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Objective To explore the interactive protein and mode of oncogene alkylglycerone phosphate synthase (AGPS) in glioma U251 cells. Methods U251 cells were routinely cultured and divided into the control group, shRAGPS-1 group and shR-AGPS-2 group, respectively, which were added with the negative control lentivirus and AGPS shRNA lentiviruse with different silencing levels. Western blotting was used to detect the expression of AGPS protein to verify the silencing efficiency. The interactive protein of AGPS was identified by immunoprecipitation and mass spectrometry, and was identified by Western blotting. The homologous modeling of the interactive proteins of AGPS was established by computer simulation and the interaction mode was predicted. Results Compared with the control group, the expression of AGPS decreased in the shR-AGPS-1 group and shR-AGPS-2 group and the expression of AGPS was lower in the shRAGPS-1 than in the shR-AGPS-2 group (all P<0. 05). It was predicted that heterogeneous nuclear ribonucleoprotein K (HNRNPK) was the target protein of AGPS, and both AGPS and HNRNPK were detected in the AGPS immunoprecipitation lysate, which indicated that AGPS and HNRNPK formed complexes, and both of them were expressed in the nucleus. The results of computer simulation showed that AGPS and HNRNPK were interacted through amino acid residues based on hydrogen bond, conjugation, hydrophobic bond and electrostatic force. Conclusion The HNRNPK is the interactive protein of AGPS in glioma, and the interaction of hydrogen bond, conjugation, hydrophobic bond and electrostatic force may be the main modes of action of AGPS. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Chinese Institute of Food Science & Technology / Zhongguo Shipin Xuebao is the property of Journal of Chinese Institute of Food Science & Technology Periodical Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Food & Machinery is the property of Food & Machinery Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of South China Fisheries Science is the property of South China Fisheries Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Objective: This study focused on improving the production of chitosan oligosaccharides by chitinase degradation of chitin. Methods: Using genetic engineering methods to clone, prokaryotic expressing, and investigating enzymatic properties of the chitinase from Streptomyces diastaticus, and the chitinase activity was explored by homology modeling, amino acid comparison of the catalytic domain, and site-directed mutagenesis. Results: After cloning and prokaryotic expression, the enzyme production cycle was shortened from 7 d to 24 h, and the enzyme activity reached 132 U/L, which was 32% higher than the original bacterial enzyme activity （100 U/L）. The amino acids that determine the activity of chitinase was Asp at position 128, 130, and Glu at position 132 of the catalytic domain. Conclusion: Clonal expression of the chitinase gene resulted in a shorter enzyme production cycle and increased enzyme activity.

To explore the binding modes of succinate dehydrogenase inhibitor（SDHI） fungicides with Botrytis cinerea succinate dehydrogenase（Bc SDH） and elucidate the resistance mechanism of Bc SDH to SDHI in structural biology, the three-dimensional structure of Bc SDH was constructed by homology modeling. In this work, the resistance mechanism of Bc SDH to SDHI was analyzed according to the changes of binding affinity and interactions between five SDHI（isofetamid, fluopyram, luxapyroxad,penthiopyrad and boscalid） and wild-type or mutant Bc SDH. The mutation types of Bc SDH were predicted by conservative analysis. The results indicated that there was a strong binding interaction between the five SDHI and Bc SDH, including hydrophobic action, hydrogen bond, halogen bond, π-πstacking and π-cation interaction. Based on these interactions, the acid part of SDHI inserted into the pocket bottom of Bc SDH, and the amine part located outside the pocket. With the B-P225 F residue mutation, the pocket narrowed. Therefore, the fungicidal acid part could not enter the pocket. With the B-P225 L residue mutation, the binding modes of isofetamid, fluopyram and penthiopyrad with the SDH changed and the binding affinity of them reduced. With the B-H272 R residue mutation, the pocket bottom narrowed, which led to binding affinity reduction. In addition, homology analysis showed that B-P225 and B-H272 located in the conservative region of Bc SDH, and the B-P225 F, B-H272 R and BH272 L residue mutations might be random mutations. These results suggested that B-P225 F and BH272 R residue mutations of Bc SDH migh be the main cause of the resistance of B. cinerea to five fungicides, and might also be one of the main causes of cross-resistance to SDHI. The B-P225 L residue mutation may reduce the sensibility of B. cinerea to parts of SDHI, rather than the primary cause of cross-resistance to SDHI. Therefore, reasonable and effective resistance monitoring and management strategies should be adopted to delay the development of the resistance of B. cinerea to SDHI in practical production. And the B-P225 F, B-H272 R and B-P225 L residue mutations should also be considered to avoid cross-resistance in the design of novel SDHI molecules. [ABSTRACT FROM AUTHOR]

