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Yu X, Li H, Tian W, Ge Y, Wang T, Qi Z, Liu J. Single-layer semiconductor-decorated flexible 2D protein nanosheets by engineered anchoring for efficient photocatalytic hydrogen production. Int J Biol Macromol 2024; 261:129819. [PMID: 38290631 DOI: 10.1016/j.ijbiomac.2024.129819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 02/01/2024]
Abstract
Protein self-assembly can be accurately manipulated to form ordered nanostructures through various supramolecular forces. This strategy is expected to make significant breakthroughs in the field of new biomimetic functional materials. Specifically, the construction of photocatalytic systems on two-dimensional (2D) flexible protein nanosheets meets a great challenge. We introduce a synthetic methodology for creating single-layer semiconductor-decorated protein 2D materials under mild conditions with enhanced light-driven hydrogen production. This approach employs a bioengineered green fluorescent protein (E4P) with the addition of a Cd-binding peptide, enabling precise control of the assembly of CdS quantum dots (QDs) on the protein's surface. Consequently, we obtained 4.3 nm-thin single-layer 2D protein nanosheets with substantial surface areas ideal for accommodating CdS QDs. By orthogonal incorporation of metal-binding peptides and supramolecular coordination, significantly enhancing the overall photocatalytic efficiency. Our findings demonstrate the potential for stable and efficient hydrogen production, highlighting the adaptability and biocompatibility of protein scaffolds for photocatalysis.
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Affiliation(s)
- Xiaoxuan Yu
- Sino-German Joint Research Lab for Space Biomaterials and Translational Technology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China; Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, China
| | - Hui Li
- Sino-German Joint Research Lab for Space Biomaterials and Translational Technology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China; Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, China
| | - Wei Tian
- Shaanxi Key Laboratory of Macromolecular Science and Technology, MOE Key Laboratory of Material Physics and Chemistry under Extraordinary Conditions, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Yan Ge
- Sino-German Joint Research Lab for Space Biomaterials and Translational Technology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Tingting Wang
- Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, China
| | - Zhenhui Qi
- Sino-German Joint Research Lab for Space Biomaterials and Translational Technology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Junqiu Liu
- Key Laboratory of Organosilicon Chemistry and Material Technology, Ministry of Education, College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 311121, China.
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Pan S, Manabe N, Ohno S, Komatsu S, Fujimura T, Yamaguchi Y. Each N-glycan on human IgA and J-chain uniquely affects oligomericity and stability. Biochim Biophys Acta Gen Subj 2024; 1868:130536. [PMID: 38070292 DOI: 10.1016/j.bbagen.2023.130536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 11/24/2023] [Accepted: 11/30/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Immunoglobulin A (IgA) plays a pivotal role in various immune responses, especially that of mucosal immunity. IgA is usually assembled into dimers with the contribution of J-chains. There are two N-glycosylation sites in human IgA1-Fc and one in the J-chain. There is no consensus as yet on the functional role of the N-glycosylation. METHODS To gain a better understanding of their role, we designed a series of IgA1-Fc mutants, which were expressed in the absence or presence of the J-chain. RESULTS IgA1-Fc without the J-chain, was predominantly expressed as a monomer, and in its presence dimers and some polymers appeared. N263 (Fc Cα2), N459 (Fc tailpiece) and N49 (J-chain) were shown to be site-specifically modified with N-glycans by mass spectrometry analysis. Mutant IgA1-Fc N459Q failed to form a proper dimer in the presence of the J-chain, instead higher-order aggregates appeared. Fluorescence experiments suggest that the N459-glycans cover a hydrophobic surface at the Fc tailpiece that prevents other Fc molecules from approaching the dimeric IgA. A thermofluor assay revealed that the N-glycans at N263 (Fc) and N49 (J-chain) both contribute in different ways to the thermal stability of the Fc-J-chain complex. NMR analysis of 13C-labeled Fc suggests that the N459-glycan is relatively flexible while the N263-glycan is more rigid. CONCLUSIONS We conclude that the N459-glycan of IgA1-Fc is essential for dimer formation and prevention of higher-order aggregates while those at N263 (Fc) and N49 (J-chain) stabilize the Fc-J-chain complex. GENERAL SIGNIFICANCE Site-specific role for N-glycan in molecular assembly is addressed.
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Affiliation(s)
- Shunli Pan
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Miyagi, Japan
| | - Noriyoshi Manabe
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Miyagi, Japan
| | - Shiho Ohno
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Miyagi, Japan
| | - Sachiko Komatsu
- Division of Bioanalytical Chemistry, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Miyagi, Japan
| | - Tsutomu Fujimura
- Division of Bioanalytical Chemistry, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Miyagi, Japan
| | - Yoshiki Yamaguchi
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Miyagi, Japan.
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Jing XH, Zhao GY, Wang GB, Huang QL, Zou WS, Huang LN, Li W, Qiu ZY, Xin RH. Naringin alleviates pneumonia caused by Klebsiella pneumoniae infection by suppressing NLRP3 inflammasome. Biomed Pharmacother 2024; 170:116028. [PMID: 38113627 DOI: 10.1016/j.biopha.2023.116028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/14/2023] [Accepted: 12/14/2023] [Indexed: 12/21/2023] Open
Abstract
Klebsiella pneumoniae (Kpn) is an important pathogen of hospital-acquired pneumonia, which can lead to sepsis and death in severe cases. In this study, we simulated pneumonia induced by Kpn infection in mice to investigate the therapeutic effect of naringin (NAR) on bacterial-induced lung inflammation. Mice infected with Kpn exhibited increases in white blood cells (WBC) and neutrophils in the peripheral blood and pathological severe injury of the lungs. This injury was manifested by increased expression of the inflammatory cytokines interleukin (IL)- 18, IL-1β, tumor necrosis factor-α (TNF-α) and IL-6, and elevated the expression of NLRP3 protein. NAR treatment could decrease the protein expression of NLRP3, alleviate lung inflammation, and reduce lung injury in mice caused by Kpn. Meanwhile, molecular docking results suggest NAR could bind to NLRP3 and Surface Plasmon Resonance (SPR) analyses also confirm this result. In vitro trials, we found that pretreated with NAR not only inhibited nuclear translocation of nuclear factor (NF)-κB protein P65 but also attenuated the protein interaction of NLRP3, caspase-1 and ASC and inhibited the assembly of NLRP3 inflammasome in mice AMs. Additionally, NAR could reduce intracellular potassium (K+) efflux, inhibiting NLRP3 inflammasome activation. These results indicated that NAR could protect against Kpn-induced pneumonia by inhibiting the overactivation of the NLRP3 inflammasome signaling pathway. The results of this study confirm the efficacy of NAR in treating bacterial pneumonia, refine the mechanism of action of NAR, and provide a theoretical basis for the research and development of NAR as an anti-inflammatory adjuvant.
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Affiliation(s)
- Xiao-Han Jing
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences (CAAS), China; Engineering and Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, China; Key Laboratory of Veterinary Pharmaceutical Development of Ministry of Agriculture and Rural Affairs of P.R. China, China
| | - Guan-Yu Zhao
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, Gansu 730000, China
| | - Gui-Bo Wang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences (CAAS), China; Engineering and Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, China; Key Laboratory of Veterinary Pharmaceutical Development of Ministry of Agriculture and Rural Affairs of P.R. China, China
| | - Qi-Lin Huang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences (CAAS), China; Engineering and Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, China; Key Laboratory of Veterinary Pharmaceutical Development of Ministry of Agriculture and Rural Affairs of P.R. China, China
| | - Wen-Shu Zou
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences (CAAS), China; Engineering and Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, China; Key Laboratory of Veterinary Pharmaceutical Development of Ministry of Agriculture and Rural Affairs of P.R. China, China
| | - Li-Na Huang
- School of Pharmacy, State Key Laboratory of Applied Organic Chemistry, Lanzhou University, China
| | - Wei Li
- Lanzhou Center for Disease Control and Prevention, Lanzhou, China.
| | - Zheng-Ying Qiu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences (CAAS), China; Engineering and Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, China; Key Laboratory of Veterinary Pharmaceutical Development of Ministry of Agriculture and Rural Affairs of P.R. China, China.
| | - Rui-Hua Xin
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences (CAAS), China; Engineering and Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province, China; Key Laboratory of Veterinary Pharmaceutical Development of Ministry of Agriculture and Rural Affairs of P.R. China, China.
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4
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Zhou P, Gao C, Song W, Wei W, Wu J, Liu L, Chen X. Engineering status of protein for improving microbial cell factories. Biotechnol Adv 2024; 70:108282. [PMID: 37939975 DOI: 10.1016/j.biotechadv.2023.108282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 10/23/2023] [Accepted: 11/05/2023] [Indexed: 11/10/2023]
Abstract
With the development of metabolic engineering and synthetic biology, microbial cell factories (MCFs) have provided an efficient and sustainable method to synthesize a series of chemicals from renewable feedstocks. However, the efficiency of MCFs is usually limited by the inappropriate status of protein. Thus, engineering status of protein is essential to achieve efficient bioproduction with high titer, yield and productivity. In this review, we summarize the engineering strategies for metabolic protein status, including protein engineering for boosting microbial catalytic efficiency, protein modification for regulating microbial metabolic capacity, and protein assembly for enhancing microbial synthetic capacity. Finally, we highlight future challenges and prospects of improving microbial cell factories by engineering status of protein.
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Affiliation(s)
- Pei Zhou
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Wanqing Wei
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China.
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Abstract
Protein self-association is a widespread phenomenon that results in the formation of multimeric protein structures with critical roles in cellular processes. Protein self-association can lead to finite protein complexes or open-ended, and potentially, infinite structures. This review explores the concept of protein agglomeration, a process that results from the infinite self-assembly of folded proteins. We highlight its differences from other better-described processes with similar macroscopic features, such as aggregation and liquid-liquid phase separation. We review the sequence, structural, and biophysical factors influencing protein agglomeration. Lastly, we briefly discuss the implications of agglomeration in evolution, disease, and aging. Overall, this review highlights the need to study protein agglomeration for a better understanding of cellular processes.
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Affiliation(s)
- M. L. Romero-Romero
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology, Dresden, Germany
| | - H. Garcia-Seisdedos
- Department of Structural and Molecular Biology, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain
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Thewasano N, Germany EM, Maruno Y, Nakajima Y, Shiota T. Categorization of Escherichia coli Outer Membrane Proteins by Dependence on Accessory Proteins of the β-barrel Assembly Machinery Complex. J Biol Chem 2023:104821. [PMID: 37196764 PMCID: PMC10300371 DOI: 10.1016/j.jbc.2023.104821] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 04/20/2023] [Accepted: 05/08/2023] [Indexed: 05/19/2023] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria is populated by various outer membrane proteins (OMPs) that fold into a unique β-barrel transmembrane domain. Most OMPs are assembled into the OM by the β-barrel assembly machinery (BAM) complex. In Escherichia coli, the BAM complex is composed of two essential proteins (BamA and BamD) and three non-essential accessory proteins (BamB, BamC, and BamE). The currently proposed molecular mechanisms of the BAM complex involve only essential subunits, with the function of the accessory proteins remaining largely unknown. Here, we compared the accessory protein requirements for the assembly of seven different OMPs, 8- to 22-stranded, by our in vitro reconstitution assay using an E. coli mid-density membrane (EMM). BamE was responsible for the full efficiency of the assembly of all tested OMPs, as it enhanced the stability of essential subunit binding. BamB increased the assembly efficiency of more than 16-stranded OMPs, whereas BamC was not required for the assembly of any tested OMPs. Our categorization of the requirements of BAM complex accessory proteins in the assembly of substrate OMPs enables us to identify potential targets for the development of new antibiotics.
