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Kar A, Jana M, Malik V, Sarkar A, Mandal K. Total Chemical Synthesis of the SARS-CoV-2 Spike Receptor-Binding Domain. Chemistry 2024; 30:e202302969. [PMID: 37815536 DOI: 10.1002/chem.202302969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/11/2023]
Abstract
SARS-CoV-2 and its global spread have created an unprecedented public health crisis. The spike protein of SARS-CoV-2 has gained significant attention due to its crucial role in viral entry into host cells and its potential as both a prophylactic and a target for therapeutic interventions. Herein, we report the first successful total synthesis of the SARS-CoV-2 spike protein receptor binding domain (RBD), highlighting the key challenges and the strategies employed to overcome them. Appropriate utilization of advanced solid phase peptide synthesis and cutting-edge native chemical ligation methods have facilitated the synthesis of this moderately large protein molecule. We discuss the problems encountered during the chemical synthesis and approaches taken to optimize the yield and the purity of the synthetic protein molecule. Furthermore, we demonstrate that the chemically synthesized homogeneous spike RBD efficiently binds to the known mini-protein binder LCB1. The successful chemical synthesis of the spike RBD presented here can be utilized to gain valuable insights into SARS-CoV-2 spike RBD biology, advancing our understanding and aiding the development of intervention strategies to combat future coronavirus outbreaks. The modular synthetic approach described in this study can be effectively implemented in the synthesis of other mutated variants or enantiomer of the spike RBD for mirror-image drug discovery.
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Affiliation(s)
- Abhisek Kar
- Tata Institute of Fundamental Research Hyderabad, 36/p Gopanpally, Hyderabad, Telangana, 500046, India
| | - Mrinmoy Jana
- Tata Institute of Fundamental Research Hyderabad, 36/p Gopanpally, Hyderabad, Telangana, 500046, India
| | - Vishal Malik
- Tata Institute of Fundamental Research Hyderabad, 36/p Gopanpally, Hyderabad, Telangana, 500046, India
| | - Arighna Sarkar
- Tata Institute of Fundamental Research Hyderabad, 36/p Gopanpally, Hyderabad, Telangana, 500046, India
| | - Kalyaneswar Mandal
- Tata Institute of Fundamental Research Hyderabad, 36/p Gopanpally, Hyderabad, Telangana, 500046, India
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2
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Wei T, Liu J, Li C, Tan Y, Wei R, Wang J, Wu H, Li Q, Liu H, Tang Y, Li X. Revealing the extracellular function of HMGB1 N-terminal region acetylation assisted by a protein semi-synthesis approach. Chem Sci 2023; 14:10297-10307. [PMID: 37772093 PMCID: PMC10530822 DOI: 10.1039/d3sc01109g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 09/05/2023] [Indexed: 09/30/2023] Open
Abstract
HMGB1 (high-mobility group box 1) is a non-histone chromatin-associated protein that has been widely reported as a representative damage-associated molecular pattern (DAMP) and to play a pivotal role in the proinflammatory process once it is in an extracellular location. Accumulating evidence has shown that HMGB1 undergoes extensive post-translational modifications (PTMs) that actively regulate its conformation, localization, and intermolecular interactions. However, fully characterizing the functional implications of these PTMs has been challenging due to the difficulty in accessing homogeneous HMGB1 with site-specific PTMs of interest. In this study, we developed a streamlined protein semi-synthesis strategy via salicylaldehyde ester-mediated chemical ligations (Ser/Thr ligation and Cys/Pen ligation, STL/CPL). This methodology enabled us to generate a series of N-terminal region acetylated HMGB1 proteins. Further studies revealed that acetylation regulates HMGB1-heparin interaction and modulates HMGB1's stability against thrombin, representing a regulatory switch to control HMGB1's extracellular activity.
