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Ning M, Guo P, Qi J, Cui Y, Wang K, Du G, Wang Z, Yuan Y, Yue T. Detoxification of Mycotoxin Patulin by the Yeast Kluyveromyces marxianus YG-4 in Apple Juice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38772384 DOI: 10.1021/acs.jafc.4c02963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Patulin (PAT) is a mycotoxin produced by Penicillium species, which often contaminates fruit and fruit-derived products, posing a threat to human health and food safety. This work aims to investigate the detoxification of PAT by Kluyveromyces marxianus YG-4 (K. marxianus YG-4) and its application in apple juice. The results revealed that the detoxification effect of K. marxianus YG-4 on PAT includes adsorption and degradation. The adsorption binding sites were polysaccharides, proteins, and some lipids on the cell wall of K. marxianus YG-4, and the adsorption groups were hydroxyl groups, amino acid side chains, carboxyl groups, and ester groups, which were combined through strong forces (ion interactions, electrostatic interactions, and hydrogen bonding) and not easily eluted. The degradation active substance was an intracellular enzyme, and the degradation product was desoxypatulinic acid (DPA) without cytotoxicity. K. marxianus YG-4 can also effectively adsorb and degrade PAT in apple juice. The contents of organic acids and polyphenols significantly increased after detoxification, significantly improving the quality of apple juice. The detoxification ability of K. marxianus YG-4 toward PAT would be a novel approach for the elimination of PAT contamination.
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Affiliation(s)
- Mengge Ning
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
| | - Peng Guo
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
| | - Jianrui Qi
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
| | - Yuanyuan Cui
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
| | - Kai Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
| | - Gengan Du
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
| | - Zhouli Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
| | - Yahong Yuan
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
- College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Tianli Yue
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
- College of Food Science and Technology, Northwest University, Xi'an 710069, China
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2
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Gu S, Yu J, Du L, Zhang D, Zhao L, Xie J. Characterization, Semirational Design for pH Robustness, and the Application in Bioactive Peptide Production of a X-Prolyl Dipeptidyl Aminopeptidase from Lactococcus lactis MY-3. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:7279-7290. [PMID: 38519413 DOI: 10.1021/acs.jafc.4c00146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
Abstract
PepXLcMY-3, an X-prolyl dipeptidyl aminopeptidase derived from Lactobacillus lactis MY-3, was screened and recombinantly expressed in Escherichia coli. The enzyme could exhibit about 40% activity within the pH range of 6.0-10. To further improve the pH robustness, site E396 located in the active pocket was discovered through alanine scanning. The mutant E396I displayed both developed activity and kcat/Km. The optimal pH of E396I shifted from 6.0 to 10 compared to WT, with the relative activity within the pH range of 6.0-10 significantly increased. The site K648 was then proposed by semirational design. The activity of mutant E396I/K648D reached 4.03 U/mg. The optimal pH was restored to 6.0, and the pH stability was further improved. E396I/K648D could totally hydrolyze β-casomorphin 7 within 30 min. The hydrolysate showed 64.5% inhibition on angiotensin I converting enzyme, which was more efficient than those produced by E396I and WT, 23.2 and 44.7%, respectively.
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Affiliation(s)
- Shengdi Gu
- State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Junjie Yu
- State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, P. R. China
- Shanghai Institute of Supervision and Inspection on Food Products and Cosmetics Quality, Shanghai 200233, P. R. China
| | - Lei Du
- State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Daihui Zhang
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forestry, Nanjing 210042, Jiangsu, P. R. China
| | - Li Zhao
- State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Jingli Xie
- State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, P. R. China
- Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai 200237, P. R. China
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3
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Borovsky D, Rougé P. Heliothis virescens chymotrypsin is translationally controlled by AeaTMOF binding ABC putative receptor. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 114:1-24. [PMID: 37526204 DOI: 10.1002/arch.22042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/19/2023] [Accepted: 07/22/2023] [Indexed: 08/02/2023]
Abstract
Heliothis virescens larval chymotrypsin (GenBank accession number AF43709) was cloned, sequenced and its three dimensional (3D) conformation modeled. The enzyme's transcript was first detected 6 days after larval emergence and the transcript level was shown to fall between larval ecdysis periods. Comparisons between the activities of larval gut chymotrypsin and trypsin shows that chymotrypsin activity is only 16% of the total trypsin activity and the pH optimum of the larval chymotrypsin is between pH 9-10, however the enzyme also exhibited a broad activity between pH 4-6. Injections of AeaTMOF and several shorter analogues into 3rd instar larvae followed by Northern blot analyses showed that although the chymotrypsins activities were inhibited by 60%-80% the transcript level of the sequenced chymotrypsin was not reduced and was similar to controls in which the chymotrypsin activity was not inhibited, indicating that AeaTMOF and its analogues exert a translational control. Based on these observations a putative AeaTMOF receptor (ABCC4) homologous to the Ae. aegypti ABC receptor sequence was found in the H. virescens genome. 3D molecular modeling and docking of the AeaTMOF and several of its analogues to the ABCC4 receptor showed that it can bind AeaTMOF and its analogues as was shown before for the Ae. aegypti receptor.
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Affiliation(s)
- Dov Borovsky
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz School of Medicine, Aurora, Colorado, USA
| | - Pierre Rougé
- UMR 152 Pharma-Dev, Faculté des Sciences Pharmaceutiques, Institut de Recherche et Développement, Université Toulouse 3, Toulouse, France
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4
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Borovsky D, Rougé P. Cloning and characterization of Aedes aegypti blood downregulated chymotrypsin II. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 113:e22018. [PMID: 37106507 DOI: 10.1002/arch.22018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 06/17/2023]
Abstract
Aedes aegypti adult and larval blood downregulated chymotrypsin II was cloned, sequenced and its 3D conformation modeled. Cloning of the enzymes from adult and larval guts indicated that both genes sit at the same location on Chromosome 2. Genomic analyses showed that larval and adult genes are the same and both have four exons and three introns that are located on an 8.32 Kb DNA in direction with the Ae. aegypti genome. The adult and larval transcript synthesis is controlled by alternative splicing explaining small difference in the amino acids sequences. Chymotrypsin II that was extracted from guts of sugar-fed and at 48 after blood feeding showed a pH optimum of 4-5 with a broad shoulder of activity from pH 6 to 10. Dot blot analyses show that the enzyme's transcript is downregulated after females take a blood meal and upregulated at 48 h after the blood meal. A Chymotrypsin II transcript was also detected in the larval gut during different times of larval developmental stages, indication that Ae. aegypti chymotrypsin II is synthesized by adults and larval guts. The possibility that JH III and 20HE play an active role in the regulation is discussed.
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Affiliation(s)
- Dov Borovsky
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz School of Medicine, Aurora, Colorado, USA
| | - Pierre Rougé
- UMR 152 Pharma-Dev, Faculté des Sciences Pharmaceutiques, Institut de Recherche et Développement, Université Toulouse 3, Toulouse, France
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5
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Yu MM, Fan YC, Li DY, Liu YX, Jiang PF, Zhou DY, Zhu BW. Differences in texture and digestive properties of different parts in boiled abalone muscles. Food Chem 2023; 404:134514. [DOI: 10.1016/j.foodchem.2022.134514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/14/2022] [Accepted: 10/02/2022] [Indexed: 11/06/2022]
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6
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Wang XX, Zhou ZK, Chen CG. In vitro digestion of a mixed gel of pork muscle and resistant starch: Salt-soluble protein perspective. Food Chem 2022; 394:133478. [PMID: 35716500 DOI: 10.1016/j.foodchem.2022.133478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/19/2022] [Accepted: 06/12/2022] [Indexed: 11/04/2022]
Abstract
The in vitro digestion of a mixed gel (MS) of pork muscle and resistant starch (RS) was investigated and the role of the salt-soluble protein (SSP) in the function promotion of the mixed gel was clarified. The results showed that the mixed muscle gel (MS) and the addition of RS to muscle gel (M + S) presented an improved protein digestion, as indicated by a reduced particle size of the hydrolysates, more degradation of proteins with large molecular weight and more generation of free amino acids compared with the RS-free muscle gel (M). Meanwhile, the hydrolysates of the M + S and MS showed intensified DPPH radical scavenging activities. Specifically, the MS exerted preferable properties in protein digestion and antioxidant activity. Similar digestion characteristics were noticed in mixed SSP gels.The current study revealed that the reinforced functionality of the mixed muscle gel was associated with the binding relationships between SSP and RS during cooking.
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Affiliation(s)
- Xi-Xi Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, Anhui Province, People's Republic of China.
| | - Zhong-Kai Zhou
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China.
| | - Cong-Gui Chen
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, Anhui Province, People's Republic of China.
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7
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Yamada Y, Obuchi K, Kikuchi N, Almarasy AA, Fujimori A. Immobilization of Trypsin from the Subphase to the Langmuir Monolayer of Fluorocarbon-Modified Single-Walled Carbon Nanotube and Its Activity Maintenance. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:5692-5701. [PMID: 35465664 DOI: 10.1021/acs.langmuir.2c00283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Single-walled carbon nanotubes (SWCNTs) synthesized by the improved arc discharge method were modified with a fluorocarbon chain, and the maintenance of trypsin activity upon adsorption from the subphase to the interfacial monolayer of SWCNTs was evaluated. The adsorption of trypsin on the fluorocarbon-modified SWCNT monolayer was confirmed by morphological and spectroscopic evaluations. Fiber morphology studies revealed that the fluorocarbon-modified SWCNT monolayer was covered by trypsin, and a trypsin-derived amide band was detected in the infrared spectra of the multilayers. After adsorption onto the fluorocarbon-modified SWCNT film, the ability of trypsin to cleave the fluorescent casein chain was maintained even at 160 °C. Furthermore, circular dichroism (CD) spectra showed that the second-order structure of the activity of trypsin adsorbed on the fluorocarbon-modified SWCNT was maintained up to nearly 200 °C. At 200 °C, the enhancement of emission intensity by casein chain cleavage was negligible, and the CD signal resulting from the negative Cotton effect was completely altered at 250 °C.