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Affiliation(s)
- Nakajohn Thewasano
- Organization for Promotion of Tenure Track, University of Miyazaki, Nishi 1-1 Gakuen Kibanadai, Miyazaki, 889-2192, Japan; Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Edward M Germany
- Organization for Promotion of Tenure Track, University of Miyazaki, Nishi 1-1 Gakuen Kibanadai, Miyazaki, 889-2192, Japan; Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Yuki Maruno
- Organization for Promotion of Tenure Track, University of Miyazaki, Nishi 1-1 Gakuen Kibanadai, Miyazaki, 889-2192, Japan; Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Yukari Nakajima
- Organization for Promotion of Tenure Track, University of Miyazaki, Nishi 1-1 Gakuen Kibanadai, Miyazaki, 889-2192, Japan; Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Takuya Shiota
- Organization for Promotion of Tenure Track, University of Miyazaki, Nishi 1-1 Gakuen Kibanadai, Miyazaki, 889-2192, Japan; Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan.
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7
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Alkhaldi HA, Vik SB. Subunits E-F-G of E. coli Complex I can form an active complex when expressed alone, but in time-delayed assembly co-expression of B-CD-E-F-G is optimal. Biochim Biophys Acta Bioenerg 2022; 1863:148593. [PMID: 35850264 PMCID: PMC9783743 DOI: 10.1016/j.bbabio.2022.148593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/15/2022] [Accepted: 07/11/2022] [Indexed: 12/27/2022]
Abstract
Respiratory Complex I from E. coli is a proto-type of the mitochondrial enzyme, consisting of a 6-subunit peripheral arm (B-CD-E-F-G-I) and a 7-subunit membrane arm. When subunits E-F-G (N-module), were expressed alone they formed an active complex as determined by co-immunoprecipitation and native gel electrophoresis. When co-expressed with subunits B and CD, only a complex of E-F-G was found. When these five subunits were co-expressed with subunit I and two membrane subunits, A and H, a complex of B-CD-E-F-G-I was membrane-bound, constituting the N- and Q-modules. Assembly of Complex I was also followed by splitting the genes between two plasmids, in three different groupings, and expressing them simultaneously, or with time-delay of expression from one plasmid. When the B-CD-E-F-G genes were co-expressed after a time-delay, assembly was over 90 % of that when the whole operon was expressed together. In summary, E-F-G was the only soluble subcomplex detected in these studies, but assembly was not optimal when these subunits were expressed either first or last. Co-expression of subunits B and CD with E-F-G provided a higher level of assembly, indicating that integrated assembly of N- and Q-modules provides a more efficient pathway.
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Affiliation(s)
- Hind A Alkhaldi
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Steven B Vik
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA.
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8
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Liu Y, Zang J, Leng X, Zhao G. A short helix regulates conversion of dimeric and 24-meric ferritin architectures. Int J Biol Macromol 2022; 203:535-542. [PMID: 35120932 DOI: 10.1016/j.ijbiomac.2022.01.174] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 12/28/2022]
Abstract
The inter-subunit interaction at the protein interfaces plays a key role in protein self-assembly, through which enabling protein self-assembly controllable is of great importance for preparing the novel nanoscale protein materials with unexplored properties. Different from normal 24-meric ferritin, archaeal ferritin, Thermotoga maritima ferritin (TmFtn) naturally occurs as a dimer, which can assemble into a 24-mer nanocage induced by salts. However, the regulation mechanism of protein self-assembly underlying this phenomenon remains unclear. Here, a combination of the computational energy simulation and key interface reconstruction revealed that a short helix involved interactions at the C4 interface are mainly responsible for the existence of such dimer. Agreeing with this idea, deletion of such short helix of each subunit triggers it to be a stable dimer, which losses the ability to reassemble into 24-meric ferritin in the presence of salts in solution. Further support for this idea comes from the observation that grafting a small helix from human H ferritin onto archaeal subunit resulted in a stable 24-mer protein nanocage even in the absence of salts. Thus, these findings demonstrate that adjusting the interactions at the protein interfaces appears to be a facile, effective approach to control subunit assembly into different protein architectures.
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Affiliation(s)
- Yu Liu
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China
| | - Jiachen Zang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China
| | - Xiaojing Leng
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
| | - Guanghua Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
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Miyazaki R, Mori H, Akiyama Y. A Photo-Crosslinking Approach to Monitoring the Assembly of an LptD Intermediate with LptE in a Living Cell. Methods Mol Biol 2022; 2548:97-107. [PMID: 36151494 DOI: 10.1007/978-1-0716-2581-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Elucidating the dynamic behavior of proteins in living cells is extremely important for understanding the physiological roles of biological processes. The site-specific in vivo photo-crosslinking approach using a photoreactive unnatural amino acid enables the analysis of protein interactions with high spatial resolution in vivo. Recently, by improving the photo-crosslinking technique, we developed the "PiXie" method for the analysis of dynamic interactions of newly synthesized proteins. Here, we describe the detailed protocols of the "PiXie" method and its application to the analysis of the assembly processes of the lipopolysaccharide translocon components, a β-barrel outer membrane protein, LptD, and a lipoprotein, LptE.
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Affiliation(s)
- Ryoji Miyazaki
- Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Hiroyuki Mori
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yoshinori Akiyama
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
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10
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Wei Q, Xia J. Self-Assembled Multienzyme Nanostructures for Biocatalysis in Cellulo. Methods Mol Biol 2022; 2487:197-204. [PMID: 35687238 DOI: 10.1007/978-1-0716-2269-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Multienzyme complexes naturally exist in cells to catalyze cascade reactions in metabolic pathways. By clustering the enzymes in close proximity, these nanomachineries achieve effective conversion of metabolites. Bioengineers are working on the development of synthetic versions of multienzyme complexes in cells to synergize heterologous biosynthesis. Assembling enzymes on protein scaffolds through protein-protein interactions is a viable and facile way to form synthetic multienzyme complexes. Here, we describe the general methods to construct self-assembled multienzyme nanostructures in Escherichia coli for biosynthesis of valuable chemicals.
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Affiliation(s)
- Qixin Wei
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Jiang Xia
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong, SAR, China.
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Ikami Y, Terasawa K, Sakamoto K, Ohtake K, Harada H, Watabe T, Yokoyama S, Hara-Yokoyama M. The two-domain architecture of LAMP2A regulates its interaction with Hsc70. Exp Cell Res 2021; 411:112986. [PMID: 34942188 DOI: 10.1016/j.yexcr.2021.112986] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 12/11/2021] [Accepted: 12/19/2021] [Indexed: 11/04/2022]
Abstract
Chaperone-mediated autophagy (CMA) is a unique proteolytic pathway, in which cytoplasmic proteins recognized by heat shock cognate protein 70 (Hsc70/HSPA8) are transported into lysosomes for degradation. The substrate/chaperone complex binds to the cytosolic tail of the lysosomal-associated membrane protein type 2A (LAMP2A), but whether the interaction between Hsc70 and LAMP2A is direct or mediated by other molecules has remained to be elucidated. The structure of LAMP2A comprises a large lumenal domain composed of two domains, both with the β-prism fold, a transmembrane domain and a short cytoplasmic tail. We previously reported the structural basis for the homophilic interaction of the lumenal domains of LAMP2A, using site-specific photo-crosslinking and/or steric hindrance within cells. In the present study, we introduced a photo-crosslinker into the cytoplasmic tail of LAMP2A and successfully detected its crosslinking with Hsc70, revealing this direct interaction for the first time. Furthermore, we demonstrated that the truncation of the membrane-distal domain within the lumenal domain of LAMP2A reduced the amount of Hsc70 that coimmunoprecipitated with LAMP2A. Our present results suggested that the two-domain architecture of the lumenal domains of LAMP2A underlies the interaction with Hsc70 at the cytoplasmic surface of the lysosome.
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Affiliation(s)
- Yuta Ikami
- Department of Oral and Maxillofacial Surgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Yushima 1-5-45, Bunkyo-ku, Tokyo, 113-8549, Japan; Department of Biochemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Yushima 1-5-45, Bunkyo-ku, Tokyo, 113-8549, Japan
| | - Kazue Terasawa
- Department of Biochemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Yushima 1-5-45, Bunkyo-ku, Tokyo, 113-8549, Japan
| | - Kensaku Sakamoto
- RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Kazumasa Ohtake
- RIKEN Center for Biosystems Dynamics Research (BDR), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Hiroyuki Harada
- Department of Oral and Maxillofacial Surgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Yushima 1-5-45, Bunkyo-ku, Tokyo, 113-8549, Japan
| | - Tetsuro Watabe
- Department of Biochemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Yushima 1-5-45, Bunkyo-ku, Tokyo, 113-8549, Japan
| | - Shigeyuki Yokoyama
- RIKEN Cluster for Science, Technology and Innovation Hub, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Miki Hara-Yokoyama
- Department of Biochemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Yushima 1-5-45, Bunkyo-ku, Tokyo, 113-8549, Japan.
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12
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Tomazic N, Overkamp KE, Wegner H, Gu B, Mahler F, Aras M, Keller S, Pierik AJ, Hofmann E, Frankenberg-Dinkel N. Exchange of a single amino acid residue in the cryptophyte phycobiliprotein lyase GtCPES expands its substrate specificity. Biochim Biophys Acta Bioenerg 2021; 1862:148493. [PMID: 34537203 DOI: 10.1016/j.bbabio.2021.148493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/26/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
Cryptophytes are among the few eukaryotes employing phycobiliproteins (PBP) for light harvesting during oxygenic photosynthesis. In contrast to cyanobacterial PBP that are organized in membrane-associated phycobilisomes, those from cryptophytes are soluble within the chloroplast thylakoid lumen. Their light-harvesting capacity is due to covalent linkage of several open-chain tetrapyrrole chromophores (phycobilins). Guillardia theta utilizes the PBP phycoerythrin 545 with 15,16-dihydrobiliverdin (DHBV) in addition to phycoerythrobilin (PEB) as chromophores. The assembly of PBPs in cryptophytes involves the action of PBP-lyases as shown for cyanobacterial PBP. PBP-lyases facilitate the attachment of the chromophore in the right configuration and stereochemistry. Here we present the functional characterization of the eukaryotic S-type PBP lyase GtCPES. We show GtCPES-mediated transfer and covalent attachment of PEB to the conserved Cys82 of the acceptor PBP β-subunit (PmCpeB) of Prochlorococcus marinus MED4. On the basis of the previously solved crystal structure, the GtCPES binding pocket was investigated using site-directed mutagenesis. Thereby, amino acid residues involved in phycobilin binding and transfer were identified. Interestingly, exchange of a single amino acid residue Met67 to Ala extended the substrate specificity to phycocyanobilin (PCB), most likely by enlarging the substrate-binding pocket. Variant GtCPES_M67A binds both PEB and PCB forming a stable, colored complex in vitro and produced in Escherichia coli. GtCPES_M67A is able to mediate PCB transfer to Cys82 of PmCpeB. Based on these findings, we postulate that this single amino acid residue has a crucial role for bilin binding specificity of S-type phycoerythrin lyases but additional factors regulate handover to the target protein.
