101
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Zhao C, Song H, Scott P, Zhao A, Tateishi-Karimata H, Sugimoto N, Ren J, Qu X. Mirror-Image Dependence: Targeting Enantiomeric G-Quadruplex DNA Using Triplex Metallohelices. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809207] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Chuanqi Zhao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P. R. China
| | - Hualong Song
- Department of Chemistry; University of Warwick; Gibbet Hill Road Coventry CV4 7AL UK
| | - Peter Scott
- Department of Chemistry; University of Warwick; Gibbet Hill Road Coventry CV4 7AL UK
| | - Andong Zhao
- University of Chinese Academy of Sciences; Beijing 100039 P. R. China
| | | | | | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P. R. China
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102
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Zhao C, Song H, Scott P, Zhao A, Tateishi-Karimata H, Sugimoto N, Ren J, Qu X. Mirror-Image Dependence: Targeting Enantiomeric G-Quadruplex DNA Using Triplex Metallohelices. Angew Chem Int Ed Engl 2018; 57:15723-15727. [PMID: 30311333 DOI: 10.1002/anie.201809207] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/21/2018] [Indexed: 12/22/2022]
Abstract
Natural d-DNA and l-DNA are mirror-image counterparts. However, because of the inherent flexibility and conformation diversity of DNA, it is still not clear how enantiomeric compounds recognize d-DNA and l-DNA. Herein, taking G-quadruplex (G4) DNA as an example that has diverse conformations and distinct biofunctions, the binding of ten pairs of iron triplex metallohelices to d- and l-G4 DNA were evaluated. The Δ-enantiomer binds to d-DNA and the Λ-enantiomer binds to l-DNA, exhibiting almost the same stabilization effect and binding affinity. The binding affinity of the Δ-metallohelix with d-G4 is nearly 70-fold higher than that of Λ-metallohelix binding d-G4. Δ-Metallohelix binding to d-G4 follows a two-step binding process driven by a favorable enthalpy contribution to compensate for the associated unfavorable entropy.
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Affiliation(s)
- Chuanqi Zhao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
| | - Hualong Song
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Peter Scott
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Andong Zhao
- University of Chinese Academy of Sciences, Beijing, 100039, P. R. China
| | | | | | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
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103
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Jin K, Li X. Advances in Native Chemical Ligation-Desulfurization: A Powerful Strategy for Peptide and Protein Synthesis. Chemistry 2018; 24:17397-17404. [DOI: 10.1002/chem.201802067] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Indexed: 11/12/2022]
Affiliation(s)
- Kang Jin
- Department of Chemistry; State Key Laboratory of Synthetic Chemistry; The University of Hong Kong; Hong Kong P. R. China
| | - Xuechen Li
- Department of Chemistry; State Key Laboratory of Synthetic Chemistry; The University of Hong Kong; Hong Kong P. R. China
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104
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Röthlisberger P, Hollenstein M. Aptamer chemistry. Adv Drug Deliv Rev 2018; 134:3-21. [PMID: 29626546 DOI: 10.1016/j.addr.2018.04.007] [Citation(s) in RCA: 218] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/28/2018] [Accepted: 04/03/2018] [Indexed: 12/12/2022]
Abstract
Aptamers are single-stranded DNA or RNA molecules capable of tightly binding to specific targets. These functional nucleic acids are obtained by an in vitro Darwinian evolution method coined SELEX (Systematic Evolution of Ligands by EXponential enrichment). Compared to their proteinaceous counterparts, aptamers offer a number of advantages including a low immunogenicity, a relative ease of large-scale synthesis at affordable costs with little or no batch-to-batch variation, physical stability, and facile chemical modification. These alluring properties have propelled aptamers into the forefront of numerous practical applications such as the development of therapeutic and diagnostic agents as well as the construction of biosensing platforms. However, commercial success of aptamers still proceeds at a weak pace. The main factors responsible for this delay are the susceptibility of aptamers to degradation by nucleases, their rapid renal filtration, suboptimal thermal stability, and the lack of functional group diversity. Here, we describe the different chemical methods available to mitigate these shortcomings. Particularly, we describe the chemical post-SELEX processing of aptamers to include functional groups as well as the inclusion of modified nucleoside triphosphates into the SELEX protocol. These methods will be illustrated with successful examples of chemically modified aptamers used as drug delivery systems, in therapeutic applications, and as biosensing devices.
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105
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Bi S, Liu P, Ling B, Yuan X, Jiang Y. Mechanism of N-to-S acyl transfer of N-(2-hydroxybenzyl) cysteine derivatives and origin of phenol acceleration effect. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2017.11.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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106
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Qu Q, Gao S, Li YM. Racemic crystal structures of peptide toxins, GsMTx4 prepared by protein total synthesis. J Pept Sci 2018; 24:e3112. [PMID: 30009430 DOI: 10.1002/psc.3112] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 06/12/2018] [Accepted: 06/13/2018] [Indexed: 01/28/2023]
Abstract
The Piezo channel is a versatile mechanosensitive cation channel that mediates tactile, vascular development, and proprioception. GsMTx4 is the only reported inhibitor specifically targeting Piezo channels. Although the sequence of GsMTx4 is reported, the crystal structure of GsMTx4 is still unknown. Here, we achieved the two-segment synthesis of GsMTx4 and its enantiomer, enGsMTx4, through hydrazide based Native Chemical Ligation, and analyzed the crystal structure of GsMTx4 through the racemic crystallization technology. By analyzing the structure, we found that there is a hydrophobic patch surrounded by aromatic residues and charged residues.