Copyright of Shipin Kexue/ Food Science is the property of Food Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

[Objectives] The purpose of this study was to clone chi8 gene from a beneficial strain Trichoderma guizhouense NJAU4742, and then to obtain the pure Chi8 protein through the heterologous expression by Escherichia coli expression system and the enzymology characteristics of Chi8 by evaluating the enzyme activity under different conditions, and to analyze the hydrolysates by using colloidal chitin as substrate, which will provide theoretical basis for its practical application in agricultural wastes treatment. [Methods] The homology of chi8 gene with other chitinase genes was obtained by sequence alignment, and the open reading flank of chi8 was amplified based on specific primers and then heterologously expressed in E.coli BL21 by using the pET-29a vector. The enzymology characteristics of Chi8 was obtained by determining the activities at different conditions with DNS method after purification by nickel gel, and the MALDI-TOF /MS method was used to detect the final product of colloidal chitin hydrolyzed by Chi8. Construction of three-dimensional model of Chi8 and docking results with chitohexaose hydrochloride was based on homologous modeling. [Results] Chi8 encoded by Trichoderma guizhouense NJAU4742 owned a highest sequence similarity ( 93. 38%) with the chitinase from Trichoderma harzianum ( ACM47359). Chi8 owned high enzyme activities and maintained a considerable thermal stability between 30 °C and 40 °C, meanwhile the enzyme activity was the highest when the pH value reached 6. 0. Ca2+ could increase the activity of Chi8 significantly,and the activity reached to 110.62% of that in CK, while the co-reaction with Co2+, Cu2+ and Fe3+ showed inhibitory effects with only 89.70%,60.17% and 5.93% of the enzyme activity by compared to CK, respectively. Under the condition of weak acid, colloidal chitin was used as the substrate for hydrolysis, and the final product was mainly chitobiose ( GlcNAc),. The protein homologous structure model of Chi8 indicated that it contained 18 helices,md 15 /3-hm-rd, with,m IMD residue as the imidazole ring at the end. The substrate docking results showed that Asn 197, Trp 110, T)T218, Arg274 and Arg3 l in Chi8 could form hydrogen bond with chitohexaose hydrochloride, which might he the active center of this protein. [ Conclusions] Chi8 owned a considerable capacity of efficient decompose colloidal chitin to generate chitosan oligosaccharides ., and the major products were ( GlcNAc), and chitin monosaccharide. [ABSTRACT FROM AUTHOR]

Copyright of Chinese Journal of Applied Entomology is the property of Chinese Journal of Applied Entomology, Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Shipin Kexue/ Food Science is the property of Food Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Objective: To search for the key regions used as protein-ligand interactions by simulating and analyzing the E6 protein structure of HPV16 and 18. Methods: The HPV16 E6 protein was used as a template for homology modeling of HPV18 E6 protein, the crystal structure model of HPV(18, 16) E6-protein was studied by molecular dynamics simulation. By analyzing the microscopic loop and the macroscopic motion, we study the similarities and differences of structural changes of HPV18 E6 and HPV16 E6 in aqueous solvents. Results: The results indicated loop in the N-terminal region played a role of "gatekeeper"that could mediate ligand, water and ion in the process of protein-ligand interactions and reveal the changes of the conformation of two proteins in aqueous solvents.Conclusions: The movement mechanisms of HPV18 E6 and HPV16 E6 in aqueous solvents, as well as the role of loop that acting as a "gatekeeper" were elucidated. Meanwhile, these simulation results interpret the changes of the conformation of two proteins in aqueous solvents and provide theoretical basis for drug design based on two proteins. [ABSTRACT FROM AUTHOR]

