1
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Zhang J, Wang X, Huang Q, Ye J, Wang J. Genetically Encoded Epoxide Warhead for Precise and Versatile Covalent Targeting of Proteins. J Am Chem Soc 2024; 146:16173-16183. [PMID: 38819260 DOI: 10.1021/jacs.4c03974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Genetically encoding a proximal reactive warhead into the protein binder/drug has emerged as an efficient strategy for covalently binding to protein targets, enabling broad applications. To expand the reactivity scope for targeting the diverse natural residues under physiological conditions, the development of a genetically encoded reactive warhead with excellent stability and broad reactivity is highly desired. Herein, we reported the genetic encoding of epoxide-containing tyrosine (EPOY) for developing covalent protein drugs. Our study demonstrates that EPOY, when incorporated into a nanobody (KN035), can cross-link with different side chains (mutations) at the same position of PD-L1 protein. Significantly, a single genetically encoded reactive warhead that is capable of covalent and site-specific targeting to 10 different nucleophilic residues was achieved for the first time. This would largely expand the scope of covalent warhead and inspire the development of covalent warheads for both small-molecule drugs and protein drugs. Furthermore, we incorporate the EPOY into a designed ankyrin repeat protein (DarpinK13) to create the covalent binders of KRAS. This covalent KRAS binder holds the potential to achieve pan-covalent targeting of KRAS based on the structural similarity among all oncogenic KRAS mutants while avoiding off-target binding to NRAS/HRAS through a covalent interaction with KRAS-specific residues (H95 and E107). We envision that covalently targeting to H95 will be a promising strategy for the development of covalent pan-KRAS inhibitors in the future.
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Affiliation(s)
- Jinpeng Zhang
- Department of Chemistry, Research Center for Chemical Biology and Omics Analysis, College of Science, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xia Wang
- Department of Chemistry, Research Center for Chemical Biology and Omics Analysis, College of Science, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Qingjun Huang
- Department of Chemistry, Research Center for Chemical Biology and Omics Analysis, College of Science, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jinsong Ye
- Department of Chemistry, Research Center for Chemical Biology and Omics Analysis, College of Science, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jie Wang
- Department of Chemistry, Research Center for Chemical Biology and Omics Analysis, College of Science, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
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2
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Yi HB, Lee S, Seo K, Kim H, Kim M, Lee HS. Cellular and Biophysical Applications of Genetic Code Expansion. Chem Rev 2024; 124:7465-7530. [PMID: 38753805 DOI: 10.1021/acs.chemrev.4c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein-protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.
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Affiliation(s)
- Han Bin Yi
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Seungeun Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Kyungdeok Seo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyeongjo Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Minah Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
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3
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Weyh M, Jokisch ML, Nguyen TA, Fottner M, Lang K. Deciphering functional roles of protein succinylation and glutarylation using genetic code expansion. Nat Chem 2024; 16:913-921. [PMID: 38531969 PMCID: PMC11164685 DOI: 10.1038/s41557-024-01500-5] [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: 09/19/2023] [Accepted: 03/01/2024] [Indexed: 03/28/2024]
Abstract
Post-translational modifications (PTMs) dynamically regulate cellular processes. Lysine undergoes a range of acylations, including malonylation, succinylation (SucK) and glutarylation (GluK). These PTMs increase the size of the lysine side chain and reverse its charge from +1 to -1 under physiological conditions, probably impacting protein structure and function. To understand the functional roles of these PTMs, homogeneously modified proteins are required for biochemical studies. While the site-specific encoding of PTMs and their mimics via genetic code expansion has facilitated the characterization of the functional roles of many PTMs, negatively charged lysine acylations have defied this approach. Here we describe site-specific incorporation of SucK and GluK into proteins via temporarily masking their negative charge through thioester derivatives. We prepare succinylated and glutarylated bacterial and mammalian target proteins, including non-refoldable multidomain proteins. This allows us to study how succinylation and glutarylation impact enzymatic activity of metabolic enzymes and regulate protein-DNA and protein-protein interactions in biological processes from replication to ubiquitin signalling.
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Affiliation(s)
- Maria Weyh
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Marie-Lena Jokisch
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Tuan-Anh Nguyen
- Department of Chemistry, Laboratory for Synthetic Biochemistry, Technical University of Munich Institute for Advanced Study, Garching, Germany
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Maximilian Fottner
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
| | - Kathrin Lang
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
- Department of Chemistry, Laboratory for Synthetic Biochemistry, Technical University of Munich Institute for Advanced Study, Garching, Germany.
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4
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Guo QR, Cao YJ. Applications of genetic code expansion technology in eukaryotes. Protein Cell 2024; 15:331-363. [PMID: 37847216 PMCID: PMC11074999 DOI: 10.1093/procel/pwad051] [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: 07/04/2023] [Accepted: 09/26/2023] [Indexed: 10/18/2023] Open
Abstract
Unnatural amino acids (UAAs) have gained significant attention in protein engineering and drug development owing to their ability to introduce new chemical functionalities to proteins. In eukaryotes, genetic code expansion (GCE) enables the incorporation of UAAs and facilitates posttranscriptional modification (PTM), which is not feasible in prokaryotic systems. GCE is also a powerful tool for cell or animal imaging, the monitoring of protein interactions in target cells, drug development, and switch regulation. Therefore, there is keen interest in utilizing GCE in eukaryotic systems. This review provides an overview of the application of GCE in eukaryotic systems and discusses current challenges that need to be addressed.
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Affiliation(s)
- Qiao-ru Guo
- State Key Laboratory of Chemical Oncogenomic, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yu J Cao
- State Key Laboratory of Chemical Oncogenomic, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
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5
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Liu J, Yang B, Wang L. Residue selective crosslinking of proteins through photoactivatable or proximity-enabled reactivity. Curr Opin Chem Biol 2023; 74:102285. [PMID: 36913752 PMCID: PMC10225350 DOI: 10.1016/j.cbpa.2023.102285] [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: 12/27/2022] [Revised: 02/08/2023] [Accepted: 02/12/2023] [Indexed: 03/13/2023]
Abstract
Photo- and chemical crosslinking of proteins have offered various avenues for studying protein structure and protein interactions with biomolecules. Conventional photoactivatable groups generally lack reaction selectivity toward amino acid residues. New photoactivatable groups reacting with selected residues have emerged recently, increasing crosslinking efficiency and facilitating crosslink identification. Traditional chemical crosslinking usually employs highly reactive functional groups, while recent advance has developed latent reactive groups with reactivity triggered by proximity, which reduce spurious crosslinks and improve biocompatibility. The employment of these residue selective chemical functional groups, activated by light or proximity, in small molecule crosslinkers and in genetically encoded unnatural amino acids is summarized. Together with new software development in identifying protein crosslinks, residue selective crosslinking has enhanced the research of elusive protein-protein interactions in vitro, in cell lysate, and in live cells. Residue selective crosslinking is expected to expand to other methods for the investigation of various protein-biomolecule interactions.
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Affiliation(s)
- Jun Liu
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Bing Yang
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Lei Wang
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94158, USA.
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6
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Update of the Pyrrolysyl-tRNA Synthetase/tRNA Pyl Pair and Derivatives for Genetic Code Expansion. J Bacteriol 2023; 205:e0038522. [PMID: 36695595 PMCID: PMC9945579 DOI: 10.1128/jb.00385-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The cotranslational incorporation of pyrrolysine (Pyl), the 22nd proteinogenic amino acid, into proteins in response to the UAG stop codon represents an outstanding example of natural genetic code expansion. Genetic encoding of Pyl is conducted by the pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA, tRNAPyl. Owing to the high tolerance of PylRS toward diverse amino acid substrates and great orthogonality in various model organisms, the PylRS/tRNAPyl-derived pairs are ideal for genetic code expansion to insert noncanonical amino acids (ncAAs) into proteins of interest. Since the discovery of cellular components involved in the biosynthesis and genetic encoding of Pyl, synthetic biologists have been enthusiastic about engineering PylRS/tRNAPyl-derived pairs to rewrite the genetic code of living cells. Recently, considerable progress has been made in understanding the molecular phylogeny, biochemical properties, and structural features of the PylRS/tRNAPyl pair, guiding its further engineering and optimization. In this review, we cover the basic and updated knowledge of the PylRS/tRNAPyl pair's unique characteristics that make it an outstanding tool for reprogramming the genetic code. In addition, we summarize the recent efforts to create efficient and (mutually) orthogonal PylRS/tRNAPyl-derived pairs for incorporation of diverse ncAAs by genome mining, rational design, and advanced directed evolution methods.
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7
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Guo AD, Chen XH. Genetically Encoded Noncanonical Amino Acids in Proteins to Investigate Lysine Benzoylation. Methods Mol Biol 2023; 2676:131-146. [PMID: 37277629 DOI: 10.1007/978-1-0716-3251-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Posttranslational modifications (PTMs) of lysine residues are major regulators of gene expression, protein-protein interactions, and protein localization and degradation. Histone lysine benzoylation is a recently identified epigenetic marker associated with active transcription, which has physiological relevance distinct from histone acetylation and can be regulated by debenzoylation of sirtuin 2 (SIRT2). Herein, we provide a protocol for the incorporation of benzoyllysine and fluorinated benzoyllysine into full-length histone proteins, which further serve as benzoylated histone probes with NMR or fluorescence signal for investigating the dynamics of SIRT2-mediated debenzoylation.