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Affiliation(s)
- Tongyao Wei
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR P. R. China
| | - Jiamei Liu
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR P. R. China
| | - Can Li
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR P. R. China
| | - Yi Tan
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR P. R. China
| | - Ruohan Wei
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR P. R. China
| | - Jinzheng Wang
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR P. R. China
| | - Hongxiang Wu
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR P. R. China
| | - Qingrong Li
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR P. R. China
| | - Heng Liu
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR P. R. China
| | - Yubo Tang
- 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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3
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Zitterbart R, Berger N, Reimann O, Noble GT, Lüdtke S, Sarma D, Seitz O. Traceless parallel peptide purification by a first-in-class reductively cleavable linker system featuring a safety-release. Chem Sci 2021; 12:2389-2396. [PMID: 34164003 PMCID: PMC8179278 DOI: 10.1039/d0sc06285e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/07/2021] [Indexed: 12/26/2022] Open
Abstract
Hundreds of peptides can be synthesized by automated parallel synthesizers in a single run. In contrast, the most widely used peptide purification method - high-pressure liquid chromatography (HPLC) - only allows one-by-one processing of each sample. The chromatographic purification of many peptides, therefore, remains a time-consuming and costly effort. Catch-and-release methods can be processed in parallel and potentially provide a remedy. However, no such system has yet provided a true alternative to HPLC. Herein we present the development of a side-reaction free, reductively cleavable linker. The linker is added to the target peptide as the last building block during peptide synthesis. After acidic cleavage from synthetic resin, the linker-tagged full-length peptide is caught onto an aldehyde-modified solid support by rapid oxime ligation, allowing removal of all impurities lacking the linker by washing. Reducing the aryl azide to an aniline sensitizes the linker for cleavage. However, scission does not occur at non-acidic pH enabling wash out of reducing agent. Final acidic treatment safely liberates the peptide by an acid-catalysed 1,6-elimination. We showcase this first-in-class reductively cleavable linker system in the parallel purification of a personalized neoantigen cocktail, containing 20 peptides for cancer immunotherapy within six hours.
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Affiliation(s)
| | - Nadja Berger
- Belyntic GmbH Richard-Willstätter-Str. 11 12489 Berlin Germany
| | - Oliver Reimann
- Belyntic GmbH Richard-Willstätter-Str. 11 12489 Berlin Germany
| | - Gavin T Noble
- Bachem (UK) Ltd. Delph Court, Sullivans Way, St. Helens Merseyside WA9 5GL UK
| | - Stephan Lüdtke
- Belyntic GmbH Richard-Willstätter-Str. 11 12489 Berlin Germany
| | - Dominik Sarma
- Belyntic GmbH Richard-Willstätter-Str. 11 12489 Berlin Germany
| | - Oliver Seitz
- Humboldt-Universität zu Berlin Brook-Taylor-Str. 2 12489 Berlin Germany
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4
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Liu X, Liu J, Wu Z, Chen L, Wang S, Wang P. Photo-cleavable purification/protection handle assisted synthesis of giant modified proteins with tandem repeats. Chem Sci 2019; 10:8694-8700. [PMID: 31803444 PMCID: PMC6849634 DOI: 10.1039/c9sc03693h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 08/04/2019] [Indexed: 12/15/2022] Open
Abstract
Proteins with tandem repeats have essential physical or biological roles in cells and have been widely investigated as biomaterials or vaccines. Chemically derived proteins with tandem repeats would be beneficial for research, owing to their accurate structures, possibly with precise modifications, produced by chemical synthesis. Traditional protein synthesis often leads to severe handling loss due to multiple ligations and HPLC purifications. To improve the protein synthesis efficiency, we developed a purification/protection handle consisting of a His6 tag and a photo-labile linker. This handle has great potential to facilitate purification with immobilized metal affinity chromatography techniques and also provides orthogonal protection for N-terminal Cys. The synthesis of the model proteins Muc1 and antifreeze glycoprotein mimics shows that the handle decreases the requirement for HPLC and enables both convergent and sequential assembly of peptide segments.
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Affiliation(s)
- Xueyi Liu
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs , School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , P. R. China .
| | - Jiazhi Liu
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs , School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , P. R. China .
| | - Zhichao Wu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources , Ministry of Education , College of Fisheries and Life Science , Shanghai Ocean University , Shanghai 201306 , China
| | - Liangbiao Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources , Ministry of Education , College of Fisheries and Life Science , Shanghai Ocean University , Shanghai 201306 , China
| | - Siyao Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs , School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , P. R. China .
| | - Ping Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs , School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , P. R. China .
