1
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Saikia B, Baruah A. In silico design of misfolding resistant proteins: the role of structural similarity of a competing conformational ensemble in the optimization of frustration. SOFT MATTER 2024; 20:3283-3298. [PMID: 38529658 DOI: 10.1039/d4sm00171k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Most state-of-the-art in silico design methods fail due to misfolding of designed sequences to a conformation other than the target. Thus, a method to design misfolding resistant proteins will provide a better understanding of the misfolding phenomenon and will also increase the success rate of in silico design methods. In this work, we optimize the conformational ensemble to be selected for negative design purposes based on the similarity of the conformational ensemble to the target. Five ensembles with different degrees of similarity to the target are created and destabilized and the target is stabilized while designing sequences using mean field theory and Monte Carlo simulation methods. The results suggest that the degree of similarity of the non-native conformations to the target plays a prominent role in designing misfolding resistant protein sequences. The design procedures that destabilize the conformational ensemble with moderate similarity to the target have proven to be more promising. Incorporation of either highly similar or highly dissimilar conformations to the target conformation into the non-native ensemble to be destabilized may lead to sequences with a higher misfolding propensity. This will significantly reduce the conformational space to be considered in any protein design procedure. Interestingly, the results suggest that a sequence with higher frustration in the target structure does not necessarily lead to a misfold prone sequence. A successful design method may purposefully choose a frustrated sequence in the target conformation if that sequence is even more frustrated in the competing non-native conformations.
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Affiliation(s)
- Bondeepa Saikia
- Department of Chemistry, Dibrugarh University, Dibrugarh 786004, India.
| | - Anupaul Baruah
- Department of Chemistry, Dibrugarh University, Dibrugarh 786004, India.
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2
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Mickael M, Łazarczyk M, Kubick N, Gurba A, Kocki T, Horbańczuk JO, Atanasov AG, Sacharczuk M, Religa P. FEZF2 and AIRE1: An Evolutionary Trade-off in the Elimination of Auto-reactive T Cells in the Thymus. J Mol Evol 2024; 92:72-86. [PMID: 38285197 DOI: 10.1007/s00239-024-10157-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/15/2024] [Indexed: 01/30/2024]
Abstract
Autoimmune Regulator 1 (AIRE1) and Forebrain Embryonic Zinc Finger-Like Protein 2 (FEZF2) play pivotal roles in orchestrating the expression of tissue-restricted antigens (TRA) to facilitate the elimination of autoreactive T cells. AIRE1's presence in the gonads of various vertebrates has raised questions about its potential involvement in gene expression control for germline cell selection. Nevertheless, the evolutionary history of these genes has remained enigmatic, as has the rationale behind their apparent redundancy in vertebrates. Furthermore, the origin of the elimination process itself has remained elusive. To shed light on these mysteries, we conducted a comprehensive evolutionary analysis employing a range of tools, including multiple sequence alignment, phylogenetic tree construction, ancestral sequence reconstruction, and positive selection assessment. Our investigations revealed intriguing insights. AIRE1 homologs emerged during the divergence of T cells in higher vertebrates, signifying its role in this context. Conversely, FEZF2 exhibited multiple homologs spanning invertebrates, lampreys, and higher vertebrates. Ancestral sequence reconstruction demonstrated distinct origins for AIRE1 and FEZF2, underscoring that their roles in regulating TRA have evolved through disparate pathways. Furthermore, it became evident that both FEZF2 and AIRE1 govern a diverse repertoire of genes, encompassing ancient and more recently diverged targets. Notably, FEZF2 demonstrates expression in both vertebrate and invertebrate embryos and germlines, accentuating its widespread role. Intriguingly, FEZF2 harbors motifs associated with autophagy, such as DKFPHP, SYSELWKSSL, and SYSEL, a process integral to cell selection in invertebrates. Our findings suggest that FEZF2 initially emerged to regulate self-elimination in the gonads of invertebrates. As organisms evolved toward greater complexity, AIRE1 likely emerged to complement FEZF2's role, participating in the regulation of cell selection for elimination in both gonads and the thymus. This dynamic interplay between AIRE1 and FEZF2 underscores their multifaceted contributions to TRA expression regulation across diverse evolutionary contexts.
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Affiliation(s)
- Michel Mickael
- Department of Experimental Genomics, Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Postępu 36A, 05-552, Jastrzebiec, Poland.
- Department of Immunology, PM Forskningscentreum, Väpnaregatan 22, 58649, Linköping, Sweden.
| | - Marzena Łazarczyk
- Department of Experimental Genomics, Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Postępu 36A, 05-552, Jastrzebiec, Poland
| | - Norwin Kubick
- Department of Biology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Agata Gurba
- Department of Pharmacodynamics, Faculty of Pharmacy, Warsaw Medical University, L Banacha 1, 02-697, Warsaw, Poland
| | - Tomasz Kocki
- Department of Experimental and Clinical Pharmacology, Medical University of Lublin, Jaczewskiego 8B, 20090, Lublin, Poland
| | - Jarosław Olav Horbańczuk
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Postępu 36A, 05-552, Jastrzebiec, Poland
| | - Atanas G Atanasov
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Postępu 36A, 05-552, Jastrzebiec, Poland
- Ludwig Boltzmann Institute Digital Health and Patient Safety, Medical University of Vienna, Vienna, Austria
| | - Mariusz Sacharczuk
- Department of Experimental Genomics, Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Postępu 36A, 05-552, Jastrzebiec, Poland
- Department of Pharmacodynamics, Faculty of Pharmacy, Warsaw Medical University, L Banacha 1, 02-697, Warsaw, Poland
| | - Piotr Religa
- Department of Medicine, Karolinska Institute, 171 77, Solna, Sweden.
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3
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Negi S, Hamori M, Sato A, Shimizu K, Kawahara-Nakagawa Y, Manabe T, Shibata N, Kitagishi H, Mashimo M, Sugiura Y. Transpeptidation reaction mediated by ligand- and metal cofactor-substituted Sortase A from Staphylococcus aureus. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20220098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Shigeru Negi
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto 610-0395
| | - Mami Hamori
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto 610-0395
| | - Ayaka Sato
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto 610-0395
| | - Kyoko Shimizu
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto 610-0395
| | - Yuka Kawahara-Nakagawa
- Graduate School of Faculty of Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo, 678-1297
| | - Takayuki Manabe
- Clinical Research Support Center, Asahikawa Medical University Hospital, 2-1-1-1 Midorigaoka Higashi, Asahikawa 078-8510
| | - Nobuhito Shibata
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto 610-0395
| | - Hiroaki Kitagishi
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321
| | - Masato Mashimo
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto 610-0395
| | - Yukio Sugiura
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto 610-0395
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4
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Negi S, Hamori M, Kawahara-Nakagawa Y, Imanishi M, Kurehara M, Kitada C, Kawahito Y, Kishi K, Manabe T, Kawamura N, Kitagishi H, Mashimo M, Shibata N, Sugiura Y. Importance of two-dimensional cation clusters induced by protein folding in intrinsic intracellular membrane permeability. RSC Chem Biol 2022; 3:1076-1084. [PMID: 35975000 PMCID: PMC9347356 DOI: 10.1039/d2cb00098a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/11/2022] [Indexed: 11/21/2022] Open
Abstract
Two-dimensional cation clusters formed on the surface of proteins play an important role in their intracellular translocation.
