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Hsieh PC, Yu PS, Fan WL, Wang CC, Chao CY, Wu YR. A New Phenotype of TUBB4A Mutation in a Family With Adult-Onset Progressive Spastic Paraplegia and Isolated Hypomyelination Leukodystrophy: A Case Report and Literature Review. J Mov Disord 2024; 17:94-98. [PMID: 37867417 PMCID: PMC10846974 DOI: 10.14802/jmd.23142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/25/2023] [Accepted: 10/23/2023] [Indexed: 10/24/2023] Open
Abstract
Tubulin beta 4A class IVa (TUBB4A) spectrum disorders include autosomal dominant dystonia type 4 or hypomyelination with atrophy of the basal ganglia and cerebellum (H-ABC syndrome). However, in rare cases, only mild hypomyelination in the cortex with no basal ganglia atrophy may be observed. We report a case of a family with TUBB4A mutation and complicated hereditary spasticity paraplegia (HSP). We performed quadro whole-exome sequencing (WES) on the family to identify the causative gene of progressive spastic paraparesis with isolated hypomyelination leukodystrophy. We identified a novel TUBB4A p.F341L mutation, which was present in all three affected patients but absent in the unaffected father. The affected patients presented with adult-onset TUBB4A disorder, predominant spastic paraparesis with/without ataxia, and brain hypomyelination with no cognitive impairment or extrapyramidal symptoms. In the literature, HSP is considered a TUBB4A spectrum disorder.
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Affiliation(s)
- Pei-Chen Hsieh
- Department of Neurology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Pei Shan Yu
- Department of Neurology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Wen-Lang Fan
- Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Chun-Chieh Wang
- Department of Neurology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Chih-Ying Chao
- Department of Neurology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Yih-Ru Wu
- Department of Neurology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
- Department of Neurology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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2
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Bureau JA, Oliva ME, Dong Y, Ignea C. Engineering yeast for the production of plant terpenoids using synthetic biology approaches. Nat Prod Rep 2023; 40:1822-1848. [PMID: 37523210 DOI: 10.1039/d3np00005b] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
Covering: 2011-2022The low amounts of terpenoids produced in plants and the difficulty in synthesizing these complex structures have stimulated the production of terpenoid compounds in microbial hosts by metabolic engineering and synthetic biology approaches. Advances in engineering yeast for terpenoid production will be covered in this review focusing on four directions: (1) manipulation of host metabolism, (2) rewiring and reconstructing metabolic pathways, (3) engineering the catalytic activity, substrate selectivity and product specificity of biosynthetic enzymes, and (4) localizing terpenoid production via enzymatic fusions and scaffolds, or subcellular compartmentalization.
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Affiliation(s)
| | | | - Yueming Dong
- Department of Bioengineering, McGill University, Montreal, QC, H3A 0C3, Canada.
| | - Codruta Ignea
- Department of Bioengineering, McGill University, Montreal, QC, H3A 0C3, Canada.
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Parveen A, Malashetty VB, Shetty PR, Patil V, Deshpande R. Rapid and easy identification of genes associated with nanoparticles from plant protein structure database. OPENNANO 2022. [DOI: 10.1016/j.onano.2022.100071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Expanding the terpene biosynthetic code with non-canonical 16 carbon atom building blocks. Nat Commun 2022; 13:5188. [PMID: 36057727 PMCID: PMC9440906 DOI: 10.1038/s41467-022-32921-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 08/23/2022] [Indexed: 11/08/2022] Open
Abstract
Humankind relies on specialized metabolites for medicines, flavors, fragrances, and numerous other valuable biomaterials. However, the chemical space occupied by specialized metabolites, and, thus, their application potential, is limited because their biosynthesis is based on only a handful of building blocks. Engineering organisms to synthesize alternative building blocks will bypass this limitation and enable the sustainable production of molecules with non-canonical chemical structures, expanding the possible applications. Herein, we focus on isoprenoids and combine synthetic biology with protein engineering to construct yeast cells that synthesize 10 non-canonical isoprenoid building blocks with 16 carbon atoms. We identify suitable terpene synthases to convert these building blocks into C16 scaffolds and a cytochrome P450 to decorate the terpene scaffolds and produce different oxygenated compounds. Thus, we reconstruct the modular structure of terpene biosynthesis on 16-carbon backbones, synthesizing 28 different non-canonical terpenes, some of which have interesting odorant properties.
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Wang Y, Binning JM, Pintilie GD, Chiu W, Amarasinghe GK, Leung DW, Su Z. Cryo-EM analysis of Ebola virus nucleocapsid-like assembly. STAR Protoc 2022; 3:101030. [PMID: 34977676 PMCID: PMC8689349 DOI: 10.1016/j.xpro.2021.101030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
This protocol describes the reconstitution of the filamentous Ebola virus nucleocapsid-like assembly in vitro. This is followed by solving the cryo-EM structure using helical reconstruction, and flexible fitting of the existing model into the 5.8 Å cryo-EM map. The protocol can be applied to other filamentous viral protein assemblies, particularly those with high flexibility and moderate resolution maps, which present technical challenges to model building. For complete details on the use and execution of this profile, please refer to Su et al. (2018). Preparation of Ebola nucleocapsid-like assembly for cryo-EM Cryo-EM helical reconstruction of flexible filamentous protein assembly Flexible fitting of protein model into cryo-EM density at moderate resolution
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Affiliation(s)
- Yan Wang
- The State Key Laboratory of Biotherapy and Cancer Center, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan 610044, China
| | - Jennifer M. Binning
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Grigore D. Pintilie
- Department of Bioengineering and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Wah Chiu
- Department of Bioengineering and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Gaya K. Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Corresponding author
| | - Daisy W. Leung
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Corresponding author
| | - Zhaoming Su
- The State Key Laboratory of Biotherapy and Cancer Center, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan 610044, China
- Corresponding author
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Sridharan R, Krishnaswamy V, Kumar PS, Vidhya TA, Sivamurugan V, Kumar DT, Doss CGP, Vo DVN. Analysis and effective separation of toxic pollutants from water resources using MBBR: Pathway prediction using alkaliphilic P. mendocina. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:149135. [PMID: 34311373 DOI: 10.1016/j.scitotenv.2021.149135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/11/2021] [Accepted: 07/14/2021] [Indexed: 06/13/2023]
Abstract
Azo dyes are highly toxic, which acts as a notable mutagen and carcinogen. This has a significant effect on human health, plants, animals, aquatic and terrestrial environments. Thus, the degradation of the azo dyes is exclusively studied using the conventional methods of which biodegradation is an eco-friendly approach. Hence, the present study is focused on the elucidation of reactive mixed azo dye degradation pathway using MBBR and laccase enzyme produced by an alkaliphilic bacterium P. mendocina. Synthetic wastewater treatment performed using MBBR was very effective which reduced the COD and BOD to 90 mg/L and 460 mg/L. The potential degrader P. mendocina was isolated and laccase enzyme was screened. Finally, the degradation pathway was elucidated. The in silico toxicity analysis predicted Reactive Red and Reactive Brown as developmental toxicants during Reactive Black as Developmental non-toxicant. Docking studies were performed to understand interaction of laccase with compounds evolved from dyes.
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Affiliation(s)
- Rajalakshmi Sridharan
- Department of Biotechnology, Stella Maris College (Autonomous) Affiliated to University of Madras, Chennai, Tamil Nadu 600 086, India
| | - Veenagayathri Krishnaswamy
- Department of Biotechnology, Stella Maris College (Autonomous) Affiliated to University of Madras, Chennai, Tamil Nadu 600 086, India.
| | - P Senthil Kumar
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Chennai 603110, India; Centre of Excellence in Water Research (CEWAR), Sri Sivasubramaniya Nadar College of Engineering, Chennai 603110, India.
| | - T Akshaya Vidhya
- Department of Biotechnology, Stella Maris College (Autonomous) Affiliated to University of Madras, Chennai, Tamil Nadu 600 086, India
| | | | - D Thirumal Kumar
- Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai 602 105, India
| | - C George Priya Doss
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632 014, India
| | - Dai-Viet N Vo
- Institute of Environmental Sciences, Nguyen Tat Thanh University, Ho Chi Minh City, Viet Nam
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The potentials of Calotropis procera against filarial elephantiasis: an in-silico approach. J Parasit Dis 2021; 46:384-394. [DOI: 10.1007/s12639-021-01456-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 09/17/2021] [Indexed: 10/20/2022] Open
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Ardila-Leal LD, Monterey-Gutiérrez PA, Poutou-Piñales RA, Quevedo-Hidalgo BE, Galindo JF, Pedroza-Rodríguez AM. Recombinant laccase rPOXA 1B real-time, accelerated and molecular dynamics stability study. BMC Biotechnol 2021; 21:37. [PMID: 34088291 PMCID: PMC8178886 DOI: 10.1186/s12896-021-00698-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/24/2021] [Indexed: 12/28/2022] Open
Abstract
Background Laccases (EC 1.10.3.2) are multi-copper oxidoreductases with great biotechnological importance due to their high oxidative potential and utility for removing synthetic dyes, oxidizing phenolic compounds, and degrading pesticides, among others. Methods A real-time stability study (RTS) was conducted for a year, by using enzyme concentrates from 3 batches (L1, L3, and L4). For which, five temperatures 243.15, 277.15, 298.15, 303.15, 308.15, and 313.15 K were assayed. Using RTS data and the Arrhenius equation, we calculated the rPOXA 1B accelerated stability (AS). Molecular dynamics (MD) computational study results were very close to those obtained experimentally at four different temperatures 241, 278, 298, and 314 K. Results In the RTS, 101.16, 115.81, 75.23, 46.09, 5.81, and 4.83% of the relative enzyme activity were recovered, at respective assayed temperatures. AS study, showed that rPOXA 1B is stable at 240.98 ± 5.38, 277.40 ± 1.32 or 297.53 ± 3.88 K; with t1/2 values of 230.8, 46.2, and 12.6 months, respectively. Kinetic and thermodynamic parameters supported the high stability of rPOXA 1B, with an Ed value of 41.40 KJ mol− 1, a low variation of KM and Vmax, at 240.98 ± 5.38, and 297.53 ± 3.88 K, and ∆G values showing deactivation reaction does not occur. The MD indicates that fluctuations in loop, coils or loops with hydrophilic or intermediate polarity amino acids as well as in some residues of POXA 1B 3D structure, increases with temperature; changing from three fluctuating residues at 278 K to six residues at 298 K, and nine residues at 314 K. Conclusions Laccase rPOXA 1B demonstrated experimentally and computationally to be a stable enzyme, with t1/2 of 230.8, 46.2 or 12.6 months, if it is preserved impure without preservatives at temperatures of 240.98 ± 5.38, 277.40 ± 1.32 or 297.53 ± 3.88 K respectively; this study could be of great utility for large scale producers. Supplementary Information The online version contains supplementary material available at 10.1186/s12896-021-00698-3.