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5
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Agouridas V, El Mahdi O, Diemer V, Cargoët M, Monbaliu JCM, Melnyk O. Native Chemical Ligation and Extended Methods: Mechanisms, Catalysis, Scope, and Limitations. Chem Rev 2019; 119:7328-7443. [DOI: 10.1021/acs.chemrev.8b00712] [Citation(s) in RCA: 243] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Vangelis Agouridas
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Ouafâa El Mahdi
- Faculté Polydisciplinaire de Taza, University Sidi Mohamed Ben Abdellah, BP 1223 Taza Gare, Morocco
| | - Vincent Diemer
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Marine Cargoët
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
| | - Jean-Christophe M. Monbaliu
- Center for Integrated Technology and Organic Synthesis, Department of Chemistry, University of Liège, Building B6a, Room 3/16a, Sart-Tilman, B-4000 Liège, Belgium
| | - Oleg Melnyk
- UMR CNRS 8204, Centre d’Immunité et d’Infection de Lille, University of Lille, CNRS, Institut Pasteur de Lille, F-59000 Lille, France
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6
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Whedon SD, Parker MK, Tyson EL, Ritterhoff T, Shelton PMM, Chatterjee C. A clickable glutamine (CliQ) derivative for the traceless reversible modification of peptides and proteins. Chem Commun (Camb) 2019; 55:2043-2045. [DOI: 10.1039/c8cc09404g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Cu(i)-mediated click reaction of proteins with affinity tags enables their selective isolation from complex mixtures.
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7
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Zitterbart R, Krumrey M, Seitz O. Immobilization methods for the rapid total chemical synthesis of proteins on microtiter plates. J Pept Sci 2017; 23:539-548. [DOI: 10.1002/psc.3006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/24/2017] [Accepted: 03/24/2017] [Indexed: 12/11/2022]
Affiliation(s)
| | - Michael Krumrey
- Department of Chemistry; Humboldt University Berlin; Berlin Germany
| | - Oliver Seitz
- Department of Chemistry; Humboldt University Berlin; Berlin Germany
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8
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Haspel N, Zheng J, Aleman C, Zanuy D, Nussinov R. A Protocol for the Design of Protein and Peptide Nanostructure Self-Assemblies Exploiting Synthetic Amino Acids. Methods Mol Biol 2017; 1529:323-352. [PMID: 27914060 PMCID: PMC7900906 DOI: 10.1007/978-1-4939-6637-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
Abstract
In recent years there has been increasing interest in nanostructure design based on the self-assembly properties of proteins and polymers. Nanodesign requires the ability to predictably manipulate the properties of the self-assembly of autonomous building blocks, which can fold or aggregate into preferred conformational states. The design includes functional synthetic materials and biological macromolecules. Autonomous biological building blocks with available 3D structures provide an extremely rich and useful resource. Structural databases contain large libraries of protein molecules and their building blocks with a range of sizes, shapes, surfaces, and chemical properties. The introduction of engineered synthetic residues or short peptides into these building blocks can greatly expand the available chemical space and enhance the desired properties. Herein, we summarize a protocol for designing nanostructures consisting of self-assembling building blocks, based on our recent works. We focus on the principles of nanostructure design with naturally occurring proteins and synthetic amino acids, as well as hybrid materials made of amyloids and synthetic polymers.
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Affiliation(s)
- Nurit Haspel
- Department of Computer Science, The University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA, 02125, USA.
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Carlos Aleman
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028, Barcelona, Spain
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n, E-08028, Barcelona, Spain
| | - David Zanuy
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028, Barcelona, Spain
| | - Ruth Nussinov
- Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Inst. of Molecular Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
- Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA
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9
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Recent advances in the preparation of Fmoc-SPPS-based peptide thioester and its surrogates for NCL-type reactions. Sci China Chem 2016. [DOI: 10.1007/s11426-016-0381-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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10
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Loibl SF, Harpaz Z, Zitterbart R, Seitz O. Total chemical synthesis of proteins without HPLC purification. Chem Sci 2016; 7:6753-6759. [PMID: 28451120 PMCID: PMC5355786 DOI: 10.1039/c6sc01883a] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/02/2016] [Indexed: 12/13/2022] Open
Abstract
This work presents the first method for the rapid chemical total on-resin synthesis of proteins that proceeds without a single HPLC-purification step.