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Affiliation(s)
- Shigeru Negi
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto 610-0395, Japan
| | - Mami Hamori
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto 610-0395, Japan
| | - Yuka Kawahara-Nakagawa
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo, 678-1297, Japan
| | - Miki Imanishi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Miku Kurehara
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto 610-0395, Japan
| | - Chieri Kitada
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto 610-0395, Japan
| | - Yuri Kawahito
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto 610-0395, Japan
| | - Kanae Kishi
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi Minami-ku, Hiroshima, 734-8553, Japan
| | - Takayuki Manabe
- Clinical Research Support Center, Asahikawa Medical University Hospital, 2-1-1-1 Midorigaokahigashi, Asahikawa 078-8510, Japan
| | - Nobuyuki Kawamura
- Education Center for Pharmacy, Faculty of Pharmaceutical Sciences, Niigata University of Pharmacy and Applied Life Sciences, 265-1 Higashijima, Akiha-ku, Niigata City, Niigata 956-8603, Japan
| | - Hiroaki Kitagishi
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| | - Masato Mashimo
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto 610-0395, Japan
| | - Nobuhito Shibata
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto 610-0395, Japan
| | - Yukio Sugiura
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto 610-0395, Japan
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5
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Chen S, He Z, Peng T, Zhou F, Wang G, Qian K, Ju L, Xiao Y, Wang X. PRR11 promotes ccRCC tumorigenesis by regulating E2F1 stability. JCI Insight 2021; 6:e145172. [PMID: 34499617 PMCID: PMC8525590 DOI: 10.1172/jci.insight.145172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 09/01/2021] [Indexed: 01/03/2023] Open
Abstract
Proline rich 11 (PRR11), a novel tumor-related gene, has been identified in different tumors. However, the relevant biological functions of PRR11 in human clear cell renal cell carcinoma (ccRCC) have not been studied. In this study, we first identified PRR11 as a biomarker of ccRCC and predictor of poor prognosis by bioinformatics. Then, we showed that PRR11 silencing substantially reduced ccRCC cell proliferation and migration in vitro and in vivo. Importantly, we found that PRR11 induced the degradation of the E2F1 protein through its interaction with E2F1, and PRR11 reduced the stability of the E2F1 protein in ccRCC cells, thereby affecting cell cycle progression. Further results indicated that the downregulation of E2F1 expression partially reversed the changes in ccRCC cell biology caused by PRR11 deletion. In addition, we showed that PRR11 was a target gene of c-Myc. The transcription factor c-Myc may have promoted the expression of PRR11 in ccRCC cells by binding to the PRR11 promoter region, thereby accelerating the progression of ccRCC. In summary, we found that PRR11 served as an oncogene in ccRCC, and PRR11 reduced the protein stability of E2F1 and could be activated by c-Myc.
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Affiliation(s)
| | | | | | | | - Gang Wang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetic Resource Preservation Center of Hubei Province, Wuhan, China.,Research Center of Wuhan for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China.,Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kaiyu Qian
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetic Resource Preservation Center of Hubei Province, Wuhan, China.,Research Center of Wuhan for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China.,Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Lingao Ju
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetic Resource Preservation Center of Hubei Province, Wuhan, China.,Research Center of Wuhan for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China.,Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yu Xiao
- Department of Urology and.,Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetic Resource Preservation Center of Hubei Province, Wuhan, China.,Research Center of Wuhan for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China.,Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xinghuan Wang
- Department of Urology and.,Research Center of Wuhan for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China.,Medical Research Institute, Wuhan University, Wuhan, China
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6
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Molecular Modeling for a Comparative Analysis of Interactions Between 2LTRZFP and 2-LTR-Circle Junctions. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10175-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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7
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Lv X, Cui S, Gu Y, Li J, Du G, Liu L. Enzyme Assembly for Compartmentalized Metabolic Flux Control. Metabolites 2020; 10:E125. [PMID: 32224973 PMCID: PMC7241084 DOI: 10.3390/metabo10040125] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/25/2020] [Accepted: 03/25/2020] [Indexed: 11/16/2022] Open
Abstract
Enzyme assembly by ligand binding or physically sequestrating enzymes, substrates, or metabolites into isolated compartments can bring key molecules closer to enhance the flux of a metabolic pathway. The emergence of enzyme assembly has provided both opportunities and challenges for metabolic engineering. At present, with the development of synthetic biology and systems biology, a variety of enzyme assembly strategies have been proposed, from the initial direct enzyme fusion to scaffold-free assembly, as well as artificial scaffolds, such as nucleic acid/protein scaffolds, and even some more complex physical compartments. These assembly strategies have been explored and applied to the synthesis of various important bio-based products, and have achieved different degrees of success. Despite some achievements, enzyme assembly, especially in vivo, still has many problems that have attracted significant attention from researchers. Here, we focus on some selected examples to review recent research on scaffold-free strategies, synthetic artificial scaffolds, and physical compartments for enzyme assembly or pathway sequestration, and we discuss their notable advances. In addition, the potential applications and challenges in the applications are highlighted.
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Affiliation(s)
- Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Shixiu Cui
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yang Gu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; (X.L.); (S.C.); (Y.G.); (J.L.); (G.D.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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8
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Hussey BJ, McMillen DR. Programmable T7-based synthetic transcription factors. Nucleic Acids Res 2019; 46:9842-9854. [PMID: 30169636 PMCID: PMC6182181 DOI: 10.1093/nar/gky785] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/21/2018] [Indexed: 12/31/2022] Open
Abstract
Despite recent progress on synthetic transcription factor generation in eukaryotes, there remains a need for high-activity bacterial versions of these systems. In synthetic biology applications, it is useful for transcription factors to have two key features: they should be orthogonal (influencing only their own targets, with minimal off-target effects), and programmable (able to be directed to a wide range of user-specified transcriptional start sites). The RNA polymerase of the bacteriophage T7 has a number of appealing properties for synthetic biological designs: it can produce high transcription rates; it is a compact, single-subunit polymerase that has been functionally expressed in a variety of organisms; and its viral origin reduces the connection between its activity and that of its host's transcriptional machinery. We have created a system where a T7 RNA polymerase is recruited to transcriptional start sites by DNA binding proteins, either directly or bridged through protein–protein interactions, yielding a modular and programmable system for strong transcriptional activation of multiple orthogonal synthetic transcription factor variants in Escherichia coli. To our knowledge this is the first exogenous, programmable activator system in bacteria.
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Affiliation(s)
- Brendan J Hussey
- Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Cell and Systems Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Impact Centre, University of Toronto, Toronto, Ontario M5S 1A7, Canada
| | - David R McMillen
- Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Cell and Systems Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Impact Centre, University of Toronto, Toronto, Ontario M5S 1A7, Canada
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9
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Zhou L, Deng ZZ, Li HY, Jiang N, Wei ZS, Hong MF, Wang JH, Zhang MX, Shi YH, Lu ZQ, Huang XM. Overexpression of PRR11 promotes tumorigenic capability and is associated with progression in esophageal squamous cell carcinoma. Onco Targets Ther 2019; 12:2677-2693. [PMID: 31040705 PMCID: PMC6462166 DOI: 10.2147/ott.s180255] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
INTRODUCTION Esophageal squamous cell carcinoma (ESCC) is one of the most common malignancies of gastrointestinal tract in the world, and the long-term prognosis for ESCC patients still remains dismal due to the lack of effective early diagnosis biomarkers. MATERIALS AND METHODS Western blot and immunochemistry were used to determine the expression of PRR11 in 201 clinicopathologically characterized ESCC specimens. The effects of PRR11 on stem cell-like traits and tumorigenicity were examined by tumor sphere formation assay and SP assays in vitro and by a tumorigenesis model in vivo. The mechanism by which PRR11 mediated Wnt/β-catenin signaling was explored using luciferase reporter, immuno-chemistry, and real time-PCR (RT-PCR) assays. RESULTS We found that PRR11 was markedly upregulated, at the level of both transcription and translation, in ESCC cell lines as compared with normal esophageal epithelial cells (NECCs). Immunohistochemical analysis showed that 69.2% paraffin-embedded archival ESCC specimens exhibited high levels of PRR11 expression, and multivariate analysis revealed that PRR11 upregulation might be an independent prognostic indicator for the survival of patients with ESCC. Furthermore, overexpression of PRR11 dramatically enhanced, whereas inhibition of PRR11 reduced the capability of cancer stem cell (CSC)-like phenotypes and tumorigenicity of ESCC cells both in vitro and in vivo. Mechanically, we demonstrated PRR11-enhanced tumorigenicity of ESCC cells via activating Wnt/β-catenin signaling, and PRR11 expression is found to be significantly correlated with β-catenin nuclear location in ESCC. CONCLUSION Our findings suggest that the PRR11 might represent a novel and valuable prognostic marker for ESCC progression and play a role during the development and progression of this malignancy.