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Affiliation(s)
- Leidy D Ardila-Leal
- Departamento de Microbiología. Facultad de Ciencias. Pontificia Universidad Javeriana (PUJ). Bogotá, Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Bogotá, D.C, Colombia
| | - Pedro A Monterey-Gutiérrez
- Vicerrectoría Académica. Universidad Antonio Nariño, Programa de Maestría y Doctorado en Educación Matemática, Bogotá, D.C, Colombia
| | - Raúl A Poutou-Piñales
- Departamento de Microbiología. Facultad de Ciencias. Pontificia Universidad Javeriana (PUJ). Bogotá, Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Bogotá, D.C, Colombia.
| | - Balkys E Quevedo-Hidalgo
- Departamento de Microbiología. Facultad de Ciencias. Pontificia Universidad Javeriana (PUJ), Laboratorio de Biotecnología Aplicada, Grupo de Biotecnología Ambiental e Industrial (GBAI), Bogotá, D.C, Colombia.
| | - Johan F Galindo
- Departamento de Química, Universidad Nacional de Colombia, Bogotá, D.C, Colombia.
| | - Aura M Pedroza-Rodríguez
- Departamento de Microbiología. Facultad de Ciencias. Pontificia Universidad Javeriana (PUJ). Bogotá, Laboratorio de Microbiología Ambiental y de Suelos, Grupo de Biotecnología Ambiental e Industrial (GBAI), Bogotá, D.C, Colombia
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Tan Y, Henehan GT, Kinsella GK, Ryan BJ. An extracellular lipase from Amycolatopsis mediterannei is a cutinase with plastic degrading activity. Comput Struct Biotechnol J 2021; 19:869-879. [PMID: 33598102 PMCID: PMC7851449 DOI: 10.1016/j.csbj.2021.01.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/08/2021] [Accepted: 01/14/2021] [Indexed: 11/04/2022] Open
Abstract
Amycolatopsis mediterranei lipase (AML) exhibits cutinase-like structural features. AML shows 60–70% sequence similarity to a few plastic degrading cutinases. AML has the ability to degrade poly(caprolactone) and poly(butylene succinate).
An extracellular lipase from Amycolatopsis mediteranei (AML) with potential applications in process biotechnology was recently cloned and examined in this laboratory. In the present study, the 3D structure of AML was elucidated by comparative modelling. AML lacked the ‘lid’ structure observed in most true lipases and shared similarities with plastic degrading enzymes. Modelling and substrate specificity studies showed that AML was a cutinase with a relatively exposed active site and specificity for medium chain fatty acyl moieties. AML rapidly hydrolysed the aliphatic plastics poly(ε-caprolactone) and poly(1,4-butylene succinate) extended with 1,6-diisocyanatohexane under mild conditions. These plastics are known to be slow to degrade in landfill. Poly(L-lactic acid) was not hydrolysed by AML, nor was the aromatic plastic Polyethylene Terephthalate (PET). The specificity of AML is partly explained by active site topology and analysis reveals that minor changes in the active site region can have large effects on substrate preference. These findings show that extracellular Amycolatopsis enzymes are capable of degrading a wider range of plastics than is generally recognised. The potential for application of AML in the bioremediation of plastics is discussed.
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Affiliation(s)
- Yeqi Tan
- School of Food Sciences and Environmental Health, Technological University Dublin, Grangegorman, Dublin 7 D07 H6K8, Ireland
| | - Gary T Henehan
- School of Food Sciences and Environmental Health, Technological University Dublin, Grangegorman, Dublin 7 D07 H6K8, Ireland
| | - Gemma K Kinsella
- School of Food Sciences and Environmental Health, Technological University Dublin, Grangegorman, Dublin 7 D07 H6K8, Ireland
| | - Barry J Ryan
- School of Food Sciences and Environmental Health, Technological University Dublin, Grangegorman, Dublin 7 D07 H6K8, Ireland
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Lanjanian H, Moazzam-Jazi M, Hedayati M, Akbarzadeh M, Guity K, Sedaghati-Khayat B, Azizi F, Daneshpour MS. SARS-CoV-2 infection susceptibility influenced by ACE2 genetic polymorphisms: insights from Tehran Cardio-Metabolic Genetic Study. Sci Rep 2021; 11:1529. [PMID: 33452303 PMCID: PMC7810897 DOI: 10.1038/s41598-020-80325-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 12/16/2020] [Indexed: 01/29/2023] Open
Abstract
The genetic variations among individuals are one of the notable factors determining disease severity and drug response. Nowadays, COVID-19 pandemic has been adversely affecting many aspects of human life. We used the Tehran Cardio-Metabolic Genetic Study (TCGS) data that is an ongoing genetic study including the whole-genome sequencing of 1200 individuals and chip genotyping of more than 15,000 participants. Here, the effect of ACE2 variations by focusing on the receptor-binding site of SARS-CoV-2 and ACE2 cleavage by TMPRSS2 protease were investigated through simulations study. After analyzing TCGS data, 570 genetic variations on the ACE2 gene, including single nucleotide polymorphisms (SNP) and insertion/deletion (INDEL) were detected. Interestingly, two observed missense variants, K26R and S331F, which only the first one was previously reported, can reduce the receptor affinity for the viral Spike protein. Moreover, our bioinformatics simulation of 3D structures and docking of proteins explains important details of ACE2-Spike and ACE2-TMPRSS2 interactions, especially the critical role of Arg652 of ACE2 for protease function of TMPRSS2 was uncovered. As our results show that the genetic variation of ACE2 can at least influence the affinity of this receptor to its partners, we need to consider the genetic variations on ACE2 as well as other genes in the pathways that contribute to the pathogenesis of COVID-19 for designing efficient drugs and vaccines.
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Affiliation(s)
- Hossein Lanjanian
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, POBox: 19195-4763, Tehran, Iran
| | - Maryam Moazzam-Jazi
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, POBox: 19195-4763, Tehran, Iran
| | - Mehdi Hedayati
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, POBox: 19195-4763, Tehran, Iran
| | - Mahdi Akbarzadeh
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, POBox: 19195-4763, Tehran, Iran
| | - Kamran Guity
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, POBox: 19195-4763, Tehran, Iran
| | - Bahareh Sedaghati-Khayat
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, POBox: 19195-4763, Tehran, Iran
| | - Fereidoun Azizi
- Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam S Daneshpour
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, POBox: 19195-4763, Tehran, Iran.
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Do HQ, Hewetson A, Borcik CG, Hastert MC, Whelly S, Wylie BJ, Sutton RB, Cornwall GA. Cross-seeding between the functional amyloidogenic CRES and CRES3 family members and their regulation of Aβ assembly. J Biol Chem 2021; 296:100250. [PMID: 33384380 PMCID: PMC7948811 DOI: 10.1074/jbc.ra120.015307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 11/24/2022] Open
Abstract
Accumulating evidence shows that amyloids perform biological roles. We previously showed that an amyloid matrix composed of four members of the CRES subgroup of reproductive family 2 cystatins is a normal component of the mouse epididymal lumen. The cellular mechanisms that control the assembly of these and other functional amyloid structures, however, remain unclear. We speculated that cross-seeding between CRES members could be a mechanism to control the assembly of the endogenous functional amyloid. Herein we used thioflavin T assays and negative stain transmission electron microscopy to explore this possibility. We show that CRES3 rapidly formed large networks of beaded chains that possessed the characteristic cross-β reflections of amyloid when examined by X-ray diffraction. The beaded amyloids accelerated the amyloidogenesis of CRES, a less amyloidogenic family member, in seeding assays during which beads transitioned into films and fibrils. Similarly, CRES seeds expedited CRES3 amyloidogenesis, although less efficiently than the CRES3 seeding of CRES. These studies suggest that CRES and CRES3 hetero-oligomerize and that CRES3 beaded amyloids may function as stable preassembled seeds. The CRES3 beaded amyloids also facilitated assembly of the unrelated amyloidogenic precursor Aβ by providing a surface for polymerization though, intriguingly, CRES3 (and CRES) monomer/early oligomer profoundly inhibited Aβ assembly. The cross-seeding between the CRES subgroup members is similar to that which occurs between bacterial curli proteins suggesting that it may be an evolutionarily conserved mechanism to control the assembly of some functional amyloids. Further, interactions between unrelated amyloidogenic precursors may also be a means to regulate functional amyloid assembly.
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Affiliation(s)
- Hoa Quynh Do
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Aveline Hewetson
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Collin G Borcik
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | | | - Sandra Whelly
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Benjamin J Wylie
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Roger Bryan Sutton
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Gail A Cornwall
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas, USA.
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Jindani S, Ganguly B. Exploiting the role of stereoelectronic effects to design the antagonists of the human complement C3a receptor. NEW J CHEM 2021. [DOI: 10.1039/d1nj00730k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Stereoelectronic effects are crucial in governing the conformational behaviour of small molecules bearing heterocyclic rings adjacent to amides.
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Affiliation(s)
- Sana Jindani
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility)
- CSIR-Central Salt and Marine Chemicals Research Institute
- Bhavnagar 364002
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility)
- CSIR-Central Salt and Marine Chemicals Research Institute
- Bhavnagar 364002
- India
- Academy of Scientific and Innovative Research (AcSIR)
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13
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Li F, Shrivastava IH, Hanlon P, Dagda RK, Gasanoff ES. Molecular Mechanism by which Cobra Venom Cardiotoxins Interact with the Outer Mitochondrial Membrane. Toxins (Basel) 2020; 12:E425. [PMID: 32605112 PMCID: PMC7404710 DOI: 10.3390/toxins12070425] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/23/2020] [Accepted: 06/26/2020] [Indexed: 12/29/2022] Open
Abstract
Cardiotoxin CTII from Najaoxiana cobra venom translocates to the intermembrane space (IMS) of mitochondria to disrupt the structure and function of the inner mitochondrial membrane. At low concentrations, CTII facilitates ATP-synthase activity, presumably via the formation of non-bilayer, immobilized phospholipids that are critical in modulating ATP-synthase activity. In this study, we investigated the effects of another cardiotoxin CTI from Najaoxiana cobra venom on the structure of mitochondrial membranes and on mitochondrial-derived ATP synthesis. By employing robust biophysical methods including 31P-NMR and 1H-NMR spectroscopy, we analyzed the effects of CTI and CTII on phospholipid packing and dynamics in model phosphatidylcholine (PC) membranes enriched with 2.5 and 5.0 mol% of cardiolipin (CL), a phospholipid composition that mimics that in the outer mitochondrial membrane (OMM). These experiments revealed that CTII converted a higher percentage of bilayer phospholipids to a non-bilayer and immobilized state and both cardiotoxins utilized CL and PC molecules to form non-bilayer structures. Furthermore, in order to gain further understanding on how cardiotoxins bind to mitochondrial membranes, we employed molecular dynamics (MD) and molecular docking simulations to investigate the molecular mechanisms by which CTII and CTI interactively bind with an in silico phospholipid membrane that models the composition similar to the OMM. In brief, MD studies suggest that CTII utilized the N-terminal region to embed the phospholipid bilayer more avidly in a horizontal orientation with respect to the lipid bilayer and thereby penetrate at a faster rate compared with CTI. Molecular dynamics along with the Autodock studies identified critical amino acid residues on the molecular surfaces of CTII and CTI that facilitated the long-range and short-range interactions of cardiotoxins with CL and PC. Based on our compiled data and our published findings, we provide a conceptual model that explains a molecular mechanism by which snake venom cardiotoxins, including CTI and CTII, interact with mitochondrial membranes to alter the mitochondrial membrane structure to either upregulate ATP-synthase activity or disrupt mitochondrial function.