The total chemical synthesis of proteins is a tedious and time-consuming endeavour. The typical steps involve solid phase synthesis of peptide thioesters and cysteinyl peptides, native chemical ligation (NCL) in solution, desulfurization or removal of ligation auxiliaries in the case of extended NCL as well as many intermediary and final HPLC purification steps. With an aim to facilitate and improve the throughput of protein synthesis we developed the first method for the rapid chemical total on-resin synthesis of proteins that proceeds without a single HPLC-purification step. The method relies on the combination of three orthogonal protein tags that allow sequential immobilization (via the N-terminal and C-terminal ends), extended native chemical ligation and release reactions. The peptide fragments to be ligated are prepared by conventional solid phase synthesis and used as crude materials in the subsequent steps. An N-terminal His6 unit permits selective immobilization of the full length peptide thioester onto Ni-NTA agarose beads. The C-terminal peptide fragment carries a C-terminal peptide hydrazide and an N-terminal 2-mercapto-2-phenyl-ethyl ligation auxiliary, which serves as a reactivity tag for the full length peptide. As a result, only full length peptides, not truncation products, react in the subsequent on-bead extended NCL. After auxiliary removal the ligation product is liberated into solution upon treatment with mild acid, and is concomitantly captured by an aldehyde-modified resin. This step allows the removal of the most frequently observed by-product in NCL chemistry, i.e. the hydrolysed peptide thioester (which does not contain a C-terminal peptide hydrazide). Finally, the target protein is released with diluted hydrazine or acid. We applied the method in the synthesis of 46 to 126 amino acid long MUC1 proteins comprising 2–6 copies of a 20mer tandem repeat sequence. Only three days were required for the parallel synthesis of 9 MUC1 proteins which were obtained in 8–33% overall yield with 90–98% purity despite the omission of HPLC purification.
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Affiliation(s)
- S F Loibl
- Humboldt-Universität zu Berlin , Institut für Chemie , Brook-Taylor-Str. 2 , 12489 Berlin , Germany . ; ; Tel: +49 030 2093 7446
| | - Z Harpaz
- Humboldt-Universität zu Berlin , Institut für Chemie , Brook-Taylor-Str. 2 , 12489 Berlin , Germany . ; ; Tel: +49 030 2093 7446
| | - R Zitterbart
- Humboldt-Universität zu Berlin , Institut für Chemie , Brook-Taylor-Str. 2 , 12489 Berlin , Germany . ; ; Tel: +49 030 2093 7446
| | - O Seitz
- Humboldt-Universität zu Berlin , Institut für Chemie , Brook-Taylor-Str. 2 , 12489 Berlin , Germany . ; ; Tel: +49 030 2093 7446
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11
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Paradís-Bas M, Tulla-Puche J, Albericio F. The road to the synthesis of "difficult peptides". Chem Soc Rev 2015; 45:631-54. [PMID: 26612670 DOI: 10.1039/c5cs00680e] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The last decade has witnessed a renaissance of peptides as drugs. This progress, together with advances in the structural behavior of peptides, has attracted the interest of the pharmaceutical industry in these molecules as potential APIs. In the past, major peptide-based drugs were inspired by sequences extracted from natural structures of low molecular weight. In contrast, nowadays, the peptides being studied by academic and industrial groups comprise more sophisticated sequences. For instance, they consist of long amino acid chains and show a high tendency to form aggregates. Some researchers have claimed that preparing medium-sized proteins is now feasible with chemical ligation techniques, in contrast to medium-sized peptide syntheses. The complexity associated with the synthesis of certain peptides is exemplified by the so-called "difficult peptides", a concept introduced in the 80's. This refers to sequences that show inter- or intra-molecular β-sheet interactions significant enough to form aggregates during peptide synthesis. These structural associations are stabilized and mediated by non-covalent hydrogen bonds that arise on the backbone of the peptide and-depending on the sequence-are favored. The tendency of peptide chains to aggregate is translated into a list of common behavioral features attributed to "difficult peptides" which hinder their synthesis. In this regard, this manuscript summarizes the strategies used to overcome the inherent difficulties associated with the synthesis of known "difficult peptides". Here we evaluate several external factors, as well as methods to incorporate chemical modifications into sequences, in order to describe the strategies that are effective for the synthesis of "difficult peptides". These approaches have been classified and ordered to provide an extensive guide for achieving the synthesis of peptides with the aforementioned features.
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Affiliation(s)
- Marta Paradís-Bas
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Spain.