Copyright of Chinese Journal of Applied Entomology is the property of Chinese Journal of Applied Entomology, Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Objective: To evaluate the reasonability and reliability of M1 muscarinic acetylcholine receptor (mAChR) constructed from different GPCR models. Methods: M1 mAChRs complexes were obtained by homology modeling from bovine rhodopsin, human β 2-adrenergic receptors, human M2 and M3 mAChRs. The receptor-ligand interactions were obtained by docking, and were compared with the crystal structure of M1 mAChR in static state. The variety of distances between ligand and crucial residues of M1 mAChR were evaluated by molecular dynamic simulation to validate the optimum model of M1 mAChR in dynamic state. Results: M2 mAChR possessed highest sequence similarities with M1 mAChR (67.9%). The mean of RMSDs between the M1 mAChR constructed by Inactive M2 (M1Rinactive-M2R) and other crystal structures was smallest (1.39 Å). The allosteric sites (K392 and E397) of M1Rinactive-M2R were closer to the binding pockets, which were corresponded with the ligand binding conformation. Docking results showed that the distances between bitopic allosteric agonist (VU0184670) and allosteric sites (Y85 and Y381) of M1Rinactive-M2R were 4.8 Å and 6.8 Å respectively, more reasonable than other M1 mAChR models. The distance between ligand and residue of Q177 was decreased from 7.4 To evaluate the reasonability and reliability of M1 muscarinic acetylcholine receptor (mAChR) constructed from different GPCR models. M1 mAChRs complexes were obtained by homology modeling from bovine rhodopsin, human β 2-adrenergic receptors, human M2 and M3 mAChRs. The receptor-ligand interactions were obtained by docking, and were compared with the crystal structure of M1 mAChR in static state. The variety of distances between ligand and crucial residues of M1 mAChR were evaluated by molecular dynamic simulation to validate the optimum model of M1 mAChR in dynamic state. M2 mAChR possessed highest sequence similarities with M1 mAChR (67.9%). The mean of RMSDs between the M1 mAChR constructed by Inactive M2 (M1Rinactive-M2R) and other crystal structures was smallest (1.39 Å). The allosteric sites (K392 and E397) of M1Rinactive-M2R were closer to the binding pockets, which were corresponded with the ligand binding conformation. Docking results showed that the distances between bitopic allosteric agonist (VU0184670) and allosteric sites (Y85 and Y381) of M1Rinactive-M2R were 4.8 Å and 6.8 Å respectively, more reasonable than other M1 mAChR models. The distance between ligand and residue of Q177 was decreased from 7.4 Tto 2.9 To evaluate the reasonability and reliability of M1 muscarinic acetylcholine receptor (mAChR) constructed from different GPCR models. M1 mAChRs complexes were obtained by homology modeling from bovine rhodopsin, human β 2-adrenergic receptors, human M2 and M3 mAChRs. The receptor-ligand interactions were obtained by docking, and were compared with the crystal structure of M1 mAChR in static state. The variety of distances between ligand and crucial residues of after dynamic simulation, indicating the rotation of VU0184670 towards Q177, which was corresponded to previously reported results. Our results have proved that the M1 mAChR constructed by Inactive M2 mAChR (M1Rinactive-M2R) exhibited high structural similarity with crystal structure of M1 mAChR and was reasonable and reliable in both static and dynamic states. Our study provides important strategies for the development of M1 mAChR drugs, and also novel paradigms for the exploration of other GPCRs.to 2.9 T after dynamic simulation, indicating the rotation of VU0184670 towards Q177, which was corresponded to previously reported results. Conclusions: Our results have proved that the M1 mAChR constructed by Inactive M2 mAChR (M1Rinactive-M2R) exhibited high structural similarity with crystal structure of M1 mAChR and was reasonable and reliable in both static and dynamic states. Our study provides important strategies for the development of M1 mAChR drugs, and also novel paradigms for the exploration of other GPCRs. [ABSTRACT FROM AUTHOR]

Pullulanase is a debranching enzyme that specifically hydrolyzes the α-1,6-glycosidic bonds in complex carbohydrates and has great potential in various industries. Here, we investigate the structural characteristics of the Bacillus naganoensispullulanase (BnPulB) by homology modeling and molecule docking. Results show that the BnPulB structure comprises the CBM41-X45a-X25-X45b-CBM48-GH13_14 multi-domain architecture and the central region of the protein forms the catalytic domain, and the highly conserved Asp619, Glu648, and Asp733 residues are identified to be catalytic triad. In addition, flexible docking studies of the enzyme-substrate system show the interactions between BnPulB and its substrate, maltotriose, and some conserved residues locate in the active centre that participate in ligand binding site are predicted. This study may provide important information for the design of new pullulanase with novel properties. [ABSTRACT FROM AUTHOR]