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Affiliation(s)
- Feng Li
- STEM Program, Science Department, Chaoyang KaiWen Academy, Yard 46, 3rd Baoquan Street, Chaoyang District, Beijing 100018, China; (F.L.); (P.H.); (E.S.G.)
| | - Indira H. Shrivastava
- Department of Computational and System Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA;
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Paul Hanlon
- STEM Program, Science Department, Chaoyang KaiWen Academy, Yard 46, 3rd Baoquan Street, Chaoyang District, Beijing 100018, China; (F.L.); (P.H.); (E.S.G.)
| | - Ruben K. Dagda
- Reno School of Medicine, Department of Pharmacology, University of Nevada, Reno, NV 89557, USA
| | - Edward S. Gasanoff
- STEM Program, Science Department, Chaoyang KaiWen Academy, Yard 46, 3rd Baoquan Street, Chaoyang District, Beijing 100018, China; (F.L.); (P.H.); (E.S.G.)
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14
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Orengo C, Velankar S, Wodak S, Zoete V, Bonvin AMJJ, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, Helmer-Citterich M, Hospital A, Orozco M, Perrakis A, Rarey M, Soares C, Sussman JL, Thornton JM, Tuffery P, Tusnady G, Wierenga R, Salminen T, Schneider B. A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community). F1000Res 2020; 9. [PMID: 32566135 PMCID: PMC7284151 DOI: 10.12688/f1000research.20559.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/05/2020] [Indexed: 12/11/2022] Open
Abstract
Structural bioinformatics provides the scientific methods and tools to analyse, archive, validate, and present the biomolecular structure data generated by the structural biology community. It also provides an important link with the genomics community, as structural bioinformaticians also use the extensive sequence data to predict protein structures and their functional sites. A very broad and active community of structural bioinformaticians exists across Europe, and 3D-Bioinfo will establish formal platforms to address their needs and better integrate their activities and initiatives. Our mission will be to strengthen the ties with the structural biology research communities in Europe covering life sciences, as well as chemistry and physics and to bridge the gap between these researchers in order to fully realize the potential of structural bioinformatics. Our Community will also undertake dedicated educational, training and outreach efforts to facilitate this, bringing new insights and thus facilitating the development of much needed innovative applications e.g. for human health, drug and protein design. Our combined efforts will be of critical importance to keep the European research efforts competitive in this respect. Here we highlight the major European contributions to the field of structural bioinformatics, the most pressing challenges remaining and how Europe-wide interactions, enabled by ELIXIR and its platforms, will help in addressing these challenges and in coordinating structural bioinformatics resources across Europe. In particular, we present recent activities and future plans to consolidate an ELIXIR 3D-Bioinfo Community in structural bioinformatics and propose means to develop better links across the community. These include building new consortia, organising workshops to establish data standards and seeking community agreement on benchmark data sets and strategies. We also highlight existing and planned collaborations with other ELIXIR Communities and other European infrastructures, such as the structural biology community supported by Instruct-ERIC, with whom we have synergies and overlapping common interests.
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Affiliation(s)
- Christine Orengo
- Structural and Molecular Biology Department, University College, London, UK
| | - Sameer Velankar
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Shoshana Wodak
- VIB-VUB Center for Structural Biology, Brussels, Belgium
| | - Vincent Zoete
- Department of Oncology, Lausanne University, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Alexandre M J J Bonvin
- Bijvoet Center, Faculty of Science - Chemistry, Utrecht University, Utrecht, 3584CH, The Netherlands
| | - Arne Elofsson
- Science for Life Laboratory, Stockholm University, Solna, S-17121, Sweden
| | - K Anton Feenstra
- Dept. Computer Science, Center for Integrative Bioinformatics VU (IBIVU), Vrije Universiteit, Amsterdam, 1081 HV, The Netherlands
| | - Dietland L Gerloff
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, L-4367, Luxembourg
| | - Thomas Hamelryck
- Bioinformatics center, Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | | | | | - Adam Hospital
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, 08028, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, 08028, Spain
| | | | - Matthias Rarey
- ZBH - Center for Bioinformatics, Universität Hamburg, Hamburg, D-20146, Germany
| | - Claudio Soares
- Instituto de Tecnologia Química e Biológica Antonio Xavier, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Joel L Sussman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Pierre Tuffery
- Ressource Parisienne en Bioinformatique Structurale, Université de Paris, Paris, F-75205, France
| | - Gabor Tusnady
- Membrane Bioinformatics Research Group, Institute of Enzymology, Budapest, H-1117, Hungary
| | | | - Tiina Salminen
- Structural Bioinformatics Laboratory, Åbo Akademi University, Turku, FI-20500, Finland
| | - Bohdan Schneider
- Institute of Biotechnology of the Czech Academy of Sciences, Vestec, CZ-25250, Czech Republic
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15
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Saxena R, Stanley CB, Kumar P, Cuneo MJ, Patil D, Jha J, Weiss KL, Chattoraj DK, Crooke E. A nucleotide-dependent oligomerization of the Escherichia coli replication initiator DnaA requires residue His136 for remodeling of the chromosomal origin. Nucleic Acids Res 2020; 48:200-211. [PMID: 31665475 PMCID: PMC7145717 DOI: 10.1093/nar/gkz939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/30/2019] [Accepted: 10/08/2019] [Indexed: 12/03/2022] Open
Abstract
Escherichia coli replication initiator protein DnaA binds ATP with high affinity but the amount of ATP required to initiate replication greatly exceeds the amount required for binding. Previously, we showed that ATP-DnaA, not ADP-DnaA, undergoes a conformational change at the higher nucleotide concentration, which allows DnaA oligomerization at the replication origin but the association state remains unclear. Here, we used Small Angle X-ray Scattering (SAXS) to investigate oligomerization of DnaA in solution. Whereas ADP-DnaA was predominantly monomeric, AMP–PNP–DnaA (a non-hydrolysable ATP-analog bound-DnaA) was oligomeric, primarily dimeric. Functional studies using DnaA mutants revealed that DnaA(H136Q) is defective in initiating replication in vivo. The mutant retains high-affinity ATP binding, but was defective in producing replication-competent initiation complexes. Docking of ATP on a structure of E. coli DnaA, modeled upon the crystallographic structure of Aquifex aeolicus DnaA, predicts a hydrogen bond between ATP and imidazole ring of His136, which is disrupted when Gln is present at position 136. SAXS performed on AMP–PNP–DnaA (H136Q) indicates that the protein has lost its ability to form oligomers. These results show the importance of high ATP in DnaA oligomerization and its dependence on the His136 residue.
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Affiliation(s)
- Rahul Saxena
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Christopher B Stanley
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Pankaj Kumar
- Department of Biochemistry, Jamia Hamdard University, Delhi 110062, India
| | - Matthew J Cuneo
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Digvijay Patil
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Jyoti Jha
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kevin L Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Dhruba K Chattoraj
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Elliott Crooke
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA.,Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA
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16
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Lu X, Chen J, Jiao L, Zhong L, Lu Z, Zhang C, Lu F. Improvement of the activity of l-asparaginase I improvement of the catalytic activity of l-asparaginase I from Bacillus megaterium H-1 by in vitro directed evolution. J Biosci Bioeng 2019; 128:683-689. [DOI: 10.1016/j.jbiosc.2019.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 05/17/2019] [Accepted: 06/04/2019] [Indexed: 10/26/2022]
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17
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Zhu HE, Yin JY, Chen DX, He S, Chen H. Agmatinase promotes the lung adenocarcinoma tumorigenesis by activating the NO-MAPKs-PI3K/Akt pathway. Cell Death Dis 2019; 10:854. [PMID: 31699997 PMCID: PMC6838094 DOI: 10.1038/s41419-019-2082-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/13/2019] [Accepted: 10/17/2019] [Indexed: 12/24/2022]
Abstract
Lung adenocarcinoma (LUAD) is one of the leading causes of cancer-related death worldwide. There is an urgent need to uncover the pathogenic mechanism to develop new treatments. Agmatinase (AGMAT) expression and its association with clinicopathological characteristics were analyzed via GEO, Oncomine, and TCGA databases, and IHC staining in human LUAD specimens. An EdU cell proliferation kit, propidiumiodide staining, colony formation, cell migration, and invasion assays, and a xenograft tumor model were used to detect the biological function of AGMAT in LUAD. Furthermore, the expression level of nitric oxide (NO) was detected using a DAF-FMDA fluorescent probe or nitrite assay kit, and further validated with Carboxy-PTIO (a NO scavenger). The roles of three isoforms of nitric oxide synthases (nNOS, eNOS, and iNOS) were validated using L-NAME (eNOS inhibitor), SMT (iNOS inhibitor), and spermidine (nNOS inhibitor). AGMAT expression was up-regulated in LUAD tissues. LUAD patients with high AGMAT levels were associated with poorer prognoses. AGMAT promoted LUAD tumorigenesis in NO released by iNOS both in vitro and in vivo. Importantly, NO signaling up-regulated the expression of cyclin D1 via activating the MAPK and PI3K/Akt-dependent c-myc activity, ultimately promoting the malignant proliferation of tumor cells. On the whole, AGMAT promoted NO release via up-regulating the expression of iNOS. High levels of NO drove LUAD tumorigenesis via activating MAPK and PI3K/Akt cascades. AGMAT might be a potential diagnostic and therapeutic target for LUAD patients.
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Affiliation(s)
- Hui-Er Zhu
- Department of Emergency Surgery, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, 510150, PR China
| | - Jia-Yi Yin
- Department of Emergency Surgery, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, 510150, PR China
| | - De-Xiong Chen
- Department of Emergency Surgery, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, 510150, PR China
| | - Sheng He
- Department of Respiratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, 510150, PR China
| | - Hui Chen
- Department of Pathology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, 510150, PR China.