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Affiliation(s)
- Yuna Yamada
- Faculty of Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Kei Obuchi
- Faculty of Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Nanata Kikuchi
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Ahmed A Almarasy
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Atsuhiro Fujimori
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
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8
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Yu MM, Fan YC, Liu YX, Yin FW, Li DY, Liu XY, Zhou DY, Zhu BW. Effects of antioxidants of bamboo leaves on protein digestion and transport of cooked abalone muscles. Food Funct 2022; 13:1785-1796. [PMID: 35142324 DOI: 10.1039/d1fo03389a] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effects of oxidation on protein digestion and transport in cooked abalone muscles were investigated using a combination of simulated digestion and everted-rat-gut-sac models for the first time. Boiling heat treatments caused protein oxidation in the abalone muscles, reflected by increases in the carbonyl group and disulfide bond contents, protein hydrophobicity and aggregation degree, as well as decreases in the free sulfhydryl group and amino acid contents. Protein oxidation significantly inhibited the degree of hydrolysis, digestion rate, and digestibility of the abalone muscles in the simulated digestion model. The results from the everted-rat-gut-sac model showed that amino acid and peptide transport levels from the digestion products of the cooked abalone muscles were lower than those of the uncooked samples. In contrast, the addition of antioxidants of bamboo leaves mitigated heat-treatment-induced protein oxidation, aggregation and increased hydrophobicity, and consequently improved abalone muscle protein digestibility and transport levels.
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Affiliation(s)
- Man-Man Yu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, PR China.
| | - Ying-Chen Fan
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, PR China.
| | - Yu-Xin Liu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, PR China. .,National Engineering Research Center of Seafood, Dalian, 116034, PR China.,Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, 116034, PR China
| | - Fa-Wen Yin
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, PR China. .,National Engineering Research Center of Seafood, Dalian, 116034, PR China.,Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, 116034, PR China
| | - De-Yang Li
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, PR China. .,National Engineering Research Center of Seafood, Dalian, 116034, PR China.,Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, 116034, PR China
| | - Xiao-Yang Liu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, PR China. .,National Engineering Research Center of Seafood, Dalian, 116034, PR China.,Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, 116034, PR China
| | - Da-Yong Zhou
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, PR China. .,National Engineering Research Center of Seafood, Dalian, 116034, PR China.,Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, 116034, PR China
| | - Bei-Wei Zhu
- School of Food Science and Technology, Dalian Polytechnic University, Dalian, 116034, PR China. .,National Engineering Research Center of Seafood, Dalian, 116034, PR China.,Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, 116034, PR China
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9
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Borovsky D, Verhaert P, Rougé P, Powell CA, De Loof A. Culex quinquefasciatus Late Trypsin Biosynthesis Is Translationally Regulated by Trypsin Modulating Oostatic Factor. Front Physiol 2021; 12:764061. [PMID: 34867469 PMCID: PMC8637831 DOI: 10.3389/fphys.2021.764061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/12/2021] [Indexed: 12/02/2022] Open
Abstract
Trypsin is a serine protease that is synthesized by the gut epithelial cells of female mosquitoes; it is the enzyme that digests the blood meal. To study its molecular regulation, Culex quinquefasciatus late trypsin was purified by diethylaminoethyl (DEAE), affinity, and C18 reverse-phase high performance liquid chromatography (HPLC) steps, and the N-terminal amino acid sequence was determined for molecular cloning. Five overlapping segments of the late trypsin cDNA were amplified by PCR, cloned, and the full sequence (855 bp) was characterized. Three-dimensional models of the pro-trypsin and activated trypsin were built and compared with other trypsin models. Trypsin modulating oostatic factor (TMOF) concentrations in the hemolymph were determined by ELISA and compared with trypsin activity in the gut after the blood meal. The results showed that there was an increase in TMOF concentrations circulating in the hemolymph which has correlated to the reduction of trypsin activity in the mosquito gut. Northern blot analysis of the trypsin transcripts after the blood meal indicated that trypsin activity also followed the increase and decrease of the trypsin transcript. Injections of different amounts of TMOF (0.025 to 50 μg) decreased the amounts of trypsin in the gut. However, Northern blot analysis showed that TMOF injections did not cause a decrease in trypsin transcript abundance, indicating that TMOF probably affected trypsin translation.
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Affiliation(s)
- Dov Borovsky
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | | | - Pierre Rougé
- UMR 152 Pharma-Dev, Institut de Recherche et Développement, Université Toulouse 3, Faculté des Sciences Pharmaceutiques, Toulouse, France
| | - Charles A Powell
- UF-IFAS Indian River Research and Education Center, Fort Pierce, FL, United States
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10
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Absalan Y, Gholizadeh M, Choi HJ. Magnetized solvents: Characteristics and various applications. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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11
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Empirical Evaluation of the Use of Computational HLA Binding as an Early Filter to the Mass Spectrometry-Based Epitope Discovery Workflow. Cancers (Basel) 2021; 13:cancers13102307. [PMID: 34065814 PMCID: PMC8150281 DOI: 10.3390/cancers13102307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/06/2021] [Accepted: 05/06/2021] [Indexed: 12/22/2022] Open
Abstract
Immunopeptidomics is used to identify novel epitopes for (therapeutic) vaccination strategies in cancer and infectious disease. Various false discovery rates (FDRs) are applied in the field when converting liquid chromatography-tandem mass spectrometry (LC-MS/MS) spectra to peptides. Subsequently, large efforts have recently been made to rescue peptides of lower confidence. However, it remains unclear what the overall relation is between the FDR threshold and the percentage of obtained HLA-binders. We here directly evaluated the effect of varying FDR thresholds on the resulting immunopeptidomes of HLA-eluates from human cancer cell lines and primary hepatocyte isolates using HLA-binding algorithms. Additional peptides obtained using less stringent FDR-thresholds, although generally derived from poorer spectra, still contained a high amount of HLA-binders and confirmed recently developed tools that tap into this pool of otherwise ignored peptides. Most of these peptides were identified with improved confidence when cell input was increased, supporting the validity and potential of these identifications. Altogether, our data suggest that increasing the FDR threshold for peptide identification in conjunction with data filtering by HLA-binding prediction, is a valid and highly potent method to more efficient exhaustion of immunopeptidome datasets for epitope discovery and reveals the extent of peptides to be rescued by recently developed algorithms.
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12
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Biochemical characterization of zebrafish Prss59.1. Biochem Biophys Res Commun 2021; 560:32-36. [PMID: 33965786 DOI: 10.1016/j.bbrc.2021.04.118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 04/27/2021] [Indexed: 11/20/2022]
Abstract
Eleven genes, including prss59.1, were selected as candidate ovulation-inducing genes on the basis of microarray analysis and RNA sequencing in our previous study. To address the role of prss59.1, the prss59.1 gene knock-out zebrafish strain is currently being established by genome editing. In this study, for further phenotypic analysis of prss59.1, biochemical characterization of Prss59.1 was conducted using recombinant protein. A C-terminal histidine-tagged version of zebrafish Prss 59.1 was constructed. Although E. coli-produced recombinant Prss59.1 showed almost no activity, peptidase activities appeared after denaturation and renaturation. Zebrafish Prss59.1 showed the highest activity against Lys-MCA. The optimal temperature and pH of the activity toward Lys-MCA were 37 °C and pH 8.0, respectively. The Km value was 0.17 mM. Thus, zebrafish Prss59.1 possesses the closed character of trypsin, as expected from the DNA sequence.
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13
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Flachsenberg F, Meyder A, Sommer K, Penner P, Rarey M. A Consistent Scheme for Gradient-Based Optimization of Protein -Ligand Poses. J Chem Inf Model 2020; 60:6502-6522. [PMID: 33258376 DOI: 10.1021/acs.jcim.0c01095] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Scoring and numerical optimization of protein-ligand poses is an integral part of docking tools. Although many scoring functions exist, many of them are not continuously differentiable and they are rarely explicitly analyzed with respect to their numerical optimization behavior. Here, we present a consistent scheme for pose scoring and gradient-based pose optimization. It consists of a novel variant of the BFGS algorithm enabling step-length control, named LSL-BFGS (limited step length BFGS), and the empirical JAMDA scoring function designed for pose prediction and good numerical optimizability. The JAMDA scoring function shows a high pose prediction performance in the CASF-2016 docking power benchmark, top-ranking a pose with an RMSD of ≤2 Å in about 89% of the cases. The combination of JAMDA scoring with the LSL-BFGS algorithm shows a significantly higher optimization locality (i.e., no excessive movement of poses) than with the classical BFGS algorithm while retaining the characteristically low number of scoring function evaluations. The JAMDA scoring and optimization scheme is freely available for noncommercial use and academic research.
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Affiliation(s)
- Florian Flachsenberg
- ZBH - Center for Bioinformatics, Universität Hamburg, Bundesstraβe 43, 20146 Hamburg, Germany
| | - Agnes Meyder
- ZBH - Center for Bioinformatics, Universität Hamburg, Bundesstraβe 43, 20146 Hamburg, Germany
| | - Kai Sommer
- ZBH - Center for Bioinformatics, Universität Hamburg, Bundesstraβe 43, 20146 Hamburg, Germany
| | - Patrick Penner
- ZBH - Center for Bioinformatics, Universität Hamburg, Bundesstraβe 43, 20146 Hamburg, Germany
| | - Matthias Rarey
- ZBH - Center for Bioinformatics, Universität Hamburg, Bundesstraβe 43, 20146 Hamburg, Germany
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14
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Yu J, Wu J, Xie D, Du L, Tang YJ, Xie J, Wei D. Characterization and rational design for substrate specificity of a prolyl endopeptidase from Stenotrophomonas maltophilia. Enzyme Microb Technol 2020; 138:109548. [DOI: 10.1016/j.enzmictec.2020.109548] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/10/2020] [Accepted: 03/06/2020] [Indexed: 11/17/2022]
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15
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Perthold JW, Petrov D, Oostenbrink C. Toward Automated Free Energy Calculation with Accelerated Enveloping Distribution Sampling (A-EDS). J Chem Inf Model 2020; 60:5395-5406. [PMID: 32492343 PMCID: PMC7686955 DOI: 10.1021/acs.jcim.0c00456] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Free-energy
perturbation (FEP) methods are commonly used in drug
design to calculate relative binding free energies of different ligands
to a common host protein. Alchemical ligand transformations are usually
performed in multiple steps which need to be chosen carefully to ensure
sufficient phase-space overlap between neighboring states. With one-step
or single-step FEP techniques, a single reference state is designed
that samples phase-space not only representative of a full transformation
but also ideally resembles multiple ligand end states and hence allows
for efficient multistate perturbations. Enveloping distribution sampling
(EDS) is one example for such a method in which the reference state
is created by a mathematical combination of the different ligand end
states based on solid statistical mechanics. We have recently proposed
a novel approach to EDS which enables efficient barrier crossing between
the different end states, termed accelerated EDS (A-EDS). In this
work, we further simplify the parametrization of the A-EDS reference
state and demonstrate the automated calculation of multiple free-energy
differences between different ligands from a single simulation in
three different well-described drug design model systems.