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Affiliation(s)
- Li Zhou
- Department of Rehabilitation, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China, ,
| | - Zhe-Zhi Deng
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510000, China,
| | - Hai-Yan Li
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510000, China,
| | - Nan Jiang
- Department of Hepatic Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510000, China
| | - Zhi-Sheng Wei
- Department of Neurology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
| | - Ming-Fan Hong
- Department of Neurology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China
| | - Ji-Hui Wang
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510000, China,
| | - Ming-Xing Zhang
- Department of Rehabilitation, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China, ,
| | - Yi-Hua Shi
- Department of Rehabilitation, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China, ,
| | - Zheng-Qi Lu
- Department of Rehabilitation, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China, ,
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510000, China,
| | - Xu-Ming Huang
- Department of Rehabilitation, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510080, China, ,
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10
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Bozkurt E, Perez MAS, Hovius R, Browning NJ, Rothlisberger U. Genetic Algorithm Based Design and Experimental Characterization of a Highly Thermostable Metalloprotein. J Am Chem Soc 2018; 140:4517-4521. [DOI: 10.1021/jacs.7b10660] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Esra Bozkurt
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Marta A. S. Perez
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Ruud Hovius
- Laboratory of Protein Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Nicholas J. Browning
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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11
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Chen X, Gao C, Guo L, Hu G, Luo Q, Liu J, Nielsen J, Chen J, Liu L. DCEO Biotechnology: Tools To Design, Construct, Evaluate, and Optimize the Metabolic Pathway for Biosynthesis of Chemicals. Chem Rev 2017; 118:4-72. [DOI: 10.1021/acs.chemrev.6b00804] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xiulai Chen
- State
Key Laboratory of Food Science and Technology, 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 Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liang Guo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guipeng Hu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Qiuling Luo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jia Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jens Nielsen
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Lyngby, Denmark
| | - Jian Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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12
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Chandrasekaran AR, Anderson N, Kizer M, Halvorsen K, Wang X. Beyond the Fold: Emerging Biological Applications of DNA Origami. Chembiochem 2016; 17:1081-9. [PMID: 26928725 DOI: 10.1002/cbic.201600038] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Indexed: 01/22/2023]
Abstract
The use of DNA as a material for nanoscale construction has blossomed in the past decade. This is largely attributable to the DNA origami technique, which has enabled construction of nanostructures ranging from simple two-dimensional sheets to complex three-dimensional objects with defined curves and edges. These structures are amenable to site-specific functionalization with nanometer precision, and have been shown to exhibit cellular biocompatibility and permeability. The DNA origami technique has already found widespread use in a variety of emerging biological applications such as biosensing, enzyme cascades, biomolecular analysis, biomimetics, and drug delivery. We highlight a few of these applications and comments on the prospects for this rapidly expanding field of research.
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Affiliation(s)
| | - Nate Anderson
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Megan Kizer
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Xing Wang
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA. , .,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA. ,
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13
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Chandrasekaran AR. Programmable DNA scaffolds for spatially-ordered protein assembly. NANOSCALE 2016; 8:4436-4446. [PMID: 26852879 DOI: 10.1039/c5nr08685j] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Ever since the notion of using DNA as a material was realized, it has been employed in the construction of complex structures that facilitate the assembly of nanoparticles or macromolecules with nanometer-scale precision. Specifically, tiles fashioned from DNA strands and DNA origami sheets have been shown to be suitable as scaffolds for immobilizing proteins with excellent control over their spatial positioning. Supramolecular assembly of proteins into periodic arrays in one or more dimensions is one of the most challenging aspects in the design of scaffolds for biomolecular investigations and macromolecular crystallization. This review provides a brief overview of how various biomolecular interactions with high degree of specificity such as streptavidin-biotin, antigen-antibody, and aptamer-protein interactions have been used to fabricate linear and multidimensional assemblies of structurally intact and functional proteins. The use of DNA-binding proteins as adaptors, polyamide recognition on DNA scaffolds and oligonucleotide linkers for protein assembly are also discussed.
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14
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Van Hove B, Love AM, Ajikumar PK, De Mey M. Programming Biology: Expanding the Toolset for the Engineering of Transcription. Synth Biol (Oxf) 2016. [DOI: 10.1007/978-3-319-22708-5_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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15
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Synthetic scaffolds for pathway enhancement. Curr Opin Biotechnol 2015; 36:98-106. [DOI: 10.1016/j.copbio.2015.08.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 07/31/2015] [Accepted: 08/09/2015] [Indexed: 12/11/2022]
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16
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Negi S, Terada Y, Suzuyama M, Matsumoto H, Honbo A, Amagase Y, Mizukawa Y, Kiriyama A, Iga K, Urushidaini T, Sugiura Y. Intrinsic cell permeability of the GAGA zinc finger protein into HeLa cells. Biochem Biophys Res Commun 2015; 464:1034-1039. [PMID: 26187668 DOI: 10.1016/j.bbrc.2015.07.060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 07/11/2015] [Indexed: 11/30/2022]
Abstract
We examined the intrinsic cell permeability of a GAGA zinc finger obtained from the Drosophila melanogaster transcription factor and analyzed its mechanism of cellular uptake using confocal microscopy and flow cytometry. HeLa cells were treated with the Cy5-labeld GAGA peptides (containing a fluorescent chromophore) to detect fluorescence signals from the fluorescent labeling peptides by confocal microscopy. The results clearly indicated that GAGA peptides possess intrinsic cell permeability for HeLa cells. Based on the results of the flow cytometry analysis and the theoretical net positive charge of the GAGA peptides, the efficiency of cellular uptake of the GAGA peptides was predicted to depend on the net positive charge of the GAGA peptide as well as the cationic component ratio of Arg residues to Lys residues.
