used as substrate. The half-life of the enzyme（0.2 mg/mL） at 90 °C was about 16 h, indicating that the enzyme exhibits a favorable thermostability. The activity of ST0779 could still remain over 85% after being treated at 25 °C in different buffers with pH range from 6.0 to10.0 for 24 h, which indicates ST0779 is stable in neutral or slight alkali environment. Under neutral or slightly alkali conditions, the enzyme exhibits really high catalytic efficiency against acyl-peptide, and the optimal substrate is Ac-Ala3. Most metal ions have no inhibition effect on the activity of ST0779, while 4% activity of ST0779 is inhibited in the presence of K＋. This enzyme was supposed to be applied in the analysis of protein sequencing and the synthesis of small peptides.

关键词： Sulfolobus tokodaii Thermostablity Acyl-peptide releasing enzyme Characterization

High-throughput Screening of the Enantioselectivity of Hyperthermophilic Mutant Esterases from Archaeon Aeropyrum pernix K1 for Resolution of (R,S)-2-Octanol Acetate

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Chemical Research in Chinese Universities 2007年第3期23卷 319-324页

作者： ZHANG gui-rong GAO Ren-jun ZHANG Ai-jun RAO Lang cao shu-gui Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education Jilin University Changchun 130021 P. R. China

To identify the desired hypertherrnophilic variants within a mutant esterase library for the resolution of （R, S）-2- octanol acetate, a simple, reliable, and versatile method was developed in this study. We built a screening strategy including two steps, first we selected agar plate with substrate to screen the enzymatic activity; secondly we used a pH indicator to screen the enantioselectivity. This method could rapidly detect favorable mutants with high activity and enantioselectivity. A total of 96. 2% of tedious screening work can be precluded using this screening strategy. It is an effective screening for alkyl ester and can be applied to relative screening researches. The four improved mutants were screened from the mutant esterase library. Their enantioselectivities, activities, and structures were investigated at different temperatures.

关键词： High-throughput screening Enantioselectivity Hyperthermophilic esterase Directed evolution

Molecular Basis for Stereospecific Hydrolysis of Ethyl Mandelate by Thermophilic Esterase

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Chemical Research in Chinese Universities 2011年第5期27卷 841-844页

作者： ZHANG Guo-yan TAO Jin ZHENG Liang-yu cao shu-gui Key Laboratory for Molecular Enzymology and Engineering Ministry of Education College of Chemistry Jilin University Changchun 130012 P. R. China

The stereospecific hydrolysis of mandelate can be effectively catalyzed by hyperthermophilic acylpeptide esterase APE 1547（Aeropyrum pernix esterase 1547）. APE 1547 used in this reaction showed a remarkable stereodi-scrimination in favour of R-mandelic acid（99% e.e.） with an enantiomeric ratio E〉200. The results of computer simulation are consistent with the experimental results. It can be inferred that the R-substrate adopted a binding mode productive of the reaction due to the formation of the hydrogen bond at the active site of APE 1547.

关键词： Hyperthermophilic acylpeptide esterase Biocatalyst Stereospecific hydrolysis Mandelic acid Computer simulation

Efficacy and safety of Yangxue Qingnao Granules in treatment of migraine:A systematic review and meta-analysis

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World Journal of Clinical Cases 2024年第2期12卷 335-345页

作者： Bo Zhou gui-shu Wang Yu-Ning Yao Tong Hao Huan-Qin Li Ke-Gang cao Department of Neurology Xiyuan HospitalChina Academy of Chinese Medical SciencesBeijing 100091China Department of Infectious Disease Dongfang HospitalBeijing University of Chinese MedicineBeijing 100078China Institute for Brain Disorders Beijing University of Chinese MedicineBeijing 100700China Department of Acupuncture and Moxibustion Beijing Hospital of Traditional Chinese Medicine Affiliated to Capital Medical UniversityBeijing 100010China

BACKGROUND Yangxue Qingnao Granules(YXQN)is a Chinese patent medicine that has been commonly used in the clinical treatment of *** To assess the efficacy and safety of YXQN alone for the treatment of *** We searched 10 databases to identify relevant randomized controlled trials(RCTs)published before September *** review authors independently searched and screened the literature,extracted the data,and assessed the methodological quality of the studies using criteria from ROB 2.0,and analyzed the data using Review Manager 5.4 *** A total of 12 RCTs including 767 participants with migraine met the selection *** divided these studies into comparisons of YXQN with placebo,routine treatment drugs,and other Chinese patent *** meta-analysis showed the following:(1)Efficacy:The YXQN group outperformed the placebo group[relative risk(RR)=0.29,95%confidence interval(95%CI):0.15–0.43,P<0.00001],routine treatment group(RR=0.18,95%CI:0.09–0.27,P<0.0001),and Chinese patent medicine group(RR=0.27,95%CI:0.13–0.41,P<0.001);(2)frequency of headache:There was a significant difference between YXQN vs placebo[mean difference(MD)=-1.25,95%CI:-1.60 to-0.90,P<0.00001],routine treatment drugs(MD=-0.85,95%CI:-1.15 to-0.56,P<0.00001),and Chinese patent medicine(MD=-0.91,95%CI:-1.35 to-0.46,P<0.0001);(3)headache duration:We found great heterogeneity between studies,with no differences between YXQN and placebo(MD=-0.61,95%CI:-1.53 to-0.31,P=0.19)and routine treatment drugs(MD=-0.22,95%CI:-0.89 to 0.46,P<0.53).YXQN was more effective than other Chinese patent medicines in reducing headache duration(MD=-1.24,95%CI:-1.70 to-0.77,P<0.00001);and(4)headache severity:There was no significant difference between YXQN vs placebo(MD=-1.67,95%CI:-3.52 to 0.19,P=0.08),routine treatment drugs(MD=-0.53,95%CI:-2.02 to 0.96,P=0.68),and other Chinese patent medicines(MD=-0.49,95%CI:-2.83 to 1.85,P=0.68).Mild gastrointestinal adverse reactions were reported