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Affiliation(s)
- Natascha Tomazic
- Microbiology, Faculty for Biology, Technische Universität Kaiserslautern (TUK), Germany
| | - Kristina E Overkamp
- Microbiology, Faculty for Biology, Technische Universität Kaiserslautern (TUK), Germany
| | - Helen Wegner
- Microbiology, Faculty for Biology, Technische Universität Kaiserslautern (TUK), Germany
| | - Bin Gu
- Microbiology, Faculty for Biology, Technische Universität Kaiserslautern (TUK), Germany
| | - Florian Mahler
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Germany
| | - Marco Aras
- Microbiology, Faculty for Biology, Technische Universität Kaiserslautern (TUK), Germany
| | - Sandro Keller
- Molecular Biophysics, Technische Universität Kaiserslautern (TUK), Germany; Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Austria; Field of Excellence BioHealth, University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Antonio J Pierik
- Biochemistry, Faculty for Chemistry, Technische Universität Kaiserslautern (TUK), Germany
| | - Eckhard Hofmann
- Proteincrystallography, Faculty for Biology and Biotechnology, Ruhr-Universität Bochum, Germany
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13
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Abstract
The ionic currents passing through nanopores can be used to sequence DNA and identify molecules at the single-molecule level. Recently, researchers have started using nanopores for the detection and analysis of proteins, providing a new platform for single-molecule enzymology studies and more efficient biomolecular sensing applications. For this approach, the homo-oligomeric Cytolysin A (ClyA) nanopore has been demonstrated as a powerful tool. Here, we describe a simple protocol allowing the production of ClyA nanopores. Monomers of ClyA are expressed in Escherichia coli and oligomerized in the presence of detergent. Subsequently, different oligomer variants are electrophoretically resolved and stored in a gel matrix for long-term use.
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Affiliation(s)
- Nicole Stéphanie Galenkamp
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Veerle Van Meervelt
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Natalie Lisa Mutter
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Nieck Jordy van der Heide
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Carsten Wloka
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
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14
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Wang R, Sun F. The Spy that links: Creation of nonlinear protein architectures and materials using SpyTag/SpyCatcher chemistry. Methods Enzymol 2020; 647:283-301. [PMID: 33482993 DOI: 10.1016/bs.mie.2020.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The peptide/protein pair, SpyTag/SpyCatcher, which is derived from split immunoglobulin-like collagen adhesin domain (CnaB2) from Streptococcus pyogenes, can spontaneously form a stable Lys-Asp isopeptide bond under physiological conditions. This enabling technology- also known as genetically encoded click chemistry owing to its marked efficiency and specificity-has led to a variety of applications in protein engineering, materials science and synthetic biology in recent years. In this chapter, we discuss the use of SpyTag/SpyCatcher chemistry to create nonlinear protein architectures and materials, with emphasis on its role in shaping up topology engineering as an emerging branch of protein engineering. The synthesis of entirely protein-based molecular networks, Spy networks, is highlighted. The protocols for preparing Spy networks and applications thereof are also illustrated.
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Affiliation(s)
- Ri Wang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, People's Republic of China
| | - Fei Sun
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, People's Republic of China.
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15
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Shafqat W, Jaskani MJ, Maqbool R, Sattar Khan A, Abbas Naqvi S, Ali Z, Ahmad Khan I. Genome Wide Analysis of Citrus sinensis Heat Shock Proteins. Iran J Biotechnol 2020; 18:e2529. [PMID: 34056019 PMCID: PMC8148642 DOI: 10.30498/ijb.2020.2529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background Plant and animal cells possess a ubiquitous protein known as heat shock proteins (HSPs). Hsps were originally described in relation to heat shock and against abiotic and biotic stresses. Heat shock protein was classified in other crops on the bases of single classes or all classes but in Citrus sinensis Hsps groups, classes, subfamilies and members were not classified and characterized up to our knowledge. Objectives Present study was focused on the identification and grouping of C. sinensis Hsps (CsHsps) classes, members among classes, their phylogenetic relationship, gene structure, conserved motifs and identification of proteins by using bioinformatics tools and analyses. Materials and Methods Genomic, Peptide and CDS sequences of CsHsps were downloaded from phytozome. MEGA 7 used for the phylogenetic analysis, GSDS for gene structure, UGENE for the multiple sequence alignment and MEME suite for the conserved motif analysis. Results The genome size of C. sinensis was 367 Mb, Chromosome number (2n)18, having 151 Hsps with six groups CsHsp10, 20, 40, 60,70 and 90. CsHsp20 was the largest group having 54 members, followed by CsHsp60 and CsHsp70 both having 30 members respectively. Conclusion CsHsps members within a class shared more similar gene and protein structure. CsHsp 60, CsHsp 70 and CsHsp90 shared more conserved and similar amino acid pattern. Each class had some important proteins such as Cpn in CsHsp10, Hypothetical proteins in CsHsp20 and 40, Dnak in CsHsp60, Molecular chaperone in CsHsp70 and Hsp90 in CsHsp90. These proteins are produced by cells in response to stresses in citrus. Chaperonins and some hypothetical proteins identified in CsHsps, help in ATP synthesis and protein degradation. This is genome wide analysis and classification sets the groundwork for future investigations to fully characterize functionally the Citrus Hsps families and underscores the relevance of Hsps response to abiotic and biotic stresses in Citrus.
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Affiliation(s)
- Waqar Shafqat
- Institute of Horticultural Sciences, Faculty of Agriculture, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Jafar Jaskani
- Institute of Horticultural Sciences, Faculty of Agriculture, University of Agriculture, Faisalabad, Pakistan
| | - Rizwana Maqbool
- Center for Advanced Studies, University of Agriculture, Faisalabad, Pakistan.,Department of Plant Breeding and Genetics, Faculty of Agriculture, University of Agriculture, Faisalabad, Pakistan
| | - Ahmad Sattar Khan
- Institute of Horticultural Sciences, Faculty of Agriculture, University of Agriculture, Faisalabad, Pakistan
| | - Summar Abbas Naqvi
- Institute of Horticultural Sciences, Faculty of Agriculture, University of Agriculture, Faisalabad, Pakistan
| | - Zulfiqar Ali
- Plant Breeding and Genetics, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
| | - Iqrar Ahmad Khan
- Institute of Horticultural Sciences, Faculty of Agriculture, University of Agriculture, Faisalabad, Pakistan
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16
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Klasek L, Ganesan I, Theg SM. Methods for studying protein targeting to and within the chloroplast. Methods Cell Biol 2020; 160:37-59. [PMID: 32896329 DOI: 10.1016/bs.mcb.2020.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Distinct protein complements impart each of the chloroplast's three membranes and three aqueous spaces with specific functions essential for plant growth and development. Chloroplasts capture light energy, synthesize macromolecular building blocks and specialized metabolites, and communicate environmental signals to the nucleus. Establishing and maintaining these processes requires approximately 3000 proteins derived from nuclear genes, constituting approximately 95% of the chloroplast proteome. These proteins are imported into chloroplasts from the cytosol, sorted to the correct subcompartment, and assembled into functioning complexes. In vitro import assays can reconstitute these processes in isolated chloroplasts. We describe methods for monitoring in vitro protein import using Pisum sativum chloroplasts and for protease protection, fractionation, and native protein electrophoresis that are commonly combined with the import assay. These techniques facilitate investigation of the import and sorting processes, of where a protein resides, and of how that protein functions.
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Affiliation(s)
- Laura Klasek
- Department of Plant Biology, University of California-Davis, Davis, CA, United States
| | - Iniyan Ganesan
- Department of Plant Biology, University of California-Davis, Davis, CA, United States
| | - Steven M Theg
- Department of Plant Biology, University of California-Davis, Davis, CA, United States.
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17
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Nüske E, Marini G, Richter D, Leng W, Bogdanova A, Franzmann TM, Pigino G, Alberti S. Filament formation by the translation factor eIF2B regulates protein synthesis in starved cells. Biol Open 2020; 9:bio046391. [PMID: 32554487 PMCID: PMC7358136 DOI: 10.1242/bio.046391] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/26/2020] [Indexed: 12/11/2022] Open
Abstract
Cells exposed to starvation have to adjust their metabolism to conserve energy and protect themselves. Protein synthesis is one of the major energy-consuming processes and as such has to be tightly controlled. Many mechanistic details about how starved cells regulate the process of protein synthesis are still unknown. Here, we report that the essential translation initiation factor eIF2B forms filaments in starved budding yeast cells. We demonstrate that filamentation is triggered by starvation-induced acidification of the cytosol, which is caused by an influx of protons from the extracellular environment. We show that filament assembly by eIF2B is necessary for rapid and efficient downregulation of translation. Importantly, this mechanism does not require the kinase Gcn2. Furthermore, analysis of site-specific variants suggests that eIF2B assembly results in enzymatically inactive filaments that promote stress survival and fast recovery of cells from starvation. We propose that translation regulation through filament assembly is an efficient mechanism that allows yeast cells to adapt to fluctuating environments.
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Affiliation(s)
- Elisabeth Nüske
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Guendalina Marini
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Doris Richter
- Department of Cellular Biochemistry Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Weihua Leng
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Aliona Bogdanova
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Titus M Franzmann
- Department of Cellular Biochemistry Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Gaia Pigino
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
- Department of Cellular Biochemistry Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
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18
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Karuka SR, Hennen J, Hur KH, Mueller JD. Time-shifted mean-segmented Q data of a luminal protein measured at the nuclear envelope by fluorescence fluctuation microscopy. Data Brief 2020; 28:105005. [PMID: 32226805 PMCID: PMC7093802 DOI: 10.1016/j.dib.2019.105005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/25/2019] [Accepted: 12/05/2019] [Indexed: 11/25/2022] Open
Abstract
Fluorescence fluctuation microscopy is a widely used method to determine the mobility and oligomeric state of proteins in the live cell environment. Existing analysis methods rely on statistical evaluation of data segments with the implicit assumption that no significant signal fluctuations occur on the time scale of a data segment. Recent work on extending fluorescence fluctuation methods to the nuclear envelope of living cells identified a slow fluctuation process that is associated with the undulations of the nuclear membranes, which lead to intensity fluctuations due to local volume changes at the nuclear envelope. This environment violates the above-mentioned assumption and is associated with biased evaluation of fluorescence fluctuation data by traditional analysis methods, such as the autocorrelation function. This challenge was overcome by the introduction of the time-shifted mean-segmented Q function, which relies on a sliding scale of data segment lengths. Here, we share experimental fluorescence fluctuation data taken at the nuclear envelope and demonstrate the calculation of the time-shifted mean-segmented Q function from the raw data. The data and analysis should be valuable for researchers interested in fluorescence fluctuation techniques and provides an opportunity to examine the influence of slow fluctuations on existing data analysis methods. The data is related to the research article titled "Protein oligomerization and mobility within the nuclear envelope evaluated by the time-shifted mean-segmented Q factor" [1].