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Affiliation(s)
- Shigeru Negi
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto, 610-0395, Japan.
| | - Yuka Terada
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto, 610-0395, Japan
| | - Misato Suzuyama
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto, 610-0395, Japan
| | - Haruka Matsumoto
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto, 610-0395, Japan
| | - Akino Honbo
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto, 610-0395, Japan
| | - Yoko Amagase
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto, 610-0395, Japan
| | - Yumiko Mizukawa
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto, 610-0395, Japan
| | - Akiko Kiriyama
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto, 610-0395, Japan
| | - Katsumi Iga
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto, 610-0395, Japan
| | - Tetsuro Urushidaini
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto, 610-0395, Japan
| | - Yukio Sugiura
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto, 610-0395, Japan
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Negi S, Yoshioka M, Mima H, Mastumoto M, Suzuki M, Yokoyama M, Kano K, Sugiura Y. Efficient cleavage of DNA oligonucleotides by a non-FokI-type zinc finger nuclease containing one His₄-type finger domain derived from the first finger domain of Sp1. Bioorg Med Chem Lett 2015; 25:4074-7. [PMID: 26316464 DOI: 10.1016/j.bmcl.2015.08.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 08/12/2015] [Accepted: 08/14/2015] [Indexed: 12/28/2022]
Abstract
In this study, we sought to improve the hydrolytic activity of a His4-type single finger domain (f2), which was previously derived from the second finger domain (f2') of the Sp1 zinc finger protein (Sp1wt), which has 3 tandem finger domains (f1', f2', and f3'). To this end, 2 His4-type single finger domains were generated by mutating 2 Cys residues participating in Zn(II) coordination with the His residues in the first (f1') and third finger (f3') domains of Sp1wt. Circular dichroism spectroscopy results showed that the first and second His4-type zinc finger domains (f1 and f2) adopted folded ββα structures in the presence of Zn(II), but that the third His4-type zinc finger domain (f3) did not. Non-FokI-type zinc finger nucleases containing 3 or 4 finger domains were also prepared by combining a His4-type zinc finger domain with the Sp1wt scaffold. We studied their DNA-binding abilities and hydrolytic activities against DNA oligonucleotides by performing gel-mobility-shift assays. The results showed that f1 had higher hydrolytic activity for a DNA oligonucleotide with a GC box (5'-GGG GCG GGG-3'), compared with that of f2, although both His4-type single finger domains had similar DNA-binding affinities. The difference in the hydrolytic activity between f1 and f2 was ascribed not only to the zinc coordinate structure, but also to its folding structure and the stability of finger domain.
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Affiliation(s)
- Shigeru Negi
- Faculty of Pharmaceutical Science, Doshisha Women's University, 97-1 Minamihokotachi, Koudo, Kyotanabe, Kyoto 610-0395, Japan.
| | - Michiko Yoshioka
- Faculty of Pharmaceutical Science, Doshisha Women's University, 97-1 Minamihokotachi, Koudo, Kyotanabe, Kyoto 610-0395, Japan
| | - Hiroko Mima
- Faculty of Pharmaceutical Science, Doshisha Women's University, 97-1 Minamihokotachi, Koudo, Kyotanabe, Kyoto 610-0395, Japan
| | - Makoto Mastumoto
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| | - Michiko Suzuki
- Faculty of Pharmaceutical Science, Doshisha Women's University, 97-1 Minamihokotachi, Koudo, Kyotanabe, Kyoto 610-0395, Japan
| | - Mao Yokoyama
- Faculty of Pharmaceutical Science, Doshisha Women's University, 97-1 Minamihokotachi, Koudo, Kyotanabe, Kyoto 610-0395, Japan
| | - Koji Kano
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| | - Yukio Sugiura
- Faculty of Pharmaceutical Science, Doshisha Women's University, 97-1 Minamihokotachi, Koudo, Kyotanabe, Kyoto 610-0395, Japan
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Identifying key interactions stabilizing DOF zinc finger-DNA complexes using in silico approaches. J Theor Biol 2015; 382:150-9. [PMID: 26092376 DOI: 10.1016/j.jtbi.2015.06.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/09/2015] [Accepted: 06/06/2015] [Indexed: 11/21/2022]
Abstract
DOF (DNA-binding with one finger) proteins, a family of DNA-binding transcription factors, are members of zinc fingers unique to plants. They are associated with different plant specific phenomena including germination, dormancy, light and defense responses. Until now, there is no report of experimentally solved structure for DOF proteins, making empirical investigation of DOF-DNA interaction more challenging. It has been shown that comparative modeling can be used to reliably predict the three-dimensional (3D) model of structurally unknown proteins whenever a suitable template is available. Furthermore, current molecular mechanics force fields allow prediction of interaction energies for macromolecular complexes. Therefore, the approaches considered in this work were to model the 3D structures of DOF zinc fingers (ZFs) from Arabidopsis thaliana complexed with DNA molecule, to calculate their binding energies, to identify key interactions established between ZFs and DNA, and to determine the impact of the different interactions on the binding energies. The results were used to predict the binding affinities for the novel designed ZFs and may be used in engineering DNA binding proteins.
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19
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Blackstock D, Sun Q, Chen W. Fluorescent protein-based molecular beacons by zinc finger protein-guided assembly. Biotechnol Bioeng 2014; 112:236-41. [DOI: 10.1002/bit.25441] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/30/2014] [Accepted: 08/18/2014] [Indexed: 01/20/2023]
Affiliation(s)
- Daniel Blackstock
- Department of Chemical and Biomolecular Engineering; University of Delaware; Newark Delaware 19716
| | - Qing Sun
- Department of Chemical and Biomolecular Engineering; University of Delaware; Newark Delaware 19716
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering; University of Delaware; Newark Delaware 19716
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20
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Funabashi H, Yanagi S, Suzuki S, Mie M, Kobatake E. Assembly of zinc finger motif-fused enzymes on a dsDNA scaffold for catalyzing consecutive reactions with a proximity effect. Biotechnol Lett 2014; 37:109-14. [PMID: 25216646 DOI: 10.1007/s10529-014-1644-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 08/14/2014] [Indexed: 11/25/2022]
Abstract
The feasibility of assembling enzymes, catalyzing consecutive reactions, on to a double-stranded DNA (dsDNA) scaffold utilizing zinc finger motifs is described. The catalytic activities of two zinc finger motif-fused enzymes catalyzing a bioluminescence reaction with energy recycling, namely pyruvate phosphate dikinase and firefly luciferase, have been evaluated. Bioluminescence measurements with dsDNA scaffolds coding a different distance between the binding sites for each zinc finger motif-fused enzyme confirmed the effect of the distance, proving the proximity effect of ATP recycling presumed to be the result of efficient intermediate diffusion. Thus, fusion to zinc finger motifs offers a promising option for the assembly of bi-enzymes, catalyzing a consecutive reaction, onto a dsDNA scaffold with a proximity effect.
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Affiliation(s)
- Hisakage Funabashi
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan,
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21
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Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 340] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fangting Yu
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | | | - Alison G. Tebo
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Leela Ruckthong
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hira Qayyum
- University of Michigan, Ann Arbor, Michigan 48109, United States
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22
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Imanishi M. [Design of artificial DNA binding proteins toward control and elucidation of cellular functions]. YAKUGAKU ZASSHI 2014. [PMID: 23208050 DOI: 10.1248/yakushi.12-00228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An artificial transcription factor that can regulate the expression of specific genes at a desired time is very useful for research in chemical biology, cell biology, and future gene therapy. A C2H2 zinc finger motif, one of zinc-containing proteins, is known as the most ubiquitous DNA binding motif. The motif is attractive for designing artificial transcription factors with desired DNA binding specificities because of its characteristic DNA binding properties: (1) recognition of 3 bp per motif, (2) tandemly connected modular structure, and (3) binding to non-palindrome sequences as a monomer. Taking advantage of these properties, artificial DNA binding proteins with new DNA binding characteristics have been designed. By changing the linker region between two 3-zinc finger domains, artificial 6-zinc finger proteins were developed and shown to skip DNA sequences. Zinc-responsive transcription factors were created by altering one of the zinc ligands. An artificial zinc finger transcription factor targeting a core clock gene induced phase shifts of the cellular "circadian rhythm". Herein, I will summarize creation and function of the above-mentioned artificial zinc finger-type DNA binding proteins and transcription factors.
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Affiliation(s)
- Miki Imanishi
- Institute for Chemical Research, Kyoto University, Kyoto, Japan.