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18
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Li F, Li D, Dewer Y, Qu C, Yang Z, Tian J, Luo C. Discrimination of Oviposition Deterrent Volatile β-Ionone by Odorant-Binding Proteins 1 and 4 in the Whitefly Bemisia tabaci. Biomolecules 2019; 9:biom9100563. [PMID: 31623354 PMCID: PMC6843521 DOI: 10.3390/biom9100563] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 11/16/2022] Open
Abstract
: The whitefly, Bemisia tabaci, is an important invasive economic pest of agricultural crops worldwide. β-ionone has a significant oviposition repellent effect against B. tabaci, but the olfactory molecular mechanism of this insect for recognizing β-ionone is unclear. To clarify the binding properties of odorant-binding proteins (OBPs) with β-ionone, we performed gene cloning, evolution analysis, bacterial expression, fluorescence competitive binding assay, and molecular docking to study the binding function of OBP1 and OBP4 on β-ionone. The results showed that after the OBP1 and OBP4 proteins were recombined, the compound β-ionone exhibited a reduction in the fluorescence binding affinity to <50%, with a dissociation constant of 5.15 and 3.62 μM for OBP1 and OBP4, respectively. Our data indicate that β-ionone has high affinity for OBP1 and OBP4, which play a crucial role in the identification of oviposition sites in B. tabaci. The findings of this study suggest that whiteflies employ β-ionone compound in the selection of the suitable egg-laying sites on host plants during the oviposition behavior.
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Affiliation(s)
- Fengqi Li
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| | - Du Li
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Hubei Key Laboratory of Insect Resource Application and Sustainable Pest Control, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Youssef Dewer
- Bioassay Research Department, Central Agricultural Pesticide Laboratory, Sabahia Plant Protection Research Station, Agricultural Research Center, Alexandria 21616, Egypt.
| | - Cheng Qu
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| | - Zhen Yang
- Tianjin University of Traditional Chinese Medicine, Tianjin 300000, China.
| | - Jiahui Tian
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| | - Chen Luo
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
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19
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Jiang T, Saito T, Nanbu S. Theoretical Molecular Dynamics Simulation of the DIF-1 Receptor Activation. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20190071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Tianlong Jiang
- Department of Materials and Life Sciences, Sophia University, Tokyo 102-8554, Japan
| | - Tamao Saito
- Department of Materials and Life Sciences, Sophia University, Tokyo 102-8554, Japan
| | - Shinkoh Nanbu
- Department of Materials and Life Sciences, Sophia University, Tokyo 102-8554, Japan
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20
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Orthogonal monoterpenoid biosynthesis in yeast constructed on an isomeric substrate. Nat Commun 2019; 10:3799. [PMID: 31444322 PMCID: PMC6707142 DOI: 10.1038/s41467-019-11290-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 07/03/2019] [Indexed: 01/29/2023] Open
Abstract
Synthetic biology efforts for the production of valuable chemicals are frequently hindered by the structure and regulation of the native metabolic pathways of the chassis. This is particularly evident in the case of monoterpenoid production in Saccharomyces cerevisiae, where the canonical terpene precursor geranyl diphosphate is tightly coupled to the biosynthesis of isoprenoid compounds essential for yeast viability. Here, we establish a synthetic orthogonal monoterpenoid pathway based on an alternative precursor, neryl diphosphate. We identify structural determinants of isomeric substrate selectivity in monoterpene synthases and engineer five different enzymes to accept the alternative substrate with improved efficiency and specificity. We combine the engineered enzymes with dynamic regulation of metabolic flux to harness the potential of the orthogonal substrate and improve the production of industrially-relevant monoterpenes by several-fold compared to the canonical pathway. This approach highlights the introduction of synthetic metabolism as an effective strategy for high-value compound production.
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21
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Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, Heer FT, de Beer TAP, Rempfer C, Bordoli L, Lepore R, Schwede T. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res 2019; 46:W296-W303. [PMID: 29788355 PMCID: PMC6030848 DOI: 10.1093/nar/gky427] [Citation(s) in RCA: 6875] [Impact Index Per Article: 1375.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/07/2018] [Indexed: 11/13/2022] Open
Abstract
Homology modelling has matured into an important technique in structural biology, significantly contributing to narrowing the gap between known protein sequences and experimentally determined structures. Fully automated workflows and servers simplify and streamline the homology modelling process, also allowing users without a specific computational expertise to generate reliable protein models and have easy access to modelling results, their visualization and interpretation. Here, we present an update to the SWISS-MODEL server, which pioneered the field of automated modelling 25 years ago and been continuously further developed. Recently, its functionality has been extended to the modelling of homo- and heteromeric complexes. Starting from the amino acid sequences of the interacting proteins, both the stoichiometry and the overall structure of the complex are inferred by homology modelling. Other major improvements include the implementation of a new modelling engine, ProMod3 and the introduction a new local model quality estimation method, QMEANDisCo. SWISS-MODEL is freely available at https://swissmodel.expasy.org.
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Affiliation(s)
- Andrew Waterhouse
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland
| | - Martino Bertoni
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland
| | - Stefan Bienert
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland
| | - Gabriel Studer
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland
| | - Gerardo Tauriello
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland
| | - Rafal Gumienny
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland
| | - Florian T Heer
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland
| | - Tjaart A P de Beer
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland
| | - Christine Rempfer
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland
| | - Lorenza Bordoli
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland
| | - Rosalba Lepore
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland
| | - Torsten Schwede
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland
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22
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The Functional Mammalian CRES (Cystatin-Related Epididymal Spermatogenic) Amyloid is Antiparallel β-Sheet Rich and Forms a Metastable Oligomer During Assembly. Sci Rep 2019; 9:9210. [PMID: 31239483 PMCID: PMC6593142 DOI: 10.1038/s41598-019-45545-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 06/06/2019] [Indexed: 12/15/2022] Open
Abstract
An amyloid matrix composed of several family 2 cystatins, including the reproductive cystatin CRES, is an integral structure in the mouse epididymal lumen and has proposed functions in sperm maturation and protection. Understanding how CRES amyloid assembles in vitro may provide clues on how the epididymal amyloid matrix forms in vivo. We therefore purified full-length CRES under nondenaturing conditions and followed its aggregation from monomer to amyloid under conditions that may approximate those in the epididymal lumen. CRES transitioned into a metastable oligomer that was resistant to aggregation and only over extended time formed higher-ordered amyloids. High protein concentrations facilitated oligomer assembly and also were required to maintain the metastable state since following dilution the oligomer was no longer detected. Similar to other amyloid precursors, the formation of CRES amyloids correlated with a loss of α-helix and a gain of β-sheet content. However, CRES is unique in that its amyloids are rich in antiparallel β-sheets instead of the more common parallel β-sheets. Taken together, our studies suggest that early metastable oligomers may serve as building blocks for functional amyloid assembly and further reveal that antiparallel β-sheet-rich amyloids can be functional forms.
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23
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Adrian J, Bonsignore P, Hammer S, Frickey T, Hauck CR. Adaptation to Host-Specific Bacterial Pathogens Drives Rapid Evolution of a Human Innate Immune Receptor. Curr Biol 2019; 29:616-630.e5. [PMID: 30744974 DOI: 10.1016/j.cub.2019.01.058] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/12/2018] [Accepted: 01/22/2019] [Indexed: 12/25/2022]
Abstract
The selective pressure by infectious agents is a major driving force in the evolution of humans and other mammals. Members of the carcinoembryonic antigen-related cell adhesion molecule (CEACAM) family serve as receptors for bacterial pathogens of the genera Haemophilus, Helicobacter, Neisseria, and Moraxella, which engage CEACAMs via distinct surface adhesins. While microbial attachment to epithelial CEACAMs facilitates host colonization, recognition by CEACAM3, a phagocytic receptor expressed by granulocytes, eliminates CEACAM-binding bacteria. Sequence analysis of primate CEACAM3 orthologs reveals that this innate immune receptor is one of the most rapidly evolving human proteins. In particular, the pathogen-binding extracellular domain of CEACAM3 shows a high degree of non-synonymous versus synonymous nucleotide exchanges, indicating an exceptionally strong positive selection. Using CEACAM3 domains derived from different primates, we find that the amino acid alterations found in CEACAM3 translate into characteristic binding patterns for bacterial adhesins. One such amino acid residue is F62 in human and chimp CEACAM3, which is not present in other primates and which is critical for binding the OMP P1 adhesin of Haemophilus aegyptius. Incorporation of the F62-containing motif into gorilla CEACAM3 results in a gain-of-function phenotype with regard to phagocytosis of H. aegyptius. Moreover, CEACAM3 polymorphisms found in human subpopulations widen the spectrum of recognized bacterial adhesins, suggesting an ongoing multivariate selection acting on this innate immune receptor. The species-specific detection of diverse bacterial adhesins helps to explain the exceptionally fast evolution of CEACAM3 within the primate lineage and provides an example of Red Queen dynamics in the human genome.
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Affiliation(s)
- Jonas Adrian
- Lehrstuhl für Zellbiologie, Fachbereich Biologie, Universität Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Patrizia Bonsignore
- Lehrstuhl für Zellbiologie, Fachbereich Biologie, Universität Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Sebastian Hammer
- Lehrstuhl für Zellbiologie, Fachbereich Biologie, Universität Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Tancred Frickey
- Forest Industry Informatics, Scion, Te Papa Tipu Innovation Park, 49 Sala Street, 3015 Rotorua, New Zealand; Konstanz Research School-Chemical Biology, Universität Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Christof R Hauck
- Lehrstuhl für Zellbiologie, Fachbereich Biologie, Universität Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany; Konstanz Research School-Chemical Biology, Universität Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
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24
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Ignea C, Pontini M, Motawia MS, Maffei ME, Makris AM, Kampranis SC. Synthesis of 11-carbon terpenoids in yeast using protein and metabolic engineering. Nat Chem Biol 2018; 14:1090-1098. [DOI: 10.1038/s41589-018-0166-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 10/11/2018] [Indexed: 12/12/2022]
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25
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Makhouri FR, Ghasemi JB. High-throughput Docking and Molecular Dynamics Simulations towards the Identification of Novel Peptidomimetic Inhibitors against CDC7. Mol Inform 2018; 37:e1800022. [DOI: 10.1002/minf.201800022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/18/2018] [Indexed: 11/05/2022]
Affiliation(s)
- Farahnaz Rezaei Makhouri
- Chemistry Department, Faculty of Sciences; K.N. Toosi University of Technology; Tehran 1969764499 Iran
| | - Jahan B. Ghasemi
- Chemistry Department, Faculty of Sciences; K.N. Toosi University of Technology; Tehran 1969764499 Iran
- Chemistry Department, Faculty of Sciences; University of Tehran; Tehran 1417466191 Iran
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26
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Abstract
Proteins undergo both cold and heat denaturation, but often cold denaturation cannot be detected because it occurs at temperatures below water freezing. Proteins undergoing detectable cold as well as heat denaturation yield a reliable curve of protein stability. Here we use bacterial IscU, an essential and ancient protein involved in iron cluster biogenesis, to show an important example of unbiased cold denaturation, based on electrostatic frustration caused by a dualism between iron–sulfur cluster binding and the presence of a functionally essential electrostatic gate. We explore the structural determinants and the universals that determine cold denaturation with the aid of a coarse grain model. Our results set a firm point in our understanding of cold denaturation and give us general rules to induce and predict protein cold denaturation. The conflict between ligand binding and stability hints at the importance of the structure–function dualism in protein evolution.