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Affiliation(s)
| | - Jared Hennen
- School of Physics and Astronomy, University of Minnesota, MN, 55455, United States
| | - Kwang-Ho Hur
- School of Physics and Astronomy, University of Minnesota, MN, 55455, United States
| | - Joachim D Mueller
- School of Physics and Astronomy, University of Minnesota, MN, 55455, United States
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19
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Martin GM, Sung MW, Shyng SL. Pharmacological chaperones of ATP-sensitive potassium channels: Mechanistic insight from cryoEM structures. Mol Cell Endocrinol 2020; 502:110667. [PMID: 31821855 PMCID: PMC6994177 DOI: 10.1016/j.mce.2019.110667] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/22/2019] [Accepted: 11/22/2019] [Indexed: 02/07/2023]
Abstract
ATP-sensitive potassium (KATP) channels are uniquely evolved protein complexes that couple cell energy levels to cell excitability. They govern a wide range of physiological processes including hormone secretion, neuronal transmission, vascular dilation, and cardiac and neuronal preconditioning against ischemic injuries. In pancreatic β-cells, KATP channels composed of Kir6.2 and SUR1, encoded by KCNJ11 and ABCC8, respectively, play a key role in coupling blood glucose concentration to insulin secretion. Mutations in ABCC8 or KCNJ11 that diminish channel function result in congenital hyperinsulinism. Many of these mutations principally hamper channel biogenesis and hence trafficking to the cell surface. Several small molecules have been shown to correct channel biogenesis and trafficking defects. Here, we review studies aimed at understanding how mutations impair channel biogenesis and trafficking and how pharmacological ligands overcome channel trafficking defects, particularly highlighting recent cryo-EM structural studies which have shed light on the mechanisms of channel assembly and pharmacological chaperones.
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Affiliation(s)
- Gregory M Martin
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Min Woo Sung
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Show-Ling Shyng
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, 97239, USA.
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20
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Abstract
Symmetry is very common among proteins found in structural databases such as the Protein Data Bank (PDB). We present novel software, called AnAnaS, that finds positions and orientations of the symmetry axes in all types of symmetrical protein assemblies. It deals with five symmetry groups: cyclic, dihedral, tetrahedral, octahedral, and icosahedral. The software also assesses the quality of symmetry and can detect symmetries in incomplete cyclic assemblies. Internally, AnAnaS comprises discrete and continuous optimization steps and is applicable to assemblies with multiple chains in the asymmetric subunits or to those with pseudosymmetry. The method is very fast as most of the steps are performed analytically.
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Affiliation(s)
- Guillaume Pagès
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP, LJK, Grenoble, France
| | - Sergei Grudinin
- Univ. Grenoble Alpes, Inria, CNRS, Grenoble INP, LJK, Grenoble, France.
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21
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Abstract
Collagen molecules are crucial extracellular players in animal tissue development and in functions ranging from ultrafiltration to organism locomotion. Among the 28 types of collagen found in human, type IV collagen stands out as a primordial type found in all species of the animal kingdom. Collagen IV forms smart scaffolds for basement membranes, sheet-like acellular structures that isolate, coordinate, and direct cells during morphogenesis. Collagen IV is also involved in multiple functions in developed tissues. As part of the basement membrane, collagen IV scaffolds provide mechanical strength, spatially tether extracellular macromolecules and directly signal to cells via receptor binding sites. Proper assembly and structure of the scaffolds are critical for development and function of multiple types of basement membranes. Within last 5 years it was established that Cl- concentration is a key factor for initiating collagen IV scaffold assembly. The biological role of Cl- in multiple physiological processes and detailed mechanisms for its signaling and structural impacts are well established. Cl- gradients are generated across the plasma and intracellular organelle membranes. As collagen IV molecules are secreted outside the cell, they experience a switch from low to high Cl- concentration. This transition works as a trigger for collagen IV scaffold assembly. Within the scaffold, collagen IV remains to be a Cl- sensor as its structural integrity continues to depend on Cl- concentration. Here, we review recent findings and set future directions for studies on the role of Cl- in type IV collagen assembly, function, and disease.
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Affiliation(s)
- Sergey V Ivanov
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ryan Bauer
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Elena N Pokidysheva
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sergei P Boudko
- Department of Medicine, Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN, USA. .,Vanderbilt Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN, USA. .,Department of Biochemistry, Vanderbilt University, Nashville, TN, USA.
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22
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Rose J, Visser F, Müller B, Senft M, Groscurth S, Sicking KF, Twyman RM, Prüfer D, Noll GA. Identification and molecular analysis of interaction sites in the MtSEO-F1 protein involved in forisome assembly. Int J Biol Macromol 2019; 144:603-614. [PMID: 31843608 DOI: 10.1016/j.ijbiomac.2019.12.092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/11/2019] [Accepted: 12/11/2019] [Indexed: 11/26/2022]
Abstract
Forisomes are large mechanoprotein complexes found solely in legumes such as Medicago truncatula. They comprise several "sieve element occlusion by forisome" (SEO-F) subunits, with MtSEO-F1 as the major structure-forming component. SEO-F proteins possess three conserved domains -an N-terminal domain (SEO-NTD), a potential thioredoxin fold, and a C-terminal domain (SEO-CTD)- but structural and biochemical data are scarce and little is known about the contribution of these domains to forisome assembly. To identify key amino acids involved in MtSEO-F1 dimerization and complex formation, we investigated protein-protein interactions by bimolecular fluorescence complementation and the analysis of yeast two-hybrid and random mutagenesis libraries. We identified a SEO-NTD core region as the major dimerization site, with abundant hydrophobic residues and rare charged residues suggesting dimerization is driven by the hydrophobic effect. We also found that ~45% of the full-length MtSEO-F1 sequence must be conserved for higher-order protein assembly, indicating that large interaction surfaces facilitate stable interactions, contributing to the high resilience of forisome bodies. Interestingly, the removal of 62 amino acids from the C-terminus did not disrupt forisome assembly. This is the first study unraveling interaction sites and mechanisms within the MtSEO-F1 protein at the level of dimerization and complex formation.
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Affiliation(s)
- Judith Rose
- Institute for Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany
| | - Franziska Visser
- Institute for Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany
| | - Boje Müller
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, 48143 Münster, Germany
| | - Matthias Senft
- Leibniz Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Sira Groscurth
- Stem Cell Network North Rhine-Westphalia, Merowingerplatz 1, 40225 Düsseldorf, Germany
| | - Kevin F Sicking
- Institute for Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany
| | | | - Dirk Prüfer
- Institute for Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, 48143 Münster, Germany
| | - Gundula A Noll
- Institute for Plant Biology and Biotechnology, University of Münster, Schlossplatz 8, 48143 Münster, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, 48143 Münster, Germany.
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23
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Nelea V, Reinhardt DP. Biophysical Techniques to Analyze Elastic Tissue Extracellular Matrix Proteins Interacting with ADAMTS Proteins. Methods Mol Biol 2020; 2043:213-35. [PMID: 31463915 DOI: 10.1007/978-1-4939-9698-8_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Multidomain matrix-associated zinc extracellular proteases ADAMTS and ADAMTS-like proteins have important biological activities in cells and tissues. Beyond their traditional role in procollagen and von Willebrand factor processing and proteoglycan cleavage, ADAMTS/ADAMTSL likely participate in or at least have some role in ECM assembly as some of these proteins bind ECM proteins including fibrillins, fibronectin, and LTBPs. In this chapter, we present four biophysical techniques largely used for the characterization, multimerization, and interaction of proteins: surface plasmon resonance spectroscopy, dynamic light scattering, atomic force microscopy, and circular dichroism spectroscopy.
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24
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de Alba E. Structure, interactions and self-assembly of ASC-dependent inflammasomes. Arch Biochem Biophys 2019; 670:15-31. [PMID: 31152698 PMCID: PMC8455077 DOI: 10.1016/j.abb.2019.05.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 05/10/2019] [Accepted: 05/28/2019] [Indexed: 12/12/2022]
Abstract
The inflammasome is a multi-protein platform that assembles upon the presence of cues derived from infection or tissue damage, and triggers the inflammatory response. Inflammasome components include sensor proteins that detect danger signals, procaspase 1 and the adapter ASC (apoptosis-associated speck-like protein containing a CARD) tethering these molecules together. Upon inflammasome assembly, procaspase 1 self-activates and renders functional cytokines to arbitrate in the defense mechanism. This assembly is mediated by self-association and protein interactions via Death Domains. The inflammasome plays a critical role in innate immunity and its dysregulation is the culprit of many autoimmune disorders. An in-depth understanding of the factors involved in inflammasome assembly could help fight these conditions. This review describes our current knowledge on the biophysical aspects of inflammasome formation from the perspective of ASC. The specific characteristics of the three-dimensional solution structure and interdomain dynamics of ASC are explained in relation to its function in inflammasome assembly. Additionally, the review elaborates on the identification of ASC interacting surfaces at the amino acid level using NMR techniques. Finally, the macrostructures formed by full-length ASC and its two Death Domains studied with Transmission Electron Microscopy are compared in the context of a directional model for inflammasome assembly.
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Affiliation(s)
- Eva de Alba
- Department of Bioengineering. School of Engineering. University of California, Merced, 5200 North Lake Road, Merced, CA, 95343, USA.
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25
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Müller SI, Aschenbrenner I, Zacharias M, Feige MJ. An Interspecies Analysis Reveals Molecular Construction Principles of Interleukin 27. J Mol Biol 2019; 431:2383-2393. [PMID: 31034891 DOI: 10.1016/j.jmb.2019.04.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/18/2019] [Accepted: 04/19/2019] [Indexed: 01/12/2023]
Abstract
Interleukin 27 (IL-27) is a cytokine that regulates inflammatory responses. It is composed of an α subunit (IL-27α) and a β subunit (EBI3), which together form heterodimeric IL-27. Despite this general principle, IL-27 from different species shows distinct characteristics: Human IL-27α is not secreted autonomously while EBI3 is. In mice, the subunits show a reciprocal behavior. The molecular basis and the evolutionary conservation of these differences have remained unclear. They are biologically important, however, since secreted IL-27 subunits can act as cytokines on their own. Here, we show that formation of a single disulfide bond is an evolutionary conserved trait, which determines secretion-competency of IL-27α. Furthermore, combining cell-biological with computational approaches, we provide detailed structural insights into IL-27 heterodimerization and find that it relies on a conserved interface. Lastly, our study reveals a hitherto unknown construction principle of IL-27: one secretion-competent subunit generally pairs with one that depends on the other to induce its secretion. Taken together, these findings significantly extend our understanding of IL-27 biogenesis as a key cytokine and highlight how protein assembly can influence immunoregulation.