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23
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Zastrow M, Pecoraro VL. Designing hydrolytic zinc metalloenzymes. Biochemistry 2014; 53:957-78. [PMID: 24506795 PMCID: PMC3985962 DOI: 10.1021/bi4016617] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 01/23/2014] [Indexed: 12/15/2022]
Abstract
Zinc is an essential element required for the function of more than 300 enzymes spanning all classes. Despite years of dedicated study, questions regarding the connections between primary and secondary metal ligands and protein structure and function remain unanswered, despite numerous mechanistic, structural, biochemical, and synthetic model studies. Protein design is a powerful strategy for reproducing native metal sites that may be applied to answering some of these questions and subsequently generating novel zinc enzymes. From examination of the earliest design studies introducing simple Zn(II)-binding sites into de novo and natural protein scaffolds to current studies involving the preparation of efficient hydrolytic zinc sites, it is increasingly likely that protein design will achieve reaction rates previously thought possible only for native enzymes. This Current Topic will review the design and redesign of Zn(II)-binding sites in de novo-designed proteins and native protein scaffolds toward the preparation of catalytic hydrolytic sites. After discussing the preparation of Zn(II)-binding sites in various scaffolds, we will describe relevant examples for reengineering existing zinc sites to generate new or altered catalytic activities. Then, we will describe our work on the preparation of a de novo-designed hydrolytic zinc site in detail and present comparisons to related designed zinc sites. Collectively, these studies demonstrate the significant progress being made toward building zinc metalloenzymes from the bottom up.
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Affiliation(s)
| | - Vincent L. Pecoraro
- Department of Chemistry, University
of Michigan, Ann Arbor, Michigan 48109, United
States
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Sun Q, Madan B, Tsai SL, DeLisa MP, Chen W. Creation of artificial cellulosomes on DNA scaffolds by zinc finger protein-guided assembly for efficient cellulose hydrolysis. Chem Commun (Camb) 2014; 50:1423-5. [DOI: 10.1039/c3cc47215a] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Colombo J, Provazzi PJS, Calmon MF, Pires LC, Rodrigues NC, Petl P, Fossey MA, de Souza FP, Canduri F, Rahal P. Expression, purification and molecular analysis of the human ZNF706 protein. Biol Proced Online 2013; 15:10. [PMID: 24060497 PMCID: PMC3848911 DOI: 10.1186/1480-9222-15-10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 09/14/2013] [Indexed: 01/14/2023] Open
Abstract
Background The ZNF706 gene encodes a protein that belongs to the zinc finger family of proteins and was found to be highly expressed in laryngeal cancer, making the structure and function of ZNF706 worthy of investigation. In this study, we expressed and purified recombinant human ZNF706 that was suitable for structural analysis in Escherichia coli BL21(DH3). Findings ZNF706 mRNA was extracted from a larynx tissue sample, and cDNA was ligated into a cloning vector using the TOPO method. ZNF706 protein was expressed according to the E. coli expression system procedures and was purified using a nickel-affinity column. The structural qualities of recombinant ZNF706 and quantification alpha, beta sheet, and other structures were obtained by spectroscopy of circular dichroism. ZNF706's structural modeling showed that it is composed of α-helices (28.3%), β-strands (19.4%), and turns (20.9%), in agreement with the spectral data from the dichroism analysis. Conclusions We used circular dichroism and molecular modeling to examine the structure of ZNF706. The results suggest that human recombinant ZNF706 keeps its secondary structures and is appropriate for functional and structural studies. The method of expressing ZNF706 protein used in this study can be used to direct various functional and structural studies that will contribute to the understanding of its function as well as its relationship with other biological molecules and its putative role in carcinogenesis.
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Affiliation(s)
- Jucimara Colombo
- Department of Biology, São Paulo State University - UNESP, CEP: 15054-000, São José do Rio Preto /SP, Brazil
| | | | - Marilia Freitas Calmon
- Department of Biology, São Paulo State University - UNESP, CEP: 15054-000, São José do Rio Preto /SP, Brazil
| | - Lilian Campos Pires
- Department of Biology, São Paulo State University - UNESP, CEP: 15054-000, São José do Rio Preto /SP, Brazil
| | - Nathália Campos Rodrigues
- Institute of Chemistry of São Carlos, Department of Chemistry and Molecular Physics, University of São Paulo - USP, CEP: 13560-970, São Carlos /SP, Brazil
| | - Paulo Petl
- Department of Biology, São Paulo State University - UNESP, CEP: 15054-000, São José do Rio Preto /SP, Brazil
| | - Marcelo Andrés Fossey
- Department of Physics, São Paulo State University - UNESP, CEP: 15054-000, São José do Rio Preto /SP, Brazil
| | - Fátima Pereira de Souza
- Department of Physics, São Paulo State University - UNESP, CEP: 15054-000, São José do Rio Preto /SP, Brazil
| | - Fernanda Canduri
- Institute of Chemistry of São Carlos, Department of Chemistry and Molecular Physics, University of São Paulo - USP, CEP: 13560-970, São Carlos /SP, Brazil
| | - Paula Rahal
- Department of Biology, São Paulo State University - UNESP, CEP: 15054-000, São José do Rio Preto /SP, Brazil
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Anand P, Schug A, Wenzel W. Structure based design of protein linkers for zinc finger nuclease. FEBS Lett 2013; 587:3231-5. [PMID: 23994524 DOI: 10.1016/j.febslet.2013.08.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 08/05/2013] [Accepted: 08/12/2013] [Indexed: 12/18/2022]
Abstract
Zinc finger nucleases are a promising tool to edit DNA in many biological applications, in particular for gene knockout. Despite many efforts the number of genes that can be effectively targeted with ZFNs remains severely limited, as available constructs cannot address arbitrary gene sequences. Here, we develop a novel concept to significantly enhance the number of DNA sequences that can be targeted by ZFN. Using an efficient computational model, we provide an extensive library of possible linker molecules between individual zinc finger motifs in the construct that can skip up to 10 base pairs between adjacent zinc finger recognition sites in the DNA sequence, which increases the number of genes that can be efficiently targeted by more than an order of magnitude.
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Affiliation(s)
- Priya Anand
- Institute of Nanotechnology, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
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27
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Rhoden Smith A, Iverson BL. Threading polyintercalators with extremely slow dissociation rates and extended DNA binding sites. J Am Chem Soc 2013; 135:12783-9. [PMID: 23919778 DOI: 10.1021/ja4057344] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The development of small molecules that bind DNA sequence specifically has the potential to modulate gene expression in a general way. One mode of DNA binding is intercalation, or the insertion of molecules between DNA base pairs. We have developed a modular polyintercalation system in which intercalating naphthalene diimide (NDI) units are connected by flexible linkers that alternate between the minor and major grooves of DNA when bound. We recently reported a threading tetraintercalator with a dissociation half-life of 16 days, the longest reported to date, from its preferred 14 bp binding site. Herein, three new tetraintercalator derivatives were synthesized with one, two, and three additional methylene units in the central major groove-binding linker. These molecules displayed dissociation half-lives of 57, 27, and 18 days, respectively, from the 14 bp site. The optimal major groove-binding linker was used in the design of an NDI hexaintercalator that was analyzed by gel-shift assays, DNase I footprinting, and UV-vis spectroscopy. The hexaintercalator bound its entire 22 bp binding site, the longest reported specific binding site for a synthetic, non-nucleic acid-based DNA binding molecule, but with a significantly faster dissociation rate compared to the tetraintercalators.