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Affiliation(s)
- An-Di Guo
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xiao-Hua Chen
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
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8
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Li P, Li J, Ren H. Capture and mass spectrometry analysis of effector-substrate complexes using genetically incorporated photo-crosslinkers in host cells. STAR Protoc 2022; 3:101882. [PMID: 36595886 PMCID: PMC9700014 DOI: 10.1016/j.xpro.2022.101882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/10/2022] [Accepted: 11/03/2022] [Indexed: 11/24/2022] Open
Abstract
Interactions between effectors and their host targets are often weak or transient, making them difficult to identify. We describe a protocol for covalent capture of effector substrates in living cells using genetic code expansion technology. The effector-substrate complexes are captured by the crosslinker and subsequently purified with tandem chromatography. We detail steps for mass spectrum analysis and substrate verification. While the steps here are specific for substrates of enteropathogenic E. coli in HEK293T cells, the protocol has broader applications. For complete details on the use and execution of this protocol, please refer to Li et al. (2021).1.
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Affiliation(s)
- Pan Li
- Division of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu 610041, China,Corresponding author
| | - Jingxiang Li
- Division of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu 610041, China,Corresponding author
| | - Haiyan Ren
- Division of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu 610041, China,Collaborative Innovation Center of Biotherapy, Chengdu 610041, China,Corresponding author
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9
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Gueta O, Amiram M. Expanding the chemical repertoire of protein-based polymers for drug-delivery applications. Adv Drug Deliv Rev 2022; 190:114460. [PMID: 36030987 DOI: 10.1016/j.addr.2022.114460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/12/2022] [Indexed: 01/24/2023]
Abstract
Expanding the chemical repertoire of natural and artificial protein-based polymers (PBPs) can enable the production of sequence-defined, yet chemically diverse, biopolymers with customized or new properties that cannot be accessed in PBPs composed of only natural amino acids. Various approaches can enable the expansion of the chemical repertoire of PBPs, including chemical and enzymatic treatments or the incorporation of unnatural amino acids. These techniques are employed to install a wide variety of chemical groups-such as bio-orthogonally reactive, cross-linkable, post-translation modifications, and environmentally responsive groups-which, in turn, can facilitate the design of customized PBP-based drug-delivery systems with modified, fine-tuned, or entirely new properties and functions. Here, we detail the existing and emerging technologies for expanding the chemical repertoire of PBPs and review several chemical groups that either demonstrate or are anticipated to show potential in the design of PBP-based drug delivery systems. Finally, we provide our perspective on the remaining challenges and future directions in this field.
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Affiliation(s)
- Osher Gueta
- The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel
| | - Miriam Amiram
- The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel.
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10
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Homodimerized cytoplasmic domain of PD-L1 regulates its complex glycosylation in living cells. Commun Biol 2022; 5:887. [PMID: 36042378 PMCID: PMC9427764 DOI: 10.1038/s42003-022-03845-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022] Open
Abstract
Whether membrane-anchored PD-L1 homodimerizes in living cells is controversial. The biological significance of the homodimer waits to be expeditiously explored. However, characterization of the membrane-anchored full-length PD-L1 homodimer is challenging, and unconventional approaches are needed. By using genetically incorporated crosslinkers, we showed that full length PD-L1 forms homodimers and tetramers in living cells. Importantly, the homodimerized intracellular domains of PD-L1 play critical roles in its complex glycosylation. Further analysis identified three key arginine residues in the intracellular domain of PD-L1 as the regulating unit. In the PD-L1/PD-L1-3RE homodimer, mutations result in a decrease in the membrane abundance and an increase in the Golgi of wild-type PD-L1. Notably, PD-1 binding to abnormally glycosylated PD-L1 on cancer cells was attenuated, and subsequent T-cell induced toxicity increased. Collectively, our study demonstrated that PD-L1 indeed forms homodimers in cells, and the homodimers play important roles in PD-L1 complex glycosylation and T-cell mediated toxicity. Membrane-anchored PD-L1 homodimerizes in cells. N-glycosylation of PD-L1 regulates its homodimerization. The formation of PD-L1 homodimers further regulates their glycan processing, localization to the plasma membrane, and binding to PD-1.
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11
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Ji Y, Sun L, Chen Y, Qin H, Xuan W. Sirtuin‐Derived Covalent Binder for the Selective Recognition of Protein Crotonylation. Angew Chem Int Ed Engl 2022; 61:e202205522. [DOI: 10.1002/anie.202205522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Yanli Ji
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Lin Sun
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
| | - Yao Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences (CAS) Dalian 116023 China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry Dalian Institute of Chemical Physics Chinese Academy of Sciences (CAS) Dalian 116023 China
| | - Weimin Xuan
- State Key Laboratory and Institute of Elemento-Organic Chemistry College of Chemistry Nankai University Tianjin 300071 China
- School of Life Sciences Tianjin University Tianjin 300072 China
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12
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Sirtuin‐Derived Covalent Binder for the Selective Recognition of Protein Crotonylation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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13
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Van Fossen EM, Grutzius S, Ruby CE, Mourich DV, Cebra C, Bracha S, Karplus PA, Cooley RB, Mehl RA. Creating a Selective Nanobody Against 3-Nitrotyrosine Containing Proteins. Front Chem 2022; 10:835229. [PMID: 35265586 PMCID: PMC8899190 DOI: 10.3389/fchem.2022.835229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/25/2022] [Indexed: 12/15/2022] Open
Abstract
A critical step in developing therapeutics for oxidative stress-related pathologies is the ability to determine which specific modified protein species are innocuous by-products of pathology and which are causative agents. To achieve this goal, technologies are needed that can identify, characterize and quantify oxidative post translational modifications (oxPTMs). Nanobodies (Nbs) represent exquisite tools for intracellular tracking of molecules due to their small size, stability and engineerability. Here, we demonstrate that it is possible to develop a selective Nb against an oxPTM protein, with the key advance being the use of genetic code expansion (GCE) to provide an efficient source of the large quantities of high-quality, homogenous and site-specific oxPTM-containing protein needed for the Nb selection process. In this proof-of-concept study, we produce a Nb selective for a 3-nitrotyrosine (nitroTyr) modified form of the 14-3-3 signaling protein with a lesser recognition of nitroTyr in other protein contexts. This advance opens the door to the GCE-facilitated development of other anti-PTM Nbs.
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Affiliation(s)
- Elise M. Van Fossen
- Oregon State University, Department of Biochemistry and Biophysics, Agricultural and Life Sciences, Corvallis, OR, United States
| | - Sonia Grutzius
- Oregon State University, Department of Biochemistry and Biophysics, Agricultural and Life Sciences, Corvallis, OR, United States
| | - Carl E. Ruby
- Oregon State University, Department of Clinical Sciences, College of Veterinary Medicine, Corvallis, OR, United States
| | - Dan V. Mourich
- Oregon State University, Department of Clinical Sciences, College of Veterinary Medicine, Corvallis, OR, United States
| | - Chris Cebra
- Oregon State University, Department of Clinical Sciences, College of Veterinary Medicine, Corvallis, OR, United States
| | - Shay Bracha
- Department of Small Animal Clinical Sciences (VSCS), Texas A&M College of Veterinary Medicine and Biomedical Sciences, College Station, TX, United States
| | - P. Andrew Karplus
- Oregon State University, Department of Biochemistry and Biophysics, Agricultural and Life Sciences, Corvallis, OR, United States
| | - Richard B. Cooley
- Oregon State University, Department of Biochemistry and Biophysics, Agricultural and Life Sciences, Corvallis, OR, United States
| | - Ryan A. Mehl
- Oregon State University, Department of Biochemistry and Biophysics, Agricultural and Life Sciences, Corvallis, OR, United States
- *Correspondence: Ryan A. Mehl,
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14
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Shu X, Asghar S, Yang F, Li ST, Wu H, Yang B. Uncover New Reactivity of Genetically Encoded Alkyl Bromide Non-Canonical Amino Acids. Front Chem 2022; 10:815991. [PMID: 35252115 PMCID: PMC8894327 DOI: 10.3389/fchem.2022.815991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/27/2022] [Indexed: 11/15/2022] Open
Abstract
Genetically encoded non-canonical amino acids (ncAAs) with electrophilic moieties are excellent tools to investigate protein-protein interactions (PPIs) both in vitro and in vivo. These ncAAs, including a series of alkyl bromide-based ncAAs, mainly target cysteine residues to form protein-protein cross-links. Although some reactivities towards lysine and tyrosine residues have been reported, a comprehensive understanding of their reactivity towards a broad range of nucleophilic amino acids is lacking. Here we used a recently developed OpenUaa search engine to perform an in-depth analysis of mass spec data generated for Thioredoxin and its direct binding proteins cross-linked with an alkyl bromide-based ncAA, BprY. The analysis showed that, besides cysteine residues, BprY also targeted a broad range of nucleophilic amino acids. We validated this broad reactivity of BprY with Affibody/Z protein complex. We then successfully applied BprY to map a binding interface between SUMO2 and SUMO-interacting motifs (SIMs). BprY was further applied to probe SUMO2 interaction partners. We identified 264 SUMO2 binders, including several validated SUMO2 binders and many new binders. Our data demonstrated that BprY can be effectively used to probe protein-protein interaction interfaces even without cysteine residues, which will greatly expand the power of BprY in studying PPIs.
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Affiliation(s)
- Xin Shu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Sana Asghar
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Fan Yang
- Department of Biophysics, Kidney Disease Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shang-Tong Li
- Glbizzia Biosciences Co., Ltd, Beijing, China
- *Correspondence: Shang-Tong Li, ; Haifan Wu, ; Bing Yang,
| | - Haifan Wu
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, KS, United States
- *Correspondence: Shang-Tong Li, ; Haifan Wu, ; Bing Yang,
| | - Bing Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
- *Correspondence: Shang-Tong Li, ; Haifan Wu, ; Bing Yang,
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15
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Cao L, Wang L. New covalent bonding ability for proteins. Protein Sci 2022; 31:312-322. [PMID: 34761448 PMCID: PMC8819847 DOI: 10.1002/pro.4228] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 10/28/2021] [Accepted: 10/28/2021] [Indexed: 02/03/2023]
Abstract
To expand protein's covalent bonding ability, latent bioreactive unnatural amino acids have been designed and genetically encoded into proteins, which react with specific natural amino acid residues through proximity-enabled bioreactivity. The resultant new covalent bonds can be selectively created within and between proteins in vitro, in cells, and in vivo. Offering diverse properties previously unattainable, these covalent linkages have been harnessed to enhance protein properties, to modulate protein function, to probe ligand-receptor binding, to identify elusive protein interactions, and to develop covalent protein drugs. Selective introduction of covalent bonds into proteins is affording novel avenues for biological studies, synthetic biology, and biotherapeutics.
