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Recent developments in protein modeling and design

Progress in Natural Science:Materials International 1995年第1期 3-7页

作者：来鲁华徐筱杰唐有祺 Beijing 100871 China Department of Chemistry Peking University State Key Laboratory for Structural Chemistry of Unstable and Stable Species

1 protein modeling and molecular design The chemical reacitivity and biological activity of proteins are mainly determined by their three-dimensional structures. So a study on them is essential to protein *** X-ray crystallography is one of the most efficient methods for determining the protein structures, but it encounters difficulty in crystal growth. The recently developed multi-dimensional NMR can be directly used for determining protein structures in solu-tion, but it needs relatively large quantity of high-purity samples and requires the

关键词： protein modeling molecular design protein backbone structure phelctic tree rational drug design.

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Nuclear Targeting of Methyl-Recycling Enzymes in Arabidopsis thaliana Is Mediated by Specific protein Interactions

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Molecular Plant 2012年第1期5卷 231-248页

作者： Sanghyun Lee Andrew C. Doxey Brendan J. McConkey Barbara A. Moffatt Department of Biology University of Waterloo Waterloo ON N2L 3G1 Canada Department of Developmental Biology Stanford University Stanford CA 94305 USA

Numerous transmethylation reactions are required for normal plant growth and development. S-adenosylhomocysteine hydrolase （SAHH） and adenosine kinase （ADK） act coordinately to recycle the by-product of these reactions, S-adenosylhomocysteine （SAH） that would otherwise competitively inhibit methyltransferase （MT） activities. Here, we report on investigations to understand how the SAH produced in the nucleus is metabolized by SAHH and ADK. Localization analyses using green fluorescent fusion proteins demonstrated that both enzymes are capable of localizing to the cytoplasm and the nucleus, although no obvious nuclear localization signal was found in their sequences. Deletion analysis revealed that a 41-amino-acid segment of SAHH （GlylS^-Lys19~） is required for nuclear targeting of this enzyme. This segment is surface exposed, shows unique sequence conservation patterns in plant SAHHs, and possesses additional features of protein-protein interaction motifs. ADK and SAHH interact in Arabidopsb via this segment and also interact with an mRNA cap MT. We propose that the targeting of this complex is directed by the nuclear localization signal of the MT; other MTs may similarly target SAHH/ADK to other subcellular compartments to ensure uninterrupted transmethylation.

关键词： Transmethylation subcellular localization S-adenosylhomocysteine hydrolase adenosine kinase nuclear targeting protein docking protein modeling protein motif analysis.

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Local Conformational Constraint of Firefly Luciferase Can Affect the Energy of Bioluminescence and Enzyme Stability

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CCS Chemistry 2022年第5期4卷 1695-1707页

作者： Chao Zhang Xiaoguang Bai Shengxi Chen Larisa M.Dedkova Sidney M.Hecht Biodesign Center for Bioenergetics Arizona State UniversityTempeArizona 85287 School of Molecular Sciences Arizona State UniversityTempeArizona 85287

Conformational dynamics contribute importantly to enzyme catalysis,such that targeted conformational constraint may affect *** luciferases undergo extensive structural change during catalysis;key residues form a hydrophobic pocket,excluding water and enabling maximally energetic light *** mutants almost always luminesce at longer wavelengths(lower energy)than the wild *** constraint,using dipeptide analogue 3 at a position critical for optimized excited state structure,produced luciferase emission at a shorter wavelength by∼10 ***,introduction of conformationally constrained analogues 4,5,or 7 afforded luciferases emitting at longer wavelengths,while a related unconstrained luciferase(analogue 6)exhibited wild-type *** constrained luciferases tested were more stable than the wild *** modeling demonstrated that the“inside”or“outside”orientation of the conformationally constrained dipeptide led to the shorter or longer emission wavelength,*** broadly,these results suggest that local conformational constraint can control specific elements of enzyme behavior,both in vitro and in *** represents the first example of studying enzyme function by introducing conformationally constrained dipeptides at a specific protein *** principles discovered here in luciferase modification will enable studies to control the wavelength emission and photophysical properties of modified luciferases.