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12
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Seenaiah M, Jbara M, Mali SM, Brik A. Convergent Versus Sequential Protein Synthesis: The Case of Ubiquitinated and Glycosylated H2B. Angew Chem Int Ed Engl 2015; 54:12374-8. [DOI: 10.1002/anie.201503309] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/13/2015] [Indexed: 11/11/2022]
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13
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Seenaiah M, Jbara M, Mali SM, Brik A. Convergent Versus Sequential Protein Synthesis: The Case of Ubiquitinated and Glycosylated H2B. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503309] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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14
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Jbara M, Seenaiah M, Brik A. Solid phase chemical ligation employing a rink amide linker for the synthesis of histone H2B protein. Chem Commun (Camb) 2015; 50:12534-7. [PMID: 25196573 DOI: 10.1039/c4cc06499b] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Presented here is a solid phase chemical ligation strategy employing native chemical ligation and the commercially available Rink-amide linker as a key element in our approach. The method was applied for the synthesis of histone H2B, which sets the ground for the rapid preparation of posttranslationally modified analogues of this protein.
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Affiliation(s)
- Muhammad Jbara
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel.
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15
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Wang JX, Fang GM, He Y, Qu DL, Yu M, Hong ZY, Liu L. Peptideo-Aminoanilides as Crypto-Thioesters for Protein Chemical Synthesis. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408078] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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16
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Wang JX, Fang GM, He Y, Qu DL, Yu M, Hong ZY, Liu L. Peptideo-Aminoanilides as Crypto-Thioesters for Protein Chemical Synthesis. Angew Chem Int Ed Engl 2014; 54:2194-8. [DOI: 10.1002/anie.201408078] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 11/18/2014] [Indexed: 12/29/2022]
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17
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Reimann O, Smet‐Nocca C, Hackenberger CPR. Spurlose Aufreinigung und Desulfurierung von Ligationsprodukten des Tau‐Proteins. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408674] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Oliver Reimann
- Leibniz‐Institut für Molekulare Pharmakologie (FMP), Robert‐Rössle‐Straße 10, 13125 Berlin (Deutschland)
- Humboldt Universität zu Berlin, Department Chemie, Brook‐Taylor‐Straße 2, 12489 Berlin (Deutschland)
- Freie Universität Berlin, Institut für Chemie und Biochemie, Takustraße 3, 14195 Berlin (Deutschland)
| | - Caroline Smet‐Nocca
- UMR CNRS 8576, Lille 1 Science and Technology University, 59655 Villeneuve d'Ascq Cedex (Frankreich)
| | - Christian P. R. Hackenberger
- Leibniz‐Institut für Molekulare Pharmakologie (FMP), Robert‐Rössle‐Straße 10, 13125 Berlin (Deutschland)
- Humboldt Universität zu Berlin, Department Chemie, Brook‐Taylor‐Straße 2, 12489 Berlin (Deutschland)
- Freie Universität Berlin, Institut für Chemie und Biochemie, Takustraße 3, 14195 Berlin (Deutschland)
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18
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Reimann O, Smet‐Nocca C, Hackenberger CPR. Traceless Purification and Desulfurization of Tau Protein Ligation Products. Angew Chem Int Ed Engl 2014; 54:306-10. [DOI: 10.1002/anie.201408674] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Indexed: 01/09/2023]
Affiliation(s)
- Oliver Reimann
- Leibniz‐Institut für Molekulare Pharmakologie (FMP), Robert‐Rössle‐Strasse 10, 13125 Berlin (Germany)
- Humboldt Universität zu Berlin, Department Chemie, Brook‐Taylor‐Strasse 2, 12489 Berlin (Germany)
- Freie Universität Berlin, Institut für Chemie und Biochemie, Takustrasse 3, 14195 Berlin (Germany)
| | - Caroline Smet‐Nocca
- UMR CNRS 8576—Lille 1 Science and Technology University, 59655 Villeneuve d'Ascq Cedex (France)
| | - Christian P. R. Hackenberger
- Leibniz‐Institut für Molekulare Pharmakologie (FMP), Robert‐Rössle‐Strasse 10, 13125 Berlin (Germany)
- Humboldt Universität zu Berlin, Department Chemie, Brook‐Taylor‐Strasse 2, 12489 Berlin (Germany)
- Freie Universität Berlin, Institut für Chemie und Biochemie, Takustrasse 3, 14195 Berlin (Germany)
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19
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Thapa P, Zhang RY, Menon V, Bingham JP. Native chemical ligation: a boon to peptide chemistry. Molecules 2014; 19:14461-83. [PMID: 25221869 PMCID: PMC6271921 DOI: 10.3390/molecules190914461] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/02/2014] [Accepted: 09/02/2014] [Indexed: 11/16/2022] Open
Abstract
The use of chemical ligation within the realm of peptide chemistry has opened various opportunities to expand the applications of peptides/proteins in biological sciences. Expansion and refinement of ligation chemistry has made it possible for the entry of peptides into the world of viable oral therapeutic drugs through peptide backbone cyclization. This progression has been a journey of chemical exploration and transition, leading to the dominance of native chemical ligation in the present advances of peptide/protein applications. Here we illustrate and explore the historical and current nature of peptide ligation, providing a clear indication to the possibilities and use of these novel methods to take peptides outside their typically defined boundaries.