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Affiliation(s)
- Jan Walther Perthold
- Institute for Molecular Modeling and Simulation, Department for Material Sciences and Process Engineering, University of Natural Resources and Life Sciences (BOKU), Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Dražen Petrov
- Institute for Molecular Modeling and Simulation, Department for Material Sciences and Process Engineering, University of Natural Resources and Life Sciences (BOKU), Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, Department for Material Sciences and Process Engineering, University of Natural Resources and Life Sciences (BOKU), Vienna, Muthgasse 18, 1190 Vienna, Austria
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16
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Zhao D, He J, Zou X, Xie Y, Xu X, Zhou G, Li C. Influence of hydrothermal treatment on the structural and digestive changes of actomyosin. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:6209-6218. [PMID: 31250450 DOI: 10.1002/jsfa.9893] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/30/2019] [Accepted: 06/21/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Heat treatment induces both structural and digestive change of meat protein. However, little has been revealed regarding the associations between structural changes and digested peptides of myofibrillar proteins. This work investigated the effects of heat treatment on the structures and in vitro digestibility of actomyosin, and the peptidomics of the digests were analyzed using liquid chromatography tandem mass spectrometry (LC-MS/MS). RESULTS Heat treatment resulted in unfolding and aggregation behavior of actomyosin according to the results of surface hydrophobicity and particle size. Formation of disulfide bonds and increase in carbonyl groups that occurred during heat treatment of actomyosin indicated the oxidation of specific residues. Unfolding behavior could elevate digestibility of actomyosin by exposing residues, based on the identification of peptides in digests of actomyosin using LC-MS/MS. However, the disulfide bond proved to reduce the action of digestive proteases, since the peptides number (increased from 56 to 86 in sample heated at 70 °C for 30 min) and peptides intensity in digests largely increased after the addition of dithiothreitol (DTT). Heating at higher temperature (100 °C) induced severer aggregation and oxidation, which resulted in lower digestibility of actomyosin than that heated at 70 °C by burying or damaging partial cleavage sites for digestive proteases. CONCLUSIONS This work highlights the huge influence of heat treatment on the multi-scale structures of myofibrillar proteins, which largely changed the peptides composition in protein digests. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Di Zhao
- Key Laboratory of Meat Processing (MOA), Key Laboratory of Meat Processing and Quality Control (MOE), Jiang Synergetic Innovation Center of Meat Production, Processing and Quality Control, Nanjing Agricultural University, Nanjing, P. R. China
| | - Jing He
- Key Laboratory of Meat Processing (MOA), Key Laboratory of Meat Processing and Quality Control (MOE), Jiang Synergetic Innovation Center of Meat Production, Processing and Quality Control, Nanjing Agricultural University, Nanjing, P. R. China
| | - Xiaoyu Zou
- Key Laboratory of Meat Processing (MOA), Key Laboratory of Meat Processing and Quality Control (MOE), Jiang Synergetic Innovation Center of Meat Production, Processing and Quality Control, Nanjing Agricultural University, Nanjing, P. R. China
| | - Yunting Xie
- Key Laboratory of Meat Processing (MOA), Key Laboratory of Meat Processing and Quality Control (MOE), Jiang Synergetic Innovation Center of Meat Production, Processing and Quality Control, Nanjing Agricultural University, Nanjing, P. R. China
| | - Xinglian Xu
- Key Laboratory of Meat Processing (MOA), Key Laboratory of Meat Processing and Quality Control (MOE), Jiang Synergetic Innovation Center of Meat Production, Processing and Quality Control, Nanjing Agricultural University, Nanjing, P. R. China
| | - Guanghong Zhou
- Key Laboratory of Meat Processing (MOA), Key Laboratory of Meat Processing and Quality Control (MOE), Jiang Synergetic Innovation Center of Meat Production, Processing and Quality Control, Nanjing Agricultural University, Nanjing, P. R. China
| | - Chunbao Li
- Key Laboratory of Meat Processing (MOA), Key Laboratory of Meat Processing and Quality Control (MOE), Jiang Synergetic Innovation Center of Meat Production, Processing and Quality Control, Nanjing Agricultural University, Nanjing, P. R. China
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17
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Liu L, Yu H, Du K, Wang Z, Gan Y, Huang H. Enhanced trypsin thermostability in Pichia pastoris through truncating the flexible region. Microb Cell Fact 2018; 17:165. [PMID: 30359279 PMCID: PMC6201580 DOI: 10.1186/s12934-018-1012-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 10/19/2018] [Indexed: 12/03/2022] Open
Abstract
Background High thermostability is required for trypsin to have wider industrial applications. Target mutagenesis at flexible regions has been proved to be an efficient protein engineering method to enhance the protein thermostability. Results The flexible regions in porcine trypsin were predicted using the methods including molecular dynamic simulation, FlexPred, and FoldUnfold. The amino acids 78–90 was predicted to be the highly flexible region simultaneously by the three methods and hence selected to be the mutation target. We constructed five variants (D3, D5, D7, D9, and D11) by truncating the region. And the variant D9 showed higher thermostability, with a 5 °C increase in Topt, 5.8 °C rise in \documentclass[12pt]{minimal}
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\begin{document}$$T_{50}^{10}$$\end{document}T5010, and a 4.5 °C rise in Tm, compared to the wild-type. Moreover, the half-life value of the variant D9 was also found to be dramatically improved by 46 min. Circular dichroism and intrinsic fluorescence indicated that the structures had no significant change between the variant D9 and the wild-type. The surface hydrophobicity of D9 was measured to be lower than that of wild-type, indicating the increased hydrophobic interaction, which could have contributed to the improved thermostability of D9. Conclusions These results showed that the thermostability of variant D9 was increased. The variant D9 could be expected to be a promising tool enzyme for its wider industrial applications. The method of truncating the flexible region used in our study has the potential to be used for enhancing the thermostability of other proteins. Electronic supplementary material The online version of this article (10.1186/s12934-018-1012-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lin Liu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China.,Key Laboratory of System Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300350, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300350, China
| | - Haoran Yu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China.,Key Laboratory of System Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300350, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300350, China.,Department of Biochemical Engineering, University College London, Gordon Street, London, WC1H 0AH, UK
| | - Kun Du
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China.,Key Laboratory of System Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300350, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300350, China
| | - Zhiyan Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China.,Key Laboratory of System Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300350, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300350, China
| | - Yiru Gan
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China.,Key Laboratory of System Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300350, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300350, China
| | - He Huang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China. .,Key Laboratory of System Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300350, China. .,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, 300350, China.
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18
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Jesús-de la Cruz K, Álvarez-González CA, Peña E, Morales-Contreras JA, Ávila-Fernández Á. Fish trypsins: potential applications in biomedicine and prospects for production. 3 Biotech 2018; 8:186. [PMID: 29556440 DOI: 10.1007/s13205-018-1208-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 03/09/2018] [Indexed: 11/28/2022] Open
Abstract
In fishes, trypsins are adapted to different environmental conditions, and the biochemical and kinetic properties of a broad variety of native isoforms have been studied. Proteolytic enzymes remain in high demand in the detergent, food, and feed industries; however, our analysis of the literature showed that, in the last decade, some fish trypsins have been studied for the synthesis of industrial peptides and for specific biomedical uses as antipathogenic agents against viruses and bacteria, which have been recently patented. In addition, innovative strategies of trypsin administration have been studied to ensure that trypsins retain their properties until they exert their action. Biomedical uses require the production of high-quality enzymes. In this context, the production of recombinant trypsins is an alternative. For this purpose, E. coli-based systems have been tested for the production of fish trypsins; however, P. pastoris-based systems also seem to show great potential in the production of fish trypsins with higher production quality. On the other hand, there is a lack of information regarding the specific structures, biochemical and kinetic properties, and characteristics of trypsins produced using heterologous systems. This review describes the potential uses of fish trypsins in biomedicine and the enzymatic and structural properties of native and recombinant fish trypsins obtained to date, outlining some prospects for their study.
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Affiliation(s)
- Kristal Jesús-de la Cruz
- Laboratorio de Acuacultura, DACBiol-UJAT, Carr. Villahermosa-Cárdenas Km 0.5, 86139 Villahermosa, Tabasco México
| | | | - Emyr Peña
- Laboratorio de Acuacultura, DACBiol-UJAT, Carr. Villahermosa-Cárdenas Km 0.5, 86139 Villahermosa, Tabasco México
- Cátedra Consejo Nacional de Ciencia y Tecnología-UJAT, Villahermosa, Tabasco México
| | - José Antonio Morales-Contreras
- 2Centro de Investigación, DACS-Universidad Juárez Autónoma de Tabasco, Av. Gregorio Méndez No. 2838-A. Col. Tamulté, 86150 Villahermosa, Tabasco México
| | - Ángela Ávila-Fernández
- 2Centro de Investigación, DACS-Universidad Juárez Autónoma de Tabasco, Av. Gregorio Méndez No. 2838-A. Col. Tamulté, 86150 Villahermosa, Tabasco México
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19
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Morey M, Pandit A. Responsive triggering systems for delivery in chronic wound healing. Adv Drug Deliv Rev 2018; 129:169-193. [PMID: 29501700 DOI: 10.1016/j.addr.2018.02.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/27/2018] [Accepted: 02/26/2018] [Indexed: 12/31/2022]
Abstract
Non-communicable diseases including cancer, cardiovascular disease, diabetes, and neuropathy are chronic in nature. Treatment of these diseases with traditional delivery systems is limited due to lack of site-specificity, non-spatiotemporal release and insufficient doses. Numerous responsive delivery systems which respond to both physiological and external stimuli have been reported in the literature. However, effective strategies incorporating a multifactorial approach are required to control these complex wounds. This can be achieved by fabricating spatiotemporal release systems, multimodal systems or dual/multi-stimuli responsive delivery systems loaded with one or more bioactive components. Critically, these next generation stimuli responsive delivery systems that are at present not feasible are required to treat chronic wounds. This review provides a critical assessment of recent developments in the field of responsive delivery systems, highlighting their limitations and providing a perspective on how these challenges can be overcome.