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Affiliation(s)
- Stephanie I Müller
- Center for Integrated Protein Science at the Department of Chemistry and Institute for Advanced Study, Technical University of Munich, 85748 Garching, Germany
| | - Isabel Aschenbrenner
- Center for Integrated Protein Science at the Department of Chemistry and Institute for Advanced Study, Technical University of Munich, 85748 Garching, Germany
| | - Martin Zacharias
- Center for Integrated Protein Science at the Physics Department, Technical University of Munich, 85748 Garching, Germany.
| | - Matthias J Feige
- Center for Integrated Protein Science at the Department of Chemistry and Institute for Advanced Study, Technical University of Munich, 85748 Garching, Germany.
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Chen C, Yang H, Xuan J, Cui Q, Feng Y. Resonance assignments of a cellulosomal double-dockerin from Clostridium thermocellum. Biomol NMR Assign 2019; 13:97-101. [PMID: 30377946 DOI: 10.1007/s12104-018-9859-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 10/24/2018] [Indexed: 06/08/2023]
Abstract
Cellulosomes are highly efficient multienzyme complexes for lignocellulose degradation secreted by some lignocellulolytic bacteria. Cellulosomes are assembled through protein modules named cohesin and dockerin, and multiple cohesin modules in the scaffold protein generally determine the complexity of the cellulosomes. Some cellulosomal proteins contain multiple dockerin modules, which may generate more complex cellulosomal architectures. Genome mining revealed that cellulosomal proteins containing double dockerin modules and a protease module exist in many cellulosome-producing bacteria, and these proteins together with cellulosomal protease inhibitors were proposed to have regulatory roles. However, the structures and functions of these multiple-dockerin proteins in cellulosome have not been reported before. In this paper, we present the NMR chemical shift assignments of the double-dockerin of a cellulosomal protease from Clostridium thermocellum DSM1313. The secondary structures predicted from the chemical shifts agree with the structural arrangement of the tandem dockerin modules. The chemical shift assignments here provide the basis for the structural and functional studies of multiple-dockerin proteins in future.
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Affiliation(s)
- Chao Chen
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Hongwu Yang
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Jinsong Xuan
- Department of Biological Science and Engineering, School of Chemical and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
| | - Qiu Cui
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Yingang Feng
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
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Degiacomi MT. On the Effect of Sphere-Overlap on Super Coarse-Grained Models of Protein Assemblies. J Am Soc Mass Spectrom 2019; 30:113-117. [PMID: 29736599 PMCID: PMC6318233 DOI: 10.1007/s13361-018-1974-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 04/17/2018] [Accepted: 04/18/2018] [Indexed: 05/06/2023]
Abstract
Ion mobility mass spectrometry (IM/MS) can provide structural information on intact protein complexes. Such data, including connectivity and collision cross sections (CCS) of assemblies' subunits, can in turn be used as a guide to produce representative super coarse-grained models. These models are constituted by ensembles of overlapping spheres, each representing a protein subunit. A model is considered plausible if the CCS and sphere-overlap levels of its subunits fall within predetermined confidence intervals. While the first is determined by experimental error, the latter is based on a statistical analysis on a range of protein dimers. Here, we first propose a new expression to describe the overlap between two spheres. Then we analyze the effect of specific overlap cutoff choices on the precision and accuracy of super coarse-grained models. Finally, we propose a method to determine overlap cutoff levels on a per-case scenario, based on collected CCS data, and show that it can be applied to the characterization of the assembly topology of symmetrical homo-multimers. Graphical Abstract.
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Affiliation(s)
- Matteo T Degiacomi
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE, UK.
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Abstract
ASC (apoptosis-associated speck-like protein containing a CARD) is a modular protein that functions as an adapter of the inflammasome, a multi-protein complex that triggers the inflammatory response in the presence of infection or cell damage. ASC bridges the inflammasome components (PYD-containing sensors and procaspase 1) via homotypic interactions mediated by its two death domains, PYD and CARD. The self-assembly and oligomerization of multiple copies of these three proteins result in the activation of procaspase 1, in turn rendering different cytokines functional. An in-depth understanding of ASC binding capabilities is crucial to decipher the molecular mechanisms of its role in inflammasome formation. In this chapter, we discuss the use of solution NMR to identify specific interacting surfaces of the inflammasome adapter ASC, and describe detailed protocols to perform NMR titrations with Death Domains to obtain apparent dissociation constants of the resulting complexes. The incorporation of NMR restraints in molecular docking to obtain models of these protein assemblies is presented.
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Affiliation(s)
- Pedro Diaz-Parga
- Department of Bioengineering, School of Engineering, University of California, Merced, CA, United States,Quantitative Systems Biology Graduate Program, University of California, Merced, CA, United States
| | - Eva de Alba
- Department of Bioengineering, School of Engineering, University of California, Merced, CA, United States,Corresponding author:
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Li F, Pincet F. SNAREpin Assembly: Kinetic and Thermodynamic Approaches. Methods Mol Biol 2019; 1860:71-93. [PMID: 30317499 DOI: 10.1007/978-1-4939-8760-3_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Proteins constantly interact and often form molecular complexes. The dynamics of most biological processes strongly rely on the kinetics and thermodynamics of assembly and disassembly of these complexes. Consequently an accurate characterization of these kinetics and thermodynamics that underlie them provides key information to better understand these processes. Here, we present two efficient techniques to quantify the assembly and disassembly of protein complexes: isothermal titration calorimetry and fluorescence anisotropy. As an example we focus on the formation of SNAREpins and also present how to prepare SNARE proteins to use in these experimental setups. We then show how to use these techniques to determine the critical factors that activate assembly kinetics.
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Kahle M, Ter Beek J, Hosler JP, Ädelroth P. The insertion of the non-heme Fe B cofactor into nitric oxide reductase from P. denitrificans depends on NorQ and NorD accessory proteins. Biochim Biophys Acta Bioenerg 2018; 1859:1051-1058. [PMID: 29874552 DOI: 10.1016/j.bbabio.2018.05.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 05/27/2018] [Accepted: 05/31/2018] [Indexed: 10/14/2022]
Abstract
Bacterial NO reductases (NOR) catalyze the reduction of NO into N2O, either as a step in denitrification or as a detoxification mechanism. cNOR from Paracoccus (P.) denitrificans is expressed from the norCBQDEF operon, but only the NorB and NorC proteins are found in the purified NOR complex. Here, we established a new purification method for the P. denitrificans cNOR via a His-tag using heterologous expression in E. coli. The His-tagged enzyme is both structurally and functionally very similar to non-tagged cNOR. We were also able to express and purify cNOR from the structural genes norCB only, in absence of the accessory genes norQDEF. The produced protein is a stable NorCB complex containing all hemes and it can bind gaseous ligands (CO) to heme b3, but it is catalytically inactive. We show that this deficient cNOR lacks the non-heme iron cofactor FeB. Mutational analysis of the nor gene cluster revealed that it is the norQ and norD genes that are essential to form functional cNOR. NorQ belongs to the family of MoxR P-loop AAA+ ATPases, which are in general considered to facilitate enzyme activation processes often involving metal insertion. Our data indicates that NorQ and NorD work together in order to facilitate non-heme Fe insertion. This is noteworthy since in many cases Fe cofactor binding occurs spontaneously. We further suggest a model for NorQ/D-facilitated metal insertion into cNOR.
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Affiliation(s)
- Maximilian Kahle
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Josy Ter Beek
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jonathan P Hosler
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS 39216, United States
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.
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31
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Sánchez M, Palacios Ò, Buchensky C, Sabio L, Gomez-Casati DF, Pagani MA, Capdevila M, Atrian S, Dominguez-Vera JM. Copper redox chemistry of plant frataxins. J Inorg Biochem 2018; 180:135-140. [PMID: 29277024 DOI: 10.1016/j.jinorgbio.2017.11.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 11/22/2017] [Accepted: 11/24/2017] [Indexed: 01/15/2023]
Abstract
The presence of a conserved cysteine residue in the C-terminal amino acid sequences of plant frataxins differentiates these frataxins from those of other kingdoms and may be key in frataxin assembly and function. We report a full study on the ability of Arabidopsis (AtFH) and Zea mays (ZmFH-1 and ZmFH-2) frataxins to assemble into disulfide-bridged dimers by copper-driven oxidation and to revert to monomers by chemical reduction. We monitored the redox assembly-disassembly process by electrospray ionization mass spectrometry, electrophoresis, UV-Vis spectroscopy, and fluorescence measurements. We conclude that plant frataxins AtFH, ZmFH-1 and ZmFH-2 are oxidized by Cu2+ and exhibit redox cysteine monomer - cystine dimer interexchange. Interestingly, the tendency to interconvert is not the same for each protein. Through yeast phenotypic rescue experiments, we show that plant frataxins are important for plant survival under conditions of excess copper, indicating that these proteins might be involved in copper metabolism.
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Affiliation(s)
- Manu Sánchez
- Departamento de Química Inorgánica, Facultad de Ciencias, Instituto de Biotecnología, Universidad de Granada, 18071 Granada, Spain
| | - Òscar Palacios
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Celeste Buchensky
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, CONICET, 2000 Rosario, Argentina
| | - Laura Sabio
- Departamento de Química Inorgánica, Facultad de Ciencias, Instituto de Biotecnología, Universidad de Granada, 18071 Granada, Spain
| | - Diego Fabian Gomez-Casati
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, CONICET, 2000 Rosario, Argentina
| | - Maria Ayelen Pagani
- Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario, CONICET, 2000 Rosario, Argentina
| | - Mercè Capdevila
- Departament de Química, Facultat de Ciències, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain.
| | - Silvia Atrian
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - Jose M Dominguez-Vera
- Departamento de Química Inorgánica, Facultad de Ciencias, Instituto de Biotecnología, Universidad de Granada, 18071 Granada, Spain.
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Gupta S, Tycko R. Segmental isotopic labeling of HIV-1 capsid protein assemblies for solid state NMR. J Biomol NMR 2018; 70:103-114. [PMID: 29464399 PMCID: PMC5832360 DOI: 10.1007/s10858-017-0162-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/28/2017] [Indexed: 05/09/2023]
Abstract
Recent studies of noncrystalline HIV-1 capsid protein (CA) assemblies by our laboratory and by Polenova and coworkers (Protein Sci 19:716-730, 2010; J Mol Biol 426:1109-1127, 2014; J Biol Chem 291:13098-13112, 2016; J Am Chem Soc 138:8538-8546, 2016; J Am Chem Soc 138:12029-12032, 2016; J Am Chem Soc 134:6455-6466, 2012; J Am Chem Soc 132:1976-1987, 2010; J Am Chem Soc 135:17793-17803, 2013; Proc Natl Acad Sci USA 112:14617-14622, 2015; J Am Chem Soc 138:14066-14075, 2016) have established the capability of solid state nuclear magnetic resonance (NMR) measurements to provide site-specific structural and dynamical information that is not available from other types of measurements. Nonetheless, the relatively high molecular weight of HIV-1 CA leads to congestion of solid state NMR spectra of fully isotopically labeled assemblies that has been an impediment to further progress. Here we describe an efficient protocol for production of segmentally labeled HIV-1 CA samples in which either the N-terminal domain (NTD) or the C-terminal domain (CTD) is uniformly 15N,13C-labeled. Segmental labeling is achieved by trans-splicing, using the DnaE split intein. Comparisons of two-dimensional solid state NMR spectra of fully labeled and segmentally labeled tubular CA assemblies show substantial improvements in spectral resolution. The molecular structure of HIV-1 assemblies is not significantly perturbed by the single Ser-to-Cys substitution that we introduce between NTD and CTD segments, as required for trans-splicing.