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Affiliation(s)
- Qian Qu
- Department of Chemistry, Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, 100084, China.,School of Biological and Medical Engineering, Hefei University of Technology, Anhui, Hefei, 230009, China
| | - Shuai Gao
- Department of Chemistry, Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Yi-Ming Li
- School of Biological and Medical Engineering, Hefei University of Technology, Anhui, Hefei, 230009, China
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107
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Liu X, Zhu TF. Sequencing Mirror-Image DNA Chemically. Cell Chem Biol 2018; 25:1151-1156.e3. [PMID: 30017914 DOI: 10.1016/j.chembiol.2018.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/15/2018] [Accepted: 05/01/2018] [Indexed: 11/24/2022]
Abstract
The development of mirror-image biology systems faces a crucial barrier of lacking an L-DNA sequencing technique. Here, we developed a practical method for sequencing mirror-image DNA by adopting the Maxam-Gilbert sequencing approach, through which specific nucleobases in an end-labeled L-DNA are cleaved by achiral chemicals. This technique may facilitate the therapeutic application of nuclease-resistant L-aptamer drugs, and bring the vision of building an alternative, mirror-image self-replicating system closer to reality.
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Affiliation(s)
- Xianyu Liu
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
| | - Ting F Zhu
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China.
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108
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Liang LJ, Si Y, Tang S, Huang D, Wang ZA, Tian C, Zheng JS. Biochemical properties of K11,48-branched ubiquitin chains. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.03.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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109
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Du JJ, Xin LM, Lei Z, Zou SY, Xu WB, Wang CW, Zhang L, Gao XF, Guo J. Glycopeptide ligation via direct aminolysis of selenoester. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.04.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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110
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Total synthesis of snake toxin α-bungarotoxin and its analogues by hydrazide-based native chemical ligation. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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111
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Chen C, Gao S, Qu Q, Mi P, Tao A, Li YM. Chemical synthesis and structural analysis of guanylate cyclase C agonist linaclotide. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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112
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Chu GC, Bai JS, Kong YF, Fan J, Sun SS, Xu HJ, Shi J, Li YM. Efficient semi-synthesis of ubiquitin-7-amino-4-methylcoumarin. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.05.081] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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113
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114
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Lu X, He SJ, Cheng WM, Shi J. Transition-metal-catalyzed C H functionalization for late-stage modification of peptides and proteins. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.05.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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115
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Fang GM, Chen XX, Yang QQ, Zhu LJ, Li NN, Yu HZ, Meng XM. Discovery, structure, and chemical synthesis of disulfide-rich peptide toxins and their analogs. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.02.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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116
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Qu Q, Pan M, Gao S, Zheng Q, Yu Y, Su J, Li X, Hu H. A Highly Efficient Synthesis of Polyubiquitin Chains. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2018; 5:1800234. [PMID: 30027052 PMCID: PMC6051384 DOI: 10.1002/advs.201800234] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 04/17/2018] [Indexed: 06/08/2023]
Abstract
A robust, microwave-assisted, highly efficient, solid-phase peptide synthesis method for preparing isopeptide-linked 62-mer and 76-mer isoubiquitins and polyubiquitin is developed. The strategy avoids the use of costly resins and pseudoprolines, and the isopeptide-linked building blocks can be assembled with high initial purity within 1 day. All seven diubiquitins are successfully synthesized on a multi-milligram scale; a four-segment, three-ligation method is used to obtain a K33-/K11-linked mixed triubiquitin in excellent yield. Circular dichroism and crystallographic analyses are used to verify the structures of the well-folded, synthetic polyubiquitin chains. The facile synthetic strategy is expected to be generally applicable for the rapid synthesis of isopeptide-linked isoUbs and to pave the way for the study of longer polyubiquitin chains.
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Affiliation(s)
- Qian Qu
- School of PharmacySecond Military Medical University325 Guohe RoadShanghai200433China
- Tsinghua‐Peking Center for Life SciencesTsinghua UniversityBeijing100084China
| | - Man Pan
- Tsinghua‐Peking Center for Life SciencesTsinghua UniversityBeijing100084China
| | - Shuai Gao
- Tsinghua‐Peking Center for Life SciencesTsinghua UniversityBeijing100084China
| | - Qing‐Yun Zheng
- Tsinghua‐Peking Center for Life SciencesTsinghua UniversityBeijing100084China
| | - Yuan‐Yuan Yu
- Tsinghua‐Peking Center for Life SciencesTsinghua UniversityBeijing100084China
| | - Jia‐Can Su
- Changhai HospitalSecond Military Medical University168 Changhai RoadShanghai200433China
| | - Xiang Li
- School of PharmacySecond Military Medical University325 Guohe RoadShanghai200433China
| | - Hong‐Gang Hu
- School of PharmacySecond Military Medical University325 Guohe RoadShanghai200433China
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117
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118
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Kurczynska M, Kotulska M. Automated method to differentiate between native and mirror protein models obtained from contact maps. PLoS One 2018; 13:e0196993. [PMID: 29787567 PMCID: PMC5963800 DOI: 10.1371/journal.pone.0196993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 04/24/2018] [Indexed: 11/23/2022] Open
Abstract
Mirror protein structures are often considered as artifacts in modeling protein structures. However, they may soon become a new branch of biochemistry. Moreover, methods of protein structure reconstruction, based on their residue-residue contact maps, need methodology to differentiate between models of native and mirror orientation, especially regarding the reconstructed backbones. We analyzed 130 500 structural protein models obtained from contact maps of 1 305 SCOP domains belonging to all 7 structural classes. On average, the same numbers of native and mirror models were obtained among 100 models generated for each domain. Since their structural features are often not sufficient for differentiating between the two types of model orientations, we proposed to apply various energy terms (ETs) from PyRosetta to separate native and mirror models. To automate the procedure for differentiating these models, the k-means clustering algorithm was applied. Using total energy did not allow to obtain appropriate clusters–the accuracy of the clustering for class A (all helices) was no more than 0.52. Therefore, we tested a series of different k-means clusterings based on various combinations of ETs. Finally, applying two most differentiating ETs for each class allowed to obtain satisfying results. To unify the method for differentiating between native and mirror models, independent of their structural class, the two best ETs for each class were considered. Finally, the k-means clustering algorithm used three common ETs: probability of amino acid assuming certain values of dihedral angles Φ and Ψ, Ramachandran preferences and Coulomb interactions. The accuracies of clustering with these ETs were in the range between 0.68 and 0.76, with sensitivity and selectivity in the range between 0.68 and 0.87, depending on the structural class. The method can be applied to all fully-automated tools for protein structure reconstruction based on contact maps, especially those analyzing big sets of models.