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Affiliation(s)
- Mangesh Morey
- CÚRAM, Centre for Research in Medical Devices, National University of Ireland Galway, Galway, Ireland.
| | - Abhay Pandit
- CÚRAM, Centre for Research in Medical Devices, National University of Ireland Galway, Galway, Ireland.
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20
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Stender EGP, Koutina G, Almdal K, Hassenkam T, Mackie A, Ipsen R, Svensson B. Isoenergic modification of whey protein structure by denaturation and crosslinking using transglutaminase. Food Funct 2018; 9:797-805. [DOI: 10.1039/c7fo01451a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structural effect of denaturation of whey protein by heat or pH and subsequent crosslinking by transglutaminase.
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Affiliation(s)
- Emil G. P. Stender
- Department of Biotechnology and Biomedicine
- Technical University of Denmark
- Denmark
| | - Glykeria Koutina
- Department of Food Science
- University of Copenhagen
- Copenhagen
- Denmark
| | - Kristoffer Almdal
- Department of Micro- and Nanotechnology
- Technical University of Denmark
- Denmark
| | - Tue Hassenkam
- Department of Chemistry
- University of Copenhagen
- Copenhagen
- Denmark
| | - Alan Mackie
- Institute of Food Research
- Norwich Research Park
- Colney
- UK
- School of Food Science and Nutrition
| | - Richard Ipsen
- Department of Food Science
- University of Copenhagen
- Copenhagen
- Denmark
| | - Birte Svensson
- Department of Biotechnology and Biomedicine
- Technical University of Denmark
- Denmark
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21
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Korkmaz AG, Popov T, Peisl L, Codrea MC, Nahnsen S, Steimle A, Velic A, Macek B, von Bergen M, Bernhardt J, Frick JS. Proteome and phosphoproteome analysis of commensally induced dendritic cell maturation states. J Proteomics 2017; 180:11-24. [PMID: 29155090 DOI: 10.1016/j.jprot.2017.11.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 09/18/2017] [Accepted: 11/14/2017] [Indexed: 01/18/2023]
Abstract
Dendritic cells (DCs) can shape the immune system towards an inflammatory or tolerant state depending on the bacterial antigens and the environment they encounter. In this study we provide a proteomic catalogue of differentially expressed proteins between distinct DC maturation states, brought about by bacteria that differ in their endotoxicity. To achieve this, we have performed proteomics and phosphoproteomics on murine DC cultures. Symbiont and pathobiont bacteria were used to direct dendritic cells into a semi-mature and fully-mature state, respectively. The comparison of semi-mature and fully-mature DCs revealed differential expression in 103 proteins and differential phosphorylation in 118 phosphosites, including major regulatory factors of central immune processes. Our analyses predict that these differences are mediated by upstream elements such as SOCS1, IRF3, ABCA1, TLR4, and PTGER4. Our analyses indicate that the symbiont bacterial strain affects DC proteome in a distinct way, by downregulating inflammatory proteins and activating anti-inflammatory upstream regulators. Biological significance In this study we have investigated the responses of immune cells to distinct bacterial stimuli. We have used the symbiont bacterial strain B. vulgatus and the pathobiont E. coli strain to stimulate cultured primary dendritic cells and performed a shotgun proteome analysis to investigate the protein expression and phosphorylation level differences on a genome level. We have observed expression and phosphorylation level differences in key immune regulators, transcription factors and signal transducers. Moreover, our subsequent bioinformatics analysis indicated regulation at several signaling pathways such as PPAR signaling, LXR/RXR activation and glucocorticoid signaling pathways, which are not studied in detail in an inflammation and DC maturation context. Our phosphoproteome analysis showed differential phosphorylation in 118 phosphosites including those belonging to epigenetic regulators, transcription factors and major cell cycle regulators. We anticipate that our study will facilitate further investigation of immune cell proteomes under different inflammatory and non-inflammatory conditions.
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Affiliation(s)
- Ali Giray Korkmaz
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Germany.
| | - Todor Popov
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Germany
| | - Loulou Peisl
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Germany
| | | | - Sven Nahnsen
- Quantitative Biology Center, University of Tübingen, Germany
| | - Alexander Steimle
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Germany
| | - Ana Velic
- Proteome Center, University of Tübingen, Germany
| | - Boris Macek
- Proteome Center, University of Tübingen, Germany
| | | | - Joerg Bernhardt
- Ernst-Moritz-Arndt Universität Greifswald, Institute for Microbiology, Germany
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22
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Schiebel J, Gaspari R, Sandner A, Ngo K, Gerber HD, Cavalli A, Ostermann A, Heine A, Klebe G. Charges Shift Protonation: Neutron Diffraction Reveals that Aniline and 2-Aminopyridine Become Protonated Upon Binding to Trypsin. Angew Chem Int Ed Engl 2017; 56:4887-4890. [DOI: 10.1002/anie.201701038] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Johannes Schiebel
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Germany
- CompuNet; Istituto Italiano di Tecnologia; Via Morego 30 16163 Genova Italy
| | - Roberto Gaspari
- CompuNet; Istituto Italiano di Tecnologia; Via Morego 30 16163 Genova Italy
| | - Anna Sandner
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Germany
| | - Khang Ngo
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Germany
| | - Hans-Dieter Gerber
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Germany
| | - Andrea Cavalli
- CompuNet; Istituto Italiano di Tecnologia; Via Morego 30 16163 Genova Italy
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum; Technische Universität München; Lichtenbergstraße 1 85748 Garching Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Germany
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23
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Ladungen verschieben Protonierungen: Neutronenbeugung zeigt, dass Anilin und 2-Aminopyridin protoniert an Trypsin binden. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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24
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Fu R, Yao K, Zhang Q, Jia D, Zhao J, Chi Y. Collagen Hydrolysates of Skin Shavings Prepared by Enzymatic Hydrolysis as a Natural Flocculant and Their Flocculating Property. Appl Biochem Biotechnol 2016; 182:55-66. [PMID: 27832513 DOI: 10.1007/s12010-016-2310-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 10/30/2016] [Indexed: 11/26/2022]
Abstract
A series of collagen hydrolysates (CHs) were prepared from pigskin shavings by using pepsin (PCH), trypsin (TCH), Alcalase (ACH), HCl (HCH), and NaOH (NCH). Their physicochemical properties, including degree of collagen hydrolysis, molecular weight distribution, electric charge, and microstructure, were investigated, and their flocculation performance was evaluated in a kaolin suspension, at varied pHs and concentrations. PCH exhibited high flocculation capability under acidic and neutral conditions, and its efficiency for removing suspended particles was approximately 80% at a concentration of 0.05 g/L. TCH, ACH, HCH, and NCH showed almost no flocculation capability. The flocculation capability of PCH could be mainly due to a combination of optimal molecular weight distribution and electric charge. This study could provide an environment-friendly natural flocculant and also proposes a promising approach for the reuse of collagen wastes. Graphical Abstract ᅟ.
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Affiliation(s)
- Ruijie Fu
- Department of Food Engineering, Sichuan University, Chengdu, 610065, People's Republic of China
| | - Kai Yao
- Department of Food Engineering, Sichuan University, Chengdu, 610065, People's Republic of China
| | - Qisheng Zhang
- Sichuan Academy of Food and Fermentation Industries, Chengdu, 611130, People's Republic of China
| | - Dongying Jia
- Department of Food Engineering, Sichuan University, Chengdu, 610065, People's Republic of China
| | - Jiayuan Zhao
- Department of Food Engineering, Sichuan University, Chengdu, 610065, People's Republic of China
| | - Yuanlong Chi
- Department of Food Engineering, Sichuan University, Chengdu, 610065, People's Republic of China.
- Chengdu Food and Drug Administration Research Institute, Chengdu, 610041, People's Republic of China.
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25
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Pillay P, Kunert KJ, van Wyk S, Makgopa ME, Cullis CA, Vorster BJ. Agroinfiltration contributes to VP1 recombinant protein degradation. Bioengineered 2016; 7:459-477. [PMID: 27459147 PMCID: PMC5094629 DOI: 10.1080/21655979.2016.1208868] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 06/24/2016] [Accepted: 06/28/2016] [Indexed: 10/21/2022] Open
Abstract
There is a growing interest in applying tobacco agroinfiltration for recombinant protein production in a plant based system. However, in such a system, the action of proteases might compromise recombinant protein production. Protease sensitivity of model recombinant foot-and-mouth disease (FMD) virus P1-polyprotein (P1) and VP1 (viral capsid protein 1) as well as E. coli glutathione reductase (GOR) were investigated. Recombinant VP1 was more severely degraded when treated with the serine protease trypsin than when treated with the cysteine protease papain. Cathepsin L- and B-like as well as legumain proteolytic activities were elevated in agroinfiltrated tobacco tissues and recombinant VP1 was degraded when incubated with such a protease-containing tobacco extract. In silico analysis revealed potential protease cleavage sites within the P1, VP1 and GOR sequences. The interaction modeling of the single VP1 protein with the proteases papain and trypsin showed greater proximity to proteolytic active sites compared to modeling with the entire P1-polyprotein fusion complex. Several plant transcripts with differential expression were detected 24 hr post-agroinfiltration when the RNA-seq technology was applied to identify changed protease transcripts using the recently available tobacco draft genome. Three candidate genes were identified coding for proteases which included the Responsive-to-Desiccation-21 (RD21) gene and genes for coding vacuolar processing enzymes 1a (NbVPE1a) and 1b (NbVPE1b). The data demonstrates that the tested recombinant proteins are sensitive to protease action and agroinfiltration induces the expression of potential proteases that can compromise recombinant protein production.