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Affiliation(s)
- Sebanti Gupta
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
- National Institutes of Health, Building 5, Room 409, Bethesda, MD, 20892-0520, USA.
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Weems E, Singha UK, Smith JT, Chaudhuri M. The divergent N-terminal domain of Tim17 is critical for its assembly in the TIM complex in Trypanosoma brucei. Mol Biochem Parasitol 2017; 218:4-15. [PMID: 28965880 DOI: 10.1016/j.molbiopara.2017.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 09/18/2017] [Accepted: 09/25/2017] [Indexed: 10/18/2022]
Abstract
Trypanosoma brucei Tim17(TbTim17), the single member of the Tim17/23/22 protein family, is an essential component of the translocase of the mitochondrial inner membrane (TIM). In spite of the conserved secondary structure, the primary sequence of TbTim17, particularly the N-terminal hydrophilic region, is significantly divergent. In order to understand the function of this region we expressed two N-terminal deletion mutants (Δ20 and Δ30) of TbTim17 in T. brucei. Both of these mutants of TbTim17 were targeted to mitochondria, however, they failed to complement the growth defect of TbTim17 RNAi cells. In addition, the import defect of other nuclear encoded proteins into TbTim17 knockdown mitochondria were not restored by expression of the N-terminal deletion mutants but complemented by knock-in of the full-length protein. Further analysis revealed that Δ20-TbTim17 and Δ30-TbTim17 mutants were not localized in the mitochondrial inner membrane. Analysis of the protein complexes in the wild type and mutant mitochondria by two-dimensional Blue-native/SDS-PAGE revealed that none of these mutants are assembled into the TbTim17 protein complex. However, FL-TbTim17 was integrated into the mitochondrial inner membrane and assembled into TbTim17 complex. Co-immunoprecipitation analysis showed that unlike the FL-TbTim17, mutant proteins are not associated with the endogenous TbTim17 as well as its interacting partner TbTim62, a novel trypanosome specific Tim. Together, these results show that the N-terminal domain of TbTim17 plays unique and essential roles for its sorting and assembly into the TbTim17 protein complex.
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Affiliation(s)
- Ebony Weems
- Department of Microbiology and Immunology, Meharry Medical College, Nashville, TN, 37209, United States
| | - Ujjal K Singha
- Department of Microbiology and Immunology, Meharry Medical College, Nashville, TN, 37209, United States
| | - Joseph T Smith
- Department of Microbiology and Immunology, Meharry Medical College, Nashville, TN, 37209, United States
| | - Minu Chaudhuri
- Department of Microbiology and Immunology, Meharry Medical College, Nashville, TN, 37209, United States.
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Habenstein B, Loquet A. Bacterial Filamentous Appendages Investigated by Solid-State NMR Spectroscopy. Methods Mol Biol 2017; 1615:415-48. [PMID: 28667627 DOI: 10.1007/978-1-4939-7033-9_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The assembly of filamentous appendages at the surface of bacteria is essential in many infection mechanisms. The extent of mechanical, dynamical, and functional properties of such appendages is very diverse, ranging from a structural scaffold of the pathogen-host cell interaction to cell motility, surface adhesion, or the export of virulence effectors. In particular, the architectures of several bacterial secretion systems have revealed the presence of filamentous architectures, known as pili, fimbriae, andneedles. At the macroscopic level, filamentous bacterial appendages appear as thin extracellular filaments of several nanometers in diameter and up to several microns in length. The structural characterization of these appendages at atomic-scale resolution represents an extremely challenging task because of their inherent noncrystallinity and very poor solubility. Here, we describe protocols based on recent advances in solid-state NMR spectroscopy to investigate the secondary structure, subunit-subunit protein interactions, symmetry parameters, and atomic architecture of bacterial filaments.
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Hammack LJ, Firestone K, Chang W, Kusmierczyk AR. Molecular chaperones of the Hsp70 family assist in the assembly of 20S proteasomes. Biochem Biophys Res Commun 2017; 486:438-443. [PMID: 28322792 DOI: 10.1016/j.bbrc.2017.03.059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 03/14/2017] [Indexed: 10/19/2022]
Abstract
The eukaryotic 26S proteasome is a large protease comprised of two major sub assemblies, the 20S proteasome, or core particle (CP), and the 19S regulatory particle (RP). Assembly of the CP and RP is assisted by an expanding list of dedicated assembly factors. For the CP, this includes Ump1 and the heterodimeric Pba1-Pba2 and Pba3-Pba4 proteins. It is not known how many additional proteins that assist in proteasome biogenesis remain to be discovered. Here, we demonstrate that two members of the Hsp70 family in yeast, Ssa1 and Ssa2, play a direct role in CP assembly. Ssa1 and Ssa2 interact genetically and physically with proteasomal components. Specifically, they associate tightly with known CP assembly intermediates, but not with fully assembled CP, through an extensive purification protocol. And, in yeast lacking both Ssa1 and Ssa2, specific defects in CP assembly are observed.
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Affiliation(s)
- Lindsay J Hammack
- Department of Biology, Indiana University-Purdue University Indianapolis, 723 West Michigan Street, Indianapolis, IN 46202, USA
| | - Kyle Firestone
- Department of Biology, Indiana University-Purdue University Indianapolis, 723 West Michigan Street, Indianapolis, IN 46202, USA
| | - William Chang
- Department of Biology, Indiana University-Purdue University Indianapolis, 723 West Michigan Street, Indianapolis, IN 46202, USA
| | - Andrew R Kusmierczyk
- Department of Biology, Indiana University-Purdue University Indianapolis, 723 West Michigan Street, Indianapolis, IN 46202, USA.
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Moulisová V, Gonzalez-García C, Cantini M, Rodrigo-Navarro A, Weaver J, Costell M, Sabater I Serra R, Dalby MJ, García AJ, Salmerón-Sánchez M. Engineered microenvironments for synergistic VEGF - Integrin signalling during vascularization. Biomaterials 2017; 126:61-74. [PMID: 28279265 DOI: 10.1016/j.biomaterials.2017.02.024] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 02/17/2017] [Accepted: 02/18/2017] [Indexed: 12/24/2022]
Abstract
We have engineered polymer-based microenvironments that promote vasculogenesis both in vitro and in vivo through synergistic integrin-growth factor receptor signalling. Poly(ethyl acrylate) (PEA) triggers spontaneous organization of fibronectin (FN) into nanonetworks which provide availability of critical binding domains. Importantly, the growth factor binding (FNIII12-14) and integrin binding (FNIII9-10) regions are simultaneously available on FN fibrils assembled on PEA. This material platform promotes synergistic integrin/VEGF signalling which is highly effective for vascularization events in vitro with low concentrations of VEGF. VEGF specifically binds to FN fibrils on PEA compared to control polymers (poly(methyl acrylate), PMA) where FN remains in a globular conformation and integrin/GF binding domains are not simultaneously available. The vasculogenic response of human endothelial cells seeded on these synergistic interfaces (VEGF bound to FN assembled on PEA) was significantly improved compared to soluble administration of VEGF at higher doses. Early onset of VEGF signalling (PLCγ1 phosphorylation) and both integrin and VEGF signalling (ERK1/2 phosphorylation) were increased only when VEGF was bound to FN nanonetworks on PEA, while soluble VEGF did not influence early signalling. Experiments with mutant FN molecules with impaired integrin binding site (FN-RGE) confirmed the role of the integrin binding site of FN on the vasculogenic response via combined integrin/VEGF signalling. In vivo experiments using 3D scaffolds coated with FN and VEGF implanted in the murine fat pad demonstrated pro-vascularization signalling by enhanced formation of new tissue inside scaffold pores. PEA-driven organization of FN promotes efficient presentation of VEGF to promote vascularization in regenerative medicine applications.
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Tsuruyama T. Kinetic stability analysis of protein assembly on the center manifold around the critical point. BMC Syst Biol 2017; 11:13. [PMID: 28153012 DOI: 10.1186/s12918-017-0391-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 01/05/2017] [Indexed: 11/22/2022]
Abstract
Background Non-linear kinetic analysis is a useful method for illustration of the dynamic behavior of cellular biological systems. To date, center manifold theory (CMT) has not been sufficiently applied for stability analysis of biological systems. The aim of this study is to demonstrate the application of CMT to kinetic analysis of protein assembly and disassembly, and to propose a novel framework for nonlinear multi-parametric analysis. We propose a protein assembly model with nonlinear kinetics provided by the fluctuation in monomer concentrations during their diffusion. Results When the diffusion process of a monomer is self-limited to give kinetics non-linearity, numerical simulations suggest the probability that the assembly and disassembly oscillate near the critical point. We applied CMT to kinetic analysis of the center manifold around the critical point in detail, and successfully demonstrated bifurcation around the critical point, which explained the observed oscillation. Conclusions The stability kinetics of the present model based on CMT illustrates a unique feature of protein assembly, namely non-linear behavior. Our findings are expected to provide methodology for analysis of biological systems.
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Abstract
The assembly of individual protein subunits into large-scale structures is important in many biological contexts. Proteins may assemble into geometrical cages or extended lattices that are characterized by a high degree of symmetry; examples include viral capsids and bacterial S-layers. The precisely defined higher order structure exhibited by these assemblies has inspired efforts to design such structures de novo by applying the principles of symmetry evident in natural protein assemblies. Here we discuss progress towards this goal and also examples of natural protein cages and lattices that have been engineered to repurpose them towards a diverse range of applications in materials science and nano-medicine.
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Affiliation(s)
- Aaron Sciore
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - E Neil G Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
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Abstract
Protein assemblies have recently become known as potential molecular scaffolds for applications in materials science and bio-nanotechnology. Efforts to design protein assemblies for construction of protein-based hybrid materials with metal ions, metal complexes, nanomaterials and proteins now represent a growing field with a common aim of providing novel functions and mimicking natural functions. However, the important roles of protein assemblies in coordination and biosupramolecular chemistry have not been systematically investigated and characterized. In this personal account, we focus on our recent progress in rational design of protein assemblies using bioinorganic chemistry for (1) exploration of unnatural reactions, (2) construction of functional protein architectures, and (3) in vivo applications.