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Expression and Activity of the BioH Esterase of Biotin Synthesis is Independent of Genome Context. Sci Rep 2017; 7:2141. [PMID: 28526858 PMCID: PMC5438404 DOI: 10.1038/s41598-017-01490-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 03/28/2017] [Indexed: 01/15/2023] Open
Abstract
BioH is an α/β-hydrolase required for synthesis of the pimelate moiety of biotin in diverse bacteria. The bioH gene is found in different genomic contexts. In some cases (e.g., Escherichia coli) the gene is not located within a biotin synthetic operon and its transcription is not coregulated with the other biotin synthesis genes. In other genomes such as Pseudomonas aeruginosa the bioH gene is within a biotin synthesis operon and its transcription is coregulated with the other biotin operon genes. The esterases of pimelate moiety synthesis show remarkable genomic plasticity in that in some biotin operons bioH is replaced by other α/ß hydrolases of diverse sequence. The “wild card” nature of these enzymes led us to compare the paradigm “freestanding” E. coli BioH with the operon-encoded P. aeruginosa BioH. We hypothesized that the operon-encoded BioH might differ in its expression level and/or activity from the freestanding BioH gene. We report this is not the case. The two BioH proteins show remarkably similar hydrolase activities and substrate specificity. Moreover, Pseudomonas aeruginosa BioH is more highly expressed than E. coli BioH. Despite the enzymatic similarities of the two BioH proteins, bioinformatics analysis places the freestanding and operon-encoded BioH proteins into distinct clades.
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Figueroa-Villar JD, Sales EM. The importance of nucleoside hydrolase enzyme (NH) in studies to treatment of Leishmania: A review. Chem Biol Interact 2016; 263:18-27. [PMID: 27939867 DOI: 10.1016/j.cbi.2016.12.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 11/08/2016] [Accepted: 12/04/2016] [Indexed: 11/16/2022]
Abstract
Leishmania is a genus of trypanosomes, which are responsible for leishmaniasis disease, a major trypanosome infection in humans. In recent years, published studies have shown that the search for new drugs for Leishmania treatments has intensified. Through technique modeling it has been possible to develop new compounds, which act as nucleoside hydrolase (NH) inhibitors. The effect of these enzymes is the hydrolysis of certain RNA nucleotides, which include uridine and inosine, necessary for the protozoa to transform certain nucleosides obtained from infected individuals into nucleobases for the preparation of their DNA. The obtention of NH inhibitors is very important to eliminate leishmaniasis disease in infected individuals. The aim of this study is to discuss the research and development of new agents for the treatment of Leishmania, and to stimulate the formulation of new NH inhibitors.
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Affiliation(s)
- José D Figueroa-Villar
- Medicinal Chemistry Group, Department of Chemistry, Military Institute of Engineering, Praça General Tibúrcio 80, 22290-270 Rio de Janeiro, Brazil.
| | - Edijane M Sales
- Medicinal Chemistry Group, Department of Chemistry, Military Institute of Engineering, Praça General Tibúrcio 80, 22290-270 Rio de Janeiro, Brazil
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SÁENZ-SUÁREZ H, POUTOU-PIÑALES RA, GONZÁLEZ-SANTOS J, BARRETO GE, RIETO-NAVARRERA LP, SÁENZ-MORENO JA, LANDÁZURI P, BARRERA-AVELLANEDA LA. Prediction of glycation sites: new insights from protein structural analysis. Turk J Biol 2016. [DOI: 10.3906/biy-1501-71] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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30
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Yuan S, Li R, Wang L, Chen H, Zhang C, Chen L, Hao Q, Shan Z, Zhang X, Chen S, Yang Z, Qiu D, Zhou X. Search for Nodulation and Nodule Development-Related Cystatin Genes in the Genome of Soybean ( Glycine max). FRONTIERS IN PLANT SCIENCE 2016; 7:1595. [PMID: 27826313 PMCID: PMC5078837 DOI: 10.3389/fpls.2016.01595] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 10/10/2016] [Indexed: 05/12/2023]
Abstract
Nodulation, nodule development and senescence directly affects nitrogen fixation efficiency, and previous studies have shown that inhibition of some cysteine proteases delay nodule senescence, so their nature inhibitors, cystatin genes, are very important in nodulation, nodule development, and senescence. Although several cystatins are actively transcribed in soybean nodules, their exact roles and functional diversities in legume have not been well explored in genome-wide survey studies. In this report, we performed a genome-wide survey of cystatin family genes to explore their relationship to nodulation and nodule development in soybean and identified 20 cystatin genes that encode peptides with 97-245 amino acid residues, different isoelectric points (pI) and structure characteristics, and various putative plant regulatory elements in 3000 bp putative promoter fragments upstream of the 20 soybean cystatins in response to different abiotic/biotic stresses, hormone signals, and symbiosis signals. The expression profiles of these cystatin genes in soybean symbiosis with rhizobium strain Bradyrhizobium japonicum strain 113-2 revealed that 7 cystatin family genes play different roles in nodulation as well as nodule development and senescence. However, these genes were not root nodule symbiosis (RNS)-specific and did not encode special clade cystatin protein with structures related to nodulation and nodule development. Besides, only two of these soybean cystatins were not upregulated in symbiosis after ABA treatment. The functional analysis showed that a candidate gene Glyma.15G227500 (GmCYS16) was likely to play a positive role in soybean nodulation. Besides, evolutionary relationships analysis divided the cystatin genes from Arabidopsis thaliana, Nicotiana tabacum, rice, barley and four legume plants into three groups. Interestingly, Group A cystatins are special in legume plants, but only include one of the above-mentioned 7 cystatin genes related to nodulation and nodule development. Overall, our results provide useful information or clues for our understanding of the functional diversity of legume cystatin family proteins in soybean nodulation and nodule development and for finding nodule-specific cysteine proteases in soybean.
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Affiliation(s)
- Songli Yuan
- Key Laboratory of Oil Crop Biology, Ministry of AgricultureWuhan, China
- Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhan, China
| | - Rong Li
- Key Laboratory of Oil Crop Biology, Ministry of AgricultureWuhan, China
- Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhan, China
| | - Lei Wang
- Bioinformatics Laboratory, College of Life Sciences, Xinyang Normal UniversityXinyang, China
| | - Haifeng Chen
- Key Laboratory of Oil Crop Biology, Ministry of AgricultureWuhan, China
- Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhan, China
| | - Chanjuan Zhang
- Key Laboratory of Oil Crop Biology, Ministry of AgricultureWuhan, China
- Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhan, China
| | - Limiao Chen
- Key Laboratory of Oil Crop Biology, Ministry of AgricultureWuhan, China
- Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhan, China
| | - Qingnan Hao
- Key Laboratory of Oil Crop Biology, Ministry of AgricultureWuhan, China
- Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhan, China
| | - Zhihui Shan
- Key Laboratory of Oil Crop Biology, Ministry of AgricultureWuhan, China
- Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhan, China
| | - Xiaojuan Zhang
- Key Laboratory of Oil Crop Biology, Ministry of AgricultureWuhan, China
- Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhan, China
| | - Shuilian Chen
- Key Laboratory of Oil Crop Biology, Ministry of AgricultureWuhan, China
- Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhan, China
| | - Zhonglu Yang
- Key Laboratory of Oil Crop Biology, Ministry of AgricultureWuhan, China
- Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhan, China
| | - Dezhen Qiu
- Key Laboratory of Oil Crop Biology, Ministry of AgricultureWuhan, China
- Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhan, China
| | - Xinan Zhou
- Key Laboratory of Oil Crop Biology, Ministry of AgricultureWuhan, China
- Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhan, China
- *Correspondence: Xinan Zhou
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Molecular Modeling and Its Applications in Protein Engineering. Synth Biol (Oxf) 2016. [DOI: 10.1007/978-3-319-22708-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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32
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Liang J, Wang Y, Ding G, Li W, Yang G, He N. Biotic stress-induced expression of mulberry cystatins and identification of cystatin exhibiting stability to silkworm gut proteinases. PLANTA 2015; 242:1139-1151. [PMID: 26070440 DOI: 10.1007/s00425-015-2345-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 06/01/2015] [Indexed: 06/04/2023]
Abstract
Biotic stresses induce the expression of mulberry cystatins. MaCPI-4 protein is stable in silkworm digestive fluid and accumulates in gut food debris and frass. Plant cystatins are considered to be involved in defense responses to insect herbivores though little is known about how cystatins from the natural host respond to a specialist herbivory and the following postingestive interaction is also poorly understood. Here, we studied the biotic stress-mediated inductions of cystatins from mulberry tree, and examined the stability of mulberry cystatin proteins in the gut of silkworm, Bombyx mori, a specialist insect feeding on mulberry leaf. First, we cloned and characterized six cystatin genes from a mulberry cultivar, Morus atropurpurea Roxb., named as MaCPI-1 to MaCPI-6. The recombinant MaCPI-1, MaCPI-3 and MaCPI-4 proteins, which showed inhibitory effects against papain in vitro, were produced. Silkworm herbivory as well as methyl jasmonate (MeJA) treatment induced the expression of five mulberry cystatin genes, and the highest inductions were observed from MaCPI-1 and MaCPI-6. Mechanical wounding led to the inductions of four cystatin genes. The differential induction occurred in MaCPI-2. The induced protein changes were detected from three mulberry cystatins comprising MaCPI-1, MaCPI-3 and MaCPI-4. In vivo and in vitro assays showed that MaCPI-1 and MaCPI-3 proteins were susceptible to silkworm digestive fluid and MaCPI-4 had an antidigestive stability, and was detected in silkworm gut and frass. Collectively, our data indicated that biotic stresses resulted in the transcriptional inductions and protein changes of mulberry cystatins (MaCPIs), and identified MaCPI-4 with stability in the gut of its specialist herbivore.
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Affiliation(s)
- Jiubo Liang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China.
| | - Yupeng Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China.
| | - Guangyu Ding
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China.
| | - Wensheng Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China.
| | - Guangwei Yang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China.
| | - Ningjia He
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China.