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Affiliation(s)
- Li Cao
- Department of Pharmaceutical Chemistry and the Cardiovascular Research InstituteUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Lei Wang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research InstituteUniversity of California San FranciscoSan FranciscoCaliforniaUSA
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16
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Nguyen T, Gronauer TF, Nast‐Kolb T, Sieber SA, Lang K. Substrate Profiling of Mitochondrial Caseinolytic Protease P via a Site‐Specific Photocrosslinking Approach. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Tuan‐Anh Nguyen
- Department of Chemistry Group of Synthetic Biochemistry Technical University of Munich Lichtenbergstr. 4 85748 Garching Germany
| | - Thomas F. Gronauer
- Center for Protein Assemblies (CPA) Department of Chemistry Chair of Organic Chemistry II Technical University of Munich Lichtenbergstr. 4 85748 Garching Germany
| | - Timon Nast‐Kolb
- Center for Protein Assemblies (CPA) and Lehrstuhl für Biophysik (E27) Physics Department Technical University of Munich Lichtenbergstr. 4 85748 Garching Germany
| | - Stephan A. Sieber
- Center for Protein Assemblies (CPA) Department of Chemistry Chair of Organic Chemistry II Technical University of Munich Lichtenbergstr. 4 85748 Garching Germany
| | - Kathrin Lang
- Department of Chemistry Group of Synthetic Biochemistry Technical University of Munich Lichtenbergstr. 4 85748 Garching Germany
- Laboratory of Organic Chemistry Department of Chemistry and Applied Biosciences Chair of Chemical Biology ETH Zürich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
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17
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Genetically encoding latent bioreactive amino acids and the development of covalent protein drugs. Curr Opin Chem Biol 2021; 66:102106. [PMID: 34968810 DOI: 10.1016/j.cbpa.2021.102106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/07/2021] [Accepted: 11/25/2021] [Indexed: 12/11/2022]
Abstract
As natural proteins generally do not bind targets in a covalent mode, the therapeutic potential of covalent protein drugs remains largely unexplored. Recently, latent bioreactive amino acids have been incorporated into proteins through genetic code expansion, which selectively react with nearby natural residues via proximity-enabled reactivity, generating diverse covalent linkages for proteins in vitro and in cells. These new covalent linkages provide novel avenues for protein research and engineering. In addition, a general platform technology, proximity-enabled reactive therapeutics (PERx), has been established for the development of covalent protein drugs. The first covalent protein drug demonstrates advantageous features in cancer immunotherapy in mice. Selective introduction of covalent bonds into proteins will advance biological studies, synthetic biology, and biotherapeutics with the power of biocompatible covalent chemistries.
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18
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Sapienza PJ, Currie MM, Lancaster NM, Li K, Aubé J, Goldfarb D, Cloer EW, Major MB, Lee AL. Visualizing an Allosteric Intermediate Using CuAAC Stabilization of an NMR Mixed Labeled Dimer. ACS Chem Biol 2021; 16:2766-2775. [PMID: 34784173 DOI: 10.1021/acschembio.1c00617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Homodimers are the most abundant type of enzyme in cells, and as such, they represent the most elemental system for studying the phenomenon of allostery. In these systems, in which the allosteric features are manifest by the effect of the first binding event on a similar event at the second site, the most informative state is the asymmetric singly bound (lig1) form, yet it tends to be thermodynamically elusive. Here we obtain milligram quantities of lig1 of the allosteric homodimer, chorismate mutase, in the form of a mixed isotopically labeled dimer stabilized by Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) between the subunits. Below, we outline several critical steps required to generate high yields of both types of unnatural amino acid-containing proteins and overcome multiple pitfalls intrinsic to CuAAC to obtain high yields of a highly purified, fully intact, active mixed labeled dimer, which provides the first glimpse of the lig1 intermediate. These data not only will make possible NMR-based investigations of allostery envisioned by us but also should facilitate other structural applications in which specific linkage of proteins is helpful.
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Affiliation(s)
- Paul J. Sapienza
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Michelle M. Currie
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Noah M. Lancaster
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kelin Li
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jeffrey Aubé
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Dennis Goldfarb
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Erica W. Cloer
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Michael B. Major
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Andrew L. Lee
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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19
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Wang YH, Jian ML, Chen PJ, Tsou JC, Truong LP, Wang YS. Ferritin Conjugates With Multiple Clickable Amino Acids Encoded by C-Terminal Engineered Pyrrolysyl-tRNA Synthetase. Front Chem 2021; 9:779976. [PMID: 34900939 PMCID: PMC8655692 DOI: 10.3389/fchem.2021.779976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 10/20/2021] [Indexed: 11/30/2022] Open
Abstract
This study reports the application of expanding genetic codes in developing protein cage-based delivery systems. The evolved Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS)•tRNAPyl pairs derived from directed evolution are examined to probe their recognition for para-substituted phenylalanine analogs. The evolved MmPylRS, AzFRS, harboring a wide range of substrates, is further engineered at the C-terminal region into another variant, AzFRS-MS. AzFRS-MS shows suppression of the elevated sfGFP protein amount up to 10 TAG stop codons when charging p-azido-l-phenylalanine (AzF, 4), which allows the occurrence of click chemistry. Since protein nanocages used as drug delivery systems that encompass multiple drugs through a site-specific loading approach remain largely unexplored, as a proof of concept, the application of AzFRS-MS for the site-specific incorporation of AzF on human heavy chain ferritin (Ftn) is developed. The Ftn-4 conjugate is shown to be able to load multiple fluorescence dyes or a therapeutic agent, doxorubicin (Dox), through the strain-promoted azide-alkyne cycloaddition (SPAAC) click reaction. Aiming to selectively target Her2+ breast cancer cells, Ftn-4-DOX conjugates fused with a HER2 receptor recognition peptide, anti-Her2/neu peptide (AHNP), is developed and demonstrated to be able to deliver Dox into the cell and to prolong the drug release. This work presents another application of evolved MmPylRS systems, whose potential in developing a variety of protein conjugates is noteworthy.
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Affiliation(s)
- Yi-Hui Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Mu-Lung Jian
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Pei-Jung Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Jo-Chu Tsou
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Le P Truong
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yane-Shih Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
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20
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Iyer S, Das C. The unity of opposites: Strategic interplay between bacterial effectors to regulate cellular homeostasis. J Biol Chem 2021; 297:101340. [PMID: 34695417 PMCID: PMC8605245 DOI: 10.1016/j.jbc.2021.101340] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 10/15/2021] [Accepted: 10/20/2021] [Indexed: 11/23/2022] Open
Abstract
Legionella pneumophila is a facultative intracellular pathogen that uses the Dot/Icm Type IV secretion system (T4SS) to translocate many effectors into its host and establish a safe, replicative lifestyle. The bacteria, once phagocytosed, reside in a vacuolar structure known as the Legionella-containing vacuole (LCV) within the host cells and rapidly subvert organelle trafficking events, block inflammatory responses, hijack the host ubiquitination system, and abolish apoptotic signaling. This arsenal of translocated effectors can manipulate the host factors in a multitude of different ways. These proteins also contribute to bacterial virulence by positively or negatively regulating the activity of one another. Such effector-effector interactions, direct and indirect, provide the delicate balance required to maintain cellular homeostasis while establishing itself within the host. This review summarizes the recent progress in our knowledge of the structure-function relationship and biochemical mechanisms of select effector pairs from Legionella that work in opposition to one another, while highlighting the diversity of biochemical means adopted by this intracellular pathogen to establish a replicative niche within host cells.
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Affiliation(s)
- Shalini Iyer
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA.
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA.
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21
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Nguyen TA, Gronauer T, Nast-Kolb T, Sieber S, Lang K. Substrate profiling of mitochondrial caseinolytic protease P via a site-specific photocrosslinking approach. Angew Chem Int Ed Engl 2021; 61:e202111085. [PMID: 34847623 PMCID: PMC9306725 DOI: 10.1002/anie.202111085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Indexed: 11/17/2022]
Abstract
Approaches for profiling protease substrates are critical for defining protease functions, but remain challenging tasks. We combine genetic code expansion, photocrosslinking and proteomics to identify substrates of the mitochondrial (mt) human caseinolytic protease P (hClpP). Site‐specific incorporation of the diazirine‐bearing amino acid DiazK into the inner proteolytic chamber of hClpP, followed by UV‐irradiation of cells, allows to covalently trap substrate proteins of hClpP and to substantiate hClpP's major involvement in maintaining overall mt homeostasis. In addition to confirming many of the previously annotated hClpP substrates, our approach adds a diverse set of new proteins to the hClpP interactome. Importantly, our workflow allows identifying substrate dynamics upon application of external cues in an unbiased manner. Identification of unique hClpP‐substrate proteins upon induction of mt oxidative stress, suggests that hClpP counteracts oxidative stress by processing of proteins that are involved in respiratory chain complex synthesis and maturation as well as in catabolic pathways.