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Affiliation(s)
- Parashar Thapa
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Rui-Yang Zhang
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Vinay Menon
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Jon-Paul Bingham
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
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20
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Repeat protein engineering: creating functional nanostructures/biomaterials from modular building blocks. Biochem Soc Trans 2014; 41:1152-8. [PMID: 24059501 DOI: 10.1042/bst20130102] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
There is enormous interest in molecular self-assembly and the development of biological systems to form smart nanostructures for biotechnology (so-called 'bottom-up fabrications'). Repeat proteins are ideal choices for development of such systems as they: (i) possess a relatively simple relationship between sequence, structure and function; (ii) are modular and non-globular in structure; (iii) act as diverse scaffolds for the mediation of a diverse range of protein-protein interactions; and (iv) have been extensively studied and successfully engineered and designed. In the present review, we summarize recent advances in the use of engineered repeat proteins in the self-assembly of novel materials, nanostructures and biosensors. In particular, we show that repeat proteins are excellent monomeric programmable building blocks that can be triggered to associate into a range of morphologies and can readily be engineered as stimuli-responsive biofunctional materials.
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21
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Zhang M, Pokharel D, Fang S. Purification of Synthetic Peptides Using a Catching Full-Length Sequence by Polymerization Approach. Org Lett 2014; 16:1290-3. [DOI: 10.1021/ol403426u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mingcui Zhang
- Department
of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931 United States
| | - Durga Pokharel
- Department
of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931 United States
| | - Shiyue Fang
- Department
of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931 United States
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22
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Dittmann M, Seidel R, Chizhov I, Engelhard M. Total chemical synthesis of a membrane protein domain analogue containing two transmembrane helices: functional reconstitution of the semisynthetic sensory rhodopsin/transducer complex. J Pept Sci 2014; 20:137-44. [DOI: 10.1002/psc.2605] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 11/25/2013] [Accepted: 11/25/2013] [Indexed: 12/15/2022]
Affiliation(s)
- Marc Dittmann
- Max Planck Institute of Molecular Physiology; Otto Hahn Str. 11 44227 Dortmund Germany
| | - Ralf Seidel
- Max Planck Institute of Molecular Physiology; Otto Hahn Str. 11 44227 Dortmund Germany
| | - Igor Chizhov
- Medizinische Hochschule Hannover; Carl-Neuberg-Str. 1 30625 Hannover Germany
| | - Martin Engelhard
- Max Planck Institute of Molecular Physiology; Otto Hahn Str. 11 44227 Dortmund Germany
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23
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Liu F, Mayer JP. Protein Chemical Synthesis in Drug Discovery. PROTEIN LIGATION AND TOTAL SYNTHESIS I 2014; 362:183-228. [DOI: 10.1007/128_2014_598] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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24
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Abstract
The chemical synthesis of peptides or small proteins is often an important step in many research projects and has stimulated the development of numerous chemical methodologies. The aim of this review is to give a substantial overview of the solid phase methods developed for the production or purification of polypeptides. The solid phase peptide synthesis (SPPS) technique has facilitated considerably the access to short peptides (<50 amino acids). However, its limitations for producing large homogeneous peptides have stimulated the development of solid phase covalent or non-covalent capture purification methods. The power of the native chemical ligation (NCL) reaction for protein synthesis in aqueous solution has also been adapted to the solid phase by the combination of novel linker technologies, cysteine protection strategies and thioester or N,S-acyl shift thioester surrogate chemistries. This review details pioneering studies and the most recent publications related to the solid phase chemical synthesis of large peptides and proteins.