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Xie W, Wen H, Chu F, Yan S, Lin B, Xie W, Liu Y, Ren G, Zhao L, Song Y, Sun C, Wang Z. Mutations in the DI-DII Linker of Human Parainfluenza Virus Type 3 Fusion Protein Result in Diminished Fusion Activity. PLoS One 2015; 10:e0136474. [PMID: 26305905 PMCID: PMC4549179 DOI: 10.1371/journal.pone.0136474] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/04/2015] [Indexed: 01/21/2023] Open
Abstract
Human parainfluenza virus type 3 (HPIV3) can cause severe respiratory tract diseases in infants and young children, but no licensed vaccines or antiviral agents are currently available for treatment. Fusing the viral and target cell membranes is a prerequisite for its entry into host cells and is directly mediated by the fusion (F) protein. Although several domains of F are known to have important effects on regulating the membrane fusion activity, the roles of the DI-DII linker (residues 369–374) of the HPIV3 F protein in the fusogenicity still remains ill-defined. To facilitate our understanding of the role of this domain might play in F-induced cell-cell fusion, nine single mutations were engineered into this domain by site-directed mutagenesis. A vaccinia virus-T7 RNA polymerase transient expression system was employed to express the wild-type or mutated F proteins. These mutants were analyzed for membrane fusion activity, cell surface expression, and interaction between F and HN protein. Each of the mutated F proteins in this domain has a cell surface expression level similar to that of wild-type F. All of them resulted in a significant reduction in fusogenic activity in all steps of membrane fusion. Furthermore, all these fusion-deficient mutants reduced the amount of the HN-F complexes at the cell surface. Together, the results of our work suggest that this region has an important effect on the fusogenic activity of F.
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Affiliation(s)
- Wenyan Xie
- Department of Virology, School of Public Health, Shandong University, Jinan, China
| | - Hongling Wen
- Department of Virology, School of Public Health, Shandong University, Jinan, China
| | - Fulu Chu
- Department of Laboratory Medicine, Provincial Hospital affiliated to Shandong University, Jinan, China
| | - Shaofeng Yan
- Department of Neurosurgery, Qilu Hospital of Shandong University, Jinan, China
| | - Bin Lin
- Shandong Center for Disease Control and Prevention, Jinan, China
| | - Wenli Xie
- Department of Laboratory Medicine, Shandong Tumor Hospital and Institute, Jinan, China
| | - Ying Liu
- Department of Virology, School of Public Health, Shandong University, Jinan, China
| | - Guijie Ren
- Institute of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, China
| | - Li Zhao
- Department of Virology, School of Public Health, Shandong University, Jinan, China
| | - Yanyan Song
- Department of Virology, School of Public Health, Shandong University, Jinan, China
| | - Chengxi Sun
- Department of Virology, School of Public Health, Shandong University, Jinan, China
| | - Zhiyu Wang
- Department of Virology, School of Public Health, Shandong University, Jinan, China
- The Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University, Jinan, China
- * E-mail:
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Valdivieso E, Perteguer MJ, Hurtado C, Campioli P, Rodríguez E, Saborido A, Martínez-Sernández V, Gómez-Puertas P, Ubeira FM, Gárate T. ANISERP: a new serpin from the parasite Anisakis simplex. Parasit Vectors 2015; 8:399. [PMID: 26215984 PMCID: PMC4517634 DOI: 10.1186/s13071-015-1006-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 07/11/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Serine proteinase inhibitors (serpins) finely regulate serine proteinase activity via a suicide substrate-like inhibitory mechanism. In parasitic nematodes, some serpins interact with host physiological processes; however, little is known about these essential molecules in Anisakis. This article reports the gene sequencing, cloning, expression and preliminary biochemical and bioinformatically-based structural characterization of a new Anisakis serpin (ANISERP). METHODS The full AniSerp gene was cloned by specific RACE-PCR after screening an Anisakis simplex (L3) cDNA library. For biochemical assays, the AniSerp gene was subcloned into both prokaryotic and eukaryotic vectors, and the recombinant proteins were purified. The inhibitory properties of the proteins were tested in classical biochemical assays using human serine peptidases and AMC substrates. Immunolocalization of ANISERP, theoretical structural analysis and bioinformatically-based structural modelling of the ANISERP protein were also conducted. RESULTS The AniSerp gene was found to have 1194 nucleotides, coding for a protein of 397 amino acid residues plus a putative N-terminal signal peptide. It showed significant similarity to other nematode, arthropod and mammalian serpins. The recombinant ANISERP expressed in the prokaryotic and eukaryotic systems inhibited the human serine proteases thrombin, trypsin and cathepsin G in a concentration-dependent manner. No inhibitory activity against Factor Xa, Factor XIa, Factor XIIa, elastase, plasmin or chymotrypsin was observed. ANISERP also acted on the cysteine protease cathepsin L. ANISERP was mainly localized in the nematode pseudocoelomic fluid, somatic muscle cell bodies and intestinal cells. The findings of molecular dynamics studies suggest that ANISERP inhibits thrombin via a suicide substrate-like inhibitory mechanism, similar to the mechanism of action of mammalian coagulation inhibitors. In contrast to findings concerning human antithrombin III, heparin had no effect on ANISERP anticoagulant inhibitory activity. CONCLUSIONS Our findings suggest that ANISERP is an internal Anisakis regulatory serpin and that the inhibitory activity against thrombin depends on a suicide substrate-like inhibitory mechanism, similar to that described for human antithrombin (AT)-III. The fact that heparin does not modulate the anticoagulant activity of ANISERP might be explained by the absence in the latter of five of the six positively charged residues usually seen at the AT-III-heparin binding site.
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Affiliation(s)
- Elizabeth Valdivieso
- Servicio de Parasitología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain.
- Laboratorio de Biología Celular de Parásitos, Instituto de Biología Experimental, Facultad de Ciencias, Universidad Central de Venezuela, 47069, Caracas, 1041-A, Venezuela.
| | - Maria J Perteguer
- Servicio de Parasitología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain.
- Parasitology Department, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain.
| | - Carolina Hurtado
- Servicio de Parasitología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain.
- Present Address: Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia, Universidad San Pablo-CEU, Campus de Montepríncipe, Urb. Montepríncipe, 28668, Madrid, Spain.
| | - Pamela Campioli
- Servicio de Parasitología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain.
| | - Esperanza Rodríguez
- Servicio de Parasitología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain.
| | - Ana Saborido
- Departamento de Bioquímica y Biología Molecular I, Facultad de Químicas, Universidad Complutense, Madrid, Spain.
| | | | - Paulino Gómez-Puertas
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM) Campus UAM. Cantoblanco, 28049, Madrid, Spain.
| | - Florencio M Ubeira
- Laboratorio de Parasitología, Facultad de Farmacia, Universidad de Santiago de Compostela, A Coruña, Spain.
| | - Teresa Gárate
- Servicio de Parasitología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain.
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Gil-Rodríguez MC, Deardorff MA, Ansari M, Tan CA, Parenti I, Baquero-Montoya C, Ousager LB, Puisac B, Hernández-Marcos M, Teresa-Rodrigo ME, Marcos-Alcalde I, Wesselink JJ, Lusa-Bernal S, Bijlsma EK, Braunholz D, Bueno-Martinez I, Clark D, Cooper NS, Curry CJ, Fisher R, Fryer A, Ganesh J, Gervasini C, Gillessen-Kaesbach G, Guo Y, Hakonarson H, Hopkin RJ, Kaur M, Keating BJ, Kibaek M, Kinning E, Kleefstra T, Kline AD, Kuchinskaya E, Larizza L, Li YR, Liu X, Mariani M, Picker JD, Pié Á, Pozojevic J, Queralt E, Richer J, Roeder E, Sinha A, Scott RH, So J, Wusik KA, Wilson L, Zhang J, Gómez-Puertas P, Casale CH, Ström L, Selicorni A, Ramos FJ, Jackson LG, Krantz ID, Das S, Hennekam RCM, Kaiser FJ, FitzPatrick DR, Pié J. De novo heterozygous mutations in SMC3 cause a range of Cornelia de Lange syndrome-overlapping phenotypes. Hum Mutat 2015; 36:454-62. [PMID: 25655089 DOI: 10.1002/humu.22761] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/21/2015] [Accepted: 01/28/2015] [Indexed: 11/09/2022]
Abstract
Cornelia de Lange syndrome (CdLS) is characterized by facial dysmorphism, growth failure, intellectual disability, limb malformations, and multiple organ involvement. Mutations in five genes, encoding subunits of the cohesin complex (SMC1A, SMC3, RAD21) and its regulators (NIPBL, HDAC8), account for at least 70% of patients with CdLS or CdLS-like phenotypes. To date, only the clinical features from a single CdLS patient with SMC3 mutation has been published. Here, we report the efforts of an international research and clinical collaboration to provide clinical comparison of 16 patients with CdLS-like features caused by mutations in SMC3. Modeling of the mutation effects on protein structure suggests a dominant-negative effect on the multimeric cohesin complex. When compared with typical CdLS, many SMC3-associated phenotypes are also characterized by postnatal microcephaly but with a less distinctive craniofacial appearance, a milder prenatal growth retardation that worsens in childhood, few congenital heart defects, and an absence of limb deficiencies. While most mutations are unique, two unrelated affected individuals shared the same mutation but presented with different phenotypes. This work confirms that de novo SMC3 mutations account for ∼ 1%-2% of CdLS-like phenotypes.
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Affiliation(s)
- María Concepción Gil-Rodríguez
- Unit of Clinical Genetics and Functional Genomics, Departments of Pharmacology-Physiology and Pediatrics, Medical School, University of Zaragoza, CIBERER-GCV and ISS-Aragon, Zaragoza, Spain
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Ignea C, Ioannou E, Georgantea P, Loupassaki S, Trikka FA, Kanellis AK, Makris AM, Roussis V, Kampranis SC. Reconstructing the chemical diversity of labdane-type diterpene biosynthesis in yeast. Metab Eng 2015; 28:91-103. [DOI: 10.1016/j.ymben.2014.12.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 11/09/2014] [Accepted: 12/02/2014] [Indexed: 01/08/2023]
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Cao X, Cronan JE. The Streptomyces coelicolor lipoate-protein ligase is a circularly permuted version of the Escherichia coli enzyme composed of discrete interacting domains. J Biol Chem 2015; 290:7280-90. [PMID: 25631049 DOI: 10.1074/jbc.m114.626879] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Lipoate-protein ligases are used to scavenge lipoic acid from the environment and attach the coenzyme to its cognate proteins, which are generally the E2 components of the 2-oxoacid dehydrogenases. The enzymes use ATP to activate lipoate to its adenylate, lipoyl-AMP, which remains tightly bound in the active site. This mixed anhydride is attacked by the ϵ-amino group of a specific lysine present on a highly conserved acceptor protein domain, resulting in the amide-linked coenzyme. The Streptomyces coelicolor genome encodes only a single putative lipoate ligase. However, this protein had only low sequence identity (<25%) to the lipoate ligases of demonstrated activity and appears to be a circularly permuted version of the known lipoate ligase proteins in that the canonical C-terminal domain seems to have been transposed to the N terminus. We tested the activity of this protein both by in vivo complementation of an Escherichia coli ligase-deficient strain and by in vitro assays. Moreover, when the domains were rearranged into a protein that mimicked the arrangement found in the canonical lipoate ligases, the enzyme retained complementation activity. Finally, when the two domains were separated into two proteins, both domain-containing proteins were required for complementation and catalysis of the overall ligase reaction in vitro. However, only the large domain-containing protein was required for transfer of lipoate from the lipoyl-AMP intermediate to the acceptor proteins, whereas both domain-containing proteins were required to form lipoyl-AMP.