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Affiliation(s)
- Tuan-Anh Nguyen
- Technical University of Munich: Technische Universitat Munchen, Chemistry, Lichtenbergstr. 4, 85748, Garching, GERMANY
| | - Thomas Gronauer
- Technical University of Munich: Technische Universitat Munchen, Chemistry, Lichtenbergstr. 4, 85748, Garching, GERMANY
| | - Timon Nast-Kolb
- Technische Universität München: Technische Universitat Munchen, Physics, GERMANY
| | - Stephan Sieber
- Technical University of Munich: Technische Universitat Munchen, Chemistry, Lichtenbergstr. 4, 85748, Garching, GERMANY
| | - Kathrin Lang
- ETH-Zürich LOC: Eidgenossische Technische Hochschule Zurich Laboratorium fur Organische Chemie, Chemistry and Applied Biosciences, Vladimir-Prelog-Weg. 3, 8093, Zürich, SWITZERLAND
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22
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Tian H, Yang J, Guo AD, Ran Y, Yang YZ, Yang B, Huang R, Liu H, Chen XH. Genetically Encoded Benzoyllysines Serve as Versatile Probes for Interrogating Histone Benzoylation and Interactions in Living Cells. ACS Chem Biol 2021; 16:2560-2569. [PMID: 34618427 DOI: 10.1021/acschembio.1c00614] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Histone posttranslational modifications (PTMs) are vital epigenetic regulators in many fundamental cell signaling pathways and diverse biological processes. Histone lysine benzoylation is a recently identified epigenetic mark associated with active transcription; however, it remains to be explored. Herein, we first report the genetic encoding of benzoyllysine and fluorinated benzoyllysines into full-length histone proteins in a site-specific manner in live cells, based on our rationally designed synthetase and fine-integrated fluorine element into benzoyllysines. The incorporated unnatural amino acids integrating unique features were demonstrated as versatile probes for investigating histone benzoylation under biological environments, conferring multiplex signals such as 19F NMR spectra with chemical clarity and fluorescence signals for benzoylation. Moreover, the site specifically incorporated lysine benzoylation within native full-length histone proteins revealed distinct dynamics of debenzoylation in the presence of debenzoylase sirtuin 2 (SIRT2). Our developed strategy for genetic encoding of benzoyllysines offers a general and novel approach to gain insights into interactions of site-specific histone benzoylation modifications with interactomes and molecular mechanisms in physiological settings, which could not be accessible with fragment histone peptides. This versatile chemical tool enables a direct and new avenue to explore benzoylation, interactions, and histone epigenetics, which will provide broad utilities in chemical biology, protein science, and basic biology research.
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Affiliation(s)
- Hongtao Tian
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiale Yang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - An-Di Guo
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Ran
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yun-Zhi Yang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Pudong, Shanghai 201203, China
| | - Bing Yang
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Ruimin Huang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiming Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiao-Hua Chen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Pudong, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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23
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Fottner M, Weyh M, Gaussmann S, Schwarz D, Sattler M, Lang K. A modular toolbox to generate complex polymeric ubiquitin architectures using orthogonal sortase enzymes. Nat Commun 2021; 12:6515. [PMID: 34764289 PMCID: PMC8585875 DOI: 10.1038/s41467-021-26812-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 10/13/2021] [Indexed: 11/09/2022] Open
Abstract
The post-translational modification of proteins with ubiquitin (Ub) and Ub-like modifiers (Ubls) represents one of the most important regulators in eukaryotic biology. Polymeric Ub/Ubl chains of distinct topologies control the activity, stability, interaction and localization of almost all cellular proteins and elicit a variety of biological outputs. Our ability to characterize the roles of distinct Ub/Ubl topologies and to identify enzymes and receptors that create, recognize and remove these modifications is however hampered by the difficulty to prepare them. Here we introduce a modular toolbox (Ubl-tools) that allows the stepwise assembly of Ub/Ubl chains in a flexible and user-defined manner facilitated by orthogonal sortase enzymes. We demonstrate the universality and applicability of Ubl-tools by generating distinctly linked Ub/Ubl hybrid chains, and investigate their role in DNA damage repair. Importantly, Ubl-tools guarantees straightforward access to target proteins, site-specifically modified with distinct homo- and heterotypic (including branched) Ub chains, providing a powerful approach for studying the functional impact of these complex modifications on cellular processes.
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Affiliation(s)
- Maximilian Fottner
- grid.6936.a0000000123222966Department of Chemistry, Lab for Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, TUM-IAS, Lichtenberg Str. 4, 85748 Garching, Germany ,grid.5801.c0000 0001 2156 2780Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Maria Weyh
- grid.6936.a0000000123222966Department of Chemistry, Lab for Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, TUM-IAS, Lichtenberg Str. 4, 85748 Garching, Germany
| | - Stefan Gaussmann
- grid.6936.a0000000123222966Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Lichtenberg Str. 4, 85748 Garching, Germany ,grid.4567.00000 0004 0483 2525Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Dominic Schwarz
- grid.6936.a0000000123222966Department of Chemistry, Lab for Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, TUM-IAS, Lichtenberg Str. 4, 85748 Garching, Germany
| | - Michael Sattler
- grid.6936.a0000000123222966Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Lichtenberg Str. 4, 85748 Garching, Germany ,grid.4567.00000 0004 0483 2525Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Kathrin Lang
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland.
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24
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Bartoschek MD, Ugur E, Nguyen TA, Rodschinka G, Wierer M, Lang K, Bultmann S. Identification of permissive amber suppression sites for efficient non-canonical amino acid incorporation in mammalian cells. Nucleic Acids Res 2021; 49:e62. [PMID: 33684219 PMCID: PMC8216290 DOI: 10.1093/nar/gkab132] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/20/2022] Open
Abstract
The genetic code of mammalian cells can be expanded to allow the incorporation of non-canonical amino acids (ncAAs) by suppressing in-frame amber stop codons (UAG) with an orthogonal pyrrolysyl-tRNA synthetase (PylRS)/tRNAPylCUA (PylT) pair. However, the feasibility of this approach is substantially hampered by unpredictable variations in incorporation efficiencies at different stop codon positions within target proteins. Here, we apply a proteomics-based approach to quantify ncAA incorporation rates at hundreds of endogenous amber stop codons in mammalian cells. With these data, we compute iPASS (Identification of Permissive Amber Sites for Suppression; available at www.bultmannlab.eu/tools/iPASS), a linear regression model to predict relative ncAA incorporation efficiencies depending on the surrounding sequence context. To verify iPASS, we develop a dual-fluorescence reporter for high-throughput flow-cytometry analysis that reproducibly yields context-specific ncAA incorporation efficiencies. We show that nucleotides up- and downstream of UAG synergistically influence ncAA incorporation efficiency independent of cell line and ncAA identity. Additionally, we demonstrate iPASS-guided optimization of ncAA incorporation rates by synonymous exchange of codons flanking the amber stop codon. This combination of in silico analysis followed by validation in living mammalian cells substantially simplifies identification as well as adaptation of sites within a target protein to confer high ncAA incorporation rates.
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Affiliation(s)
- Michael D Bartoschek
- Department of Biology II and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Enes Ugur
- Department of Biology II and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany.,Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Tuan-Anh Nguyen
- Department of Chemistry, Synthetic Biochemistry, Technical University of Munich, Garching 85748, Germany
| | - Geraldine Rodschinka
- Department of Biology II and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Kathrin Lang
- Department of Chemistry, Synthetic Biochemistry, Technical University of Munich, Garching 85748, Germany
| | - Sebastian Bultmann
- Department of Biology II and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
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25
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Li J, Guo S, Chai F, Sun Q, Li P, Gao L, Dai L, Ouyang X, Zhou Z, Zhou L, Cheng W, Qi S, Lu K, Ren H. Genetically incorporated crosslinkers reveal NleE attenuates host autophagy dependent on PSMD10. eLife 2021; 10:e69047. [PMID: 34254583 PMCID: PMC8324295 DOI: 10.7554/elife.69047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/13/2021] [Indexed: 02/05/2023] Open
Abstract
Autophagy acts as a pivotal innate immune response against infection. Some virulence effectors subvert the host autophagic machinery to escape the surveillance of autophagy. The mechanism by which pathogens interact with host autophagy remains mostly unclear. However, traditional strategies often have difficulty identifying host proteins that interact with effectors due to the weak, dynamic, and transient nature of these interactions. Here, we found that Enteropathogenic Escherichia coli (EPEC) regulates autophagosome formation in host cells dependent on effector NleE. The 26S Proteasome Regulatory Subunit 10 (PSMD10) was identified as a direct interaction partner of NleE in living cells by employing genetically incorporated crosslinkers. Pairwise chemical crosslinking revealed that NleE interacts with the N-terminus of PSMD10. We demonstrated that PSMD10 homodimerization is necessary for its interaction with ATG7 and promotion of autophagy, but not necessary for PSMD10 interaction with ATG12. Therefore, NleE-mediated PSMD10 in monomeric state attenuates host autophagosome formation. Our study reveals the mechanism through which EPEC attenuates host autophagy activity.