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Affiliation(s)
- Amy Rhoden Smith
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
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Frenkel-Morgenstern M, Valencia A. Novel domain combinations in proteins encoded by chimeric transcripts. ACTA ACUST UNITED AC 2013; 28:i67-74. [PMID: 22689780 PMCID: PMC3371848 DOI: 10.1093/bioinformatics/bts216] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Motivation: Chimeric RNA transcripts are generated by different mechanisms including pre-mRNA trans-splicing, chromosomal translocations and/or gene fusions. It was shown recently that at least some of chimeric transcripts can be translated into functional chimeric proteins. Results: To gain a better understanding of the design principles underlying chimeric proteins, we have analyzed 7,424 chimeric RNAs from humans. We focused on the specific domains present in these proteins, comparing their permutations with those of known human proteins. Our method uses genomic alignments of the chimeras, identification of the gene–gene junction sites and prediction of the protein domains. We found that chimeras contain complete protein domains significantly more often than in random data sets. Specifically, we show that eight different types of domains are over-represented among all chimeras as well as in those chimeras confirmed by RNA-seq experiments. Moreover, we discovered that some chimeras potentially encode proteins with novel and unique domain combinations. Given the observed prevalence of entire protein domains in chimeras, we predict that certain putative chimeras that lack activation domains may actively compete with their parental proteins, thereby exerting dominant negative effects. More generally, the production of chimeric transcripts enables a combinatorial increase in the number of protein products available, which may disturb the function of parental genes and influence their protein–protein interaction network. Availability: our scripts are available upon request. Contact:avalencia@cnio.es Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Milana Frenkel-Morgenstern
- Structural Biology and BioComputing Program, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
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29
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Verzele D, Madder A. Synthetic Progress in cMyc-Max Oncoprotein Miniaturization: Semi-Online Monitoring Gives Solid-Phase Access to Hydrophobic b(-HLH-)ZIP Peptidosteroid Tweezers. European J Org Chem 2012. [DOI: 10.1002/ejoc.201201235] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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30
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Nakata E, Liew FF, Uwatoko C, Kiyonaka S, Mori Y, Katsuda Y, Endo M, Sugiyama H, Morii T. Zinc-Finger Proteins for Site-Specific Protein Positioning on DNA-Origami Structures. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108199] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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31
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Nakata E, Liew FF, Uwatoko C, Kiyonaka S, Mori Y, Katsuda Y, Endo M, Sugiyama H, Morii T. Zinc-Finger Proteins for Site-Specific Protein Positioning on DNA-Origami Structures. Angew Chem Int Ed Engl 2012; 51:2421-4. [DOI: 10.1002/anie.201108199] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 12/27/2011] [Indexed: 01/22/2023]
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Fehr F, Nadler A, Brodhun F, Feussner I, Diederichsen U. Semi-synthesis and analysis of chemically modified zif268 zinc-finger domains. ChemistryOpen 2012; 1:26-32. [PMID: 24551489 PMCID: PMC3922437 DOI: 10.1002/open.201100002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Indexed: 01/10/2023] Open
Abstract
Total synthesis of proteins can be challenging despite assembling techniques, such as native chemical ligation (NCL) and expressed protein ligation (EPL). Especially, the combination of recombinant protein expression and chemically addressable solid-phase peptide synthesis (SPPS) is well suited for the redesign of native protein structures. Incorporation of analytical probes and artificial amino acids into full-length natural protein domains, such as the sequence-specific DNA binding zinc-finger motifs, are of interest combining selective DNA recognition and artificial function. The semi-synthesis of the natural 90 amino acid long sequence of the zinc-finger domain of Zif268 is described including various chemically modified constructs. Our approach offers the possibility to exchange any amino acid within the third zinc finger. The realized modifications of the natural sequence include point mutations, attachment of a fluorophore, and the exchange of amino acids at different positions in the zinc finger by artificial amino acids to create additional metal binding sites. The individual constructs were analyzed by circular dichroism (CD) spectroscopy with respect to the integrity of the zinc-finger fold and DNA binding.
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Affiliation(s)
- Friederike Fehr
- Georg-August-Universität Göttingen, Institut für Organische und Biomolekulare Chemie Tammannstrasse 2, 37077 Göttingen (Germany), E-mail:
| | - André Nadler
- Georg-August-Universität Göttingen, Institut für Organische und Biomolekulare Chemie Tammannstrasse 2, 37077 Göttingen (Germany), E-mail:
| | - Florian Brodhun
- Georg-August-Universität Göttingen, Albrecht-von-Haller Institut für Pflanzenwissenschaften Justus-von-Liebig-Weg 11, 37077 Göttingen (Germany)
| | - Ivo Feussner
- Georg-August-Universität Göttingen, Albrecht-von-Haller Institut für Pflanzenwissenschaften Justus-von-Liebig-Weg 11, 37077 Göttingen (Germany)
| | - Ulf Diederichsen
- Georg-August-Universität Göttingen, Institut für Organische und Biomolekulare Chemie Tammannstrasse 2, 37077 Göttingen (Germany), E-mail:
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Towards artificial metallonucleases for gene therapy: recent advances and new perspectives. Future Med Chem 2011; 3:1935-66. [DOI: 10.4155/fmc.11.139] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The process of DNA targeting or repair of mutated genes within the cell, induced by specifically positioned double-strand cleavage of DNA near the mutated sequence, can be applied for gene therapy of monogenic diseases. For this purpose, highly specific artificial metallonucleases are developed. They are expected to be important future tools of modern genetics. The present state of art and strategies of research are summarized, including protein engineering and artificial ‘chemical’ nucleases. From the results, we learn about the basic role of the metal ions and the various ligands, and about the DNA binding and cleavage mechanism. The results collected provide useful guidance for engineering highly controlled enzymes for use in gene therapy.
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Imanishi M, Nakamura A, Doi M, Futaki S, Okamura H. Control of Circadian Phase by an Artificial Zinc Finger Transcription Regulator. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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35
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Michalek JL, Besold AN, Michel SLJ. Cysteine and histidine shuffling: mixing and matching cysteine and histidine residues in zinc finger proteins to afford different folds and function. Dalton Trans 2011; 40:12619-32. [PMID: 21952363 DOI: 10.1039/c1dt11071c] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Zinc finger proteins utilize zinc for structural purposes: zinc binds to a combination of cysteine and histidine ligands in a tetrahedral coordination geometry facilitating protein folding and function. While much is known about the classical zinc finger proteins, which utilize a Cys(2)His(2) ligand set to coordinate zinc and fold into an anti-parallel beta sheet/alpha helical fold, there are thirteen other families of 'non-classical' zinc finger proteins for which relationships between metal coordination and protein structure/function are less defined. This 'Perspective' article focuses on two classes of these non-classical zinc finger proteins: Cys(3)His type zinc finger proteins and Cys(2)His(2)Cys type zinc finger proteins. These proteins bind zinc in a tetrahedral geometry, like the classical zinc finger proteins, yet they adopt completely different folds and target different oligonucleotides. Our current understanding of the relationships between ligand set, metal ion, fold and function for these non-classical zinc fingers is discussed.
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Affiliation(s)
- Jamie L Michalek
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, USA
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36
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Imanishi M, Nakamura A, Doi M, Futaki S, Okamura H. Control of circadian phase by an artificial zinc finger transcription regulator. Angew Chem Int Ed Engl 2011; 50:9396-9. [PMID: 21905187 DOI: 10.1002/anie.201103307] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2011] [Indexed: 11/07/2022]
Affiliation(s)
- Miki Imanishi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
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37
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Pazos E, Mosquera J, Vázquez ME, Mascareñas JL. DNA Recognition by Synthetic Constructs. Chembiochem 2011; 12:1958-73. [DOI: 10.1002/cbic.201100247] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Indexed: 12/29/2022]
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38
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Camsund D, Lindblad P, Jaramillo A. Genetically engineered light sensors for control of bacterial gene expression. Biotechnol J 2011; 6:826-36. [PMID: 21648094 DOI: 10.1002/biot.201100091] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2011] [Revised: 04/11/2011] [Accepted: 04/18/2011] [Indexed: 12/28/2022]
Abstract
Light of different wavelengths can serve as a transient, noninvasive means of regulating gene expression for biotechnological purposes. Implementation of advanced gene regulatory circuits will require orthogonal transcriptional systems that can be simultaneously controlled and that can produce several different control states. Fully genetically encoded light sensors take advantage of the favorable characteristics of light, do not need the supplementation of any chemical inducers or co-factors, and have been demonstrated to control gene expression in Escherichia coli. Herein, we review engineered light-sensor systems with potential for in vivo regulation of gene expression in bacteria, and highlight different means of extending the range of available light input and transcriptional output signals. Furthermore, we discuss advances in multiplexing different light sensors for achieving multichromatic control of gene expression and indicate developments that could facilitate the construction of efficient systems for light-regulated, multistate control of gene expression.