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Affiliation(s)
- Monika Kurczynska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Malgorzata Kotulska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wroclaw, Poland
- * E-mail:
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119
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Kalra P, Dhiman A, Cho WC, Bruno JG, Sharma TK. Simple Methods and Rational Design for Enhancing Aptamer Sensitivity and Specificity. Front Mol Biosci 2018; 5:41. [PMID: 29868605 PMCID: PMC5966647 DOI: 10.3389/fmolb.2018.00041] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/13/2018] [Indexed: 12/27/2022] Open
Abstract
Aptamers are structured nucleic acid molecules that can bind to their targets with high affinity and specificity. However, conventional SELEX (Systematic Evolution of Ligands by EXponential enrichment) methods may not necessarily produce aptamers of desired affinity and specificity. Thus, to address these questions, this perspective is intended to suggest some approaches and tips along with novel selection methods to enhance evolution of aptamers. This perspective covers latest novel innovations as well as a broad range of well-established approaches to improve the individual binding parameters (aptamer affinity, avidity, specificity and/or selectivity) of aptamers during and/or post-SELEX. The advantages and limitations of individual aptamer selection methods and post-SELEX optimizations, along with rational approaches to overcome these limitations are elucidated in each case. Further the impact of chosen selection milieus, linker-systems, aptamer cocktails and detection modules utilized in conjunction with target-specific aptamers, on the overall assay performance are discussed in detail, each with its own advantages and limitations. The simple variations suggested are easily available for facile implementation during and/or post-SELEX to develop ultrasensitive and specific assays. Finally, success studies of established aptamer-based assays are discussed, highlighting how they utilized some of the suggested methodologies to develop commercially successful point-of-care diagnostic assays.
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Affiliation(s)
- Priya Kalra
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Abhijeet Dhiman
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India.,Faculty of Pharmacy, Uttarakhand Technical University, Dehradun, India
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - John G Bruno
- Operational Technologies Corporation, San Antonio, TX, United States
| | - Tarun K Sharma
- Center for Biodesign and Diagnostics, Translational Health Science and Technology Institute, Faridabad, India.,AptaBharat Innovation Private Limited, Translational Health Science and Technology Institute Incubator, Faridabad, India
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120
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Yan B, Shi W, Ye L, Liu L. Acyl donors for native chemical ligation. Curr Opin Chem Biol 2018; 46:33-40. [PMID: 29654943 DOI: 10.1016/j.cbpa.2018.03.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 03/21/2018] [Accepted: 03/29/2018] [Indexed: 11/28/2022]
Abstract
Native chemical ligation (NCL) has become one of the most important methods in chemical syntheses of proteins. Recently, in order to expand its scope, considerable effort has been devoted to tuning the C-terminal acyl donor thioesters used in NCL. This article reviews the recent advances in the design of C-terminal acyl donors, their precursors and surrogates, and highlights some noteworthy progress that may lead the future direction of protein chemical synthesis.
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Affiliation(s)
- Bingjia Yan
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Structural Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Weiwei Shi
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Structural Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Linzhi Ye
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Structural Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Beijing Advanced Innovation Center for Structural Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China.