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25
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Gordon WR, Bang D, Hoff WD, Kent SB. Total chemical synthesis of fully functional Photoactive Yellow Protein. Bioorg Med Chem 2013; 21:3436-42. [DOI: 10.1016/j.bmc.2013.03.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 03/15/2013] [Accepted: 03/19/2013] [Indexed: 10/27/2022]
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26
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Moyal T, Hemantha HP, Siman P, Refua M, Brik A. Highly efficient one-pot ligation and desulfurization. Chem Sci 2013. [DOI: 10.1039/c3sc50239b] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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27
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Hemantha HP, Narendra N, Sureshbabu VV. Total chemical synthesis of polypeptides and proteins: chemistry of ligation techniques and beyond. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.08.059] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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28
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Aucagne V, Valverde IE, Marceau P, Galibert M, Dendane N, Delmas AF. Towards the Simplification of Protein Synthesis: Iterative Solid-Supported Ligations with Concomitant Purifications. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206428] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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29
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Aucagne V, Valverde IE, Marceau P, Galibert M, Dendane N, Delmas AF. Towards the Simplification of Protein Synthesis: Iterative Solid-Supported Ligations with Concomitant Purifications. Angew Chem Int Ed Engl 2012; 51:11320-4. [DOI: 10.1002/anie.201206428] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Indexed: 12/25/2022]
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30
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Yang R, Hou W, Zhang X, Liu CF. N-to-C Sequential Ligation Using Peptidyl N,N-Bis(2-mercaptoethyl)amide Building Blocks. Org Lett 2011; 14:374-7. [DOI: 10.1021/ol2031284] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Renliang Yang
- Structural Biology and Biochemistry Division, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Wen Hou
- Structural Biology and Biochemistry Division, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Xiaohong Zhang
- Structural Biology and Biochemistry Division, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Chuan-Fa Liu
- Structural Biology and Biochemistry Division, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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31
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Sato K, Shigenaga A, Tsuji K, Tsuda S, Sumikawa Y, Sakamoto K, Otaka A. N-sulfanylethylanilide peptide as a crypto-thioester peptide. Chembiochem 2011; 12:1840-4. [PMID: 21739560 DOI: 10.1002/cbic.201100241] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2011] [Indexed: 11/06/2022]
Affiliation(s)
- Kohei Sato
- Institute of Health Biosciences and Graduate School of Pharmaceutical Sciences, The University of Tokushima, Shomachi, Tokushima 770-8505, Japan
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32
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Fang GM, Li YM, Shen F, Huang YC, Li JB, Lin Y, Cui HK, Liu L. Protein Chemical Synthesis by Ligation of Peptide Hydrazides. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100996] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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33
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Fang GM, Li YM, Shen F, Huang YC, Li JB, Lin Y, Cui HK, Liu L. Protein chemical synthesis by ligation of peptide hydrazides. Angew Chem Int Ed Engl 2011; 50:7645-9. [PMID: 21648030 DOI: 10.1002/anie.201100996] [Citation(s) in RCA: 574] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Indexed: 11/12/2022]
Affiliation(s)
- Ge-Min Fang
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
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34
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Wang C, Guo Q, Fu Y. Theoretical Analysis of the Detailed Mechanism of Native Chemical Ligation Reactions. Chem Asian J 2011; 6:1241-51. [DOI: 10.1002/asia.201000760] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Indexed: 12/22/2022]
Affiliation(s)
- Chen Wang
- Department of Chemistry, University of Science and Technology of China, Hefei 230026 (China), Fax: (+86) 551‐3606689
| | - Qing‐Xiang Guo
- Department of Chemistry, University of Science and Technology of China, Hefei 230026 (China), Fax: (+86) 551‐3606689
| | - Yao Fu
- Department of Chemistry, University of Science and Technology of China, Hefei 230026 (China), Fax: (+86) 551‐3606689
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35
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Lee JY, Bang D. Challenges in the chemical synthesis of average sized proteins: sequential vs. convergent ligation of multiple peptide fragments. Biopolymers 2010; 94:441-7. [PMID: 20593477 DOI: 10.1002/bip.21379] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This review examines the challenges in the chemical synthesis of average sized proteins. Recent progress on sequential and convergent ligation methods, two approaches to the synthesis of proteins, is outlined. An examination of these challenges could aid in the process of finding new methodologies for the efficient chemical synthesis of average sized protein molecules.