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Affiliation(s)
- Basudev Maity
- Department of Life Science anad Technology, Tokyo Institute of Technology, B55-Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan
| | - Takafumi Ueno
- Department of Life Science anad Technology, Tokyo Institute of Technology, B55-Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan
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Terasawa K, Tomabechi Y, Ikeda M, Ehara H, Kukimoto-Niino M, Wakiyama M, Podyma-Inoue KA, Rajapakshe AR, Watabe T, Shirouzu M, Hara-Yokoyama M. Lysosome-associated membrane proteins-1 and -2 (LAMP-1 and LAMP-2) assemble via distinct modes. Biochem Biophys Res Commun 2016; 479:489-495. [PMID: 27663661 DOI: 10.1016/j.bbrc.2016.09.093] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 09/19/2016] [Indexed: 12/13/2022]
Abstract
Lysosome-associated membrane proteins 1 and 2 (LAMP-1 and LAMP-2) have a large, heavily glycosylated luminal domain composed of two subdomains, and are the most abundant protein components in lysosome membranes. LAMP-1 and LAMP-2 have distinct functions, and the presence of both proteins together is required for the essential regulation of autophagy to avoid embryonic lethality. However, the structural aspects of LAMP-1 and LAMP-2 have not been elucidated. In the present study, we demonstrated that the subdomains of LAMP-1 and LAMP-2 adopt the unique β-prism fold, similar to the domain structure of the dendritic cell-specific-LAMP (DC-LAMP, LAMP-3), confirming the conserved aspect of this family of lysosome-associated membrane proteins. Furthermore, we evaluated the effects of the N-domain truncation of LAMP-1 or LAMP-2 on the assembly of LAMPs, based on immunoprecipitation experiments. We found that the N-domain of LAMP-1 is necessary, whereas that of LAMP-2 is repressive, for the organization of a multimeric assembly of LAMPs. Accordingly, the present study suggests for the first time that the assembly modes of LAMP-1 and LAMP-2 are different, which may underlie their distinct functions.
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Affiliation(s)
- Kazue Terasawa
- Department of Biochemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo 113-8549, Japan
| | - Yuri Tomabechi
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mariko Ikeda
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Haruhiko Ehara
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mutsuko Kukimoto-Niino
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Motoaki Wakiyama
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Katarzyna A Podyma-Inoue
- Department of Biochemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo 113-8549, Japan
| | - Anupama R Rajapakshe
- Department of Biochemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo 113-8549, Japan
| | - Tetsuro Watabe
- Department of Biochemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo 113-8549, Japan
| | - Mikako Shirouzu
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Miki Hara-Yokoyama
- Department of Biochemistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo 113-8549, Japan.
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List JM, Pathmanathan JS, Lopez P, Bapteste E. Unity and disunity in evolutionary sciences: process-based analogies open common research avenues for biology and linguistics. Biol Direct 2016; 11:39. [PMID: 27544206 PMCID: PMC4992195 DOI: 10.1186/s13062-016-0145-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 08/06/2016] [Indexed: 11/13/2022] Open
Abstract
Background For a long time biologists and linguists have been noticing surprising similarities between the evolution of life forms and languages. Most of the proposed analogies have been rejected. Some, however, have persisted, and some even turned out to be fruitful, inspiring the transfer of methods and models between biology and linguistics up to today. Most proposed analogies were based on a comparison of the research objects rather than the processes that shaped their evolution. Focusing on process-based analogies, however, has the advantage of minimizing the risk of overstating similarities, while at the same time reflecting the common strategy to use processes to explain the evolution of complexity in both fields. Results We compared important evolutionary processes in biology and linguistics and identified processes specific to only one of the two disciplines as well as processes which seem to be analogous, potentially reflecting core evolutionary processes. These new process-based analogies support novel methodological transfer, expanding the application range of biological methods to the field of historical linguistics. We illustrate this by showing (i) how methods dealing with incomplete lineage sorting offer an introgression-free framework to analyze highly mosaic word distributions across languages; (ii) how sequence similarity networks can be used to identify composite and borrowed words across different languages; (iii) how research on partial homology can inspire new methods and models in both fields; and (iv) how constructive neutral evolution provides an original framework for analyzing convergent evolution in languages resulting from common descent (Sapir’s drift). Conclusions Apart from new analogies between evolutionary processes, we also identified processes which are specific to either biology or linguistics. This shows that general evolution cannot be studied from within one discipline alone. In order to get a full picture of evolution, biologists and linguists need to complement their studies, trying to identify cross-disciplinary and discipline-specific evolutionary processes. The fact that we found many process-based analogies favoring transfer from biology to linguistics further shows that certain biological methods and models have a broader scope than previously recognized. This opens fruitful paths for collaboration between the two disciplines. Reviewers This article was reviewed by W. Ford Doolittle and Eugene V. Koonin. Electronic supplementary material The online version of this article (doi:10.1186/s13062-016-0145-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Johann-Mattis List
- CRLAO/EHESS, 2 rue de Lille, Paris, 75007, France. .,Equipe AIRE, UMR 7138, Laboratoire Evolution Paris-Seine, Université Pierre et Marie Curie, 7 quai St Bernard, Paris, 75005, France.
| | - Jananan Sylvestre Pathmanathan
- Equipe AIRE, UMR 7138, Laboratoire Evolution Paris-Seine, Université Pierre et Marie Curie, 7 quai St Bernard, Paris, 75005, France
| | - Philippe Lopez
- Equipe AIRE, UMR 7138, Laboratoire Evolution Paris-Seine, Université Pierre et Marie Curie, 7 quai St Bernard, Paris, 75005, France
| | - Eric Bapteste
- Equipe AIRE, UMR 7138, Laboratoire Evolution Paris-Seine, Université Pierre et Marie Curie, 7 quai St Bernard, Paris, 75005, France
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Chait BT, Cadene M, Olinares PD, Rout MP, Shi Y. Revealing Higher Order Protein Structure Using Mass Spectrometry. J Am Soc Mass Spectrom 2016; 27:952-65. [PMID: 27080007 PMCID: PMC5125627 DOI: 10.1007/s13361-016-1385-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 03/14/2016] [Accepted: 03/15/2016] [Indexed: 05/24/2023]
Abstract
The development of rapid, sensitive, and accurate mass spectrometric methods for measuring peptides, proteins, and even intact protein assemblies has made mass spectrometry (MS) an extraordinarily enabling tool for structural biology. Here, we provide a personal perspective of the increasingly useful role that mass spectrometric techniques are exerting during the elucidation of higher order protein structures. Areas covered in this brief perspective include MS as an enabling tool for the high resolution structural biologist, for compositional analysis of endogenous protein complexes, for stoichiometry determination, as well as for integrated approaches for the structural elucidation of protein complexes. We conclude with a vision for the future role of MS-based techniques in the development of a multi-scale molecular microscope. Graphical Abstract ᅟ.
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Affiliation(s)
- Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, 10065, USA.
| | - Martine Cadene
- CBM, CNRS UPR4301, Rue Charles Sadron, CS 80054, 45071, Orleans Cedex 2, France
| | - Paul Dominic Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, 10065, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, 10065, USA
| | - Yi Shi
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, 10065, USA
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Garcia VM, Rowlett VW, Margolin W, Morano KA. Semi-automated microplate monitoring of protein polymerization and aggregation. Anal Biochem 2016; 508:9-11. [PMID: 27251433 DOI: 10.1016/j.ab.2016.05.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 05/18/2016] [Accepted: 05/20/2016] [Indexed: 11/29/2022]
Abstract
Static light scattering (SLS) is a commonly used technique for monitoring dynamics of high molecular weight protein complexes such as protein oligomers or aggregates. However, traditional methods are limited to testing a single condition and typically require large amounts of protein and specialized equipment. We show that a standard microplate reader can be used to characterize the molecular dynamics of different types of protein complexes, with the multiple advantages of microscale experimental volumes, semi-automated protocols and highly parallel processing.
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Affiliation(s)
- Veronica M Garcia
- Department of Microbiology and Molecular Genetics, University of Texas McGovern Medical School at Houston, Houston, TX, 77030, USA; University of Texas Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Veronica W Rowlett
- Department of Microbiology and Molecular Genetics, University of Texas McGovern Medical School at Houston, Houston, TX, 77030, USA; University of Texas Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - William Margolin
- Department of Microbiology and Molecular Genetics, University of Texas McGovern Medical School at Houston, Houston, TX, 77030, USA.
| | - Kevin A Morano
- Department of Microbiology and Molecular Genetics, University of Texas McGovern Medical School at Houston, Houston, TX, 77030, USA.
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Matsumoto T, Isogawa Y, Minamihata K, Tanaka T, Kondo A. Twigged streptavidin polymer as a scaffold for protein assembly. J Biotechnol 2016; 225:61-6. [PMID: 27002233 DOI: 10.1016/j.jbiotec.2016.03.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 03/15/2016] [Accepted: 03/17/2016] [Indexed: 12/11/2022]
Abstract
Protein assemblies are an emerging tool that is finding many biological and bioengineering applications. We here propose a method for the site-specific assembly of proteins on a twigged streptavidin (SA) polymer using streptavidin as a functional scaffold. SA was genetically appended with a G tag (sortase A recognition sequence) and a Y tag (HRP recognition sequence) on its N- and C-termini, respectively, to provide G-SA-Y. G-SA-Y was polymerized using HPR-mediated tyrosine coupling, then fluorescent proteins were immobilized on the polymer by biotin-SA affinity and sortase A-mediated ligation. Fluorescence measurements showed that the proteins were immobilized in close proximity to each other. Hydrolyzing enzymes were also functionally assembled on the G-SA-Y polymer. The site-specific assembly of proteins on twigged SA polymer may find new applications in various biological and bioengineering fields.
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Affiliation(s)
- Takuya Matsumoto
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Yuki Isogawa
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan
| | - Kosuke Minamihata
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Tsutomu Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan.
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan
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45
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Fischer WB, Kalita MM, Heermann D. Viral channel forming proteins--How to assemble and depolarize lipid membranes in silico. Biochim Biophys Acta 2016; 1858:1710-21. [PMID: 26806161 PMCID: PMC7094687 DOI: 10.1016/j.bbamem.2016.01.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/14/2016] [Accepted: 01/18/2016] [Indexed: 01/23/2023]
Abstract
Viral channel forming proteins (VCPs) have been discovered in the late 70s and are found in many viruses to date. Usually they are small and have to assemble to form channels which depolarize the lipid membrane of the host cells. Structural information is just about to emerge for just some of them. Thus, computational methods play a pivotal role in generating plausible structures which can be used in the drug development process. In this review the accumulation of structural data is introduced from a historical perspective. Computational performances and their predictive power are reported guided by biological questions such as the assembly, mechanism of function and drug–protein interaction of VCPs. An outlook of how coarse grained simulations can contribute to yet unexplored issues of these proteins is given. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. Early references about the discovery of viral channel forming proteins. Latest structural information about the class of proteins. Identification of structural motifs, assembly mechanism of function and drug action using computational methods. Outlook for the use of coarse grained techniques to address assembly and integration into cellular processes.