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Affiliation(s)
- Priyen Pillay
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Hillcrest, Pretoria, South Africa
| | - Karl J. Kunert
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Hillcrest, Pretoria, South Africa
| | - Stefan van Wyk
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Hillcrest, Pretoria, South Africa
| | - Matome Eugene Makgopa
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Hillcrest, Pretoria, South Africa
| | | | - Barend J. Vorster
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Hillcrest, Pretoria, South Africa
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26
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Karimi M, Ghasemi A, Sahandi Zangabad P, Rahighi R, Moosavi Basri SM, Mirshekari H, Amiri M, Shafaei Pishabad Z, Aslani A, Bozorgomid M, Ghosh D, Beyzavi A, Vaseghi A, Aref AR, Haghani L, Bahrami S, Hamblin MR. Smart micro/nanoparticles in stimulus-responsive drug/gene delivery systems. Chem Soc Rev 2016; 45:1457-501. [PMID: 26776487 PMCID: PMC4775468 DOI: 10.1039/c5cs00798d] [Citation(s) in RCA: 863] [Impact Index Per Article: 107.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
New achievements in the realm of nanoscience and innovative techniques of nanomedicine have moved micro/nanoparticles (MNPs) to the point of becoming actually useful for practical applications in the near future. Various differences between the extracellular and intracellular environments of cancerous and normal cells and the particular characteristics of tumors such as physicochemical properties, neovasculature, elasticity, surface electrical charge, and pH have motivated the design and fabrication of inventive "smart" MNPs for stimulus-responsive controlled drug release. These novel MNPs can be tailored to be responsive to pH variations, redox potential, enzymatic activation, thermal gradients, magnetic fields, light, and ultrasound (US), or can even be responsive to dual or multi-combinations of different stimuli. This unparalleled capability has increased their importance as site-specific controlled drug delivery systems (DDSs) and has encouraged their rapid development in recent years. An in-depth understanding of the underlying mechanisms of these DDS approaches is expected to further contribute to this groundbreaking field of nanomedicine. Smart nanocarriers in the form of MNPs that can be triggered by internal or external stimulus are summarized and discussed in the present review, including pH-sensitive peptides and polymers, redox-responsive micelles and nanogels, thermo- or magnetic-responsive nanoparticles (NPs), mechanical- or electrical-responsive MNPs, light or ultrasound-sensitive particles, and multi-responsive MNPs including dual stimuli-sensitive nanosheets of graphene. This review highlights the recent advances of smart MNPs categorized according to their activation stimulus (physical, chemical, or biological) and looks forward to future pharmaceutical applications.
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Affiliation(s)
- Mahdi Karimi
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Amir Ghasemi
- Department of Materials Science and Engineering, Sharif University of Technology, 11365-9466, Tehran, Iran
| | - Parham Sahandi Zangabad
- Department of Materials Science and Engineering, Sharif University of Technology, 11365-9466, Tehran, Iran
| | - Reza Rahighi
- Department of Research and Development, Sharif Ultrahigh Nanotechnologists (SUN) Company, P.O. Box: 13488-96394, Tehran, Iran and Nanotechnology Research Center, Research Institute of Petroleum Industry (RIPI), West Entrance Blvd., Olympic Village, P.O. Box: 14857-33111, Tehran, Iran
| | - S Masoud Moosavi Basri
- Bioenvironmental Research Center, Sharif University of Technology, Tehran, Iran and Civil & Environmental Engineering Department, Shahid Beheshti University, Tehran, Iran
| | - H Mirshekari
- Department of Biotechnology, University of Kerala, Trivandrum, India
| | - M Amiri
- Department of Materials Science and Engineering, Sharif University of Technology, 11365-9466, Tehran, Iran
| | - Z Shafaei Pishabad
- Department of Cell & Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - A Aslani
- Department of Materials Science and Engineering, Sharif University of Technology, 11365-9466, Tehran, Iran
| | - M Bozorgomid
- Department of Applied Chemistry, Central Branch of Islamic Azad University of Tehran, Tehran, Iran
| | - D Ghosh
- Department of Medical Nanotechnology, School of Advanced Technologies in Medicine (SATiM), Tehran University of Medical Sciences, Tehran, Iran
| | - A Beyzavi
- School of Mechanical Engineering, Boston University, Boston, MA, USA
| | - A Vaseghi
- Department of Biotechnology, Faculty of Advanced Science and Technologies of Isfahan, Isfahan, Iran
| | - A R Aref
- Department of Cancer Biology, Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Department of Genetics, Harvard Medical School, Boston, MA 02215, USA
| | - L Haghani
- School of Medicine, International Campus of Tehran University of Medical Science, Tehran, Iran
| | - S Bahrami
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA. and Department of Dermatology, Harvard Medical School, Boston, MA 02115, USA and Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA
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27
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Involvement of mast cells and proteinase-activated receptor 2 in oxaliplatin-induced mechanical allodynia in mice. Pharmacol Res 2016; 105:84-92. [PMID: 26804251 DOI: 10.1016/j.phrs.2016.01.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 01/07/2016] [Accepted: 01/12/2016] [Indexed: 12/12/2022]
Abstract
The chemotherapeutic agent oxaliplatin induces neuropathic pain, a dose-limiting side effect, but the underlying mechanisms are not fully understood. Here, we show the potential involvement of cutaneous mast cells in oxaliplatin-induced mechanical allodynia in mice. A single intraperitoneal injection of oxaliplatin induced mechanical allodynia, which peaked on day 10 after injection. Oxaliplatin-induced mechanical allodynia was almost completely prevented by congenital mast cell deficiency. The numbers of total and degranulated mast cells was significantly increased in the skin after oxaliplatin administration. Repetitive topical application of the mast cell stabilizer azelastine hydrochloride inhibited mechanical allodynia and the degranulation of mast cells without affecting the number of mast cells in oxaliplatin-treated mice. The serine protease inhibitor camostat mesilate and the proteinase-activated receptor 2 (PAR2) antagonist FSLLRY-NH2 significantly inhibited oxaliplatin-induced mechanical allodynia. However, it was not inhibited by the H1 histamine receptor antagonist terfenadine. Single oxaliplatin administration increased the activity of cutaneous serine proteases, which was attenuated by camostat and mast cell deficiency. Depletion of the capsaicin-sensitive primary afferents by neonatal capsaicin treatment almost completely prevented oxaliplatin-induced mechanical allodynia, the increase in the number of mast cells, and the activity of cutaneous serine proteases. These results suggest that serine protease(s) released from mast cells and PAR2 are involved in oxaliplatin-induced mechanical allodynia. Therefore, oxaliplatin may indirectly affect the functions of mast cells through its action on capsaicin-sensitive primary afferents.
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28
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Almlöf M, Carlsson J, Åqvist J. Improving the Accuracy of the Linear Interaction Energy Method for Solvation Free Energies. J Chem Theory Comput 2015; 3:2162-75. [PMID: 26636209 DOI: 10.1021/ct700106b] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A linear response method for estimating the free energy of solvation is presented and validated using explicit solvent molecular dynamics, thermodynamic perturbation calculations, and experimental data. The electrostatic contribution to the solvation free energy is calculated using a linear response estimate, which is obtained by comparison to the free energy calculated using thermodynamic perturbation. Systematic deviations from the value of (1)/2 in the potential energy scaling factor are observed for some types of compounds, and these are taken into account by introducing specific coefficients for different chemical groups. The derived model reduces the rms error of the linear response estimate significantly from 1.6 to 0.3 kcal/mol on a training set of 221 molecules used to parametrize the model and from 3.7 to 1.3 kcal/mol on a test set of 355 molecules that were not used in the derivation of the model. The total solvation free energy is estimated by combining the derived model with an empirical size dependent term for predicting the nonpolar contribution. Using this model, the experimental hydration free energies for 192 molecules are reproduced with an rms error of 1.1 kcal/mol. The use of LIE in simplified binding free energy calculations to predict protein-ligand binding free energies is also discussed.
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Affiliation(s)
- Martin Almlöf
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Jens Carlsson
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
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29
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Production of butyrate from lysine and the Amadori product fructoselysine by a human gut commensal. Nat Commun 2015; 6:10062. [PMID: 26620920 PMCID: PMC4697335 DOI: 10.1038/ncomms10062] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 10/29/2015] [Indexed: 12/18/2022] Open
Abstract
Human intestinal bacteria produce butyrate, which has signalling properties and can be used as energy source by enterocytes thus influencing colonic health. However, the pathways and the identity of bacteria involved in this process remain unclear. Here we describe the isolation from the human intestine of Intestinimonas strain AF211, a bacterium that can convert lysine stoichiometrically into butyrate and acetate when grown in a synthetic medium. Intestinimonas AF211 also converts the Amadori product fructoselysine, which is abundantly formed in heated foods via the Maillard reaction, into butyrate. The butyrogenic pathway includes a specific CoA transferase that is overproduced during growth on lysine. Bacteria related to Intestinimonas AF211 as well as the genetic coding capacity for fructoselysine conversion are abundantly present in colonic samples from some healthy human subjects. Our results indicate that protein can serve as a source of butyrate in the human colon, and its conversion by Intestinimonas AF211 and related butyrogens may protect the host from the undesired side effects of Amadori reaction products. Bacterial production of butyrate in the gut is associated with a healthy colon. Here the authors isolate an Intestinimonas strain from the human gut that can produce butyrate from lysine and fructoselysine, a potentially harmful compound formed in heated foods.
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30
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Wang L, Wang Z, Yuan Y, Cai R, Niu C, Yue T. Identification of Key Factors Involved in the Biosorption of Patulin by Inactivated Lactic Acid Bacteria (LAB) Cells. PLoS One 2015; 10:e0143431. [PMID: 26581099 PMCID: PMC4651504 DOI: 10.1371/journal.pone.0143431] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Accepted: 11/04/2015] [Indexed: 11/19/2022] Open
Abstract
The purpose of this study was to identify the key factors involved in patulin adsorption by heat-inactivated lactic acid bacteria (LAB) cells. For preventing bacterial contamination, a sterilization process was involved in the adsorption process. The effects of various physical, chemical, and enzymatic pre-treatments, simultaneous treatments, and post-treatments on the patulin adsorption performances of six LAB strains were evaluated. The pre-treated cells were characterized by scanning electron microscopy (SEM). Results showed that the removal of patulin by viable cells was mainly based on adsorption or degradation, depending on the specific strain. The adsorption abilities were widely increased by NaOH and esterification pre-treatments, and reduced by trypsin, lipase, iodate, and periodate pre-treatments. Additionally, the adsorption abilities were almost maintained at pH 2.2-4.0, and enhanced significantly at pH 4.0-6.0. The effects of sodium and magnesium ions on the adsorption abilities at pH 4 were slight and strain-specific. A lower proportion of patulin was released from the strain with higher adsorption ability. Analyses revealed that the physical structure of peptidoglycan was not a principal factor. Vicinal OH and carboxyl groups were not involved in patulin adsorption, while alkaline amino acids, thiol and ester compounds were important for patulin adsorption. Additionally, besides hydrophobic interaction, electrostatic interaction also participated in patulin adsorption, which was enhanced with the increase in pH (4.0-6.0).