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Affiliation(s)
- Jingxiang Li
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of BiotherapyChengduChina
| | - Shupan Guo
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of BiotherapyChengduChina
| | - Fangni Chai
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of BiotherapyChengduChina
| | - Qi Sun
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of BiotherapyChengduChina
| | - Pan Li
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of BiotherapyChengduChina
| | - Li Gao
- Department of General Practice and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, and Sichuan UniversityChengduChina
| | - Lunzhi Dai
- Department of General Practice and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, West China Hospital, and Sichuan UniversityChengduChina
| | - Xiaoxiao Ouyang
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of BiotherapyChengduChina
| | - Zhihui Zhou
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of BiotherapyChengduChina
| | - Li Zhou
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of BiotherapyChengduChina
| | - Wei Cheng
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of BiotherapyChengduChina
| | - Shiqian Qi
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of BiotherapyChengduChina
| | - Kefeng Lu
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of BiotherapyChengduChina
| | - Haiyan Ren
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of BiotherapyChengduChina
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26
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Reille‐Seroussi M, Meyer‐Ahrens P, Aust A, Feldberg A, Mootz HD. Genetic Encoding and Enzymatic Deprotection of a Latent Thiol Side Chain to Enable New Protein Bioconjugation Applications. Angew Chem Int Ed Engl 2021; 60:15972-15979. [PMID: 33844389 PMCID: PMC8361980 DOI: 10.1002/anie.202102343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/09/2021] [Indexed: 12/11/2022]
Abstract
The thiol group of the cysteine side chain is arguably the most versatile chemical handle in proteins. To expand the scope of established and commercially available thiol bioconjugation reagents, we genetically encoded a second such functional moiety in form of a latent thiol group that can be unmasked under mild physiological conditions. Phenylacetamidomethyl (Phacm) protected homocysteine (HcP) was incorporated and its latent thiol group unmasked on purified proteins using penicillin G acylase (PGA). The enzymatic deprotection depends on steric accessibility, but can occur efficiently within minutes on exposed positions in flexible sequences. The freshly liberated thiol group does not require treatment with reducing agents. We demonstrate the potential of this approach for protein modification with conceptually new schemes for regioselective dual labeling, thiol bioconjugation in presence of a preserved disulfide bond and formation of a novel intramolecular thioether crosslink.
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Affiliation(s)
| | - Pascal Meyer‐Ahrens
- Institute of BiochemistryUniversity of MünsterCorrensstraße 3648149MünsterGermany
| | - Annika Aust
- Institute of BiochemistryUniversity of MünsterCorrensstraße 3648149MünsterGermany
| | - Anna‐Lena Feldberg
- Institute of BiochemistryUniversity of MünsterCorrensstraße 3648149MünsterGermany
| | - Henning D. Mootz
- Institute of BiochemistryUniversity of MünsterCorrensstraße 3648149MünsterGermany
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27
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Reille‐Seroussi M, Meyer‐Ahrens P, Aust A, Feldberg A, Mootz HD. Genetic Encoding and Enzymatic Deprotection of a Latent Thiol Side Chain to Enable New Protein Bioconjugation Applications. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Marie Reille‐Seroussi
- Institute of Biochemistry University of Münster Corrensstraße 36 48149 Münster Germany
| | - Pascal Meyer‐Ahrens
- Institute of Biochemistry University of Münster Corrensstraße 36 48149 Münster Germany
| | - Annika Aust
- Institute of Biochemistry University of Münster Corrensstraße 36 48149 Münster Germany
| | - Anna‐Lena Feldberg
- Institute of Biochemistry University of Münster Corrensstraße 36 48149 Münster Germany
| | - Henning D. Mootz
- Institute of Biochemistry University of Münster Corrensstraße 36 48149 Münster Germany
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28
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Genetically encoded selective cross-linkers and emerging applications. Biochem Soc Trans 2021; 48:1807-1817. [PMID: 32657352 DOI: 10.1042/bst20200508] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/05/2020] [Accepted: 06/11/2020] [Indexed: 02/08/2023]
Abstract
There has been a large amount of interest in the development of genetically encoded cross-linkers that target functional groups naturally present in cells. Recently, a new class of unnatural amino acids that specifically react with target residues were developed and genetically incorporated. The selective reaction shows higher cross-linking efficiency, lower background and predictable cross-linking sites. It has been applied to enhance protein/peptide stability, pinpoint protein-protein interactions, stabilize protein complexes, engineer covalent protein inhibitors, identify phosphatases in living cells, etc. These new covalent linkages provide excellent new tools for protein engineering and biological studies. Their applications in biotherapy will provide considerable opportunities for innovating and improving biomolecular medicines.
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29
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Row RD, Nguyen SS, Ferreira AJ, Prescher JA. Chemically triggered crosslinking with bioorthogonal cyclopropenones. Chem Commun (Camb) 2021; 56:10883-10886. [PMID: 32808608 DOI: 10.1039/d0cc04600k] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We report a proximity-driven crosslinking strategy featuring bioorthogonal cyclopropenones. These motifs react with phosphines to form electrophilic ketene-ylides. Such intermediates can be trapped by neighboring proteins to form covalent adducts. Successful crosslinking was achieved using a model split reporter, and the rate of crosslinking could be tuned using different phosphine triggers. We further demonstrated that the reaction can be performed in cell lysate. Based on these features, we anticipate that cyclopropenones will enable unique studies of protein-protein and other biomolecule interactions.
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Affiliation(s)
- R David Row
- Department of Chemistry, University of California, Irvine, California 92697, USA.
| | - Sean S Nguyen
- Department of Chemistry, University of California, Irvine, California 92697, USA.
| | - Andrew J Ferreira
- Department of Chemistry, University of California, Irvine, California 92697, USA.
| | - Jennifer A Prescher
- Department of Chemistry, University of California, Irvine, California 92697, USA. and Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697, USA and Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
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30
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Fauser J, Itzen A, Gulen B. Current Advances in Covalent Stabilization of Macromolecular Complexes for Structural Biology. Bioconjug Chem 2021; 32:879-890. [PMID: 33861574 DOI: 10.1021/acs.bioconjchem.1c00118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Structural characterization of macromolecular assemblies is often limited by the transient nature of the interactions. The development of specific chemical tools to covalently tether interacting proteins to each other has played a major role in various fundamental discoveries in recent years. To this end, protein engineering techniques such as mutagenesis, incorporation of unnatural amino acids, and methods using synthetic substrate/cosubstrate derivatives were employed. In this review, we give an overview of both commonly used and recently developed biochemical methodologies for covalent stabilization of macromolecular complexes enabling structural investigation via crystallography, nuclear magnetic resonance, and cryo-electron microscopy. We divided the strategies into nonenzymatic- and enzymatic-driven cross-linking and further categorized them in either naturally occurring or engineered covalent linkage. This review offers a compilation of recent advances in diverse scientific fields where the structural characterization of macromolecular complexes was achieved by the aid of intermolecular covalent linkage.
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Affiliation(s)
- Joel Fauser
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, 85747 Garching, Germany.,Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
| | - Aymelt Itzen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, 85747 Garching, Germany.,Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
| | - Burak Gulen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, 85747 Garching, Germany.,Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
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31
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Tremel S, Ohashi Y, Morado DR, Bertram J, Perisic O, Brandt LTL, von Wrisberg MK, Chen ZA, Maslen SL, Kovtun O, Skehel M, Rappsilber J, Lang K, Munro S, Briggs JAG, Williams RL. Structural basis for VPS34 kinase activation by Rab1 and Rab5 on membranes. Nat Commun 2021; 12:1564. [PMID: 33692360 PMCID: PMC7946940 DOI: 10.1038/s41467-021-21695-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/01/2021] [Indexed: 02/07/2023] Open
Abstract
The lipid phosphatidylinositol-3-phosphate (PI3P) is a regulator of two fundamental but distinct cellular processes, endocytosis and autophagy, so its generation needs to be under precise temporal and spatial control. PI3P is generated by two complexes that both contain the lipid kinase VPS34: complex II on endosomes (VPS34/VPS15/Beclin 1/UVRAG), and complex I on autophagosomes (VPS34/VPS15/Beclin 1/ATG14L). The endosomal GTPase Rab5 binds complex II, but the mechanism of VPS34 activation by Rab5 has remained elusive, and no GTPase is known to bind complex I. Here we show that Rab5a–GTP recruits endocytic complex II to membranes and activates it by binding between the VPS34 C2 and VPS15 WD40 domains. Electron cryotomography of complex II on Rab5a-decorated vesicles shows that the VPS34 kinase domain is released from inhibition by VPS15 and hovers over the lipid bilayer, poised for catalysis. We also show that the GTPase Rab1a, which is known to be involved in autophagy, recruits and activates the autophagy-specific complex I, but not complex II. Both Rabs bind to the same VPS34 interface but in a manner unique for each. These findings reveal how VPS34 complexes are activated on membranes by specific Rab GTPases and how they are recruited to unique cellular locations. The phosphatidylinositol-3-phosphate (PI3P) is generated by the lipid kinase VPS34, in the context of VPS34 complex I on autophagosomes or complex II on endosomes. Biochemical and structural analyses provide insights into the mechanism of both VPS34 complexes recruitment to and activation on membranes by specific Rab GTPases.
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Affiliation(s)
| | - Yohei Ohashi
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Dustin R Morado
- MRC Laboratory of Molecular Biology, Cambridge, UK.,Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | | | - Olga Perisic
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Marie-Kristin von Wrisberg
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Lab for Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, TUM-IAS, Garching, Germany
| | - Zhuo A Chen
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | | | | | - Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.,Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Kathrin Lang
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Lab for Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, TUM-IAS, Garching, Germany
| | - Sean Munro
- MRC Laboratory of Molecular Biology, Cambridge, UK.
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32
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Du J, Wrisberg MKV, Gulen B, Stahl M, Pett C, Hedberg C, Lang K, Schneider S, Itzen A. Rab1-AMPylation by Legionella DrrA is allosterically activated by Rab1. Nat Commun 2021; 12:460. [PMID: 33469029 PMCID: PMC7815794 DOI: 10.1038/s41467-020-20702-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/16/2020] [Indexed: 01/29/2023] Open
Abstract
Legionella pneumophila infects eukaryotic cells by forming a replicative organelle - the Legionella containing vacuole. During this process, the bacterial protein DrrA/SidM is secreted and manipulates the activity and post-translational modification (PTM) states of the vesicular trafficking regulator Rab1. As a result, Rab1 is modified with an adenosine monophosphate (AMP), and this process is referred to as AMPylation. Here, we use a chemical approach to stabilise low-affinity Rab:DrrA complexes in a site-specific manner to gain insight into the molecular basis of the interaction between the Rab protein and the AMPylation domain of DrrA. The crystal structure of the Rab:DrrA complex reveals a previously unknown non-conventional Rab-binding site (NC-RBS). Biochemical characterisation demonstrates allosteric stimulation of the AMPylation activity of DrrA via Rab binding to the NC-RBS. We speculate that allosteric control of DrrA could in principle prevent random and potentially cytotoxic AMPylation in the host, thereby perhaps ensuring efficient infection by Legionella.