关键词： genetic code reprogramming modified ribosomes conformational constraint luciferase bioluminescence and stability protein modeling

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Single nucleotide polymorphisms of the maternal gene and their association with fetal neural tube defects in Han ethnic group in Shanxi Province, China

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Chinese Medical Journal 2011年第3期124卷 374-379页

作者： GUO Li ZHAO Hong PEI Yu-heng HE Quan-ren LI Wan-I ZHANG Ting ZHENG Xiao-ying ZHOU Ran XIE Jun Department of Biochemistry and Molecular Biology Ministry of Education Key Laboratory of Cellular Physiology Shanxi Medical University Taiyuan Shanxi 030001China Department of Physiology Linfen Vocational and Technical College Linfen Shanxi 041000 China Department of Biochemistry and Molecular Biology Ministry of Education Key Laboratory of Cellular Physiology Shanxi Medical University Taiyuan Shanxi 030001China Department of Internal Neurology Second HospitalShanxi Medical University Taiyuan Shanxi 030001China Department of Physiology and Pharmacology University of Georgia Athens GA USA Capital Institute of Pediatrics Beijing 100020 China Institute of Population Research Peking University Beijing 100871 China Department of Prescription and Therapeutic Method Shanxi Traditional Medical College Taiyuan Shanxi 030024 China

Background Neural tube defects are the most common human birth defects. The causes are multifactorial with complex genetic and environmental factors, although the exact genetic causes are unknown. This research was conducted to study the frequency of Msx2 gene polymorphisms in 59 women with a history of pregnancy with a neural tube defect and in 73 healthy controls. We aimed to determine the effect of this genetic polymorphism on the incidence of neural tube defects in the Han Chinese *** We studied 59 mothers with at least one previous child with a neural tube defect （the case group） and 73case-control subjects during the same period, from Shanxi Province, China. We analyzed the genotypic distributions and allele frequencies of Msx2 C386T poiymorphisms in DNA samples from the case and control groups. A three-dimensional protein model was predicted using Swiss-Pdb Viewer software version 4.0. Disease association was analyzed using chi-square *** Significant differences were observed in the genotypes and allele frequencies of the Msx2 C386T allele between the case and control groups （CT： 32% vs. 15%, P=0.0073 and TT 15% vs. 4%, P=0.013, respectively）. Logistic regression analysis showed that the C386T mutation is a potential risk factor for neural tube defects （P 〈0.05; OR： 3.466;95%CI： 1.831-6.560）. Three-dimensional structure prediction revealed that the Msx2 C386T mutation results in a threonine substitution for methionine at position 129 of exon 2, which might lead to structural mutations or dysfunctions in the protein encoded by *** Maternal Msx2 C386T gene polymorphisms were associated with fetal neural tube defects in Han Chinese women in Shanxi Province.

关键词： neural tube defects Msx2 single nucleotide polymorphism protein modeling

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Polymorphisms of the maternal Slug gene in fetal neural tube defects in a Chinese population

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Neural Regeneration Research 2010年第17期5卷 1342-1346页

作者： Li Guo Hong Zhao Yuheng Pei Quanren He Wan-I Li Ting Zhang Xiaoying Zheng Ran Zhou Jun Xie Department of Biochemistry and Molecular Biology Ministry of Education Key Laboratory of Cellular PhysiologyShanxi Medical UniversityTaiyuan 030001Shanxi ProvinceChina Department of Physiology Linfen Vocational and Technical CollegeLinfen 041000Shanxi ProvinceChina Department of Internal Neurology Second HospitalShanxi Medical UniversityTaiyuan 030001Shanxi ProvinceChina Department of Physiology and Pharmacology University of GeorgiaAthens 30602GAUSA Capital Institute of Pediatrics Beijing 100020China Institute of Population Research Peking UniversityBeijing 100871China Department of Prescription and Therapeutic Method Shanxi Traditional Medical CollegeTaiyuan 030024Shanxi ProvinceChina

Several studies have demonstrated that Slug,which encodes a zinc finger of the Snail family of transcription factors,is a potential risk factor for neural tube *** tube defects tend to occur with a high rate in Shanxi province,*** present case-control study investigated genotypic distributions and allele frequencies of Slug C1548A polymorphisms in DNA samples from59 women with a history of neural tube defect pregnancies and 73 controls during the same period from Shanxi Province,*** demonstrated that women with a history of neural tube defect pregnancies had significantly greater genotypic distributions of Slug AA genotypes and A allele frequencies compared with controls,and A allele Slug C1548A was a risk factor for neural tube defects（odds ratio = 3.444;95% confidence interval;2.021-5.868,P 〈 0.05）.Three-dimensional structure prediction revealed that Slug C1548A resulted in transition of aspartic acid into glutamate at position *** indicated that these mutations could lead to damaged protein structure and *** findings suggest that Slug C1548A gene polymorphism is closely related to neural tube defects in a population of Han Chinese origin from Shanxi Province,China

关键词： neural tube defects Slug single nucleotide polymorphisms protein modeling

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