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Affiliation(s)
- Ji Yeon Lee
- Department of Chemistry, Yonsei University, Shinchon 134, Seoul 120-749, Korea
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36
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Zheng JS, Cui HK, Fang GM, Xi WX, Liu L. Chemical protein synthesis by kinetically controlled ligation of peptide O-esters. Chembiochem 2010; 11:511-5. [PMID: 20157912 DOI: 10.1002/cbic.200900789] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ji-Shen Zheng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing 100084, China
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37
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Sequential native chemical ligation utilizing peptide thioacids derived from newly developed Fmoc-based synthetic method. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.03.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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38
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Barlos KK, Gatos D, Vasileiou Z, Barlos K. An optimized chemical synthesis of human relaxin-2. J Pept Sci 2010; 16:200-11. [DOI: 10.1002/psc.1221] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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39
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Lahiri S, Seidel R, Engelhard M, Becker CFW. Photocontrol of STAT6 dimerization and translocation. MOLECULAR BIOSYSTEMS 2010; 6:2423-9. [DOI: 10.1039/c0mb00019a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Affiliation(s)
- B. Karaszewski
- Division of Clinical Neurosciences, University of Edinburgh, Edinburgh, UK
- Department of Neurology of Adults, Medical University of Gdansk, Gdansk, Poland
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41
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Abstract
Redox-active enzymes perform many key biological reactions. The electron transfer process is complex, not only because of its versatility, but also because of the intricate and delicate modulation exerted by the protein scaffold on the redox properties of the catalytic sites. Nowadays, there is a wealth of information available about the catalytic mechanisms of redox-active enzymes and the time is propitious for the development of projects based on the protein engineering of redox-active enzymes. In this review, we aim to provide an updated account of the available methods used for protein engineering, including both genetic and chemical tools, which are usually reviewed separately. Specific applications to redox-active enzymes are mentioned within each technology, with emphasis on those cases where the generation of novel functionality was pursued. Finally, we focus on two emerging fields in the protein engineering of redox-active enzymes: the construction of novel nucleic acid-based catalysts and the remodeling of intra-molecular electron transfer networks. We consider that the future development of these areas will represent fine examples of the concurrence of chemical and genetic tools.
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Affiliation(s)
- Gloria Saab-Rincón
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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42
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Bang D, Pentelute BL, Kent SBH. Kinetically controlled ligation for the convergent chemical synthesis of proteins. Angew Chem Int Ed Engl 2007; 45:3985-8. [PMID: 16639756 DOI: 10.1002/anie.200600702] [Citation(s) in RCA: 249] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Duhee Bang
- Department of Chemistry, Institute for Biophysical Dynamics, Center for Integrative Science, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
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43
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Haspel N, Zanuy D, Alemán C, Wolfson H, Nussinov R. De Novo Tubular Nanostructure Design Based on Self-Assembly of β-Helical Protein Motifs. Structure 2006; 14:1137-48. [PMID: 16843895 DOI: 10.1016/j.str.2006.05.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2006] [Revised: 04/06/2006] [Accepted: 05/01/2006] [Indexed: 12/01/2022]
Abstract
We present an approach for designing self-assembled nanostructures from naturally occurring building block segments obtained from native protein structures. We focus on structural motifs from left-handed beta-helical proteins. We selected 17 motifs. Copies of each of the motifs are stacked one atop the other. The obtained structures were simulated for long periods by using Molecular Dynamics to test their ability to retain their organization over time. We observed that a structural model based on the self-assembly of a motif from E. coli galactoside acetyltransferase produced a very stable tube. We studied the interactions that help maintain the conformational stability of the systems, focusing on the role of specific amino acids at specific positions. Analysis of these systems and a mutational study of selected candidates revealed that the presence of proline and glycine residues in the loops of beta-helical structures greatly enhances the structural stability of the systems.
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Affiliation(s)
- Nurit Haspel
- School of Computer Science, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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44
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Bang D, Pentelute BL, Kent SBH. Kinetically Controlled Ligation for the Convergent Chemical Synthesis of Proteins. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600702] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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45
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46
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Ueda S, Fujita M, Tamamura H, Fujii N, Otaka A. Photolabile Protection for One-Pot Sequential Native Chemical Ligation. Chembiochem 2005; 6:1983-6. [PMID: 16206319 DOI: 10.1002/cbic.200500272] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Satoshi Ueda
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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47
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Affiliation(s)
| | - Doug Auld
- National Institutes of Health, Bethesda, MD
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