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Affiliation(s)
- Daniel Camsund
- Department of Photochemistry and Molecular Science, Uppsala University, Ångström Laboratories, Uppsala, Sweden
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Mori H, Ueno-Noto K. A Theoretical Study of the Physicochemical Mechanisms Associated with DNA Recognition Modulation in Artificial Zinc-Finger Proteins. J Phys Chem B 2011; 115:4774-80. [DOI: 10.1021/jp1097348] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Hirotoshi Mori
- Division of Advanced Sciences, Ocha-dai Academic Production, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Kaori Ueno-Noto
- Division of Advanced Sciences, Ocha-dai Academic Production, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan
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40
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Quintal SM, dePaula QA, Farrell NP. Zinc finger proteins as templates for metal ion exchange and ligand reactivity. Chemical and biological consequences. Metallomics 2011; 3:121-39. [PMID: 21253649 DOI: 10.1039/c0mt00070a] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Zinc finger reactions with inorganic ions and coordination compounds are as diverse as the zinc fingers themselves. Use of metal ions such as Co(2+) and Cd(2+) has given structural, thermodynamic and kinetic information on zinc fingers and zinc-finger-DNA/RNA interactions. It is a general truism that alteration of the coordination sphere in the finger environment will disrupt the recognition with DNA/RNA and this has implications for mechanism of toxicity and carcinogenesis of metal ions. Structural zinc fingers are susceptible to electrophilic attack and the recognition that the coordination sphere of inorganic compounds may be modulated for control of electrophilic attack on zinc fingers raises the possibility of systematic studies of zinc fingers as drug targets using inorganic chemistry. Some inorganic compounds such as those of As(III) and Au(I) may exert their biological effects through inactivation of zinc fingers and novel approaches to specifically attack the zinc-bound ligands using Co(III)-Schiff bases and Platinum(II)-Nucleobase compounds have been proposed. The genomic importance of zinc fingers suggests that the "coordination chemistry" of zinc fingers themselves is ripe for exploration to design new targets for medicinal inorganic chemistry.
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Affiliation(s)
- Susana M Quintal
- Department of Chemistry, Virginia Commonwealth University, 1001 W. Main St., Richmond, VA 23284-2006, USA
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41
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Jolma A, Taipale J. Methods for Analysis of Transcription Factor DNA-Binding Specificity In Vitro. Subcell Biochem 2011; 52:155-173. [PMID: 21557082 DOI: 10.1007/978-90-481-9069-0_7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Transcription of genes during development and in response to environmental stimuli is determined by genomic DNA sequence. The DNA sequences regulating transcription are read by sequence-specific transcription factors (TFs) that recognize relatively short sequences, generally between four and twenty base pairs in length. Transcriptional regulation generally requires binding of multiple TFs in close proximity to each other. Mechanistic understanding of transcription in an organism thus requires detailed knowledge of binding affinities of all its TFs to all possible DNA sequences, and the co-operative interactions between the TFs. However, very little is known about such co-operative binding interactions, and even the simple TF-DNA binding information exists only for a very small proportion of all TFs - for example, mammals have approximately 1,300-2,000 TFs [1, 2], yet the largest public databases for TF binding specificity, Jaspar and Uniprobe [3, 4] currently list only approximately 500 moderate to high resolution profiles for human or mouse. This lack of knowledge is in part due to the fact that analysis of TF DNA binding has been laborious and expensive. In this chapter, we review methods that can be used to determine binding specificity of TFs to DNA, mainly focusing on recently developed assays that allow high-resolution analysis of TF binding specificity in relatively high throughput.
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Affiliation(s)
- Arttu Jolma
- Department of Biosciences and Nutrition, SE-171 77, Stockholm, Sweden,
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42
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am Ende CW, Meng HY, Ye M, Pandey AK, Zondlo NJ. Design of lanthanide fingers: compact lanthanide-binding metalloproteins. Chembiochem 2010; 11:1738-47. [PMID: 20623571 DOI: 10.1002/cbic.201000056] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Lanthanides have interesting chemical properties; these include luminescent, magnetic, and catalytic functions. Toward the development of proteins incorporating novel functions, we have designed a new lanthanide-binding motif, lanthanide fingers. These were designed based on the Zif268 zinc finger, which exhibits a beta beta alpha structural motif. Lanthanide fingers utilize an Asp(2)Glu(2) metal-coordination environment to bind lanthanides through a tetracarboxylate peptide ligand. The iterative design of a general lanthanide-binding peptide incorporated the following key elements: 1) residues with high alpha-helix and beta-sheet propensities in the respective secondary structures; 2) an optimized big box alpha-helix N-cap; 3) a Schellman alpha-helix C-cap motif; and 4) an optional D-Pro-Ser type II' beta-turn in the beta-hairpin. The peptides were characterized for lanthanide binding by circular dichroism (CD), NMR, and fluorescence spectroscopy. In all instances, stabilization of the peptide secondary structures resulted in an increase in metal affinity. The optimized protein design was a 25-residue peptide that was a general lanthanide-binding motif; this binds all lanthanides examined in a competitive aqueous environment, with a dissociation constant of 9.3 microM for binding Er(3+). CD spectra of the peptide-lanthanide complexes are similar to those of zinc fingers and other beta beta alpha proteins. Metal binding involves residues from the N-terminal beta-hairpin and the C terminal alpha-helical segments of the peptide. NMR data indicated that metal binding induced a global change in the peptide structure. The D-Pro-Ser type II' beta-turn motif could be replaced by Thr-Ile to generate genetically encodable lanthanide fingers. Replacement of the central Phe with Trp generated genetically encodable lanthanide fingers that exhibited terbium luminescence greater than that of an EF-hand peptide.
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Affiliation(s)
- Christopher W am Ende
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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43
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Zhang H, Jiang T. Synthetic circuits, devices and modules. Protein Cell 2010; 1:974-8. [PMID: 21153514 DOI: 10.1007/s13238-010-0133-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 11/09/2010] [Indexed: 12/19/2022] Open
Abstract
The aim of synthetic biology is to design artificial biological systems for novel applications. From an engineering perspective, construction of biological systems of defined functionality in a hierarchical way is fundamental to this emerging field. Here, we highlight some current advances on design of several basic building blocks in synthetic biology including the artificial gene control elements, synthetic circuits and their assemblies into devices and modules. Such engineered basic building blocks largely expand the synthetic toolbox and contribute to our understanding of the underlying design principles of living cells.