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Affiliation(s)
- Jiqing Du
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Garching, 85748, Germany.,Center for Experimental Medicine, Institute of Biochemistry and Signal Transduction, Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, 20246, Germany
| | - Marie-Kristin von Wrisberg
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Institute for Advanced Study, Garching, 85748, Germany
| | - Burak Gulen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Garching, 85748, Germany.,Center for Experimental Medicine, Institute of Biochemistry and Signal Transduction, Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, 20246, Germany
| | - Matthias Stahl
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Garching, 85748, Germany.,Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Box 1031, 171 21 Solna, Stockholm, Sweden
| | - Christian Pett
- Chemical Biology Center (KBC), Department of Chemistry, Umeå University, Linnaeus väg 10, 90187, Umeå, Sweden
| | - Christian Hedberg
- Chemical Biology Center (KBC), Department of Chemistry, Umeå University, Linnaeus väg 10, 90187, Umeå, Sweden
| | - Kathrin Lang
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Institute for Advanced Study, Garching, 85748, Germany.
| | - Sabine Schneider
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Ludwig-Maximilians-University Munich, München, 81377, Germany.
| | - Aymelt Itzen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, Garching, 85748, Germany. .,Center for Experimental Medicine, Institute of Biochemistry and Signal Transduction, Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, 20246, Germany. .,Center for Structural Systems Biology (CSSB), University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, Germany.
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33
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Shin G, Lim SI. Site-specific proximity ligation provides molecular insights into biologically relevant interfaces of protein-protein interaction. Biochem Biophys Res Commun 2020; 533:932-937. [PMID: 33008597 DOI: 10.1016/j.bbrc.2020.09.097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/10/2020] [Accepted: 09/23/2020] [Indexed: 11/30/2022]
Abstract
Dynamic protein-protein interactions (PPIs) are fundamental to spatiotemporal control of protein functions in biological systems. Dissecting binding interfaces in aqueous solution (i.e., biological interfaces) is of great importance for identifying molecular determinants that contribute to the affinity and specificity of PPIs. Herein, we describe a biochemical method, termed site-specific proximity ligation (SPL), that enables the identification and reconstruction of native binding interfaces distinct from those present in crystal structures and models from computational prediction. SPL involves the strategic incorporation of an aryl azide-containing unnatural amino acid (AZF) into residues of interest in a particular protein that forms a multiprotein complex. Depending on the interfacial role of a targeted residue, a photo-inducible highly reactive incorporated AZF moiety may react with neighboring functional groups to covalently capture an otherwise non-covalent or weak interaction with a specific partner protein, thereby revealing the landscape of biological interfaces. Using a heterotrimeric nuclear pore protein as a model, we show that the biological interfaces of the complex mapped by SPL provide new insight into dynamic molecular recognition that is missed by, or even in conflict with, static models.
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Affiliation(s)
- Goeun Shin
- Department of Chemical Engineering, Pukyong National University, Yongso-ro 45, Nam-gu, Busan, Republic of Korea
| | - Sung In Lim
- Department of Chemical Engineering, Pukyong National University, Yongso-ro 45, Nam-gu, Busan, Republic of Korea.
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34
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Zheng J, Chen X, Yang Y, Tan CSH, Tian R. Mass Spectrometry-Based Protein Complex Profiling in Time and Space. Anal Chem 2020; 93:598-619. [DOI: 10.1021/acs.analchem.0c04332] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jiangnan Zheng
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiong Chen
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yun Yang
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Chris Soon Heng Tan
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruijun Tian
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
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35
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Capturing Peptide-GPCR Interactions and Their Dynamics. Molecules 2020; 25:molecules25204724. [PMID: 33076289 PMCID: PMC7587574 DOI: 10.3390/molecules25204724] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022] Open
Abstract
Many biological functions of peptides are mediated through G protein-coupled receptors (GPCRs). Upon ligand binding, GPCRs undergo conformational changes that facilitate the binding and activation of multiple effectors. GPCRs regulate nearly all physiological processes and are a favorite pharmacological target. In particular, drugs are sought after that elicit the recruitment of selected effectors only (biased ligands). Understanding how ligands bind to GPCRs and which conformational changes they induce is a fundamental step toward the development of more efficient and specific drugs. Moreover, it is emerging that the dynamic of the ligand–receptor interaction contributes to the specificity of both ligand recognition and effector recruitment, an aspect that is missing in structural snapshots from crystallography. We describe here biochemical and biophysical techniques to address ligand–receptor interactions in their structural and dynamic aspects, which include mutagenesis, crosslinking, spectroscopic techniques, and mass-spectrometry profiling. With a main focus on peptide receptors, we present methods to unveil the ligand–receptor contact interface and methods that address conformational changes both in the ligand and the GPCR. The presented studies highlight a wide structural heterogeneity among peptide receptors, reveal distinct structural changes occurring during ligand binding and a surprisingly high dynamics of the ligand–GPCR complexes.
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36
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Tinzl M, Hilvert D. Trapping Transient Protein Species by Genetic Code Expansion. Chembiochem 2020; 22:92-99. [PMID: 32810341 DOI: 10.1002/cbic.202000523] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/18/2020] [Indexed: 12/24/2022]
Abstract
Nature employs a limited number of genetically encoded amino acids for the construction of functional proteins. By engineering components of the cellular translation machinery, however, it is now possible to genetically encode noncanonical building blocks with tailored electronic and structural properties. The ability to incorporate unique chemical functionality into proteins provides a powerful tool to probe mechanism and create novel function. In this minireview, we highlight several recent studies that illustrate how noncanonical amino acids have been used to capture and characterize reactive intermediates, fine-tune the catalytic properties of enzymes, and stabilize short-lived protein-protein complexes.
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Affiliation(s)
- Matthias Tinzl
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
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37
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Krauskopf K, Lang K. Increasing the chemical space of proteins in living cells via genetic code expansion. Curr Opin Chem Biol 2020; 58:112-120. [PMID: 32911429 DOI: 10.1016/j.cbpa.2020.07.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/20/2020] [Accepted: 07/27/2020] [Indexed: 01/30/2023]
Abstract
In recent years it has become possible to genetically encode an expanded set of designer amino acids with tailored chemical and physical properties (dubbed unnatural amino acids, UAAs) into proteins in living cells by expanding the genetic code. Together with developments in chemistries that are amenable to and selective within physiological settings, these strategies have started to have a big impact on biological studies, as they enable exciting in cellulo applications. Here we highlight recent advances to covalently stabilize transient protein-protein interactions and capture enzyme substrate-complexes in living cells using proximity-triggered and residue-selective photo-induced crosslinking approaches. Furthermore, we describe recent efforts in controlling enzyme activity with photocaged UAAs and in extending their application to a variety of enzymatic scaffolds. In addition, we discuss the site-specific incorporation of UAAs mimicking post-translational modifications (PTMs) and approaches to generate natively-linked ubiquitin-protein conjugates to probe the role of PTMs in modulating complex cellular networks.
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Affiliation(s)
- Kristina Krauskopf
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Kathrin Lang
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany.
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38
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Copley SD. The physical basis and practical consequences of biological promiscuity. Phys Biol 2020; 17:10.1088/1478-3975/ab8697. [PMID: 32244231 PMCID: PMC9291633 DOI: 10.1088/1478-3975/ab8697] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proteins interact with metabolites, nucleic acids, and other proteins to orchestrate the myriad catalytic, structural and regulatory functions that support life from the simplest microbes to the most complex multicellular organisms. These molecular interactions are often exquisitely specific, but never perfectly so. Adventitious "promiscuous" interactions are ubiquitous due to the thousands of macromolecules and small molecules crowded together in cells. Such interactions may perturb protein function at the molecular level, but as long as they do not compromise organismal fitness, they will not be removed by natural selection. Although promiscuous interactions are physiologically irrelevant, they are important because they can provide a vast reservoir of potential functions that can provide the starting point for evolution of new functions, both in nature and in the laboratory.
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Affiliation(s)
- Shelley D Copley
- Department of Molecular, Cellular and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado, UNITED STATES
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39
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A methylated lysine is a switch point for conformational communication in the chaperone Hsp90. Nat Commun 2020; 11:1219. [PMID: 32139682 PMCID: PMC7057950 DOI: 10.1038/s41467-020-15048-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 02/15/2020] [Indexed: 02/06/2023] Open
Abstract
Methylation of a conserved lysine in C-terminal domain of the molecular chaperone Hsp90 was shown previously to affect its in vivo function. However, the underlying mechanism remained elusive. Through a combined experimental and computational approach, this study shows that this site is very sensitive to sidechain modifications and crucial for Hsp90 activity in vitro and in vivo. Our results demonstrate that this particular lysine serves as a switch point for the regulation of Hsp90 functions by influencing its conformational cycle, ATPase activity, co-chaperone regulation, and client activation of yeast and human Hsp90. Incorporation of the methylated lysine via genetic code expansion specifically shows that upon modification, the conformational cycle of Hsp90 is altered. Molecular dynamics simulations including the methylated lysine suggest specific conformational changes that are propagated through Hsp90. Thus, methylation of the C-terminal lysine allows a precise allosteric tuning of Hsp90 activity via long distances. Methylation of a lysine residue in Hsp90 is a recently discovered post-translational modification but the mechanistic effects of this modification have remained unknown so far. Here the authors combine biochemical and biophysical approaches, molecular dynamics (MD) simulations and functional experiments with yeast and show that this lysine is a switch point, which specifically modulates conserved Hsp90 functions including co-chaperone regulation and client activation.