To clone the manganese peroxidase gene Ps-mnp1 from Pleurotus sapidus PS1 contributing a lot to the lignin biodegradation activity is important for the analysis of protein structure and functions of MnP and the understanding of manganese peroxidase gene function and transcriptional regulation of Pleurotus sapidus. Based on the analysis of ribosomal rDNA Intenal Transcribed Spacer (ITS) sequences, the classification status of the strain PS1 was defined. Ps-mnp1 was cloned by using the methods of Genome Walking-PCR and Reverse transcription-PCR with primers designed from some white-rot fungi which contains the conserved sequences of the known manganese peroxidase genes (GenBank No. KP189358.1). We used a variety of modern bioinformatics technology softwares to clone the manganese peroxidase gene and analyze the protein structure of Ps-mnp1. For example, after the cloning full length DNA sequence of genome walking method, prediction of the full cDNA sequence of manganese peroxidase gene by using contigexpress splicing software; comparison the DNA and cDNA nucleotide sequences alignment analysis by using BioEdit software; prediction the RNA splice site through Augustus website, following the comparison and correction of Ps-mnp1 sequences by using the NCBI database; understanding the compositions of the intron and exon by using online software Gene Structure Display Server contrast of white rot fungus manganese peroxidase gene. The results obtained in the sequence analysis of Ps-mnp1 from Pleurotus sapidus indicated that the full length of the DNA was 1 854 bp containing 14 exons and 13 introns. Meanwhile, exons and introns composition analysis of the genes Ps-mnp1 from Pleurotus sapidus, compared to other white-rot fungi manganese peroxidase genes, suggested that P. ostreatus and P. sapidus belonged to the same genus Pleurotus, but the manganese peroxidase gene structures between them were entirely different. The Ps-mnp1 gene included a signal peptide of 20 amino acids and held Open Reading Frame of 1 095 bp, with start codon ATG and stop codon TAA, encoding 364 amino acids. The results of protein phylogenetic analysis by MEGA 5.1 software revealed that Ps-mnp1 and 6 strains of white rot fungus protein clustered on short branches MnPs, and differentiated 5 long branches of MnPs group formed by disulphide bond. In addition, the 3D structures of Ps-mnp1 were built using homology modelling technique, and the results showed that the binding sites of the protein ligand included 1 Fe heme, 2 Ca ions and 1 Mn (II), and the those sites were non-conservation. The results also suggested that the modelling similarity was 72.51% compared with P. eryngii VPs. This paper could establish the basis of the study in the structure and function of the Ps-nmp1. It is further helpful to offer reference on the variation of protein engineering of the Ps-mnp1. [ABSTRACT FROM AUTHOR]

Objective: To explore the molecular biology of D variant blood group with RHD*95A genotype and the genetic mechanism of its generation., Methods: A total of 6 samples from 3 generations of a family were analyzed. RHD blood group was identified by saline test tube and microcolumn gel card method. 10 exons of RHD gene were amplified by Polymerase Chain Reaction-Sequence Specific Primer (PCR-SSP) and analyzed by direct sequencing. Homology modeling was used to compare the structural differences between mutant RHD protein and wild-type RHD protein., Results: The proband was identified as D variant by serological identification, RHD gene sequencing directly detected a c. 95 c > A mutation in exon 1 that leads to encoding the 32-bit amino acids by threonine Thr (T) into aspartic acid Asn (N), the rest of the exon sequences were normal compared with the normal RHD*01 gene. In the family, the proband's father, grandmather and uncle were all carried the same RHD*95A allele. Protein modeling results suggested that the hydrogen chain connected to the 32nd amino acid residue was changed after p.T32N mutation, which affected the structural stability of RHD protein., Conclusion: The first genetic lineage of the RHD*95A gene was identified in a Chinese population. The c.95C>A mutation in RHD gene was found in the family, which resulted in reduced expression of RHD antigen and showed D variant, the mutation could be stably inheritable. Gene identification and protein structure analysis of D variant population is helpful to explore the molecular mechanism of its formation and ensure the safety of blood transfusion.

The three-dimensional structure model of azoreductase AZR of Rhodobacter sphaeroides was constructed using homology modeling method. It is demonstrated that AZR is a flavodoxin adopting α/β structure with the central five-stranded parallel β-sheet flanked by five a helices. A flavin mononucleotide (FMN) prosthetic group lies on top of the molecule, acting as redox and reactive centers. Flavin-dependent azoreductases are classified into two families according to the results of sequence alignments. However, structure analysis indicates that they all possess similar three-dimensional structures and active sites. The study of AZR's structure lays a foundation for finding new azoreductase gene and deeply understanding AZR's function. [ABSTRACT FROM AUTHOR]

The stability of virus-like particles (VLPs) is currently the main factor affecting the quality of foot-and-mouth disease VLPs vaccines. In order to further improve the quality of the VLPs vaccine of foot-and-mouth disease (FMD), three amino acid modification sites were designed and screened through kinetic analysis software, based on the three-dimensional structure of FMDV. The three mutant recombinant plasmids were successfully prepared by the point mutation kit, transformed into Escherichia coli strain BL21 and expressed in vitro. After purification by Ni ion chromatography column, SDS-PAGE proved that the three amino acid mutations did not affect the expression of the target protein. The results of the stability study of three FMD mutant VLPs obtained by in vitro assembly show that the introduction of internal hydrophobic side chain amino acids made the morphology of VLPs more uniform (N4017W), and their stability was significantly improved compared to the other two VLPs. The internal hydrophobic force of the capsid contributes to the formation of VLPs and helps to maintain the stability of the capsid, providing new experimental ideas for improving the quality of VLPs vaccines, and helping to promote the development of VLPs vaccines.