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Affiliation(s)
- Hong Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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44
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Guerrerio AL, Berg JM. Design of single-stranded nucleic acid binding peptides based on nucleocapsid CCHC-box zinc-binding domains. J Am Chem Soc 2010; 132:9638-43. [PMID: 20586464 DOI: 10.1021/ja910942v] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The solution structures of nucleocapsid (NC)-like CCHC zinc-binding domains bound to nucleic acid targets have revealed that these domains bind guanosine residues within single-stranded nucleic acids. Here, we have performed initial studies examining the potential use of NC-like CCHC zinc-binding domains as modules to construct single-stranded nucleic acid binding peptides. The affinity for guanosine-containing single-stranded deoxyribooligonucleotides increases with the number of CCHC domains in the peptide. The length of the linker between domains affects the spacing of guanosine residues in oligonucleotides that are preferentially bound. These studies provide a proof of principle that NC-like CCHC zinc-binding domains can be utilized as a basis for designing peptides that bind specific single-stranded nucleic acid sequences.
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Affiliation(s)
- Anthony L Guerrerio
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
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45
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Zinc-finger hydrolase: Computational selection of a linker and a sequence towards metal activation with a synthetic αββ protein. Bioorg Med Chem 2010; 18:8270-6. [PMID: 21035349 DOI: 10.1016/j.bmc.2010.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 09/30/2010] [Accepted: 10/02/2010] [Indexed: 12/29/2022]
Abstract
The zinc-finger protein is targeted for computational redesign as a hydrolase enzyme. Successful in having zinc activated for hydrolase function, the study validates the stepwise approach to having the protein tuned in main-chain structure stereochemically and over side chains chemically. A leucine homopolypeptide, harboring histidines to tri coordinate zinc and d-amino-acid-nucleated α-helix and β-hairpin building blocks of an αββ protein, is taken up for modeling, first with cyana, in a mixed-chirality linker between the building blocks, and then with IDeAS, in a sequence over side chains. The designed mixed-chirality polypeptide structure is proven to order as an intended αββ fold and capture zinc to activate its role as a hydrolase catalyst. The design approach to have protein folds defined stereochemically and receptor and catalysis functions defined chemically is presented, and illustrates L- and D-α-amino-acid structures as the alphabet integrating chemical- and stereochemical-structure variables as its letters.
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46
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Jantz D, Berg JM. Probing the DNA-binding affinity and specificity of designed zinc finger proteins. Biophys J 2010; 98:852-60. [PMID: 20197039 DOI: 10.1016/j.bpj.2009.11.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Revised: 10/30/2009] [Accepted: 11/02/2009] [Indexed: 11/17/2022] Open
Abstract
Engineered transcription factors and endonucleases based on designed Cys(2)His(2) zinc finger domains have proven to be effective tools for the directed regulation and modification of genes. The introduction of this technology into both research and clinical settings necessitates the development of rapid and accurate means of evaluating both the binding affinity and binding specificity of designed zinc finger domains. Using a fluorescence anisotropy-based DNA-binding assay, we examined the DNA-binding properties of two engineered zinc finger proteins that differ by a single amino acid. We demonstrate that the protein with the highest affinity for a particular DNA site need not be the protein that binds that site with the highest degree of specificity. Moreover, by comparing the binding characteristics of the two proteins at varying salt concentrations, we show that the ionic strength makes significant and variable contributions to both affinity and specificity. These results have significant implications for zinc finger design as they highlight the importance of considering affinity, specificity, and environmental requirements in designing a DNA-binding domain for a particular application.
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Affiliation(s)
- Derek Jantz
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA
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47
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Morisaki T, Imanishi M, Futaki S, Sugiura Y. [Artificial transcription factors based on multi-zinc finger motifs]. YAKUGAKU ZASSHI 2010; 130:45-8. [PMID: 20046064 DOI: 10.1248/yakushi.130.45] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Artificial transcription factors targeting any desired genes are very attractive from the standpoint of regulating biological functions for life science studies and clinical applications. In order to generate such transcription factors, specific DNA binding domains are required to address a single site for each gene promoter. C(2)H(2) type zinc finger motif is one of the best frameworks to create new artificial DNA binding proteins for the following features: the zinc finger motif can recognize three bases DNA, be tandemly repeated by covalent linkage, and work as a monomer. Taking advantage of these features, manifold zinc finger proteins targeting various DNA sequences have been created so far. For application to a target in sequences as complex as the human genome, the significantly strict specificity in DNA binding must be required. Conjugating multiple fingers (multi-zinc fingers) enables to recognize longer sequences which are sufficient for addressing a single site in the human genome, whereas it has become known that as the number of finger motifs increases, the equilibrium time with the target sequence is significantly longer by in vitro experiments. Our recent study showed that the multi-zinc finger type artificial transcription factor could activate the reporter gene promptly. There is much interest in creating gene regulators, and the artificial transcription factors based on multi-zinc finger motifs could be a superior scaffold.
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Affiliation(s)
- Tatsuya Morisaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan.
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48
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Du K, Chen Y, Dai Z, Bi Y, Cai T, Hou L, Chai Y, Song Q, Chen S, Luo W, Chen J. Molecular cloning and functional characterization of a mouse gene upregulated by lipopolysaccharide treatment reveals alternative splicing. Biochem Biophys Res Commun 2010; 391:267-71. [PMID: 19913514 DOI: 10.1016/j.bbrc.2009.11.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Accepted: 11/07/2009] [Indexed: 12/27/2022]
Abstract
Treatment of mouse cells with lipopolysaccharide (LPS) potently initiates an inflammatory response, but the underlying mechanisms are unclear. We therefore sought to characterize cDNA sequences of a new mouse LPS-responsive gene, and to evaluate the effects of MLrg. Full-length cDNAs were obtained from LPS-treated NIH3T3 cells. We report that the MLrg gene produces two alternative splice products (GenBank Accession Nos. DQ316984 and DQ320011), respectively, encoding MLrgW and MLrgS polypeptides. Both proteins contain zinc finger and leucine zipper domains and are thus potential regulators of transcription. Expression of MLrgW and MLrgS were robustly upregulated following LPS treatment, and the proteins were localized predominantly in the nuclear membrane and cytoplasm. In stable transfectants over-expressing MLrgW the proportion of cells in G1 phase was significantly reduced, while in cells over-expressing MLrgS the proportion of cells in G2 was significantly increased; both proteins are thus potential regulators of cell cycle progression. Upregulation of MLrgW and MLrgS may be an important component of the LPS inflammatory pathway and of the host response to infection with GNB.
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Affiliation(s)
- Kejun Du
- Department of Occupational and Environmental Health, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, PR China
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Aiba Y, Komiyama M. Introduction of disulfide bond to the main chain of PNA to switch its hybridization and invasion activity. Org Biomol Chem 2009; 7:5078-83. [PMID: 20024101 DOI: 10.1039/b917405b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In order to facilitate the removal of peptide nucleic acid (PNA), when necessary, from its duplexes and invasion complexes, a disulfide bond was introduced to its main chain. The disulfide bond was readily cleaved by various reducing agents (2-mercaptoethanol, dl-dithiothreitol, and tris(2-carboxyethyl)phosphine) even when the PNA was forming a duplex with its complementary DNA. The resultant two short PNA fragments were spontaneously removed from the DNA. Double-duplex invasion complexes of two disulfide-containing PNA strands were also promptly cleaved by the reducing agents. By using this modified PNA, a desired DNA fragment was picked up from DNA mixtures, and obtained in a pure form (free from the PNA) by the reductive treatment. Importantly, this separation was achieved at low temperatures (e.g., 37 degrees C), where all the DNAs (and other biomolecules if any) should be kept intact. Strong potential of the modified PNA for various biological applications has been indicated.
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Affiliation(s)
- Yuichiro Aiba
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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50
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Zaykov A, MacKenzie K, Ball Z. Controlling Peptide Structure with Coordination Chemistry: Robust and Reversible Peptide-Dirhodium Ligation. Chemistry 2009; 15:8961-5. [DOI: 10.1002/chem.200901266] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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