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40
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Reddy PS, Langlois d'Estaintot B, Granier T, Mackereth CD, Fischer L, Huc I. Structure Elucidation of Helical Aromatic Foldamer-Protein Complexes with Large Contact Surface Areas. Chemistry 2019; 25:11042-11047. [PMID: 31257622 DOI: 10.1002/chem.201902942] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Indexed: 01/12/2023]
Abstract
The development of large synthetic ligands could be useful to target the sizeable surface areas involved in protein-protein interactions. Herein, we present long helical aromatic oligoamide foldamers bearing proteinogenic side chains that cover up to 450 Å2 of the human carbonic anhydrase II (HCA) surface. The foldamers are composed of aminoquinolinecarboxylic acids bearing proteinogenic side chains and of more flexible aminomethyl-pyridinecarboxylic acids that enhance helix handedness dynamics. Crystal structures of HCA-foldamer complexes were obtained with a 9- and a 14-mer both showing extensive protein-foldamer hydrophobic contacts. In addition, foldamer-foldamer interactions seem to be prevalent in the crystal packing, leading to the peculiar formation of an HCA superhelix wound around a rod of stacked foldamers. Solution studies confirm the positioning of the foldamer at the protein surface as well as a dimerization of the complexes.
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Affiliation(s)
- Post Sai Reddy
- CBMN (UMR5248), Univ. Bordeaux-CNRS-INP, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France
| | - Béatrice Langlois d'Estaintot
- CBMN (UMR5248), Univ. Bordeaux-CNRS-INP, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France
| | - Thierry Granier
- CBMN (UMR5248), Univ. Bordeaux-CNRS-INP, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France
| | - Cameron D Mackereth
- ARNA (U1212), Univ. Bordeaux-INSERM-CNRS, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France
| | - Lucile Fischer
- CBMN (UMR5248), Univ. Bordeaux-CNRS-INP, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France
| | - Ivan Huc
- CBMN (UMR5248), Univ. Bordeaux-CNRS-INP, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France.,Department Pharmazie and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377, München, Germany
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41
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Nödling AR, Spear LA, Williams TL, Luk LYP, Tsai YH. Using genetically incorporated unnatural amino acids to control protein functions in mammalian cells. Essays Biochem 2019; 63:237-266. [PMID: 31092687 PMCID: PMC6610526 DOI: 10.1042/ebc20180042] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/14/2019] [Accepted: 03/19/2019] [Indexed: 02/07/2023]
Abstract
Genetic code expansion allows unnatural (non-canonical) amino acid incorporation into proteins of interest by repurposing the cellular translation machinery. The development of this technique has enabled site-specific incorporation of many structurally and chemically diverse amino acids, facilitating a plethora of applications, including protein imaging, engineering, mechanistic and structural investigations, and functional regulation. Particularly, genetic code expansion provides great tools to study mammalian proteins, of which dysregulations often have important implications in health. In recent years, a series of methods has been developed to modulate protein function through genetically incorporated unnatural amino acids. In this review, we will first discuss the basic concept of genetic code expansion and give an up-to-date list of amino acids that can be incorporated into proteins in mammalian cells. We then focus on the use of unnatural amino acids to activate, inhibit, or reversibly modulate protein function by translational, optical or chemical control. The features of each approach will also be highlighted.
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Affiliation(s)
| | - Luke A Spear
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
| | - Thomas L Williams
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
| | - Louis Y P Luk
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, Wales, United Kingdom
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42
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Ming Q, Gonzalez-Perez D, Luca VC. Molecular engineering strategies for visualizing low-affinity protein complexes. Exp Biol Med (Maywood) 2019; 244:1559-1567. [PMID: 31184923 DOI: 10.1177/1535370219855401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The growing availability of complex structures in the Protein Data Bank has provided key insight into the molecular architecture of protein–protein interfaces. The remarkable diversity observed in protein binding modes is paralleled by a tremendous variation in binding affinities, with interaction half-lives ranging from days to milliseconds. Within the protein interactome, low-affinity binding events have been particularly difficult to visualize by traditional structural methods, which has spurred the development of innovative strategies for reconstituting these short-lived yet biologically essential assemblies. An important takeaway from structural studies of low-affinity systems is that there is no universal solution for stabilizing protein complexes, and approaches such as single-chain fusions, biochemical linkages, and affinity-maturation have each been successful in certain contexts. In this article, we review how advances in molecular engineering have been used to capture weakly associated complexes for structure determination, and we provide perspectives on how the continued application of these methods can shed new light on the “hidden world” of low-affinity interactions. Impact statement Low-affinity protein interactions, while biologically essential, have been difficult to visualize by traditional methods in structural biology. In this review, we describe a series of innovative molecular engineering strategies that have been used to stabilize weakly bound protein complexes for structure determination. By highlighting several examples from the literature along with potential advantages and disadvantages of the individual approaches, we hope to provide an introductory resource for structural biologists studying low-affinity systems.
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Affiliation(s)
- Qianqian Ming
- Department of Drug Discovery, Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - David Gonzalez-Perez
- Department of Drug Discovery, Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Vincent C Luca
- Department of Drug Discovery, Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
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St Amant AH, Huang F, Lin J, Rickert K, Oganesyan V, Lemen D, Mao S, Harper J, Marelli M, Wu H, Gao C, Read de Alaniz J, Christie RJ. A Diene-Containing Noncanonical Amino Acid Enables Dual Functionality in Proteins: Rapid Diels-Alder Reaction with Maleimide or Proximity-Based Dimerization. Angew Chem Int Ed Engl 2019; 58:8489-8493. [PMID: 31018033 DOI: 10.1002/anie.201903494] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Indexed: 12/19/2022]
Abstract
Here, we describe a diene-containing noncanonical amino acid (ncAA) capable of undergoing fast and selective normal electron-demand Diels-Alder (DA) reactions following its incorporation into antibodies. A cyclopentadiene derivative of lysine (CpHK) served as the reactive handle for DA transformations and the substrate for genetic incorporation. CpHK incorporated into antibodies with high efficiency and was available for maleimide conjugation or self-reaction depending on position in the amino acid sequence. CpHK at position K274 reacted with the maleimide drug-linker AZ1508 at a rate of ≈79 m-1 s-1 to produce functional antibody-drug conjugates (ADCs) in a one-step process. Incorporation of CpHK at position S239 resulted in dimerization, which covalently linked antibody heavy chains together. The diene ncAA described here is capable of producing therapeutic protein conjugates with clinically validated and widely available maleimide compounds, while also enabling proximity-based stapling through a DA dimerization reaction.
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Affiliation(s)
- Andre H St Amant
- Department of Chemistry and Biochemistry, University of California - Santa Barbara, Santa Barbara, California, 93106, USA
| | - Fengying Huang
- Antibody Discovery and Protein Engineering Department, AstraZeneca Biopharmaceuticals R&D, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Jia Lin
- Antibody Discovery and Protein Engineering Department, AstraZeneca Biopharmaceuticals R&D, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Keith Rickert
- Antibody Discovery and Protein Engineering Department, AstraZeneca Biopharmaceuticals R&D, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Vaheh Oganesyan
- Antibody Discovery and Protein Engineering Department, AstraZeneca Biopharmaceuticals R&D, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Daniel Lemen
- Antibody Discovery and Protein Engineering Department, AstraZeneca Biopharmaceuticals R&D, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Shenlan Mao
- AstraZeneca Oncology R&D, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Jay Harper
- AstraZeneca Oncology R&D, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Marcello Marelli
- Antibody Discovery and Protein Engineering Department, AstraZeneca Biopharmaceuticals R&D, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Herren Wu
- Antibody Discovery and Protein Engineering Department, AstraZeneca Biopharmaceuticals R&D, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Changshou Gao
- Antibody Discovery and Protein Engineering Department, AstraZeneca Biopharmaceuticals R&D, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Javier Read de Alaniz
- Department of Chemistry and Biochemistry, University of California - Santa Barbara, Santa Barbara, California, 93106, USA
| | - R James Christie
- Antibody Discovery and Protein Engineering Department, AstraZeneca Biopharmaceuticals R&D, One MedImmune Way, Gaithersburg, MD, 20878, USA
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St. Amant AH, Huang F, Lin J, Rickert K, Oganesyan V, Lemen D, Mao S, Harper J, Marelli M, Wu H, Gao C, Read de Alaniz J, Christie RJ. A Diene‐Containing Noncanonical Amino Acid Enables Dual Functionality in Proteins: Rapid Diels–Alder Reaction with Maleimide or Proximity‐Based Dimerization. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Andre H. St. Amant
- Department of Chemistry and BiochemistryUniversity of California – Santa Barbara Santa Barbara California 93106 USA
| | - Fengying Huang
- Antibody Discovery and Protein Engineering DepartmentAstraZeneca Biopharmaceuticals R&D One MedImmune Way Gaithersburg MD 20878 USA
| | - Jia Lin
- Antibody Discovery and Protein Engineering DepartmentAstraZeneca Biopharmaceuticals R&D One MedImmune Way Gaithersburg MD 20878 USA
| | - Keith Rickert
- Antibody Discovery and Protein Engineering DepartmentAstraZeneca Biopharmaceuticals R&D One MedImmune Way Gaithersburg MD 20878 USA
| | - Vaheh Oganesyan
- Antibody Discovery and Protein Engineering DepartmentAstraZeneca Biopharmaceuticals R&D One MedImmune Way Gaithersburg MD 20878 USA
| | - Daniel Lemen
- Antibody Discovery and Protein Engineering DepartmentAstraZeneca Biopharmaceuticals R&D One MedImmune Way Gaithersburg MD 20878 USA
| | - Shenlan Mao
- AstraZeneca Oncology R&D One MedImmune Way Gaithersburg MD 20878 USA
| | - Jay Harper
- AstraZeneca Oncology R&D One MedImmune Way Gaithersburg MD 20878 USA
| | - Marcello Marelli
- Antibody Discovery and Protein Engineering DepartmentAstraZeneca Biopharmaceuticals R&D One MedImmune Way Gaithersburg MD 20878 USA
| | - Herren Wu
- Antibody Discovery and Protein Engineering DepartmentAstraZeneca Biopharmaceuticals R&D One MedImmune Way Gaithersburg MD 20878 USA
| | - Changshou Gao
- Antibody Discovery and Protein Engineering DepartmentAstraZeneca Biopharmaceuticals R&D One MedImmune Way Gaithersburg MD 20878 USA
| | - Javier Read de Alaniz
- Department of Chemistry and BiochemistryUniversity of California – Santa Barbara Santa Barbara California 93106 USA
| | - R. James Christie
- Antibody Discovery and Protein Engineering DepartmentAstraZeneca Biopharmaceuticals R&D One MedImmune Way Gaithersburg MD 20878 USA
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Abstract
Crosslinking of proteins for their irreversible immobilization on surfaces is a proven and popular method. However, many protocols lead to random orientation and the formation of undefined or even inactive by-products. Most concepts to obtain a more targeted conjugation or immobilization requires the recombinant modification of at least one binding partner, which is often impractical or prohibitively expensive. Here a novel method is presented, which is based on the chemical preactivation of Protein A or G with selected conventional crosslinkers. In a second step, the antibody is added, which is subsequently crosslinked in the Fc part. This leads to an oriented and covalent immobilization of the immunoglobulin with a very high yield. Protocols for Protein A and Protein G with murine and human IgG are presented. This method may be useful for the preparation of columns for affinity chromatography, immunoprecipitation, antibodies conjugated to magnetic particles, permanent and oriented immobilization of antibodies in biosensor systems, microarrays, microtitration plates or any other system, where the loss of antibodies needs to be avoided, and maximum binding capacity is desired. This method is directly applicable even to antibodies in crude cell culture supernatants, raw sera or protein-stabilized antibody preparations without any purification nor enrichment of the IgG. This new method delivered much higher signals as a traditional method and, hence, seems to be preferable in many applications.