关键词： Meta-analysis Migraine Yangxue Qingnao Granules Traditional Chinese patent medicine

Analysis of a Critical Residue Determining Herbicide Efficiency Sensitivity in Carboxyltransferase Domain of Acetyl-CoA Carboxylase from Poaceae by Homology Modeling and Free Energy Simulation

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Chemical Research in Chinese Universities 2010年第5期26卷 816-821页

作者： TAO Jin ZHAO Bo TIAN Xue-mei ZHENG Liang-yu cao shu-gui Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education Jilin University Changchun 130021 P. R. China

Carboxyltransferase domain（CT） of acetyl-coenzyme A carboxylase（ACCase, EC 6.***.1.2） from a family of Poaceae is an important target of commercial herbicide APPs for controlling grass weed growth. As the abuse of APPs herbicides, the resistant ACCase due to the mutation of a single residue（Ile→Leu）, which is located in CT active site, is emergent in many populations and species of Poaceae. So it is urgent to understand the resistant mechanism so as to design new effect herbicides. Herein lies the complex of CT dimmer from Lolium rigidum and herbicide haloxyfop successfully constructed for wild type enzyme and Ile/Leu mutant, respectively, providing a basis for explaining the resistance from microscopic structure. Moreover, the binding free energy difference between wild type and mutant enzymes was predicted in good agreement with the known observation, and the various contributions to it were analyzed, by Molecular mechanics-Poisson-Boltzmann surface area（MM-PBSA） method. The results indicate the van der Waals interaction difference between the protein and inhibitor, -22.94 kJ/mol of CT wild type lower than that of mutant, is the major reason for resistance. Structure analysis further suggests that van der Waals interaction difference is originated from the steric hindrance between the side chain of mutated residue Leu and the chiral methyl group of haloxyfop. All these findings enhance the understanding of resistant mechanism of ACCase to herbicide by Ile/Leu mutation and provide an important clue for the rational design of high effective herbicides.

关键词： Molecular modeling Molecular dynamics Free energy calculation Herbicide resistance

Cloning, Expression and Purification of Wheat Acetyl-CoA Carboxylases CT Domain in E. coil

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Chemical Research in Chinese Universities 2008年第6期24卷 752-755页

作者： WANG Rui-jian YANG Xue-ying ZHENG Liang-yu YANG Ye GAO gui cao shu-gui Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education Jilin University Changchun 130021 P. R. China College of Forestry Beihua University Jilin 132013 P. R. China

The entire gene of carboxyltransferase（CT） domain of acetyl-CoA carboxylase（ACCase） from Chinese Spring wheat（CSW） plastid was cloned firstly, and the 2.3 kb gene was inserted into PET28a^＋ vector and expressed in E. coil in a soluble state. The （His）6 fusion protein was identified by SDS-PAGE and Western blot. The recombinant protein was purified by affinity chromatography, and the calculated molecular mass（Mr） was 88000. The results of the sequence analysis indicate that the cloned gene（GeneBank accession No. EU124675） was a supplement and revision of the reported ACCase CT partial cDNA from Chinese Spring wheat plastid. The recombinant protein will be significant for us to investigate the recognizing mechanism between ACCase and herbicides, and further to screen new herbicides.

关键词： Chinese Spring wheat Acetyl-CoA carboxylase Carboxyltransferase(CT) domain Cloning Expression Purification

Synthesis of (S)-N-(2-Ethyl-6-methylphenyl) alanine by Enzyme-catalyzed Resolution and Chemical Racemization

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Chemical Research in Chinese Universities 2009年第6期25卷 836-840页

作者： ZHENG Liang-yu ZHANG Suo-qin LU Xiao-li cao shu-gui Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education College of Chemistry Stomatological Hospital Jilin University Changchun 130021 P. R. China

A practical synthesis of （S）-N-（2-ethyl-6-methylphenyl）alanine, a key intermediate for （S）-metolachlor, was completed by means of lipase-catalyzed hydrolytic kinetic resolution and chemical racemization of the remaining ester. The effects of operating temperature and enzyme concentration on the activity and enantioselectivity of enzyme were initially studied, and it was found that the enantioselectivity of CAL-B towards the resolution was not high enough to obtain enantiomerically pure compound（E=12.1）. When diethyl ether（15%, volume fraction） was added in the reaction medium, the lipase gave an excellent enantioselectivity（E=117.8）, which is about 9.7-fold that in pure buffered aqueous solution. For overcoming the limitation of a maximum theoretical yield of 50%, the acid product was separated from the remaining ester by a simple extraction procedure and the remaining ester was racemized with aldehyde and acetic acid under microwave irradiation or conventional heating condition, The results show the microwave irradiation was more effective than the conventional heating method and gave the desired （R,S）-N-（2- ethyl-6-methylphenyl）alanine methyl ester a high yield（92%） with R/S=50/50 in 1 h.

关键词： Candida antarctica lipase B Resolution (S)-N-(2-Ethyl-6-methylphenyl)alanine Racemization