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121
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From Designing the Molecules of Life to Designing Life: Future Applications Derived from Advances in DNA Technologies. Angew Chem Int Ed Engl 2018; 57:4313-4328. [DOI: 10.1002/anie.201707976] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 11/14/2017] [Indexed: 12/20/2022]
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122
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Kohman RE, Kunjapur AM, Hysolli E, Wang Y, Church GM. Vom Design der Moleküle des Lebens zum Design von Leben: Zukünftige Anwendungen von DNA-Technologien. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201707976] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Richie E. Kohman
- Wyss Institute for Biologically Inspired Engineering; Harvard University; Boston MA 02115 USA
| | | | - Eriona Hysolli
- Department of Genetics; Harvard Medical School; Boston MA 02115 USA
| | - Yu Wang
- Department of Genetics; Harvard Medical School; Boston MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering; Harvard University; Boston MA 02115 USA
| | - George M. Church
- Department of Genetics; Harvard Medical School; Boston MA 02115 USA
- Wyss Institute for Biologically Inspired Engineering; Harvard University; Boston MA 02115 USA
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123
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Wang Y, Han L, Yuan N, Wang H, Li H, Liu J, Chen H, Zhang Q, Dong S. Traceless β-mercaptan-assisted activation of valinyl benzimidazolinones in peptide ligations. Chem Sci 2018; 9:1940-1946. [PMID: 29675240 PMCID: PMC5892131 DOI: 10.1039/c7sc04148a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/04/2018] [Indexed: 12/27/2022] Open
Abstract
Peptidyl thioesters or their surrogates with C-terminal β-branched hydrophobic amino acid residues usually exhibit poor reactivities in ligation reactions. Thus, activation using exogenous additives is required to ensure an acceptable reaction efficiency. Herein, we report a traceless ligation at Val-Xaa sites under mild thiol additive-free reaction conditions, whereby the introduction of β-mercaptan on the C-terminal valine residue effectively activates the otherwise unreactive N-acyl-benzimidazolinone (Nbz), and enables the use of a one-pot ligation-desulfurization strategy to generate the desired peptide products. The orthogonality between β-thiovaline-Nbz and a conventional alkyl thioester, as well as the convenient access to the former from readily available penicillamine, also allowed expedited assembly of the peptidic hormone β-LPH and hPTH analogues, based on a kinetically controlled one-pot three-segment ligation and desulfurization strategy.
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Affiliation(s)
- Yinglu Wang
- State Key Laboratory of Natural and Biomimetic Drugs , Department of Chemical Biology , School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China .
| | - Lin Han
- State Key Laboratory of Natural and Biomimetic Drugs , Department of Chemical Biology , School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China .
| | - Ning Yuan
- State Key Laboratory of Natural and Biomimetic Drugs , Department of Chemical Biology , School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China .
| | - Hanxuan Wang
- State Key Laboratory of Natural and Biomimetic Drugs , Department of Chemical Biology , School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China .
| | - Hongxing Li
- State Key Laboratory of Natural and Biomimetic Drugs , Department of Chemical Biology , School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China .
| | - Jinrong Liu
- State Key Laboratory of Natural and Biomimetic Drugs , Department of Chemical Biology , School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China .
| | - Huan Chen
- Department of Chemistry , University at Albany , Albany , New York 12222 , USA .
| | - Qiang Zhang
- Department of Chemistry , University at Albany , Albany , New York 12222 , USA .
| | - Suwei Dong
- State Key Laboratory of Natural and Biomimetic Drugs , Department of Chemical Biology , School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China .
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124
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Qi YK, Ai HS, Li YM, Yan B. Total Chemical Synthesis of Modified Histones. Front Chem 2018; 6:19. [PMID: 29473034 PMCID: PMC5810247 DOI: 10.3389/fchem.2018.00019] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/23/2018] [Indexed: 01/04/2023] Open
Abstract
In the post-genome era, epigenetics has received increasing attentions in recent years. The post-translational modifications (PTMs) of four core histones play central roles in epigenetic regulation of eukaryotic genome by either directly altering the biophysical properties of nucleosomes or by recruiting other effector proteins. In order to study the biological functions and structural mechanisms of these histone PTMs, an obligatory step is to prepare a sufficient amount of homogeneously modified histones. This task cannot be fully accomplished either by recombinant technology or enzymatic modification. In this context, synthetic chemists have developed novel protein synthetic tools and state-of-the-art chemical ligation strategies for the preparation of homologous modified histones. In this review, we summarize the recent advances in the preparation of modified histones, focusing on the total chemical synthesis strategies. The importance and potential of synthetic chemistry for the study of histone code will be also discussed.
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Affiliation(s)
- Yun-Kun Qi
- Department of Anesthesiology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Department of Medicinal Chemistry, School of Pharmacy, Qingdao University, Qingdao, China
| | - Hua-Song Ai
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Yi-Ming Li
- Department of Pharmacy, School of Biological and Medical Engineering, Hefei University of Technology, Hefei, China
| | - Baihui Yan
- Department of Anesthesiology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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125
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Racemic X-ray structure of L-type calcium channel antagonist Calciseptine prepared by total chemical synthesis. Sci China Chem 2018. [DOI: 10.1007/s11426-017-9198-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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126
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Si YY, Liang LJ, Tang S, Qi YK, Huang Y, Zheng JS. One-pot ligation strategy for atypical ubiquitin chains synthesis by using the trifluoroacetamidomethyl-protected isopeptide-linked Ub (Tfacm-isoUb) unit. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2017.12.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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127
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Jiang YY, Liu TT, Sun X, Xu ZY, Fan X, Zhu L, Bi S. Computational study of the mechanism of amide bond formation via CS2-releasing 1,3-acyl transfer. Org Biomol Chem 2018; 16:5808-5815. [DOI: 10.1039/c8ob01338a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A systematic computational study on CS2-releasing 1,3-acyl transfer was performed for the first time and provided deeper mechanistic insights.