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Affiliation(s)
- Wolfgang B Fischer
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan; Biophotonics & Molecular Imaging Center (BMIRC), National Yang-Ming University, Taipei 112, Taiwan.
| | - Monoj Mon Kalita
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan; Biophotonics & Molecular Imaging Center (BMIRC), National Yang-Ming University, Taipei 112, Taiwan
| | - Dieter Heermann
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan; Biophotonics & Molecular Imaging Center (BMIRC), National Yang-Ming University, Taipei 112, Taiwan
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Rai AK, Kundu N, Chattopadhyay K. Physicochemical constraints of elevated pH affect efficient membrane interaction and arrest an abortive membrane-bound oligomeric intermediate of the beta-barrel pore-forming toxin Vibrio cholerae cytolysin. Arch Biochem Biophys 2015; 583:9-17. [PMID: 26235489 DOI: 10.1016/j.abb.2015.07.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 07/24/2015] [Accepted: 07/24/2015] [Indexed: 11/21/2022]
Abstract
Vibrio cholerae cytolysin (VCC) is a potent membrane-damaging cytotoxic protein. VCC causes permeabilization of the target cell membranes by forming transmembrane oligomeric beta-barrel pores. Membrane pore formation by VCC involves following key steps: (i) membrane binding, (ii) formation of a pre-pore oligomeric intermediate, (iii) membrane insertion of the pore-forming motifs, and (iv) formation of the functional transmembrane pore. Membrane binding, oligomerization, and subsequent pore-formation process of VCC appear to be facilitated by multiple regulatory mechanisms that are only partly understood. Here, we have explored the role(s) of the physicochemical constraints, specifically imposed by the elevated pH conditions, on the membrane pore-formation mechanism of VCC. Elevated pH abrogates efficient interaction of VCC with the target membranes, and blocks its pore-forming activity. Under the elevated pH conditions, membrane-bound fractions of VCC remain trapped in the form of abortive oligomeric species that fail to generate the functional transmembrane pores. Such an abortive oligomeric assembly appears to represent a distinct, more advanced intermediate state than the pre-pore state. The present study offers critical insights regarding the implications of the physicochemical constraints for regulating the efficient membrane interaction and pore formation by VCC.
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47
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Luján MA, Martínez JI, Alonso PJ, Torrado A, Roncel M, Ortega JM, Sancho J, Picorel R. In vivo reconstitution of a homodimeric cytochrome b559 like structure: The role of the N-terminus α-subunit from Synechocystis sp. PCC 6803. J Photochem Photobiol B 2015; 152:308-17. [PMID: 26183783 DOI: 10.1016/j.jphotobiol.2015.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/02/2015] [Accepted: 07/06/2015] [Indexed: 11/24/2022]
Abstract
The cytochrome b559 is a heme-bridged heterodimeric protein with two subunits, α and β. Both subunits from Synechocystis sp. PCC 6803 have previously been cloned and overexpressed in Escherichia coli and in vivo reconstitution experiments have been carried out. The formation of homodimers in the bacterial membrane with endogenous heme was only observed in the case of the β-subunit (β/β) but not with the full length α-subunit. In the present work, reconstitution of a homodimer (α/α) cytochrome b559 like structure was possible using a chimeric N-terminus α-subunit truncated before the amino acid isoleucine 17, eliminating completely a short amphipathic α-helix that lays on the surface of the membrane. Overexpression and in vivo reconstitution in the bacteria was clearly demonstrated by the brownish color of the culture pellet and the use of a commercial monoclonal antibody against the fusion protein carrier, the maltoside binding protein, and polyclonal antibodies against a synthetic peptide of the α-subunit from Thermosynechococcus elongatus. Moreover, a simple partial purification after membrane solubilization with Triton X-100 confirmed that the overexpressed protein complex corresponded with the maltoside binding protein-chimeric α-subunit cytochrome b559 like structure. The features of the new structure were determined by UV-Vis, electron paramagnetic resonance and redox potentiometric techniques. Ribbon representations of all possible structures are also shown to better understand the mechanism of the cytochrome b559 maturation in the bacterial cytoplasmic membrane.
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Abstract
The proper functioning of the cell depends on preserving the cellular genome. In yeast cells, a limited number of genes are located on mitochondrial DNA. Although the mechanisms underlying nuclear genome maintenance are well understood, much less is known about the mechanisms that ensure mitochondrial genome stability. Mitochondria influence the stability of the nuclear genome and vice versa. Little is known about the two-way communication and mutual influence of the nuclear and mitochondrial genomes. Although the mitochondrial genome replicates independent of the nuclear genome and is organized by a distinct set of mitochondrial nucleoid proteins, nearly all genome stability mechanisms responsible for maintaining the nuclear genome, such as mismatch repair, base excision repair, and double-strand break repair via homologous recombination or the nonhomologous end-joining pathway, also act to protect mitochondrial DNA. In addition to mitochondria-specific DNA polymerase γ, the polymerases α, η, ζ, and Rev1 have been found in this organelle. A nuclear genome instability phenotype results from a failure of various mitochondrial functions, such as an electron transport chain activity breakdown leading to a decrease in ATP production, a reduction in the mitochondrial membrane potential (ΔΨ), and a block in nucleotide and amino acid biosynthesis. The loss of ΔΨ inhibits the production of iron-sulfur prosthetic groups, which impairs the assembly of Fe-S proteins, including those that mediate DNA transactions; disturbs iron homeostasis; leads to oxidative stress; and perturbs wobble tRNA modification and ribosome assembly, thereby affecting translation and leading to proteotoxic stress. In this review, we present the current knowledge of the mechanisms that govern mitochondrial genome maintenance and demonstrate ways in which the impairment of mitochondrial function can affect nuclear genome stability.
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Affiliation(s)
- Aneta Kaniak-Golik
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
| | - Adrianna Skoneczna
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland.
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Marreiros R, Müller-Schiffmann A, Bader V, Selvarajah S, Dey D, Lingappa VR, Korth C. Viral capsid assembly as a model for protein aggregation diseases: Active processes catalyzed by cellular assembly machines comprising novel drug targets. Virus Res 2014; 207:155-64. [PMID: 25451064 DOI: 10.1016/j.virusres.2014.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/09/2014] [Accepted: 10/01/2014] [Indexed: 11/18/2022]
Abstract
Viruses can be conceptualized as self-replicating multiprotein assemblies, containing coding nucleic acids. Viruses have evolved to exploit host cellular components including enzymes to ensure their replicative life cycle. New findings indicate that also viral capsid proteins recruit host factors to accelerate their assembly. These assembly machines are RNA-containing multiprotein complexes whose composition is governed by allosteric sites. In the event of viral infection, the assembly machines are recruited to support the virus over the host and are modified to achieve that goal. Stress granules and processing bodies may represent collections of such assembly machines, readily visible by microscopy but biochemically labile and difficult to isolate by fractionation. We hypothesize that the assembly of protein multimers such as encountered in neurodegenerative or other protein conformational diseases, is also catalyzed by assembly machines. In the case of viral infection, the assembly machines have been modified by the virus to meet the virus' need for rapid capsid assembly rather than host homeostasis. In the case of the neurodegenerative diseases, it is the monomers and/or low n oligomers of the so-called aggregated proteins that are substrates of assembly machines. Examples for substrates are amyloid β peptide (Aβ) and tau in Alzheimer's disease, α-synuclein in Parkinson's disease, prions in the prion diseases, Disrupted-in-schizophrenia 1 (DISC1) in subsets of chronic mental illnesses, and others. A likely continuum between virus capsid assembly and cell-to-cell transmissibility of aggregated proteins is remarkable. Protein aggregation diseases may represent dysfunction and dysregulation of these assembly machines analogous to the aberrations induced by viral infection in which cellular homeostasis is pathologically reprogrammed. In this view, as for viral infection, reset of assembly machines to normal homeostasis should be the goal of protein aggregation therapeutics. A key basis for the commonality between viral and neurodegenerative disease aggregation is a broader definition of assembly as more than just simple aggregation, particularly suited for the crowded cytoplasm. The assembly machines are collections of proteins that catalytically accelerate an assembly reaction that would occur spontaneously but too slowly to be relevant in vivo. Being an enzyme complex with a functional allosteric site, appropriated for a non-physiological purpose (e.g. viral infection or conformational disease), these assembly machines present a superior pharmacological target because inhibition of their active site will amplify an effect on their substrate reaction. Here, we present this hypothesis based on recent proof-of-principle studies against Aβ assembly relevant in Alzheimer's disease.
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Affiliation(s)
- Rita Marreiros
- Department Neuropathology, Heinrich Heine University Düsseldorf Medical School, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Andreas Müller-Schiffmann
- Department Neuropathology, Heinrich Heine University Düsseldorf Medical School, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Verian Bader
- Department Neuropathology, Heinrich Heine University Düsseldorf Medical School, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | | | | | | | - Carsten Korth
- Department Neuropathology, Heinrich Heine University Düsseldorf Medical School, Moorenstrasse 5, 40225 Düsseldorf, Germany.
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50
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Höhr AIC, Straub SP, Warscheid B, Becker T, Wiedemann N. Assembly of β-barrel proteins in the mitochondrial outer membrane. Biochim Biophys Acta 2014; 1853:74-88. [PMID: 25305573 DOI: 10.1016/j.bbamcr.2014.10.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 09/25/2014] [Accepted: 10/01/2014] [Indexed: 12/15/2022]
Abstract
Mitochondria evolved through endosymbiosis of a Gram-negative progenitor with a host cell to generate eukaryotes. Therefore, the outer membrane of mitochondria and Gram-negative bacteria contain pore proteins with β-barrel topology. After synthesis in the cytosol, β-barrel precursor proteins are first transported into the mitochondrial intermembrane space. Folding and membrane integration of β-barrel proteins depend on the mitochondrial sorting and assembly machinery (SAM) located in the outer membrane, which is related to the β-barrel assembly machinery (BAM) in bacteria. The SAM complex recognizes β-barrel proteins by a β-signal in the C-terminal β-strand that is required to initiate β-barrel protein insertion into the outer membrane. In addition, the SAM complex is crucial to form membrane contacts with the inner mitochondrial membrane by interacting with the mitochondrial contact site and cristae organizing system (MICOS) and shares a subunit with the endoplasmic reticulum-mitochondria encounter structure (ERMES) that links the outer mitochondrial membrane to the endoplasmic reticulum (ER).
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Affiliation(s)
- Alexandra I C Höhr
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany; Fakultät für Biologie, Universität Freiburg, 79104 Freiburg, Germany
| | - Sebastian P Straub
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany; Fakultät für Biologie, Universität Freiburg, 79104 Freiburg, Germany
| | - Bettina Warscheid
- BIOSS Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany; Abteilung Biochemie und Funktionelle Proteomik, Institut für Biologie II, Fakultät für Biologie, Universität Freiburg, 79104 Freiburg, Germany
| | - Thomas Becker
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany
| | - Nils Wiedemann
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Universität Freiburg, 79104 Freiburg, Germany.
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