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Affiliation(s)
- Ling Wang
- College of Food Science and Engineering, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Zhouli Wang
- College of Food Science and Engineering, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Yahong Yuan
- College of Food Science and Engineering, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Rui Cai
- College of Food Science and Engineering, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Chen Niu
- College of Food Science and Engineering, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Tianli Yue
- College of Food Science and Engineering, Northwest A & F University, Yangling, Shaanxi, 712100, China
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31
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Maximova K, Trylska J. Kinetics of trypsin-catalyzed hydrolysis determined by isothermal titration calorimetry. Anal Biochem 2015; 486:24-34. [DOI: 10.1016/j.ab.2015.06.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 06/13/2015] [Accepted: 06/16/2015] [Indexed: 10/23/2022]
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32
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Miranda WE, Noskov SY, Valiente PA. Improving the LIE Method for Binding Free Energy Calculations of Protein–Ligand Complexes. J Chem Inf Model 2015; 55:1867-77. [DOI: 10.1021/acs.jcim.5b00012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Williams E. Miranda
- Computational
Biology and Biomolecular Dynamics Laboratory, Center for Protein Studies,
Faculty of Biology, University of Havana, Havana, Cuba
| | - Sergei Yu. Noskov
- Centre
for Molecular Simulations and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Pedro A. Valiente
- Computational
Biology and Biomolecular Dynamics Laboratory, Center for Protein Studies,
Faculty of Biology, University of Havana, Havana, Cuba
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33
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Shu M, Shen W, Wang X, Wang F, Ma L, Zhai C. Expression, activation and characterization of porcine trypsin in Pichia pastoris GS115. Protein Expr Purif 2015; 114:149-55. [PMID: 26118809 DOI: 10.1016/j.pep.2015.06.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/26/2015] [Accepted: 06/22/2015] [Indexed: 10/23/2022]
Abstract
Trypsin is a typical member of serine protease families, specifically cleaving the carboxyl group of peptides at the basic amino acids arginine and lysine. The gene fragment of porcine trypsin with its propeptide coding sequence was optimized and synthesized according to the codon usage bias of Pichia pastoris. The optimized sequence was integrated into the genome of P. pastoris GS115 using the vector pHBM905A. The yield of the recombinant protein was 0.48mg/ml with a maximum activity of 19.2U/ml after 96-h induction in a 5-l fermenter. An optimum activity for the recombinant trypsin was observed at 35°C and pH 8.5. This is the first time to express the porcine trypsinogen with P. pastoris expression system. This report also found that the propeptide was cleaved from the recombinant protein and the enzymogen was transferred into trypsin at the later phase of the fed-batch cultivation. In particular, the activation process can be initiated by changing pH.
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Affiliation(s)
- Min Shu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, People's Republic of China
| | - Wei Shen
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, People's Republic of China
| | - Xiaojuan Wang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, People's Republic of China
| | - Fei Wang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, People's Republic of China
| | - Lixin Ma
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, People's Republic of China.
| | - Chao Zhai
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, People's Republic of China.
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34
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Pazhang M, Mehrnejad F, Pazhang Y, Falahati H, Chaparzadeh N. Effect of sorbitol and glycerol on the stability of trypsin and difference between their stabilization effects in the various solvents. Biotechnol Appl Biochem 2015; 63:206-13. [DOI: 10.1002/bab.1366] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 03/05/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Mohammad Pazhang
- Department of Cellular and Molecular Biology; Faculty of Sciences, Azarbaijan Shahid Madani University; Tabriz Iran
| | - Faramarz Mehrnejad
- Department of Life Science Engineering; Faculty of New Sciences & Technologies, University of Tehran; Tehran Iran
| | - Yaghub Pazhang
- Department of Biology; Faculty of Science, Urmia University; Urmia Iran
| | - Hanieh Falahati
- Department of Quantitative and Computational Biology; Princeton University; Princeton NJ USA
| | - Nader Chaparzadeh
- Department of Cellular and Molecular Biology; Faculty of Sciences, Azarbaijan Shahid Madani University; Tabriz Iran
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35
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Ouidir T, Cosette P, Jouenne T, Hardouin J. Proteomic profiling of lysine acetylation in Pseudomonas aeruginosa reveals the diversity of acetylated proteins. Proteomics 2015; 15:2152-7. [PMID: 25900529 DOI: 10.1002/pmic.201500056] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 03/30/2015] [Accepted: 04/17/2015] [Indexed: 12/31/2022]
Abstract
Protein lysine acetylation is a reversible and highly regulated post-translational modification with the well demonstrated physiological relevance in eukaryotes. Recently, its important role in the regulation of metabolic processes in bacteria was highlighted. Here, we reported the lysine acetylproteome of Pseudomonas aeruginosa using a proteomic approach. We identified 430 unique peptides corresponding to 320 acetylated proteins. In addition to the proteins involved in various metabolic pathways, several enzymes contributing to the lipopolysaccharides biosynthesis were characterized as acetylated. This data set illustrated the abundance and the diversity of acetylated lysine proteins in P. aeruginosa and opens opportunities to explore the role of the acetylation in the bacterial physiology.
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Affiliation(s)
- Tassadit Ouidir
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, Mont-Saint-Aignan, France.,Normandie University, UR, France.,PISSARO proteomic facility, IRIB, Mont-Saint-Aignan, France
| | - Pascal Cosette
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, Mont-Saint-Aignan, France.,Normandie University, UR, France.,PISSARO proteomic facility, IRIB, Mont-Saint-Aignan, France
| | - Thierry Jouenne
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, Mont-Saint-Aignan, France.,Normandie University, UR, France.,PISSARO proteomic facility, IRIB, Mont-Saint-Aignan, France
| | - Julie Hardouin
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, Mont-Saint-Aignan, France.,Normandie University, UR, France.,PISSARO proteomic facility, IRIB, Mont-Saint-Aignan, France
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36
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Tang K, Wong SWK, Liu JS, Zhang J, Liang J. Conformational sampling and structure prediction of multiple interacting loops in soluble and β-barrel membrane proteins using multi-loop distance-guided chain-growth Monte Carlo method. Bioinformatics 2015; 31:2646-52. [PMID: 25861965 DOI: 10.1093/bioinformatics/btv198] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 04/03/2015] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Loops in proteins are often involved in biochemical functions. Their irregularity and flexibility make experimental structure determination and computational modeling challenging. Most current loop modeling methods focus on modeling single loops. In protein structure prediction, multiple loops often need to be modeled simultaneously. As interactions among loops in spatial proximity can be rather complex, sampling the conformations of multiple interacting loops is a challenging task. RESULTS In this study, we report a new method called multi-loop Distance-guided Sequential chain-Growth Monte Carlo (M-DiSGro) for prediction of the conformations of multiple interacting loops in proteins. Our method achieves an average RMSD of 1.93 Å for lowest energy conformations of 36 pairs of interacting protein loops with the total length ranging from 12 to 24 residues. We further constructed a data set containing proteins with 2, 3 and 4 interacting loops. For the most challenging target proteins with four loops, the average RMSD of the lowest energy conformations is 2.35 Å. Our method is also tested for predicting multiple loops in β-barrel membrane proteins. For outer-membrane protein G, the lowest energy conformation has a RMSD of 2.62 Å for the three extracellular interacting loops with a total length of 34 residues (12, 12 and 10 residues in each loop). AVAILABILITY AND IMPLEMENTATION The software is freely available at: tanto.bioe.uic.edu/m-DiSGro. CONTACT jinfeng@stat.fsu.edu or jliang@uic.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ke Tang
- Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL
| | - Samuel W K Wong
- Department of Statistics, University of Florida, Gainesville, FL
| | - Jun S Liu
- Department of Statistics, Harvard University, Science Center, Cambridge, MA and
| | - Jinfeng Zhang
- Department of Statistics, Florida State University, Tallahassee, FL, USA
| | - Jie Liang
- Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL
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37
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Chen J, Wang J, Zhang Q, Chen K, Zhu W. A comparative study of trypsin specificity based on QM/MM molecular dynamics simulation and QM/MM GBSA calculation. J Biomol Struct Dyn 2015; 33:2606-18. [PMID: 25562613 DOI: 10.1080/07391102.2014.1003146] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Hydrogen bonding and polar interactions play a key role in identification of protein-inhibitor binding specificity. Quantum mechanics/molecular mechanics molecular dynamics (QM/MM MD) simulations combined with DFT and semi-empirical Hamiltonian (AM1d, RM1, PM3, and PM6) methods were performed to study the hydrogen bonding and polar interactions of two inhibitors BEN and BEN1 with trypsin. The results show that the accuracy of treating the hydrogen bonding and polar interactions using QM/MM MD simulation of PM6 can reach the one obtained by the DFT QM/MM MD simulation. Quantum mechanics/molecular mechanics generalized Born surface area (QM/MM-GBSA) method was applied to calculate binding affinities of inhibitors to trypsin and the results suggest that the accuracy of binding affinity prediction can be significantly affected by the accurate treatment of the hydrogen bonding and polar interactions. In addition, the calculated results also reveal the binding specificity of trypsin: (1) the amidinium groups of two inhibitors generate favorable salt bridge interaction with Asp189 and form hydrogen bonding interactions with Ser190 and Gly214, (2) the phenyl of inhibitors can produce favorable van der Waals interactions with the residues His58, Cys191, Gln192, Trp211, Gly212, and Cys215. This systematic and comparative study can provide guidance for the choice of QM/MM MD methods and the designs of new potent inhibitors targeting trypsin.