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Affiliation(s)
- Yuan-Ye Jiang
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- People's Republic of China
| | - Tian-Tian Liu
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- People's Republic of China
| | - Xue Sun
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- People's Republic of China
| | - Zhong-Yan Xu
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- People's Republic of China
| | - Xia Fan
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- People's Republic of China
| | - Ling Zhu
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- People's Republic of China
| | - Siwei Bi
- School of Chemistry and Chemical Engineering
- Qufu Normal University
- Qufu 273165
- People's Republic of China
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128
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Bajaj K, Agarwal DS, Sakhuja R, Pillai GG. Aziridine based electrophilic handle for aspartic acid ligation. Org Biomol Chem 2018; 16:4311-4319. [DOI: 10.1039/c8ob00676h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A one-pot ligation strategy at aspartic acid junction has been described by incorporating aziridin-2,3-dicarboxylate to the N-side of a peptide fragment that ligates with a variety of small peptide thio acids to afford native peptides in good yields.
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Affiliation(s)
- Kiran Bajaj
- Department of Chemistry
- Birla Institute of Technology and Science
- Pilani 333031
- India
| | - Devesh S. Agarwal
- Department of Chemistry
- Birla Institute of Technology and Science
- Pilani 333031
- India
| | - Rajeev Sakhuja
- Department of Chemistry
- Birla Institute of Technology and Science
- Pilani 333031
- India
| | - Girinath G. Pillai
- Computational Chemistry Division
- Zastra Innovations Pvt. Ltd
- Bengaluru 560043
- India
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129
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Xu L, Huang JF, Chen CC, Qu Q, Shi J, Pan M, Li YM. Chemical Synthesis of Natural Polyubiquitin Chains through Auxiliary-Mediated Ligation of an Expressed Ubiquitin Isomer. Org Lett 2017; 20:329-332. [DOI: 10.1021/acs.orglett.7b03515] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Ling Xu
- School
of Biological and Medical Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
- Department
of Chemistry, School of Life Science, University of Science and Technology of China, Hefei 230026, China
| | - Jian-Feng Huang
- Department
of Chemistry, School of Life Science, University of Science and Technology of China, Hefei 230026, China
| | - Chen-Chen Chen
- Department
of Chemistry, School of Life Science, University of Science and Technology of China, Hefei 230026, China
| | - Qian Qu
- School
of Biological and Medical Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Jing Shi
- Department
of Chemistry, School of Life Science, University of Science and Technology of China, Hefei 230026, China
| | - Man Pan
- Department
of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Yi-Ming Li
- School
of Biological and Medical Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
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130
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Jin K, Li T, Chow HY, Liu H, Li X. P-B Desulfurization: An Enabling Method for Protein Chemical Synthesis and Site-Specific Deuteration. Angew Chem Int Ed Engl 2017; 56:14607-14611. [PMID: 28971554 DOI: 10.1002/anie.201709097] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 09/28/2017] [Indexed: 12/13/2022]
Abstract
Cysteine-mediated native chemical ligation is a powerful method for protein chemical synthesis. Herein, we report an unprecedentedly mild system (TCEP/NaBH4 or TCEP/LiBEt3 H; TCEP=tris(2-carboxyethyl)phosphine) for chemoselective peptide desulfurization to achieve effective protein synthesis via the native chemical ligation-desulfurization approach. This method, termed P-B desulfurization, features usage of common reagents, simplicity of operation, robustness, high yields, clean conversion, and versatile functionality compatibility with complex peptides/proteins. In addition, this method can be used for incorporating deuterium into the peptides after cysteine desulfurization by running the reaction in D2 O buffer. Moreover, this method enables the clean desulfurization of peptides carrying post-translational modifications, such as phosphorylation and crotonylation. The effectiveness of this method has been demonstrated by the synthesis of the cyclic peptides dichotomin C and E and synthetic proteins, including ubiquitin, γ-synuclein, and histone H2A.
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Affiliation(s)
- Kang Jin
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
| | - Tianlu Li
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
| | - Hoi Yee Chow
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
| | - Han Liu
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
| | - Xuechen Li
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
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131
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Jin K, Li T, Chow HY, Liu H, Li X. P−B Desulfurization: An Enabling Method for Protein Chemical Synthesis and Site-Specific Deuteration. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709097] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Kang Jin
- Department of Chemistry, State Key Lab of Synthetic Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong SAR P. R. China
| | - Tianlu Li
- Department of Chemistry, State Key Lab of Synthetic Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong SAR P. R. China
| | - Hoi Yee Chow
- Department of Chemistry, State Key Lab of Synthetic Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong SAR P. R. China
| | - Han Liu
- Department of Chemistry, State Key Lab of Synthetic Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong SAR P. R. China
| | - Xuechen Li
- Department of Chemistry, State Key Lab of Synthetic Chemistry; The University of Hong Kong; Pokfulam Road Hong Kong SAR P. R. China
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132
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Jiang W, Zhang B, Fan C, Wang M, Wang J, Deng Q, Liu X, Chen J, Zheng J, Liu L, Zhu TF. Mirror-image polymerase chain reaction. Cell Discov 2017; 3:17037. [PMID: 29051832 PMCID: PMC5643884 DOI: 10.1038/celldisc.2017.37] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 09/03/2017] [Accepted: 09/03/2017] [Indexed: 01/30/2023] Open
Abstract
The construction of mirror-image biological systems may open the next frontier for biomedical technology development and discovery. Here we have designed and chemically synthesized a mutant version of the thermostable Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) consisting of d-amino acids. With a total peptide length of 358 amino acid residues, it is the largest chemically synthesized d-amino acid protein reported to date. We show that the d-polymerase is able to amplify a 120-bp l-DNA sequence coding for the Escherichia coli 5S ribosomal RNA gene rrfB by mirror-image polymerase chain reaction, and that both the natural and mirror-image systems operate with strict chiral specificity. The development of efficient miPCR systems may lead to many practical applications, such as mirror-image systematic evolution of ligands by exponential enrichment for the selection of therapeutically promising nuclease-resistant l-nucleic acid aptamers.