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Affiliation(s)
- Xinyun Cao
- From the Departments of Biochemistry and
| | - John E Cronan
- From the Departments of Biochemistry and Microbiology, University of Illinois, Urbana, Illinois 61801
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38
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Three-dimensional protein structure prediction: Methods and computational strategies. Comput Biol Chem 2014; 53PB:251-276. [DOI: 10.1016/j.compbiolchem.2014.10.001] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 10/03/2014] [Accepted: 10/07/2014] [Indexed: 01/01/2023]
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39
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Correale S, de Paola I, Morgillo CM, Federico A, Zaccaro L, Pallante P, Galeone A, Fusco A, Pedone E, Luque FJ, Catalanotti B. Structural model of the hUbA1-UbcH10 quaternary complex: in silico and experimental analysis of the protein-protein interactions between E1, E2 and ubiquitin. PLoS One 2014; 9:e112082. [PMID: 25375166 PMCID: PMC4223017 DOI: 10.1371/journal.pone.0112082] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 10/12/2014] [Indexed: 12/21/2022] Open
Abstract
UbcH10 is a component of the Ubiquitin Conjugation Enzymes (Ubc; E2) involved in the ubiquitination cascade controlling the cell cycle progression, whereby ubiquitin, activated by E1, is transferred through E2 to the target protein with the involvement of E3 enzymes. In this work we propose the first three dimensional model of the tetrameric complex formed by the human UbA1 (E1), two ubiquitin molecules and UbcH10 (E2), leading to the transthiolation reaction. The 3D model was built up by using an experimentally guided incremental docking strategy that combined homology modeling, protein-protein docking and refinement by means of molecular dynamics simulations. The structural features of the in silico model allowed us to identify the regions that mediate the recognition between the interacting proteins, revealing the active role of the ubiquitin crosslinked to E1 in the complex formation. Finally, the role of these regions involved in the E1–E2 binding was validated by designing short peptides that specifically interfere with the binding of UbcH10, thus supporting the reliability of the proposed model and representing valuable scaffolds for the design of peptidomimetic compounds that can bind selectively to Ubcs and inhibit the ubiquitylation process in pathological disorders.
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Affiliation(s)
| | - Ivan de Paola
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Napoli, Italy
| | | | - Antonella Federico
- Istituto di Endocrinologia ed Oncologia Sperimentale Consiglio Nazionale delle Ricerche, Napoli, Italy
| | - Laura Zaccaro
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Napoli, Italy
| | - Pierlorenzo Pallante
- Istituto di Endocrinologia ed Oncologia Sperimentale Consiglio Nazionale delle Ricerche, Napoli, Italy
| | - Aldo Galeone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Alfredo Fusco
- Istituto di Endocrinologia ed Oncologia Sperimentale Consiglio Nazionale delle Ricerche, Napoli, Italy
| | - Emilia Pedone
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Napoli, Italy
| | - F. Javier Luque
- Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Santa Coloma de Gramenet, Spain
| | - Bruno Catalanotti
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Napoli, Italy
- * E-mail:
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40
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Rega MF, Di Monaco R, Leone S, Donnarumma F, Spadaccini R, Cavella S, Picone D. Design of sweet protein based sweeteners: hints from structure-function relationships. Food Chem 2014; 173:1179-86. [PMID: 25466141 DOI: 10.1016/j.foodchem.2014.10.151] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 10/01/2014] [Accepted: 10/30/2014] [Indexed: 11/29/2022]
Abstract
Sweet proteins represent a class of natural molecules, which are extremely interesting regarding their potential use as safe low-calories sweeteners for individuals who need to control sugar intake, such as obese or diabetic subjects. Punctual mutations of amino acid residues of MNEI, a single chain derivative of the natural sweet protein monellin, allow the modulation of its taste. In this study we present a structural and functional comparison between MNEI and a sweeter mutant Y65R, containing an extra positive charge on the protein surface, in conditions mimicking those of typical beverages. Y65R exhibits superior sweetness in all the experimental conditions tested, has a better solubility at mild acidic pH and preserves a significant thermal stability in a wide range of pH conditions, although slightly lower than MNEI. Our findings confirm the advantages of structure-guided protein engineering to design improved low-calorie sweeteners and excipients for food and pharmaceutical preparations.
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Affiliation(s)
- Michele Fortunato Rega
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126 Naples, Italy
| | - Rossella Di Monaco
- Food Science and Agricultural Department, University of Naples - Federico II, Italy; Centre for Food Innovation and Development, University of Naples, Portici, Italy
| | - Serena Leone
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126 Naples, Italy
| | - Federica Donnarumma
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126 Naples, Italy
| | - Roberta Spadaccini
- Department of Science and Technology, University of Sannio, 82100 Benevento, Italy
| | - Silvana Cavella
- Food Science and Agricultural Department, University of Naples - Federico II, Italy; Centre for Food Innovation and Development, University of Naples, Portici, Italy
| | - Delia Picone
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, 80126 Naples, Italy.
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41
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Structure-based inhibition of protein-protein interactions. Eur J Med Chem 2014; 94:480-8. [PMID: 25253637 DOI: 10.1016/j.ejmech.2014.09.047] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 09/03/2014] [Accepted: 09/12/2014] [Indexed: 12/24/2022]
Abstract
Protein-protein interactions (PPIs) are emerging as attractive targets for drug design because of their central role in directing normal and aberrant cellular functions. These interactions were once considered "undruggable" because their large and dynamic interfaces make small molecule inhibitor design challenging. However, landmark advances in computational analysis, fragment screening and molecular design have enabled development of a host of promising strategies to address the fundamental molecular recognition challenge. An attractive approach for targeting PPIs involves mimicry of protein domains that are critical for complex formation. This approach recognizes that protein subdomains or protein secondary structures are often present at interfaces and serve as organized scaffolds for the presentation of side chain groups that engage the partner protein(s). Design of protein domain mimetics is in principle rather straightforward but is enabled by a host of computational strategies that provide predictions of important residues that should be mimicked. Herein we describe a workflow proceeding from interaction network analysis, to modeling a complex structure, to identifying a high-affinity sub-structure, to developing interaction inhibitors. We apply the design procedure to peptidomimetic inhibitors of Ras-mediated signaling.
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42
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Liu HG, Li HM, Wang SY, Huang LB, Guo HJ. Gene cloning, homology comparison and analysis of the main functional structure domains of beta estrogen receptor in Jining Gray goat. Comput Biol Chem 2014; 51:42-50. [DOI: 10.1016/j.compbiolchem.2014.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Revised: 02/20/2014] [Accepted: 04/27/2014] [Indexed: 11/25/2022]
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43
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Murashima K, Shimonaka A, Nishimura T, Baba Y, Koga J, Kubota H, Kono T. Exploring Amino Acids Responsible for the Temperature Profile of Glycoside Hydrolase Family 45 Endoglucanase EGL3 fromHumicola grisea. Biosci Biotechnol Biochem 2014; 70:2205-12. [PMID: 16960377 DOI: 10.1271/bbb.60149] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
EGL3 and RCE1 are glycoside hydrolase family 45 endoglucanases isolated from Humicola grisea and Rhizopus oryzae respectively. The amino acid sequences of the two endoglucanases are homologous; on the other hand, the optimum temperature of EGL3 is higher than that of RCE1. In this study, four chimeric endoglucanases, named ER1, ER2, ER3 and ER4, in which one of four sequential amino acid regions of the EGL3 catalytic domain (CAD) was replaced by the corresponding RCE1 amino acids, were constructed to explore the region responsible for the EGL3 temperature profile. Then their temperature profiles were compared with that of the recombinant EGL3. Replacement of the N-terminal region of EGL3 with that of RCE1 caused the EGL3 temperature profile to shift to a lower temperature. These results suggest that the N-terminal amino acids of the EGL3 are responsible for the EGL3 temperature profile.
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Affiliation(s)
- Koichiro Murashima
- Food and Health R & D Laboratories, Meiji Seika Kaisha, Ltd., Sakado-shi, Saitama, Japan.
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44
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Ignea C, Pontini M, Maffei ME, Makris AM, Kampranis SC. Engineering monoterpene production in yeast using a synthetic dominant negative geranyl diphosphate synthase. ACS Synth Biol 2014; 3:298-306. [PMID: 24847684 DOI: 10.1021/sb400115e] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Monoterpenes have an established use in the food and cosmetic industries and have recently also found application as advanced biofuels. Although metabolic engineering efforts have so far achieved significant yields of larger terpenes, monoterpene productivity is lagging behind. Here, we set out to establish a monoterpene-specific production platform in Saccharomyces cerevisiae and identified the sequential reaction mechanism of the yeast farnesyl diphosphate synthase Erg20p to be an important factor limiting monoterpene yield. To overcome this hurdle, we engineered Erg20p into a geranyl diphosphate synthase and achieved a significant increase in monoterpene titers. To further improve production, we converted the engineered geranyl diphosphate synthase into a dominant negative form, so as to decrease the ability of the endogenous Erg20p to function as a farnesyl diphosphate synthase, without entirely abolishing sterol biosynthesis. Fusion of the synthetic dominant negative Erg20p variant with the terpene synthase, combined with yeast strain engineering, further improved monoterpene yields and achieved an overall 340-fold increase in sabinene yield over the starting strain. The design described here can be readily incorporated to any dedicated yeast strain, while the developed plasmid vectors and heterozygous ERG20 deletion yeast strain can also be used as a plug-and-play system for enzyme characterization and monoterpene pathway elucidation.