In order to study the interaction between Pterocephalus hookeri and bitter taste receptors,three-dimensional structural models of bitter taste receptors TAS2 R16,TAS2 R14 and TAS2 R13 were established by homology modeling in this paper. Maestro software was used for docking the chemical constituents of P. hookeri with bitter taste receptors. The results showed that 25 chemical components of P. hookeri can regulate three bitter taste receptors. And these components were mainly iridoid glycosides and phenolic acids.This research focused on the comprehensive application of homology modeling and molecular docking technology to explore the interaction between bitter chemical constituents of P. hookeri and bitter taste receptors. This study provided assistance in revealing pharmacodynamic basis of bitter Tibetan medicine at molecular level. It also provided new ideas and methods for the study of Tibetan medicine.

A short terpene synthase gene was obtained by screening the transcriptome data of Senecio scandens. The phylogenetic tree and sequence alignment putatively identified this gene as a nerolidol synthase gene, named SsNES(GenBank MH518312). Protein homology modeling indicated that SsNES contained a complete conserved domain and folded correctly. SsNES was cloned and successfully expressed in Escherichia coli as soluble protein. The biochemical function of SsNES was characterized by E. coli metabolic engineering, which showed that SsNES catalyzed formation of trans-nerolidol with(E, E)-farnesyl diphosphate as the substrate. Nerolidol was also detected in stems and leaves of S. scandens, indicating that SsNES might act as the nerolidol synthase in plant. RT-PCR analysis indicated that SsNES was mainly expressed in stem, flowers and leaves, and no expression was observed in roots. After the treatment of SA, MeJA or Ala, SsNES was induced significantly at 6 h, indicating involvement in the defense response of S. scandens. The identification of SsNES not only clarified biosynthesis of nerolidol in S. scandens, but also provided diversity of sesquiterpene synthase, as well as theoretical basis for disease and pest defense mediated by the terpene metabolites.

Oligopeptides are one of the the key pharmaceutical effective constituents of traditional Chinese medicine(TCM). Systematic study on composition and efficacy of TCM oligopeptides is essential for the analysis of material basis and mechanism of TCM. In this study, the potential anti-hypertensive oligopeptides from Glycine max and their endothelin receptor A (ETA) antagonistic activity were discovered and predicted based on in silico technologies.Main protein sequences of G. max were collected and oligopeptides were obtained using in silico gastrointestinal tract proteolysis. Then, the pharmacophore of ETA antagonistic peptides was constructed and included one hydrophobic feature, one ionizable negative feature, one ring aromatic feature and five excluded volumes. Meanwhile, three-dimensional structure of ETA was developed by homology modeling methods for further docking studies. According to docking analysis and consensus score, the key amino acid of GLN165 was identified for ETA antagonistic activity. And 27 oligopeptides from G. max were predicted as the potential ETA antagonists by pharmacophore and docking studies.In silico proteolysis could be used to analyze the protein sequences from TCM. According to combination of in silico proteolysis and molecular simulation, the biological activities of oligopeptides could be predicted rapidly based on the known TCM protein sequence. It might provide the methodology basis for rapidly and efficiently implementing the mechanism analysis of TCM oligopeptides., Competing Interests: The authors of this article and the planning committee members and staff have no relevant financial relationships with commercial interests to disclose., (Copyright© by the Chinese Pharmaceutical Association.)

To virtual screen the compound of Chicory combined with the concentrative nucleoside transporter 2 (CNT2) in molecular docking technology.The homology model of hCNT2 was produced, and then the Vina software was employed to virtual screen the Chicory compound combined with CNT2. Compared with 7,8,3'-trihydroxyflavone, a CNT2 inhibitors, 23 score higher chicory compounds were hit.Meanwhile, the ten top compounds have been revealed that play important role in decrease the uric level. The bioactivity to CNT2 needs to be investigatedin experiment. CNT2 may be a potential target of chicory, which decreases the absorption of purine nucleoside in intestinal tract., Competing Interests: The authors of this article and the planning committee members and staff have no relevant financial relationships with commercial interests to disclose., (Copyright© by the Chinese Pharmaceutical Association.)