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Affiliation(s)
- Jianzhong Chen
- a School of Science , Shandong Jiaotong University , Jinan , 250014 , China
| | - Jinan Wang
- b Discovery and Design Center , CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai , 201203 , China
| | - Qinggang Zhang
- c College of Physics and Electronics , Shandong Normal University , Jinan , 250014 , China
| | - Kaixian Chen
- b Discovery and Design Center , CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai , 201203 , China
| | - Weiliang Zhu
- b Discovery and Design Center , CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai , 201203 , China
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38
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Catalytic activation of pre-substrates via dynamic fragment assembly on protein templates. Nat Commun 2014; 5:5170. [PMID: 25403979 DOI: 10.1038/ncomms6170] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 09/08/2014] [Indexed: 11/09/2022] Open
Abstract
Sensitive detection of small molecule fragments binding to defined sites of biomacromolecules is still a considerable challenge. Here we demonstrate that protein-binding fragments are able to induce enzymatic reactions on the protein surface via dynamic fragment ligation. Fragments binding to the S1 pocket of serine proteases containing a nitrogen, oxygen or sulphur nucleophile are found to activate electrophilic pre-substrates through a reversible, covalent ligation reaction. The dynamic ligation reaction positions the pre-substrate molecule at the active site of the protein thereby inducing its enzymatic cleavage. Catalytic activation of pre-substrates is confirmed by fluorescence spectroscopy and by high-performance liquid chromatography. The approach is investigated with 3 pre-substrates and 14 protein-binding fragments and the specific activation and the templating effect exerted by the enzyme is quantified for each protease-fragment-pre-substrate combination. The described approach enables the site-specific identification of protein-binding fragments, the functional characterization of enzymatic sites and the quantitative analysis of protein template-assisted ligation reactions.
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39
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Wu HJ, Li Y, Fan J, Deng Z, Hu Z, Liu X, Graviss EA, Ferrari M, Ma X, Hu Y. Antibody-free detection of Mycobacterium tuberculosis antigen using customized nanotraps. Anal Chem 2014; 86:1988-96. [PMID: 24446580 PMCID: PMC3983014 DOI: 10.1021/ac4027669] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Rapid
screening and diagnosis of tuberculosis disease (TB) is still
challenging and critically needed for global TB control efforts. In
this study, we present a rapid and streamlined technology, using precisely
engineered silica nanopore thin films, which are optimized for pore
size, structure, capillary force, and film thickness, to isolate Mycobacterium tuberculosis (MTB) antigens in laboratory
and clinical samples for rapid TB screening. This technology, referred
to here as on-chip fractionation, is integrated with high-throughput
matrix-assisted laser desorption/ionization time-of flight mass spectrometry
to screen and identify fragments of the MTB antigen, CFP-10, from
complex biological samples, without use of immunoaffinity agents.
With the use of this comprehensive approach, we were able to clearly
distinguish a clinical isolate of MTB from a nonTB species of the
genus Mycobacterium avium grown in
liquid culture media. This assay can reach a detection limit of 10
fmol and an isolation rate of 90% for the antigen CFP-10. Our strategy
has significant potential to fill the conceptual and technical gaps
in rapid diagnosis of active TB disease.
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Affiliation(s)
- Hung-Jen Wu
- Department of Nanomedicine, Houston Methodist Research Institute , 6670 Bertner Avenue R8-213, Houston, TX 77030, United States
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40
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Takahashi R, Gil VA, Guallar V. Monte Carlo Free Ligand Diffusion with Markov State Model Analysis and Absolute Binding Free Energy Calculations. J Chem Theory Comput 2013; 10:282-8. [PMID: 26579911 DOI: 10.1021/ct400678g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Obtaining absolute binding free energies from unbiased ligand diffusion has attracted a significant amount of attention due to its implications in drug design. Several studies have used special purpose computers and software to achieve microsecond molecular dynamics which, combined with a Markov state model analysis, are capable of providing absolute binding free energies. We have recently developed a Monte Carlo based technique, PELE, capable of performing a dynamical exploration of the protein-ligand energy landscape including free ligand diffusion into the active site, at a fraction of the computational cost of molecular dynamics techniques. We demonstrate here the capabilities of our Monte Carlo technique in obtaining absolute binding free energies for a series of benzamidine like inhibitors into trypsin. Our results are in good agreement with experimental data and other molecular dynamics simulations, indicating that PELE can be a useful tool for quick estimates of binding free energies and mechanisms.
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Affiliation(s)
- Ryoji Takahashi
- Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center , c/Jordi Girona 29, 08034 Barcelona, Spain
| | - Víctor A Gil
- Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center , c/Jordi Girona 29, 08034 Barcelona, Spain
| | - Victor Guallar
- Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center , c/Jordi Girona 29, 08034 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA) , Passeig Lluís Companys 23, 08010 Barcelona, Spain
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41
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Ismaya WT, Hasan K, Kardi I, Zainuri A, Rahmawaty RI, Permanahadi S, El Viera BV, Harinanto G, Gaffar S, Natalia D, Subroto T, Soemitro S. Chemical modification of Saccharomycopsis fibuligera R64 α-amylase to improve its stability against thermal, chelator, and proteolytic inactivation. Appl Biochem Biotechnol 2013; 170:44-57. [PMID: 23468006 DOI: 10.1007/s12010-013-0164-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 02/21/2013] [Indexed: 10/27/2022]
Abstract
α-Amylase catalyzes hydrolysis of starch to oligosaccharides, which are further degraded to simple sugars. The enzyme has been widely used in food and textile industries and recently, in generation of renewable energy. An α-amylase from yeast Saccharomycopsis fibuligera R64 (Sfamy) is active at 50 °C and capable of degrading raw starch, making it attractive for the aforementioned applications. To improve its characteristics as well as to provide information for structural study ab initio, the enzyme was chemically modified by acid anhydrides (nonpolar groups), glyoxylic acid (GA) (polar group), dimethyl adipimidate (DMA) (cross-linking), and polyethylene glycol (PEG) (hydrophilization). Introduction of nonpolar groups increased enzyme stability up to 18 times, while modification by a cross-linking agent resulted in protection of the calcium ion, which is essential for enzyme activity and integrity. The hydrophilization with PEG resulted in protection against tryptic digestion. The chemical modification of Sfamy by various modifiers has thereby resulted in improvement of its characteristics and provided systematic information beneficial for structural study of the enzyme. An in silico structural study of the enzyme improved the interpretation of the results.
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Affiliation(s)
- Wangsa Tirta Ismaya
- Biochemistry Laboratory, Department of Chemistry, Faculty of Mathematics and Natural Sciences, Padjadjaran University, Jalan Singaperbangsa No. 2, 40133 Bandung, Indonesia.
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42
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Wu X, Vellaichamy A, Wang D, Zamdborg L, Kelleher NL, Huber SC, Zhao Y. Differential lysine acetylation profiles of Erwinia amylovora strains revealed by proteomics. J Proteomics 2012; 79:60-71. [PMID: 23234799 DOI: 10.1016/j.jprot.2012.12.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 11/05/2012] [Accepted: 12/01/2012] [Indexed: 01/01/2023]
Abstract
Protein lysine acetylation (LysAc) has recently been demonstrated to be widespread in E. coli and Salmonella, and to broadly regulate bacterial physiology and metabolism. However, LysAc in plant pathogenic bacteria is largely unknown. Here we first report the lysine acetylome of Erwinia amylovora, an enterobacterium causing serious fire blight disease of apples and pears. Immunoblots using generic anti-lysine acetylation antibodies demonstrated that growth conditions strongly affected the LysAc profiles in E. amylovora. Differential LysAc profiles were also observed for two E. amylovora strains, known to have differential virulence in plants, indicating translational modification of proteins may be important in determining virulence of bacterial strains. Proteomic analysis of LysAc in two E. amylovora strains identified 141 LysAc sites in 96 proteins that function in a wide range of biological pathways. Consistent with previous reports, 44% of the proteins are involved in metabolic processes, including central metabolism, lipopolysaccharide, nucleotide and amino acid metabolism. Interestingly, for the first time, several proteins involved in E. amylovora virulence, including exopolysaccharide amylovoran biosynthesis- and type III secretion-associated proteins, were found to be lysine acetylated, suggesting that LysAc may play a major role in bacterial virulence. Comparative analysis of LysAc sites in E. amylovora and E. coli further revealed the sequence and structural commonality for LysAc in the two organisms. Collectively, these results reinforce the notion that LysAc of proteins is widespread in bacterial metabolism and virulence.
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Affiliation(s)
- Xia Wu
- Department of Plant Biology, University of Illinois, Urbana, IL 61801, USA
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Dallas DC, Underwood MA, Zivkovic AM, German JB. Digestion of Protein in Premature and Term Infants. JOURNAL OF NUTRITIONAL DISORDERS & THERAPY 2012; 2:112. [PMID: 24744976 PMCID: PMC3988022 DOI: 10.4172/2161-0509.1000112] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Premature birth rates and premature infant morbidity remain discouragingly high. Improving nourishment for these infants is the key for accelerating their development and decreasing disease risk. Dietary protein is essential for growth and development of infants. Studies on protein nourishment for premature infants have focused on protein requirements for catch-up growth, nitrogen balance, and digestive protease concentrations and activities. However, little is known about the processes and products of protein digestion in the premature infant. This review briefly summarizes the protein requirements of term and preterm infants, and the protein content of milk from women delivering preterm and at term. An in-depth review is presented of the current knowledge of term and preterm infant dietary protein digestion, including human milk protease and anti-protease concentrations; neonatal intestinal pH, and enzyme activities and concentrations; and protein fermentation by intestinal bacteria. The advantages and disadvantages of incomplete protein digestion as well as factors that increase resistance to proteolysis of particular proteins are discussed. In order to better understand protein digestion in preterm and term infants, future studies should examine protein and peptide fragment products of digestion in saliva, gastric, intestinal and fecal samples, as well as the effects of the gut micro biome on protein degradation. The confluence of new mass spectrometry technology and new bioinformatics programs will now allow thorough identification of the array of peptides produced in the infant as they are digested.