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Affiliation(s)
- Wenjun Jiang
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Baochang Zhang
- Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Chuyao Fan
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Min Wang
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Jiaxing Wang
- Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Qiang Deng
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Xianyu Liu
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Ji Chen
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
| | - Jishen Zheng
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Lei Liu
- Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Ting F Zhu
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China
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133
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134
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Yan B, Ye L, Xu W, Liu L. Recent advances in racemic protein crystallography. Bioorg Med Chem 2017; 25:4953-4965. [DOI: 10.1016/j.bmc.2017.05.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/03/2017] [Accepted: 05/09/2017] [Indexed: 10/19/2022]
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135
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Pech A, Achenbach J, Jahnz M, Schülzchen S, Jarosch F, Bordusa F, Klussmann S. A thermostable d-polymerase for mirror-image PCR. Nucleic Acids Res 2017; 45:3997-4005. [PMID: 28158820 PMCID: PMC5605242 DOI: 10.1093/nar/gkx079] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 01/27/2017] [Indexed: 01/13/2023] Open
Abstract
Biological evolution resulted in a homochiral world in which nucleic acids consist exclusively of d-nucleotides and proteins made by ribosomal translation of l-amino acids. From the perspective of synthetic biology, however, particularly anabolic enzymes that could build the mirror-image counterparts of biological macromolecules such as l-DNA or l-RNA are lacking. Based on a convergent synthesis strategy, we have chemically produced and characterized a thermostable mirror-image polymerase that efficiently replicates and amplifies mirror-image (l)-DNA. This artificial enzyme, dubbed d-Dpo4-3C, is a mutant of Sulfolobus solfataricus DNA polymerase IV consisting of 352 d-amino acids. d-Dpo4-3C was reliably deployed in classical polymerase chain reactions (PCR) and it was used to assemble a first mirror-image gene coding for the protein Sso7d. We believe that this d-polymerase provides a valuable tool to further investigate the mysteries of biological (homo)chirality and to pave the way for potential novel life forms running on a mirror-image genome.
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Affiliation(s)
- Andreas Pech
- NOXXON Pharma AG, Weinbergweg 23, 06120 Halle (Saale), Germany
| | - John Achenbach
- NOXXON Pharma AG, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Michael Jahnz
- NOXXON Pharma AG, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | | | - Florian Jarosch
- NOXXON Pharma AG, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Frank Bordusa
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
| | - Sven Klussmann
- NOXXON Pharma AG, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
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136
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Tan XL, Pan M, Zheng Y, Gao S, Liang LJ, Li YM. Sortase-mediated chemical protein synthesis reveals the bidentate binding of bisphosphorylated p62 with K63 diubiquitin. Chem Sci 2017; 8:6881-6887. [PMID: 29147513 PMCID: PMC5636944 DOI: 10.1039/c7sc02937c] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 08/03/2017] [Indexed: 12/21/2022] Open
Abstract
Phosphorylation of S403 or S407 of the autophagic receptor protein p62 has recently been discovered to enhance the binding of p62 with ubiquitinated protein substrates to upregulate selective autophagy. To elucidate the molecular mechanism of how phosphorylation regulates the recruitment of ubiquitinated proteins, we report the first chemical synthesis of homogeneously phosphorylated p62, which enables the setting up of accurate in vitro systems for biochemical studies. Our synthesis employs the technology of sortase A-mediated protein hydrazide ligation, which successfully affords three types of phosphorylated p62 at the multi-milligram scale. Quantitative biochemical measurements show that the binding affinity of S403/S407-bisphosphorylated p62 to K63 diubiquitin is significantly higher than that of mono-phosphorylated p62. This finding suggests that phosphorylated S403 and S407 sites should bind to different epitopes on the ubiquitin chain. Furthermore, glutamate mutation is found to give a significantly impaired binding affinity, implying the necessity of using chemically synthesized phosphorylated p62 for the biochemical study of selective autophagy.
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Affiliation(s)
- Xiang-Long Tan
- Tsinghua-Peking Center for Life Sciences , Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology , Department of Chemistry , Tsinghua University , Beijing 100084 , China.,School of Biological and Medical Engineering , Hefei University of Technology , Hefei , Anhui 230009 , China .
| | - Man Pan
- Tsinghua-Peking Center for Life Sciences , Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology , Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | - Yong Zheng
- School of Biological and Medical Engineering , Hefei University of Technology , Hefei , Anhui 230009 , China . .,High Magnetic Field Laboratory , Chinese Academy of Sciences , Hefei 230031 , China
| | - Shuai Gao
- Tsinghua-Peking Center for Life Sciences , Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology , Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | - Lu-Jun Liang
- Tsinghua-Peking Center for Life Sciences , Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology , Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | - Yi-Ming Li
- School of Biological and Medical Engineering , Hefei University of Technology , Hefei , Anhui 230009 , China .