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Affiliation(s)
- Codruta Ignea
- Mediterranean Agronomic Institute of Chania, P.O. Box
85, Chania 73100, Greece
| | - Marianna Pontini
- Mediterranean Agronomic Institute of Chania, P.O. Box
85, Chania 73100, Greece
- Plant
Physiology Unit, Department of Plant Biology, Innovation Centre, University of Turin, Via Quarello 11/A, 10135, Turin, Italy
| | - Massimo E. Maffei
- Plant
Physiology Unit, Department of Plant Biology, Innovation Centre, University of Turin, Via Quarello 11/A, 10135, Turin, Italy
| | - Antonios M. Makris
- Institute of Applied Biosciences − Centre for Research and Technology Hellas (INAB-CERTH), P.O. Box 60361,
Thermi 57001, Thessaloniki, Greece
| | - Sotirios C. Kampranis
- Mediterranean Agronomic Institute of Chania, P.O. Box
85, Chania 73100, Greece
- Department
of Biochemistry, School of Medicine, University of Crete, P.O. Box 2208, Heraklion 71003, Greece
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45
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Henke SK, Cronan JE. Successful conversion of the Bacillus subtilis BirA Group II biotin protein ligase into a Group I ligase. PLoS One 2014; 9:e96757. [PMID: 24816803 PMCID: PMC4016012 DOI: 10.1371/journal.pone.0096757] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 04/07/2014] [Indexed: 11/19/2022] Open
Abstract
Group II biotin protein ligases (BPLs) are characterized by the presence of an N-terminal DNA binding domain that allows transcriptional regulation of biotin biosynthetic and transport genes whereas Group I BPLs lack this N-terminal domain. The Bacillus subtilis BPL, BirA, is classified as a Group II BPL based on sequence predictions of an N-terminal helix-turn-helix motif and mutational alteration of its regulatory properties. We report evidence that B. subtilis BirA is a Group II BPL that regulates transcription at three genomic sites: bioWAFDBI, yuiG and yhfUTS. Moreover, unlike the paradigm Group II BPL, E. coli BirA, the N-terminal DNA binding domain can be deleted from Bacillus subtilis BirA without adverse effects on its ligase function. This is the first example of successful conversion of a Group II BPL to a Group I BPL with retention of full ligase activity.
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Affiliation(s)
- Sarah K. Henke
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
| | - John E. Cronan
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
- Department of Biochemistry, University of Illinois, Urbana, Illinois, United States of America
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46
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Molecular models of the Mojave rattlesnake (Crotalus scutulatus scutulatus) venom metalloproteinases reveal a structural basis for differences in hemorrhagic activities. J Biol Phys 2014; 40:193-216. [PMID: 24522289 DOI: 10.1007/s10867-013-9339-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 12/23/2013] [Indexed: 01/22/2023] Open
Abstract
Rattlesnake venom can differ in composition and in metalloproteinase-associated activities. The molecular basis for this intra-species variation in Crotalus scutulatus scutulatus (Mojave rattlesnake) remains an enigma. To understand the molecular basis for intra-species variation of metalloproteinase-associated activities, we modeled the three-dimensional structures of four metalloproteinases based on the amino acid sequence of four variations of the proteinase domain of the C. s. scutulatus metalloproteinase gene (GP1, GP2, GP3, and GP4). For comparative purposes, we modeled the atrolysin metalloproteinases of C. atrox as well. All molecular models shared the same topology. While the atrolysin metalloproteinase molecular models contained highly conserved substrate binding sites, the Mojave rattlesnake metalloproteinases showed higher structural divergence when superimposed onto each other. The highest structural divergence among the four C. s. scutulatus molecular models was located at the northern cleft wall and the S'1-pocket of the substrate binding site, molecular regions that modulate substrate selectivity. Molecular dynamics and field potential maps for each C. s. scutulatus metalloproteinase model demonstrated that the non-hemorrhagic metalloproteinases (GP2 and GP3) contain highly basic molecular and field potential surfaces while the hemorrhagic metalloproteinases GP1 and atrolysin C showed extensive acidic field potential maps and shallow but less dynamic active site pockets. Hence, differences in the spatial arrangement of the northern cleft wall, the S'1-pocket, and the physico-chemical environment surrounding the catalytic site contribute to differences in metalloproteinase activities in the Mojave rattlesnake. Our results provide a structural basis for variation of metalloproteinase-associated activities in the rattlesnake venom of the Mojave rattlesnake.
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47
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Ramos M, Menao S, Arnedo M, Puisac B, Gil-Rodríguez MC, Teresa-Rodrigo ME, Hernández-Marcos M, Pierre G, Ramaswami U, Baquero-Montoya C, Bueno G, Casale C, Hegardt FG, Gómez-Puertas P, Pié J. New case of mitochondrial HMG-CoA synthase deficiency. Functional analysis of eight mutations. Eur J Med Genet 2013; 56:411-5. [PMID: 23751782 DOI: 10.1016/j.ejmg.2013.05.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 05/27/2013] [Indexed: 11/29/2022]
Abstract
Mitochondrial HMG-CoA synthase deficiency is a rare inherited metabolic disorder that affects ketone-body synthesis. Acute episodes include vomiting, lethargy, hepatomegaly, hypoglycaemia, dicarboxylic aciduria, and in severe cases, coma. This deficiency may have been under-diagnosed owing to the absence of specific clinical and biochemical markers, limitations in liver biopsy and the lack of an effective method of expression and enzyme assay for verifying the mutations found. To date, eight patients have been reported with nine allelic variants of the HMGCS2 gene. We present a new method of enzyme expression and a modification of the activity assay that allows, for first time, the functional study of missense mutations found in patients with this deficiency. Four of the missense mutations (p.V54M, p.R188H, p.G212R and p.G388R) did not produce proteins that could have been detected in soluble form by western blot; three produced a total loss of activity (p.Y167C, p.M307T and p.R500H) and one, variant p.F174L, gave an enzyme with a catalytic efficiency of 11.5%. This indicates that the deficiency may occur with partial loss of activity of enzyme. In addition, we describe a new patient with this deficiency, in which we detected the missense allelic variant, c.1162G>A (p.G388R) and the nonsense variant c.1270C>T (p.R424X).
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Affiliation(s)
- Mónica Ramos
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology Physiology, Medical School, University of Zaragoza, Spain
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48
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de Vega M. The minimal Bacillus subtilis nonhomologous end joining repair machinery. PLoS One 2013; 8:e64232. [PMID: 23691176 PMCID: PMC3656841 DOI: 10.1371/journal.pone.0064232] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 04/10/2013] [Indexed: 11/19/2022] Open
Abstract
It is widely accepted that repair of double-strand breaks in bacteria that either sporulate or that undergo extended periods of stationary phase relies not only on homologous recombination but also on a minimal nonhomologous end joining (NHEJ) system consisting of a dedicated multifunctional ATP-dependent DNA Ligase D (LigD) and the DNA-end-binding protein Ku. Bacillus subtilis is one of the bacterial members with a NHEJ system that contributes to genome stability during the stationary phase and germination of spores, having been characterized exclusively in vivo. Here, the in vitro analysis of the functional properties of the purified B. subtilis LigD (BsuLigD) and Ku (BsuKu) proteins is presented. The results show that the essential biochemical signatures exhibited by BsuLigD agree with its proposed function in NHEJ: i) inherent polymerization activity showing preferential insertion of NMPs, ii) specific recognition of the phosphate group at the downstream 5′ end, iii) intrinsic ligase activity, iv) ability to promote realignments of the template and primer strands during elongation of mispaired 3′ ends, and v) it is recruited to DNA by BsuKu that stimulates the inherent polymerization and ligase activities of the enzyme allowing it to deal with and to hold different and unstable DNA realignments.
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Affiliation(s)
- Miguel de Vega
- Instituto de Biología Molecular Eladio Viñuela, CSIC, Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, Madrid, Spain.
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49
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Andreev SM, Giliazova AV, Khaitov MR, Kozlov DG. [Anti-peptide antibodies specifically recognize the L1 protein of human papilloma virus type 31]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2013; 38:667-75. [PMID: 23547470 DOI: 10.1134/s1068162012060039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Antibodies that specifically recognize the capsid protein (L1) of human papillomavirus (HPV) are an important tool necessary for designing vaccines against HPV infection. In this work, we have predicted and synthesized peptide fragments mimicking B cell epitopes of L1 HPV type 31 (sequences 49-65, 131-145, 172-189, 349-362 and 402-414), and conjugated their to KLH and BSA to generate the L1-31-specific anti-peptide antibodies in mice. Variants of recombinant L1-31, including full-size and mutants with C-terminal single amino acid changes and deletions and full-size L1-16 were produced in the yeast using monitoring with L1 HPV16-specific monoclonal antibody. Testing of anti-peptide antisera in ELISA showed that antibodies to peptides 49-65 and 172-189 were capable to recognize specifically L1-31 protein, but not L1-16 one. Such antibodies may be used for assay of L1-31 production in various expression systems.
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50
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Batool S, Nawaz MS, Kamal MA. In silico analysis of the amido phosphoribosyltransferase inhibition by PY873, PY899 and a derivative of isophthalic acid. Invest New Drugs 2013; 31:1355-63. [PMID: 23483322 DOI: 10.1007/s10637-013-9944-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 02/25/2013] [Indexed: 10/27/2022]
Abstract
Selectively decreasing the availability of precursors for the de novo biosynthesis of purine nucleotides is a valid approach towards seeking a cure for leukaemia. Nucleotides and deoxynucleotides are required by living cells for syntheses of RNA, DNA, and cofactors such as NADP(+), FAD(+), coenzyme A and ATP. Nucleotides contain purine and pyrimidine bases, which can be synthesized through salvage pathway as well. Amido phosphoribosyltransferase (APRT), also known as glutamine phosphoribosylpyrophosphate amidotransferase (GPAT), is an enzyme that in humans is encoded by the PPAT (phosphoribosyl pyrophosphate amidotransferase) gene. APRT catalyzes the first committed step of the de novo pathway using its substrate, phosphoribosyl pyrophosphate (PRPP). As APRT is inhibited by many folate analogues, therefore, in this study we focused on the inhibitory effects of three folate analogues on APRT activity. This is extension of our previous wet lab work to analyze and dissect molecular interaction and inhibition mechanism using molecular modeling and docking tools in the current study. Comparative molecular docking studies were carried out for three diamino folate derivatives employing a model of the human enzyme that was built using the 3D structure of Bacillus subtilis APRT (PDB ID; 1GPH) as the template. Binding orientation of interactome indicates that all compounds having nominal cluster RMSD in same active site's deep narrow polar fissure. On the basis of comparative conformational analysis, electrostatic interaction, binding free energy and binding orientation of interactome, we support the possibility that these molecules could behave as APRT inhibitors and therefore may block purine de novo biosynthesis. Consequently, we suggest that PY899 is the most active biological compound that would be a more potent inhibitor for APRT inhibition than PY873 and DIA, which also confirms previous wet lab report.
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Affiliation(s)
- Sidra Batool
- Functional Informatics Laboratory National Center for Bioinformatics, Quaid-I-Azam University, Islamabad, Pakistan
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