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Affiliation(s)
- David C Dallas
- Department of Food Science, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA
- Foods for Health Institute, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Mark A Underwood
- Foods for Health Institute, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA
- Department of Pediatrics, University of California Davis, 2315 Stockton Blvd., Sacramento, CA, 95817, USA
| | - Angela M. Zivkovic
- Department of Food Science, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA
- Foods for Health Institute, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - J. Bruce German
- Department of Food Science, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA
- Foods for Health Institute, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA
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Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores. J Comput Aided Mol Des 2012; 26:647-59. [PMID: 22476578 DOI: 10.1007/s10822-012-9567-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 03/21/2012] [Indexed: 10/28/2022]
Abstract
Two families of binding affinity estimation methodologies are described which were utilized in the SAMPL3 trypsin/fragment binding affinity challenge. The first is a free energy decomposition scheme based on a thermodynamic cycle, which included separate contributions from enthalpy and entropy of binding as well as a solvent contribution. Enthalpic contributions were estimated with PM6-DH2 semiempirical quantum mechanical interaction energies, which were modified with a statistical error correction procedure. Entropic contributions were estimated with the rigid-rotor harmonic approximation, and solvent contributions to the free energy were estimated with several different methods. The second general methodology is the empirical score LISA, which contains several physics-based terms trained with the large PDBBind database of protein/ligand complexes. Here we also introduce LISA+, an updated version of LISA which, prior to scoring, classifies systems into one of four classes based on a ligand's hydrophobicity and molecular weight. Each version of the two methodologies (a total of 11 methods) was trained against a compiled set of known trypsin binders available in the Protein Data Bank to yield scaling parameters for linear regression models. Both raw and scaled scores were submitted to SAMPL3. Variants of LISA showed relatively low absolute errors but also low correlation with experiment, while the free energy decomposition methods had modest success when scaling factors were included. Nonetheless, re-scaled LISA yielded the best predictions in the challenge in terms of RMS error, and six of these models placed in the top ten best predictions by RMS error. This work highlights some of the difficulties of predicting binding affinities of small molecular fragments to protein receptors as well as the benefit of using training data.
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de Ruiter A, Oostenbrink C. Efficient and Accurate Free Energy Calculations on Trypsin Inhibitors. J Chem Theory Comput 2012; 8:3686-95. [PMID: 26593013 DOI: 10.1021/ct200750p] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Several combinations of free energy calculation methods have been applied to determine the relative free energies of binding between eight para-substituted benzamidines in complex with the serine protease trypsin. With the aim to improve efficiency and maintain accuracy, the linear response approximation (LRA), linear interaction energy (LIE) and third power fitting (TPF) are combined with the one-step perturbation (OSP) to determine the polar and apolar contributions to the free energy, respectively. It is shown that the combination TPF/OSP gives the most accurate results and is 4.5 times more efficient than the rigorous thermodynamic integration (TI). By projecting the electrostatic preorganization energy from the OSP simulations, an increase in efficiency of a factor 7.5 can even be achieved. Loss of accuracy with respect to the TI data is limited to 3.9 and 5.6 kJ/mol, respectively, making it an attractive approach for lead optimization programs in drug research.
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Affiliation(s)
- Anita de Ruiter
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU) , Vienna, Austria
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences (BOKU) , Vienna, Austria
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Effects of Selected Anionic β-Cyclodextrins on Persistence of Blood Glucose Lowering by Insulin Glargine after Subcutaneous Injection to Rats. JOURNAL OF DRUG DELIVERY 2011; 2011:195146. [PMID: 22187651 PMCID: PMC3236511 DOI: 10.1155/2011/195146] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 09/19/2011] [Indexed: 01/26/2023]
Abstract
Insulin glargine is a synthetic long-acting insulin product used for patients with diabetes mellitus. In this study, to obtain the further desirable blood-glucose lowering profile of insulin glargine, we investigated the effects of β-cyclodextrin sulfate (Sul-β-CyD) and sulfobutylether β-cyclodextrin (SBE7-β-CyD) on physicochemical properties of insulin glargine and pharmacokinetics/pharmacodynamics of insulin glargine after subcutaneous injection to rats. Sul-β-CyD and SBE7-β-CyD increased solubility of insulin glargine. SBE7-β-CyD suppressed the formation of oligomer and enhanced the dissolution rate of insulin glargine from its precipitate, compared to that of Sul-β-CyD. Additionally, we revealed that after subcutaneous administration of an insulin glargine solution, SBE7-β-CyD, but not Sul-β-CyD, increased bioavailability and sustained the blood-glucose lowering effect, possibly due to the inhibitory effects of SBE7-β-CyD on the enzymatic degradation at the injection site. These results suggest that SBE7-β-CyD could be a useful excipient for sustained release of insulin glargine.
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Uehata K, Anno T, Hayashida K, Motoyama K, Hirayama F, Ono N, Pipkin JD, Uekama K, Arima H. Effect of sulfobutyl ether-β-cyclodextrin on bioavailability of insulin glargine and blood glucose level after subcutaneous injection to rats. Int J Pharm 2011; 419:71-6. [DOI: 10.1016/j.ijpharm.2011.07.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 06/14/2011] [Accepted: 07/14/2011] [Indexed: 11/29/2022]
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Ghasemi M, Minier MJG, Tatoulian M, Chehimi MM, Arefi-Khonsari F. Ammonia Plasma Treated Polyethylene Films for Adsorption or Covalent Immobilization of Trypsin: Quantitative Correlation between X-ray Photoelectron Spectroscopy Data and Enzyme Activity. J Phys Chem B 2011; 115:10228-38. [DOI: 10.1021/jp204097a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Mahsa Ghasemi
- Chimie ParisTech, Laboratoire de Génie des Procédés Plasma et Traitements de Surface (LGPPTS), EA 3492, 75005 Paris, France
- UPMC Univ Paris 06, 75005 Paris, France
- Chimie ParisTech, Laboratoire Charles Friedel (LCF), 75005 Paris, France
- CNRS, UMR 7223, 75005 Paris, France
| | - Michel J. G. Minier
- Chimie ParisTech, Laboratoire Charles Friedel (LCF), 75005 Paris, France
- CNRS, UMR 7223, 75005 Paris, France
| | - Michaël Tatoulian
- Chimie ParisTech, Laboratoire de Génie des Procédés Plasma et Traitements de Surface (LGPPTS), EA 3492, 75005 Paris, France
- UPMC Univ Paris 06, 75005 Paris, France
| | - Mohamed M. Chehimi
- Interfaces, Traitements, Organisation & Dynamique des Systèmes (ITODYS Lab), University Paris Diderot & CNRS, 15 rue Jean-Antoine de Baïf, 75013 Paris, France
| | - Farzaneh Arefi-Khonsari
- Chimie ParisTech, Laboratoire de Génie des Procédés Plasma et Traitements de Surface (LGPPTS), EA 3492, 75005 Paris, France
- UPMC Univ Paris 06, 75005 Paris, France
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Raman EP, Yu W, Guvench O, MacKerell AD. Reproducing crystal binding modes of ligand functional groups using Site-Identification by Ligand Competitive Saturation (SILCS) simulations. J Chem Inf Model 2011; 51:877-96. [PMID: 21456594 PMCID: PMC3090225 DOI: 10.1021/ci100462t] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The applicability of a computational method, Site Identification by Ligand Competitive Saturation (SILCS), to identify regions on a protein surface with which different types of functional groups on low-molecular weight inhibitors interact is demonstrated. The method involves molecular dynamics (MD) simulations of a protein in an aqueous solution of chemically diverse small molecules from which probability distributions of fragments types, termed FragMaps, are obtained. In the present application, SILCS simulations are performed with an aqueous solution of 1 M benzene and propane to map the affinity pattern of the protein for aromatic and aliphatic functional groups. In addition, water hydrogen and oxygen atoms serve as probes for hydrogen-bond donor and acceptor affinity, respectively. The method is tested using a set of 7 proteins for which crystal structures of complexes with several high affinity inhibitors are known. Good agreement is obtained between FragMaps and the positions of chemically similar functional groups in inhibitors as observed in the X-ray crystallographic structures. Quantitative capabilities of the SILCS approach are demonstrated by converting FragMaps to free energies, termed Grid Free Energies (GFE), and showing correlation between the GFE values and experimental binding affinities. For proteins for which ligand decoy sets are available, GFE values are shown to typically score the crystal conformation and conformations similar to it more favorable than decoys. Additionally, SILCS is tested for its ability to capture the subtle differences in ligand affinity across homologous proteins, information which may be of utility toward specificity-guided drug design. Taken together, our results show that SILCS can recapitulate the known location of functional groups of bound inhibitors for a number of proteins, suggesting that the method may be of utility for rational drug design.
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Affiliation(s)
- E. Prabhu Raman
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street HSF II, Baltimore MD 21201
| | - Wenbo Yu
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street HSF II, Baltimore MD 21201
| | - Olgun Guvench
- Department of Pharmaceutical Sciences, University of New England College of Pharmacy, 716 Stevens Ave, Portland ME 04103
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street HSF II, Baltimore MD 21201
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50
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Yang T, Wu JC, Yan C, Wang Y, Luo R, Gonzales MB, Dalby KN, Ren P. Virtual screening using molecular simulations. Proteins 2011; 79:1940-51. [PMID: 21491494 DOI: 10.1002/prot.23018] [Citation(s) in RCA: 146] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 01/24/2011] [Accepted: 02/05/2011] [Indexed: 11/05/2022]
Abstract
Effective virtual screening relies on our ability to make accurate prediction of protein-ligand binding, which remains a great challenge. In this work, utilizing the molecular-mechanics Poisson-Boltzmann (or Generalized Born) surface area approach, we have evaluated the binding affinity of a set of 156 ligands to seven families of proteins, trypsin β, thrombin α, cyclin-dependent kinase (CDK), cAMP-dependent kinase (PKA), urokinase-type plasminogen activator, β-glucosidase A, and coagulation factor Xa. The effect of protein dielectric constant in the implicit-solvent model on the binding free energy calculation is shown to be important. The statistical correlations between the binding energy calculated from the implicit-solvent approach and experimental free energy are in the range of 0.56-0.79 across all the families. This performance is better than that of typical docking programs especially given that the latter is directly trained using known binding data whereas the molecular mechanics is based on general physical parameters. Estimation of entropic contribution remains the barrier to accurate free energy calculation. We show that the traditional rigid rotor harmonic oscillator approximation is unable to improve the binding free energy prediction. Inclusion of conformational restriction seems to be promising but requires further investigation. On the other hand, our preliminary study suggests that implicit-solvent based alchemical perturbation, which offers explicit sampling of configuration entropy, can be a viable approach to significantly improve the prediction of binding free energy. Overall, the molecular mechanics approach has the potential for medium to high-throughput computational drug discovery.
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Affiliation(s)
- Tianyi Yang
- Department of Biomedical Engineering, The University of Texas, Austin, Texas 78712, USA
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