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137
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Xiao Y, Liu Q, Tang X, Yang Z, Wu L, He Y. Mirror-Image Thymidine Discriminates against Incorporation of Deoxyribonucleotide Triphosphate into DNA and Repairs Itself by DNA Polymerases. Bioconjug Chem 2017; 28:2125-2134. [PMID: 28686433 DOI: 10.1021/acs.bioconjchem.7b00301] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
DNA polymerases are known to recognize preferably d-nucleotides over l-nucleotides during DNA synthesis. Here, we report that several general DNA polymerases catalyze polymerization reactions of nucleotides directed by the DNA template containing an l-thymidine (l-T). The results display that the 5'-3' primer extension of natural nucleotides get to the end at chiral modification site with Taq and Phanta Max DNA polymerases, but the primer extension proceeds to the end of the template catalyzed by Deep Vent (exo-), Vent (exo-), and Therminator DNA polymerases. Furthermore, templating l-nucleoside displays a lag in the deoxyribonucleotide triphosphate (dNTP) incorporation rates relative to natural template by kinetics analysis, and polymerase chain reactions were inhibited with the DNA template containing two or three consecutive l-Ts. Most interestingly, no single base mutation or mismatch mixture corresponding to the location of l-T in the template was found, which is physiologically significant because they provide a theoretical basis on the involvement of DNA polymerase in the effective repair of l-T that may lead to cytotoxicity.
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Affiliation(s)
- Yating Xiao
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences , Beijing 100049, China
| | - Qingju Liu
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences , Beijing 100049, China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
| | - Li Wu
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences , Beijing 100049, China.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
| | - Yujian He
- School of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences , Beijing 100049, China.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
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138
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Yang J, Zhao J. Recent developments in peptide ligation independent of amino acid side-chain functional group. Sci China Chem 2017. [DOI: 10.1007/s11426-017-9056-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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139
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Houlihan G, Arangundy-Franklin S, Holliger P. Engineering and application of polymerases for synthetic genetics. Curr Opin Biotechnol 2017; 48:168-179. [PMID: 28601700 DOI: 10.1016/j.copbio.2017.04.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 04/18/2017] [Accepted: 04/19/2017] [Indexed: 11/26/2022]
Abstract
Organic chemistry has systematically probed the chemical determinants of function in nucleic acids by variation to the nucleobase, sugar ring and backbone moieties to build synthetic genetic polymers. Concomitantly, protein engineering has advanced to allow the discovery of polymerases capable of utilizing modified nucleotide analogs. A conjunction of these two lines of investigation in nucleotide chemistry and molecular biology has given rise to a new field of synthetic genetics dedicated to the exploration of the capacity of these novel, synthetic nucleic acids for the storage and propagation of genetic information, for evolution and for crosstalk, that is, information exchange with the natural genetic system. Here we summarize recent progress in synthetic genetics, specifically in the design of novel unnatural basepairs to expand the genetic alphabet as well as progress in engineering polymerases capable of templated synthesis, reverse transcription and evolution of synthetic genetic polymers.
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Affiliation(s)
- Gillian Houlihan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | | | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
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140
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Jacobsen MT, Erickson PW, Kay MS. Aligator: A computational tool for optimizing total chemical synthesis of large proteins. Bioorg Med Chem 2017; 25:4946-4952. [PMID: 28651912 DOI: 10.1016/j.bmc.2017.05.061] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/24/2017] [Accepted: 05/30/2017] [Indexed: 12/14/2022]
Abstract
The scope of chemical protein synthesis (CPS) continues to expand, driven primarily by advances in chemical ligation tools (e.g., reversible solubilizing groups and novel ligation chemistries). However, the design of an optimal synthesis route can be an arduous and fickle task due to the large number of theoretically possible, and in many cases problematic, synthetic strategies. In this perspective, we highlight recent CPS tool advances and then introduce a new and easy-to-use program, Aligator (Automated Ligator), for analyzing and designing the most efficient strategies for constructing large targets using CPS. As a model set, we selected the E. coli ribosomal proteins and associated factors for computational analysis. Aligator systematically scores and ranks all feasible synthetic strategies for a particular CPS target. The Aligator script methodically evaluates potential peptide segments for a target using a scoring function that includes solubility, ligation site quality, segment lengths, and number of ligations to provide a ranked list of potential synthetic strategies. We demonstrate the utility of Aligator by analyzing three recent CPS projects from our lab: TNFα (157 aa), GroES (97 aa), and DapA (312 aa). As the limits of CPS are extended, we expect that computational tools will play an increasingly important role in the efficient execution of ambitious CPS projects such as production of a mirror-image ribosome.
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Affiliation(s)
- Michael T Jacobsen
- Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East, Room 4100, Salt Lake City, UT 84112-5650, United States
| | - Patrick W Erickson
- Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East, Room 4100, Salt Lake City, UT 84112-5650, United States
| | - Michael S Kay
- Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East, Room 4100, Salt Lake City, UT 84112-5650, United States.
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141
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Wang Z, Liu YF, Yan H, Tong H, Mei Z. Theoretical Investigations of the Chiral Transition of α-Amino Acid Confined in Various Sized Armchair Boron-Nitride Nanotubes. J Phys Chem A 2017; 121:1833-1840. [PMID: 28139928 DOI: 10.1021/acs.jpca.7b00079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We computationally study the chiral transition process of the α-Ala molecule under confined different sizes of armchair SWBNNTs to explore the confinement effect. We find that the influence of a confinement environment (in armchair SWBNNTs) on the α-Ala molecule would lead to different reaction pathways. Meanwhile, the preferred reaction pathway is also different in various sizes of armchair SWBNNTs, and their energy barriers for the rate-limiting step decrease rapidly with the decreasing of the diameters of the nanotubes. It is obvious that significant decrease of the chiral transition energy barrier occurs compared with the isolated α-Ala molecule chirality conversion mechanism, by ∼15.6 kcal mol-1, highlighting the improvement in the activity the enantiomers of α-Ala molecule. We concluded that the confinement environment has a significant impact at the nanoscale on the enantiomer transformation process of the chiral molecule.