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Vallade M, Jewginski M, Fischer L, Buratto J, Bathany K, Schmitter JM, Stupfel M, Godde F, Mackereth CD, Huc I. Assessing Interactions between Helical Aromatic Oligoamide Foldamers and Protein Surfaces: A Tethering Approach. Bioconjug Chem 2019; 30:54-62. [PMID: 30395443 DOI: 10.1021/acs.bioconjchem.8b00710] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Helically folded aromatic foldamers may constitute suitable candidates for the ab initio design of ligands for protein surfaces. As preliminary steps toward the exploration of this hypothesis, a tethering approach was developed to detect interactions between a protein and a foldamer by confining the former at the surface of the latter. Cysteine mutants of two therapeutically relevant enzymes, CypA and IL4, were produced. Two series of ten foldamers were synthesized bearing different proteinogenic side chains and either a long or a short linker functionalized with an activated disulfide. Disulfide exchange between the mutated cysteines and the activated disulfides yielded 20 foldamer-IL4 and 20 foldamer-CypA adducts. Effectiveness of the reaction was demonstrated by LC-MS, by MS analysis after proteolytic digestion, and by 2D NMR. Circular dichroism then revealed diastereoselective interactions between the proteins and the foldamers confined at their surface which resulted in a preferred handedness of the foldamer helix. Helix sense bias occurred sometimes with both the short and the long linkers and sometimes with only one of them. In a few cases, helix handedness preference is found to be close to quantitative. These cases constitute valid candidates for structural elucidation of the interactions involved.
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Affiliation(s)
- Maëlle Vallade
- Université Bordeaux, CNRS, IPB, CBMN (UMR 5248), Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33600 Pessac , France
| | - Michal Jewginski
- Université Bordeaux, CNRS, IPB, CBMN (UMR 5248), Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33600 Pessac , France.,Department of Bioorganic Chemistry, Faculty of Chemistry , Wrocław University of Technology , 50-370 Wrocław , Poland
| | - Lucile Fischer
- Université Bordeaux, CNRS, IPB, CBMN (UMR 5248), Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33600 Pessac , France
| | - Jérémie Buratto
- Université Bordeaux, CNRS, IPB, CBMN (UMR 5248), Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33600 Pessac , France
| | - Katell Bathany
- Université Bordeaux, CNRS, IPB, CBMN (UMR 5248), Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33600 Pessac , France
| | - Jean-Marie Schmitter
- Université Bordeaux, CNRS, IPB, CBMN (UMR 5248), Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33600 Pessac , France
| | - Marine Stupfel
- Université Bordeaux, CNRS, IPB, CBMN (UMR 5248), Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33600 Pessac , France
| | - Frédéric Godde
- Université Bordeaux, CNRS, IPB, CBMN (UMR 5248), Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33600 Pessac , France
| | - Cameron D Mackereth
- Université Bordeaux, INSERM, CNRS, ARNA (U 1212 and UMR 5320), Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33600 Pessac , France
| | - Ivan Huc
- Université Bordeaux, CNRS, IPB, CBMN (UMR 5248), Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33600 Pessac , France.,Department Pharmazie , Ludwig-Maximilians-Universität , Butenandtstraße 5-13 , D-81377 München , Germany
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Reille-Seroussi M, Mayer SV, Dörner W, Lang K, Mootz HD. Expanding the genetic code with a lysine derivative bearing an enzymatically removable phenylacetyl group. Chem Commun (Camb) 2019; 55:4793-4796. [PMID: 30945708 DOI: 10.1039/c9cc00475k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We report the genetically encoded incorporation of phenylacetyl protected lysine (PacK) into proteins in Escherichia coli. This unnatural side-chain modification can be enzymatically removed using either penicillin G acylase (PGA) or, surprisingly, the sirtuin SrtN from Bacillus subtilis. Our approach expands the toolbox to reversibly control protein structure and function under very mild and non-denaturing conditions, as demonstrated by triggering the activity of the nonribosomal peptide synthetase GrsA.
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Affiliation(s)
- Marie Reille-Seroussi
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany.
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48
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Nguyen TA, Cigler M, Lang K. Expanding the Genetic Code to Study Protein-Protein Interactions. Angew Chem Int Ed Engl 2018; 57:14350-14361. [PMID: 30144241 DOI: 10.1002/anie.201805869] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/20/2018] [Indexed: 12/19/2022]
Abstract
Protein-protein interactions are central to many biological processes. A considerable challenge consists however in understanding and deciphering when and how proteins interact, and this can be particularly difficult when interactions are weak and transient. The site-specific incorporation of unnatural amino acids (UAAs) that crosslink with nearby molecules in response to light provides a powerful tool for mapping transient protein-protein interactions and for defining the structure and topology of protein complexes both in vitro and in vivo. Complementary strategies consist in site-specific incorporation of UAAs bearing electrophilic moieties that react with natural nucleophilic amino acids in a proximity-dependent manner, thereby chemically stabilizing low-affinity interactions and providing additional constraints on distances and geometries in protein complexes. Herein, we review how UAAs bearing fine-tuned chemical moieties that react with proteins in their vicinity can be utilized to map, study, and characterize weak and transient protein-protein interactions in living systems.
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Affiliation(s)
- Tuan-Anh Nguyen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Marko Cigler
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Kathrin Lang
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany
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49
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Nguyen TA, Cigler M, Lang K. Expanding the Genetic Code to Study Protein-Protein Interactions. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201805869] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Tuan-Anh Nguyen
- Center for Integrated Protein Science Munich (CIPSM); Department of Chemistry; Group of Synthetic Biochemistry; Technical University of Munich; Institute for Advanced Study; Lichtenbergstr. 4 85748 Garching Germany
| | - Marko Cigler
- Center for Integrated Protein Science Munich (CIPSM); Department of Chemistry; Group of Synthetic Biochemistry; Technical University of Munich; Institute for Advanced Study; Lichtenbergstr. 4 85748 Garching Germany
| | - Kathrin Lang
- Center for Integrated Protein Science Munich (CIPSM); Department of Chemistry; Group of Synthetic Biochemistry; Technical University of Munich; Institute for Advanced Study; Lichtenbergstr. 4 85748 Garching Germany
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50
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Coin I. Application of non-canonical crosslinking amino acids to study protein-protein interactions in live cells. Curr Opin Chem Biol 2018; 46:156-163. [PMID: 30077876 DOI: 10.1016/j.cbpa.2018.07.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/02/2018] [Accepted: 07/13/2018] [Indexed: 02/06/2023]
Abstract
The genetic incorporation of non-canonical amino acids (ncAAs) equipped with photo-crosslinking and chemical crosslinking moieties has found broad application in the study of protein-protein interactions from a unique perspective in live cells. We highlight here applications of photo-activatable ncAAs to map protein interaction surfaces and to capture protein-protein interactions, and we describe recent efforts to efficiently couple photo-crosslinking with mass spectrometric analysis. In addition, we describe recent advances in the development and application of ncAAs for chemical crosslinking, including protein stapling, photo-control of protein conformation, two-dimensional crosslinking, and stabilization of transient and low-affinity protein-protein interactions. We expect that the field will keep growing in the near future and enable the tackling of ambitious biological questions.
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Affiliation(s)
- Irene Coin
- University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstr. 34, 04301 Leipzig, Germany.
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