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Affiliation(s)
- Zuocheng Wang
- The Department of Physics, Baicheng Normal University , Baicheng 137000, P.R. China.,The Institute of Theoretical and Computational Research, Baicheng Normal University , Baicheng 137000, P.R. China
| | - Yan Fang Liu
- The Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao, Shandong 266101, P.R. China.,The Qingdao Key Lab of Solar Energy Utilization and Energy Storage Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao, 266101, Shandong, P.R. China
| | - Honyan Yan
- The Institute of Theoretical and Computational Research, Baicheng Normal University , Baicheng 137000, P.R. China.,Department of Computer Science, Baicheng Normal University , Baicheng 137000, P.R. China
| | - Hua Tong
- The Department of Physics, Baicheng Normal University , Baicheng 137000, P.R. China.,The Institute of Theoretical and Computational Research, Baicheng Normal University , Baicheng 137000, P.R. China
| | - Zemin Mei
- The Institute of Theoretical and Computational Research, Baicheng Normal University , Baicheng 137000, P.R. China.,Department of Chemistry, Baicheng Normal University , Baicheng 137000, P.R. China
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142
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Total chemical synthesis of a thermostable enzyme capable of polymerase chain reaction. Cell Discov 2017; 3:17008. [PMID: 28265464 PMCID: PMC5335361 DOI: 10.1038/celldisc.2017.8] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/06/2017] [Indexed: 01/30/2023] Open
Abstract
Polymerase chain reaction (PCR) has been a defining tool in modern biology. Towards realizing mirror-image PCR, we have designed and chemically synthesized a mutant version of the 352-residue thermostable Sulfolobus solfataricus P2 DNA polymerase IV with l-amino acids and tested its PCR activity biochemically. To the best of our knowledge, this enzyme is the largest chemically synthesized protein reported to date. We show that with optimization of PCR conditions, the fully synthetic polymerase is capable of amplifying template sequences of up to 1.5 kb. The establishment of this synthetic route for chemically synthesizing DNA polymerase IV is a stepping stone towards building a d-enzyme system for mirror-image PCR, which may open up an avenue for the creation of many mirror-image molecular tools such as mirror-image systematic evolution of ligands by exponential enrichment.
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143
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Modern tools for the chemical ligation and synthesis of modified peptides and proteins. Future Med Chem 2016; 8:2287-2304. [DOI: 10.4155/fmc-2016-0175] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The ability to improve nature's capacity by introducing modification of biological interest in proteins and peptides (P&P) is one of the modern challenges in synthetic chemistry. Due to the unfavorable pharmacokinetic properties, many native P&P are of little use as therapeutic agents. Today, few methods for the preparation of modified proteins are available. Initially introduced to realize the ligation between two standard peptidic sequences, and hence to afford native proteins, the modern chemical methodologies, in other words native chemical ligation, expressed ligation, Staudinger ligation, auxiliary mediated ligation, aldehyde capture, etc., can be virtually utilized to ligate a variety of peptidomimetic partners, allowing a systematic access to modified, unnatural large P&P.
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Lipi F, Chen S, Chakravarthy M, Rakesh S, Veedu RN. In vitro evolution of chemically-modified nucleic acid aptamers: Pros and cons, and comprehensive selection strategies. RNA Biol 2016; 13:1232-1245. [PMID: 27715478 PMCID: PMC5207382 DOI: 10.1080/15476286.2016.1236173] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Nucleic acid aptamers are single-stranded DNA or RNA oligonucleotide sequences that bind to a specific target molecule with high affinity and specificity through their ability to adopt 3-dimensional structure in solution. Aptamers have huge potential as targeted therapeutics, diagnostics, delivery agents and as biosensors. However, aptamers composed of natural nucleotide monomers are quickly degraded in vivo and show poor pharmacodynamic properties. To overcome this, chemically-modified nucleic acid aptamers are developed by incorporating modified nucleotides after or during the selection process by Systematic Evolution of Ligands by EXponential enrichment (SELEX). This review will discuss the development of chemically-modified aptamers and provide the pros and cons, and new insights on in vitro aptamer selection strategies by using chemically-modified nucleic acid libraries.
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Affiliation(s)
- Farhana Lipi
- a Western Australian Neuroscience Research Institute , Perth , Australia
| | - Suxiang Chen
- a Western Australian Neuroscience Research Institute , Perth , Australia.,b Centre for Comparative Genomics, Murdoch University , Perth , Australia
| | - Madhuri Chakravarthy
- a Western Australian Neuroscience Research Institute , Perth , Australia.,b Centre for Comparative Genomics, Murdoch University , Perth , Australia
| | - Shilpa Rakesh
- a Western Australian Neuroscience Research Institute , Perth , Australia
| | - Rakesh N Veedu
- a Western Australian Neuroscience Research Institute , Perth , Australia.,b Centre for Comparative Genomics, Murdoch University , Perth , Australia
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